[{"title":"Is speciation driven by cycles of mixing and isolation?","ddc":["570"],"status":"public","intvolume":" 6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6858","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":106463,"creator":"dernst","file_name":"2019_NSR_Barton.pdf","access_level":"open_access","date_updated":"2020-10-02T09:16:44Z","date_created":"2020-10-02T09:16:44Z","checksum":"571d60fa21a568607d1fd04e119da88c","success":1,"relation":"main_file","file_id":"8595"}],"type":"journal_article","issue":"2","article_type":"review","page":"291-292","publication":"National Science Review","citation":{"short":"N.H. Barton, National Science Review 6 (2019) 291–292.","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:10.1093/nsr/nwy113.","chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.","ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? National Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113","ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113","ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292."},"date_published":"2019-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","year":"2019","date_updated":"2023-08-29T07:51:09Z","date_created":"2019-09-07T14:43:02Z","volume":6,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-10-02T09:16:44Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000467957400025"]},"language":[{"iso":"eng"}],"doi":"10.1093/nsr/nwy113","month":"03","publication_identifier":{"issn":["2095-5138"],"eissn":["2053-714X"]}},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","article_type":"original","citation":{"mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151.","ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019."},"publication":"BioEssays","date_published":"2019-11-01T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop."}],"intvolume":" 41","status":"public","title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6857","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6939","checksum":"8cc7551bff70b2658f8d5630f228ee12","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-10-11T06:59:26Z","access_level":"open_access","file_name":"2019_BioEssays_Giese.pdf","file_size":193248,"content_type":"application/pdf","creator":"dernst"}],"publication_identifier":{"eissn":["1521-1878"]},"month":"11","isi":1,"quality_controlled":"1","external_id":{"isi":["000489502000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/bies.201900151","article_number":"1900151","file_date_updated":"2020-07-14T12:47:42Z","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","year":"2019","volume":41,"date_created":"2019-09-07T14:40:03Z","date_updated":"2023-08-30T06:56:26Z","author":[{"last_name":"Giese","first_name":"B","full_name":"Giese, B"},{"full_name":"Friess, J L","last_name":"Friess","first_name":"J L"},{"full_name":"Schetelig, M F ","first_name":"M F ","last_name":"Schetelig"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Philip","last_name":"Messer","full_name":"Messer, Philip"},{"last_name":"Debarre","first_name":"Florence","full_name":"Debarre, Florence"},{"first_name":"H","last_name":"Meimberg","full_name":"Meimberg, H"},{"first_name":"N","last_name":"Windbichler","full_name":"Windbichler, N"},{"last_name":"Boete","first_name":"C","full_name":"Boete, C"}]},{"year":"2019","_id":"13067","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Zagrodzka, Zuzanna","last_name":"Zagrodzka","first_name":"Zuzanna"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"}],"related_material":{"record":[{"id":"7205","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-09-06T14:48:57Z","date_created":"2023-05-23T16:36:27Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbnzwk","open_access":"1"}],"doi":"10.5061/DRYAD.TB2RBNZWK","date_published":"2019-12-02T00:00:00Z","day":"02","month":"12","article_processing_charge":"No"},{"publication":"Science Advances","citation":{"mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019).","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.","ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019."},"article_type":"original","date_published":"2019-12-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7393","status":"public","ddc":["570"],"title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","intvolume":" 5","file":[{"relation":"main_file","file_id":"7442","checksum":"af99a5dcdc66c6d6102051faf3be48d8","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-03T13:33:25Z","access_level":"open_access","file_name":"2019_ScienceAdvances_Morales.pdf","content_type":"application/pdf","file_size":1869449,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow."}],"issue":"12","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"pmid":["31840052"],"isi":["000505069600008"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"doi":"10.1126/sciadv.aav9963","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["2375-2548"]},"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"AAAS","author":[{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Tomas","last_name":"Larsson","full_name":"Larsson, Tomas"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"date_updated":"2023-09-06T15:35:56Z","date_created":"2020-01-29T15:58:27Z","volume":5,"article_number":"eaav9963","file_date_updated":"2020-07-14T12:47:57Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"edition":"4","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"date_updated":"2023-09-08T11:24:15Z","date_created":"2020-08-21T04:25:39Z","year":"2019","department":[{"_id":"NiBa"}],"editor":[{"full_name":"Balding, David","last_name":"Balding","first_name":"David"},{"full_name":"Moltke, Ida","first_name":"Ida","last_name":"Moltke"},{"last_name":"Marioni","first_name":"John","full_name":"Marioni, John"}],"publisher":"Wiley","publication_status":"published","publication_identifier":{"isbn":["9781119429142"]},"month":"07","doi":"10.1002/9781119487845.ch4","language":[{"iso":"eng"}],"external_id":{"isi":["000261343000003"]},"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it."}],"type":"book_chapter","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8281","ddc":["576"],"status":"public","title":"Mathematical models in population genetics","article_processing_charge":"No","day":"29","date_published":"2019-07-29T00:00:00Z","citation":{"ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.","short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144."},"publication":"Handbook of statistical genomics","page":"115-144"},{"date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","oa":1,"citation":{"ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019).","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"article_processing_charge":"No","day":"09","month":"01","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"40"}]},"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"oa_version":"Published Version","date_created":"2021-08-06T12:03:50Z","date_updated":"2023-09-19T10:06:07Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9805","year":"2019","department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","title":"Data from: The consequences of an introgression event","abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"type":"research_data_reference"},{"day":"11","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-03-11T00:00:00Z","page":"189","citation":{"chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071"},"abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"checksum":"e60a72de35d270b31f1a23d50f224ec0","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:05:07Z","file_id":"6072","relation":"main_file","creator":"rprizak","file_size":20995465,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf"},{"creator":"rprizak","content_type":"application/zip","file_size":85705272,"access_level":"closed","file_name":"thesis_v2_merge.zip","checksum":"67c2630333d05ebafef5f018863a8465","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:09:39Z","file_id":"6073","title":"Latex files","relation":"source_file"}],"ddc":["576"],"status":"public","title":"Coevolution of transcription factors and their binding sites in sequence space","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6071","month":"03","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:th6071","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa":1,"file_date_updated":"2020-07-14T12:47:18Z","date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z","author":[{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1358"},{"id":"955","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2019"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31505037"]},"oa":1,"quality_controlled":"1","project":[{"name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7","grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosomes and species barriers"}],"doi":"10.1111/nph.16180","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"year":"2019","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"author":[{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Brandvain","first_name":"Yaniv","full_name":"Brandvain, Yaniv"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"full_name":"Yakimowski, Sarah","last_name":"Yakimowski","first_name":"Sarah"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"},{"last_name":"Cereghetti","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","full_name":"Cereghetti, Eva"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"}],"date_updated":"2023-10-18T08:47:08Z","date_created":"2019-09-07T14:35:40Z","volume":224,"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"publication":"New Phytologist","citation":{"ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180."},"article_type":"original","page":"1035-1047","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6856","status":"public","ddc":["570"],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","intvolume":" 224","file":[{"relation":"main_file","file_id":"7011","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","checksum":"21e4c95599bbcaf7c483b89954658672","file_name":"2019_NewPhytologist_Pickup.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1511958,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.","lang":"eng"}],"issue":"3"},{"month":"03","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"quality_controlled":"1","isi":1,"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy246","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2019","pmid":1,"date_created":"2019-03-10T22:59:19Z","date_updated":"2024-02-21T13:59:17Z","volume":36,"author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5757"}]},"scopus_import":"1","day":"01","article_processing_charge":"No","page":"500-515","publication":"Molecular biology and evolution","citation":{"ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246."},"date_published":"2019-03-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"issue":"3","status":"public","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","intvolume":" 36","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6089","oa_version":"Submitted Version"},{"author":[{"first_name":"Martín","last_name":"Carballo-Pacheco","full_name":"Carballo-Pacheco, Martín"},{"full_name":"Desponds, Jonathan","first_name":"Jonathan","last_name":"Desponds"},{"last_name":"Gavrilchenko","first_name":"Tatyana","full_name":"Gavrilchenko, Tatyana"},{"full_name":"Mayer, Andreas","last_name":"Mayer","first_name":"Andreas"},{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan"},{"full_name":"Reddy, Gautam","first_name":"Gautam","last_name":"Reddy"},{"full_name":"Nemenman, Ilya","first_name":"Ilya","last_name":"Nemenman"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"}],"volume":99,"date_updated":"2024-02-28T13:12:06Z","date_created":"2019-03-10T22:59:20Z","year":"2019","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"American Physical Society","publication_status":"published","article_number":"022423","doi":"10.1103/PhysRevE.99.022423","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"external_id":{"isi":["000459916500007"]},"quality_controlled":"1","isi":1,"month":"02","oa_version":"Preprint","_id":"6090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 99","title":"Receptor crosstalk improves concentration sensing of multiple ligands","status":"public","issue":"2","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"type":"journal_article","date_published":"2019-02-26T00:00:00Z","citation":{"chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423"},"publication":"Physical Review E","article_processing_charge":"No","day":"26","scopus_import":"1"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31169497"],"isi":["000473588700001"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.7554/eLife.42014","language":[{"iso":"eng"}],"month":"06","year":"2019","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"}],"author":[{"full_name":"Castro, João Pl","first_name":"João Pl","last_name":"Castro"},{"first_name":"Michelle N.","last_name":"Yancoskie","full_name":"Yancoskie, Michelle N."},{"full_name":"Marchini, Marta","first_name":"Marta","last_name":"Marchini"},{"full_name":"Belohlavy, Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","first_name":"Stefanie","last_name":"Belohlavy"},{"first_name":"Layla","last_name":"Hiramatsu","full_name":"Hiramatsu, Layla"},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"last_name":"Beluch","first_name":"William H.","full_name":"Beluch, William H."},{"full_name":"Naumann, Ronald","last_name":"Naumann","first_name":"Ronald"},{"first_name":"Isabella","last_name":"Skuplik","full_name":"Skuplik, Isabella"},{"full_name":"Cobb, John","last_name":"Cobb","first_name":"John"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"related_material":{"record":[{"id":"9804","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"11388"}]},"date_updated":"2024-03-28T23:30:23Z","date_created":"2019-07-28T21:59:17Z","volume":8,"article_number":"e42014","file_date_updated":"2020-07-14T12:47:38Z","publication":"eLife","citation":{"ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014."},"date_published":"2019-06-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"No","has_accepted_license":"1","_id":"6713","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["576"],"status":"public","title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","intvolume":" 8","file":[{"relation":"main_file","file_id":"6721","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","date_updated":"2020-07-14T12:47:38Z","date_created":"2019-07-29T07:41:18Z","access_level":"open_access","file_name":"2019_eLife_Castro.pdf","content_type":"application/pdf","file_size":6748249,"creator":"apreinsp"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}]},{"scopus_import":1,"has_accepted_license":"1","day":"15","citation":{"chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","short":"J. Polechova, PLoS Biology 16 (2018).","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372"},"publication":"PLoS Biology","date_published":"2018-06-15T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315","intvolume":" 16","status":"public","title":"Is the sky the limit? On the expansion threshold of a species’ range","ddc":["576"],"oa_version":"Published Version","file":[{"date_created":"2019-01-22T08:30:03Z","date_updated":"2020-07-14T12:46:01Z","checksum":"908c52751bba30c55ed36789e5e4c84d","file_id":"5870","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":6968201,"file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access"}],"publication_identifier":{"issn":["15449173"]},"month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pbio.2005372","language":[{"iso":"eng"}],"article_number":"e2005372","publist_id":"7550","file_date_updated":"2020-07-14T12:46:01Z","year":"2018","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9839"}]},"author":[{"full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova"}],"volume":16,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z"},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"citation":{"ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113."},"date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","article_processing_charge":"No","month":"10","day":"09","year":"2018","_id":"9837","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6095"}]},"author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"full_name":"Lemmon, Emily M.","first_name":"Emily M.","last_name":"Lemmon"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"oa_version":"Published Version","date_created":"2021-08-09T12:46:39Z","date_updated":"2023-08-24T14:50:26Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}]},{"publist_id":"7400","ec_funded":1,"file_date_updated":"2020-07-14T12:46:25Z","article_number":"e32035","volume":7,"date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-11T12:49:17Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9840"}]},"author":[{"full_name":"Payne, Pavel","last_name":"Payne","first_name":"Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publication_status":"published","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","year":"2018","month":"03","language":[{"iso":"eng"}],"doi":"10.7554/eLife.32035","project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000431035800001"]},"abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"5689","relation":"main_file","checksum":"447cf6e680bdc3c01062a8737d876569","date_created":"2018-12-17T10:36:07Z","date_updated":"2020-07-14T12:46:25Z","access_level":"open_access","file_name":"2018_eLife_Payne.pdf","creator":"dernst","file_size":3533881,"content_type":"application/pdf"}],"intvolume":" 7","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","ddc":["576"],"status":"public","_id":"423","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","has_accepted_license":"1","day":"09","scopus_import":"1","date_published":"2018-03-09T00:00:00Z","citation":{"short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035."},"publication":"eLife"},{"date_published":"2018-03-12T00:00:00Z","doi":"10.5061/dryad.42n44","main_file_link":[{"url":"https://doi.org/10.5061/dryad.42n44","open_access":"1"}],"oa":1,"citation":{"mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44"},"article_processing_charge":"No","month":"03","day":"12","oa_version":"Published Version","date_created":"2021-08-09T13:10:02Z","date_updated":"2023-09-11T12:49:17Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"423"}]},"author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","first_name":"Pavel","last_name":"Payne","full_name":"Payne, Pavel"},{"last_name":"Geyrhofer","first_name":"Lukas","full_name":"Geyrhofer, Lukas"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","status":"public","year":"2018","_id":"9840","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"type":"research_data_reference"},{"department":[{"_id":"NiBa"}],"publisher":"Academic Press","publication_status":"published","year":"2018","volume":122,"date_created":"2018-12-11T11:47:12Z","date_updated":"2023-09-11T13:41:22Z","related_material":{"record":[{"id":"9842","relation":"research_data","status":"public"}]},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"ec_funded":1,"publist_id":"7250","file_date_updated":"2020-07-14T12:47:09Z","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000440392900014"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.11.007","month":"07","intvolume":" 122","status":"public","ddc":["519","576"],"title":"Establishment in a new habitat by polygenic adaptation","_id":"564","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","file":[{"date_created":"2019-12-21T09:36:39Z","date_updated":"2020-07-14T12:47:09Z","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_id":"7199","relation":"main_file","creator":"nbarton","content_type":"application/pdf","file_size":2287682,"file_name":"bartonetheridge.pdf","access_level":"open_access"}],"type":"journal_article","issue":"7","abstract":[{"text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population.","lang":"eng"}],"page":"110-127","article_type":"original","citation":{"chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007"},"publication":"Theoretical Population Biology","date_published":"2018-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"issue":"3","abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 208","status":"public","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","_id":"563","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-03-01T00:00:00Z","page":"1231-1245","citation":{"ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638."},"publication":"Genetics","publist_id":"7251","volume":208,"date_updated":"2023-09-11T13:42:38Z","date_created":"2018-12-11T11:47:12Z","related_material":{"record":[{"id":"200","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Ringbauer","first_name":"Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald"},{"full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"publication_status":"published","year":"2018","month":"03","language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300638","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}],"external_id":{"isi":["000426219600025"]}},{"ec_funded":1,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Genetics Society of America","year":"2018","date_updated":"2023-09-11T13:57:43Z","date_created":"2018-12-11T11:45:47Z","volume":209,"author":[{"full_name":"Bodova, Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarina","last_name":"Bodova"},{"first_name":"Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"9813","status":"public","relation":"research_data"}]},"month":"07","quality_controlled":"1","isi":1,"project":[{"name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000437171700017"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/node/80098.abstract"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.300748","type":"journal_article","abstract":[{"lang":"eng","text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants."}],"issue":"3","title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","status":"public","intvolume":" 209","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"316","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"861-883","publication":"Genetics","citation":{"chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748"},"date_published":"2018-07-01T00:00:00Z"},{"article_processing_charge":"No","day":"30","month":"04","doi":"10.25386/genetics.6148304.v1","date_published":"2018-04-30T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"citation":{"mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018."},"oa":1,"abstract":[{"lang":"eng","text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables."}],"type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"316"}]},"author":[{"last_name":"Bod'ová","first_name":"Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína"},{"first_name":"Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","full_name":"Field, David"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda"}],"oa_version":"Published Version","date_updated":"2023-09-11T13:57:42Z","date_created":"2021-08-06T13:04:32Z","year":"2018","_id":"9813","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"status":"public","title":"Supplemental material for Bodova et al., 2018"},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2018-05-01T00:00:00Z","page":"1604 - 1633","citation":{"chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2"},"publication":"Algorithmica","issue":"5","abstract":[{"lang":"eng","text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"4674","relation":"main_file","checksum":"7d92f5d7be81e387edeec4f06442791c","date_updated":"2020-07-14T12:47:54Z","date_created":"2018-12-12T10:08:14Z","access_level":"open_access","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","creator":"system","file_size":691245,"content_type":"application/pdf"}],"pubrep_id":"1014","intvolume":" 80","ddc":["576"],"status":"public","title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","_id":"723","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"05","language":[{"iso":"eng"}],"doi":"10.1007/s00453-017-0369-2","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000428239300010"]},"ec_funded":1,"publist_id":"6957","file_date_updated":"2020-07-14T12:47:54Z","volume":80,"date_created":"2018-12-11T11:48:09Z","date_updated":"2023-09-11T14:11:35Z","author":[{"full_name":"Oliveto, Pietro","last_name":"Oliveto","first_name":"Pietro"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia","first_name":"Jorge"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora"}],"publisher":"Springer","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","year":"2018"},{"issue":"4","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"282","intvolume":" 209","title":"Introgression of a block of genome under infinitesimal selection","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","citation":{"ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018."},"publication":"Genetics","page":"1279 - 1303","publist_id":"7617","author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"volume":209,"date_updated":"2023-09-13T08:22:32Z","date_created":"2018-12-11T11:45:36Z","year":"2018","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","month":"08","doi":"10.1534/genetics.118.301018","language":[{"iso":"eng"}],"external_id":{"isi":["000440014100020"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"isi":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301429","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000452315900021"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/379578v1"}],"publication_identifier":{"issn":["00166731"]},"month":"12","volume":210,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:10:29Z","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","year":"2018","date_published":"2018-12-04T00:00:00Z","page":"1411-1427","article_type":"original","citation":{"mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429"},"publication":"Genetics","article_processing_charge":"No","day":"04","scopus_import":"1","oa_version":"Preprint","intvolume":" 210","status":"public","title":"Replicability of introgression under linked, polygenic selection","_id":"39","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","abstract":[{"text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.","lang":"eng"}],"type":"journal_article"},{"type":"journal_article","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"issue":"43","_id":"38","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Selection and gene flow shape genomic islands that control floral guides","ddc":["570"],"intvolume":" 115","file":[{"file_name":"11006.full.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1911302,"file_id":"5683","relation":"main_file","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-17T08:44:03Z","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1"}],"oa_version":"Published Version","scopus_import":"1","day":"23","has_accepted_license":"1","article_processing_charge":"No","publication":"PNAS","citation":{"apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115."},"page":"11006 - 11011","date_published":"2018-10-23T00:00:00Z","file_date_updated":"2020-07-14T12:46:16Z","publist_id":"8017","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","acknowledgement":" ERC Grant 201252 (to N.H.B.)","year":"2018","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"author":[{"last_name":"Tavares","first_name":"Hugo","full_name":"Tavares, Hugo"},{"last_name":"Whitley","first_name":"Annabel","full_name":"Whitley, Annabel"},{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"full_name":"Bradley, Desmond","first_name":"Desmond","last_name":"Bradley"},{"first_name":"Matthew","last_name":"Couchman","full_name":"Couchman, Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"first_name":"Joane","last_name":"Elleouet","full_name":"Elleouet, Joane"},{"full_name":"Burrus, Monique","last_name":"Burrus","first_name":"Monique"},{"full_name":"Andalo, Christophe","first_name":"Christophe","last_name":"Andalo"},{"full_name":"Li, Miaomiao","first_name":"Miaomiao","last_name":"Li"},{"first_name":"Qun","last_name":"Li","full_name":"Li, Qun"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"first_name":"Alexandra B","last_name":"Rebocho","full_name":"Rebocho, Alexandra B"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:36:49Z","volume":115,"month":"10","publication_identifier":{"issn":["00278424"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1801832115","language":[{"iso":"eng"}]},{"publist_id":"8014","file_date_updated":"2020-07-14T12:46:22Z","volume":27,"date_updated":"2023-09-19T10:06:08Z","date_created":"2018-12-11T11:44:18Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9805"}]},"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2018","publication_identifier":{"issn":["1365294X"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1111/mec.14950","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000454600500001"],"pmid":["30599087"]},"oa":1,"issue":"24","abstract":[{"lang":"eng","text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6652","date_updated":"2020-07-14T12:46:22Z","date_created":"2019-07-19T06:54:46Z","file_name":"2018_MolecularEcology_BartonNick.pdf","access_level":"open_access","file_size":295452,"content_type":"application/pdf","creator":"apreinsp"}],"intvolume":" 27","ddc":["576"],"title":"The consequences of an introgression event","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"40","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"31","scopus_import":"1","date_published":"2018-12-31T00:00:00Z","page":"4973-4975","article_type":"letter_note","citation":{"ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975."},"publication":"Molecular Ecology"},{"month":"01","doi":"10.1534/genetics.117.300426","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}],"oa":1,"external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"isi":1,"quality_controlled":"1","publist_id":"7249","author":[{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"volume":208,"date_updated":"2023-09-19T10:12:31Z","date_created":"2018-12-11T11:47:12Z","pmid":1,"year":"2018","department":[{"_id":"NiBa"}],"publisher":"Genetics ","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","citation":{"ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426."},"publication":"Genetics","page":"377 - 382","article_type":"original","issue":"1","abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"type":"journal_article","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"565","intvolume":" 208","status":"public","title":"The spread of an inversion with migration and selection"},{"month":"04","external_id":{"isi":["000429094400005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1534/genetics.118.300786","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:26Z","publist_id":"7393","year":"2018","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"author":[{"full_name":"Novembre, John","first_name":"John","last_name":"Novembre"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"date_updated":"2023-09-19T10:17:30Z","date_created":"2018-12-11T11:46:26Z","volume":208,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Genetics","citation":{"chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786"},"page":"1351 - 1355","date_published":"2018-04-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly.","lang":"eng"}],"issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"430","status":"public","title":"Tread lightly interpreting polygenic tests of selection","ddc":["576"],"intvolume":" 208","pubrep_id":"1012","file":[{"file_id":"4958","relation":"main_file","date_updated":"2020-07-14T12:46:26Z","date_created":"2018-12-12T10:12:40Z","checksum":"3d838dc285df394376555b794b6a5ad1","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","access_level":"open_access","creator":"system","file_size":500129,"content_type":"application/pdf"}],"oa_version":"Published Version"},{"date_published":"2018-08-01T00:00:00Z","publication":"Physica D: Nonlinear Phenomena","citation":{"chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015"},"page":"108-120","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"607","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","status":"public","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"type":"journal_article","doi":"10.1016/j.physd.2017.10.015","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"external_id":{"arxiv":["1704.08757"],"isi":["000437962900012"]},"quality_controlled":"1","isi":1,"month":"08","author":[{"first_name":"Katarina","last_name":"Bodova","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina"},{"full_name":"Haskovec, Jan","last_name":"Haskovec","first_name":"Jan"},{"full_name":"Markowich, Peter","last_name":"Markowich","first_name":"Peter"}],"date_updated":"2023-09-19T10:38:34Z","date_created":"2018-12-11T11:47:28Z","volume":"376-377","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","year":"2018","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Elsevier","publist_id":"7198"},{"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"doi":"10.15479/AT:ISTA:th_963","publication_identifier":{"issn":["2663-337X"]},"month":"02","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","date_updated":"2023-09-20T12:00:56Z","date_created":"2018-12-11T11:45:10Z","related_material":{"record":[{"id":"563","status":"public","relation":"part_of_dissertation"},{"id":"1074","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Harald","last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald"}],"publist_id":"7713","file_date_updated":"2020-07-14T12:45:23Z","page":"146","citation":{"ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963."},"date_published":"2018-02-21T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"21","status":"public","title":"Inferring recent demography from spatial genetic structure","ddc":["576"],"_id":"200","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"open_access","file_name":"IST-2018-963-v1+1_thesis.pdf","file_size":5792935,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5111","checksum":"8cc534d2b528ae017acf80874cce48c9","date_created":"2018-12-12T10:14:55Z","date_updated":"2020-07-14T12:45:23Z"},{"file_id":"6224","relation":"source_file","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","date_created":"2019-04-05T09:30:12Z","date_updated":"2020-07-14T12:45:23Z","access_level":"closed","file_name":"2018_thesis_ringbauer_source.zip","creator":"dernst","content_type":"application/zip","file_size":113365}],"oa_version":"Published Version","pubrep_id":"963","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}]},{"publication":"PeerJ","citation":{"chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198"},"date_published":"2018-07-30T00:00:00Z","scopus_import":"1","day":"30","has_accepted_license":"1","article_processing_charge":"No","_id":"139","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","ddc":["576"],"status":"public","intvolume":" 2018","oa_version":"Published Version","file":[{"date_created":"2018-12-18T09:42:11Z","date_updated":"2020-07-14T12:44:48Z","checksum":"7d55ae22598a1c70759cd671600cff53","file_id":"5739","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1480792,"file_name":"2018_PeerJ_Fraisse.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.","lang":"eng"}],"issue":"7","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000440484800002"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.7717/peerj.5198","language":[{"iso":"eng"}],"month":"07","year":"2018","publication_status":"published","publisher":"PeerJ","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"full_name":"Gagnaire, Pierre","last_name":"Gagnaire","first_name":"Pierre"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"last_name":"Faivre","first_name":"Nicolas","full_name":"Faivre, Nicolas"},{"first_name":"John","last_name":"Welch","full_name":"Welch, John"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"date_created":"2018-12-11T11:44:50Z","date_updated":"2023-10-17T12:25:28Z","volume":2018,"article_number":"30083438","file_date_updated":"2020-07-14T12:44:48Z","publist_id":"7784"},{"abstract":[{"text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.","lang":"eng"}],"issue":"10","type":"journal_article","file":[{"access_level":"open_access","file_name":"2018_PeerJ_Bertl.pdf","creator":"dernst","content_type":"application/pdf","file_size":1328344,"file_id":"5692","relation":"main_file","checksum":"3334886c4b39678db4c4b74299ca14ba","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-17T10:46:06Z"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"33","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","ddc":["576"],"status":"public","intvolume":" 2018","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-10-01T00:00:00Z","publication":"PeerJ","citation":{"ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325.","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325."},"file_date_updated":"2020-07-14T12:46:06Z","publist_id":"8022","article_number":"e5325","author":[{"full_name":"Bertl, Johanna","last_name":"Bertl","first_name":"Johanna"},{"full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","first_name":"Harald"},{"last_name":"Blum","first_name":"Michaël","full_name":"Blum, Michaël"}],"date_created":"2018-12-11T11:44:16Z","date_updated":"2023-10-17T12:24:43Z","volume":2018,"year":"2018","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"PeerJ","month":"10","doi":"10.7717/peerj.5325","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30294507"],"isi":["000447204400001"]},"oa":1,"isi":1,"quality_controlled":"1"},{"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","year":"2018","acknowledgement":"ERC, Grant/Award Number: 250152","volume":18,"date_created":"2018-12-11T11:45:37Z","date_updated":"2024-02-21T13:45:00Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5583"}]},"author":[{"orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"ec_funded":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000441753000007"]},"language":[{"iso":"eng"}],"doi":"10.1111/1755-0998.12782","month":"09","intvolume":" 18","status":"public","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"286","oa_version":"None","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. "}],"page":"988 - 999","citation":{"ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782."},"publication":"Molecular Ecology Resources","date_published":"2018-09-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"has_accepted_license":"1","article_processing_charge":"No","day":"12","month":"02","doi":"10.15479/AT:ISTA:95","date_published":"2018-02-12T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.","mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.","short":"T. Ellis, (2018).","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95.","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95"},"oa":1,"file_date_updated":"2020-07-14T12:47:07Z","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"type":"research_data","datarep_id":"95","file":[{"access_level":"open_access","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","creator":"system","content_type":"text/csv","file_size":122048,"file_id":"5606","relation":"main_file","checksum":"fc6aab51439f2622ba6df8632e66fd4f","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:41Z"},{"relation":"main_file","file_id":"5607","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:42Z","checksum":"92347586ae4f8a6eb7c04354797bf314","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","access_level":"open_access","content_type":"text/csv","file_size":235980,"creator":"system"},{"checksum":"3300813645a54e6c5c39f41917228354","date_created":"2018-12-12T13:02:43Z","date_updated":"2020-07-14T12:47:07Z","relation":"main_file","file_id":"5608","content_type":"text/csv","file_size":311712,"creator":"system","access_level":"open_access","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv"},{"date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:44Z","checksum":"e739fc473567fd8f39438b445fc46147","file_id":"5609","relation":"main_file","creator":"system","content_type":"application/zip","file_size":342090,"file_name":"IST-2018-95-v1+4_faps_scripts.zip","access_level":"open_access"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:39Z","date_updated":"2024-02-21T13:45:01Z","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"related_material":{"record":[{"id":"286","status":"public","relation":"research_paper"}]},"author":[{"orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"status":"public","title":"Data and Python scripts supporting Python package FAPS","year":"2018","_id":"5583","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"research_data","ec_funded":1,"file_date_updated":"2020-07-14T12:47:11Z","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"year":"2018","_id":"5757","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"ddc":["576"],"status":"public","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","related_material":{"record":[{"id":"6089","relation":"research_paper","status":"public"}]},"contributor":[{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"}],"file":[{"content_type":"application/zip","file_size":369837892,"creator":"cfraisse","access_level":"open_access","file_name":"FileS1.zip","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:52Z","relation":"main_file","file_id":"5758"},{"creator":"cfraisse","file_size":84856909,"content_type":"application/zip","file_name":"FileS2.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"3592e467b4d8206650860b612d6e12f3","file_id":"5759","relation":"main_file"},{"file_id":"5760","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"c37ac5d5437c457338afc128c1240655","file_name":"FileS3.txt","access_level":"open_access","creator":"cfraisse","file_size":881133,"content_type":"text/plain"},{"date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","checksum":"943dfd14da61817441e33e3e3cb8cdb9","file_id":"5761","relation":"main_file","creator":"cfraisse","content_type":"text/plain","file_size":883742,"file_name":"FileS4.txt","access_level":"open_access"},{"checksum":"1c669b6c4690ec1bbca3e2da9f566d17","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","relation":"main_file","file_id":"5762","file_size":2495437,"content_type":"text/plain","creator":"cfraisse","access_level":"open_access","file_name":"FileS5.txt"},{"creator":"cfraisse","content_type":"text/plain","file_size":15913457,"file_name":"FileS6.txt","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763","relation":"main_file"},{"file_size":2584120,"content_type":"text/plain","creator":"cfraisse","access_level":"open_access","file_name":"FileS7.txt","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","date_created":"2018-12-19T14:19:50Z","date_updated":"2020-07-14T12:47:11Z","relation":"main_file","file_id":"5764"},{"date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","relation":"main_file","file_id":"5765","file_size":2446059,"content_type":"text/plain","creator":"cfraisse","file_name":"FileS8.txt","access_level":"open_access"},{"creator":"cfraisse","content_type":"text/plain","file_size":100737,"access_level":"open_access","file_name":"FileS9.txt","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","file_id":"5766","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:59:18Z","date_created":"2018-12-19T14:22:35Z","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"article_processing_charge":"No","has_accepted_license":"1","month":"12","day":"19","oa":1,"citation":{"ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","short":"C. Fraisse, (2018)."},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"doi":"10.15479/at:ista:/5757","date_published":"2018-12-19T00:00:00Z"},{"language":[{"iso":"eng"}],"conference":{"end_date":"2017-01-15","start_date":"2017-01-12","location":"Copenhagen, Denmark","name":"FOGA: Foundations of Genetic Algorithms"},"doi":"10.1145/3040718.3040729","date_published":"2017-01-12T00:00:00Z","quality_controlled":"1","page":"3 - 11","publication":"Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms","citation":{"ama":"Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729","ista":"Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.","apa":"Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729","ieee":"T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.","mla":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.","short":"T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.","chicago":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729."},"month":"01","day":"12","publication_identifier":{"isbn":["978-145034651-1"]},"scopus_import":1,"date_updated":"2021-01-12T06:48:22Z","date_created":"2018-12-11T11:50:12Z","oa_version":"None","author":[{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"last_name":"Pérez Heredia","first_name":"Jorge","full_name":"Pérez Heredia, Jorge"}],"publication_status":"published","title":"An application of stochastic differential equations to evolutionary algorithms","status":"public","department":[{"_id":"NiBa"}],"publisher":"ACM","_id":"1112","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"There has been renewed interest in modelling the behaviour of evolutionary algorithms by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogs of the additive and multiplicative drift theorems for SDEs. We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS) on two canonical problems(OneMax and LeadingOnes).","lang":"eng"}],"publist_id":"6255","type":"conference"},{"issue":"3","abstract":[{"lang":"eng","text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 79","status":"public","title":"Existence of traveling waves for the generalized F–KPP equation","_id":"1191","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":1,"date_published":"2017-03-01T00:00:00Z","page":"525-559","citation":{"ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.","ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017.","apa":"Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3","mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3.","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3."},"publication":"Bulletin of Mathematical Biology","publist_id":"6160","ec_funded":1,"volume":79,"date_updated":"2021-01-12T06:48:58Z","date_created":"2018-12-11T11:50:38Z","author":[{"last_name":"Kollár","first_name":"Richard","full_name":"Kollár, Richard"},{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"publisher":"Springer","publication_status":"published","acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","year":"2017","month":"03","language":[{"iso":"eng"}],"doi":"10.1007/s11538-016-0244-3","project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1607.00944","open_access":"1"}],"oa":1},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.28921","month":"11","publication_identifier":{"issn":["2050084X"]},"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","year":"2017","date_created":"2018-12-11T11:47:14Z","date_updated":"2021-01-12T08:03:15Z","volume":6,"author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator"},{"last_name":"Sarikas","first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan"},{"first_name":"Hande","last_name":"Acar","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","full_name":"Acar, Hande"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"article_number":"e28921","file_date_updated":"2020-07-14T12:47:10Z","ec_funded":1,"publist_id":"7244","publication":"eLife","citation":{"ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921.","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017.","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.","short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921."},"date_published":"2017-11-13T00:00:00Z","scopus_import":1,"day":"13","has_accepted_license":"1","ddc":["576"],"title":"Regulatory network structure determines patterns of intermolecular epistasis","status":"public","intvolume":" 6","_id":"570","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":8453470,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:14:42Z","checksum":"273ab17f33305e4eaafd911ff88e7c5b","relation":"main_file","file_id":"5096"},{"file_size":1953221,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","checksum":"b433f90576c7be597cd43367946f8e7f","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:14:43Z","relation":"main_file","file_id":"5097"}],"oa_version":"Published Version","pubrep_id":"918","type":"journal_article","abstract":[{"text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. ","lang":"eng"}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity."}],"publist_id":"7193","issue":"6365","status":"public","title":"Evolution of flower color pattern through selection on regulatory small RNAs","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"American Association for the Advancement of Science","intvolume":" 358","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"611","year":"2017","date_updated":"2021-01-12T08:06:10Z","date_created":"2018-12-11T11:47:29Z","oa_version":"None","volume":358,"author":[{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"last_name":"Xu","first_name":"Ping","full_name":"Xu, Ping"},{"full_name":"Mohorianu, Irina","first_name":"Irina","last_name":"Mohorianu"},{"first_name":"Annabel","last_name":"Whibley","full_name":"Whibley, Annabel"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"last_name":"Tavares","first_name":"Hugo","full_name":"Tavares, Hugo"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"full_name":"Copsey, Lucy","last_name":"Copsey","first_name":"Lucy"},{"first_name":"Rosemary","last_name":"Carpenter","full_name":"Carpenter, Rosemary"},{"last_name":"Li","first_name":"Miaomiao","full_name":"Li, Miaomiao"},{"first_name":"Qun","last_name":"Li","full_name":"Li, Qun"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"full_name":"Dalmay, Tamas","first_name":"Tamas","last_name":"Dalmay"},{"full_name":"Coen, Enrico","last_name":"Coen","first_name":"Enrico"}],"scopus_import":1,"day":"17","month":"11","publication_identifier":{"issn":["00368075"]},"quality_controlled":"1","page":"925 - 928","publication":"Science","citation":{"chicago":"Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aao3526.","short":"D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928.","mla":"Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:10.1126/science.aao3526.","ieee":"D. Bradley et al., “Evolution of flower color pattern through selection on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017.","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao3526","ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","ama":"Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 2017;358(6365):925-928. doi:10.1126/science.aao3526"},"language":[{"iso":"eng"}],"doi":"10.1126/science.aao3526","date_published":"2017-11-17T00:00:00Z"},{"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"}],"date_created":"2018-12-11T11:47:34Z","date_updated":"2021-01-12T08:06:50Z","volume":118,"year":"2017","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Academic Press","file_date_updated":"2020-07-14T12:47:25Z","publist_id":"7169","ec_funded":1,"doi":"10.1016/j.tpb.2017.06.001","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"month":"12","publication_identifier":{"issn":["00405809"]},"pubrep_id":"908","file":[{"access_level":"open_access","file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf","content_type":"application/pdf","file_size":1133924,"creator":"system","relation":"main_file","file_id":"4964","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8","date_created":"2018-12-12T10:12:45Z","date_updated":"2020-07-14T12:47:25Z"}],"oa_version":"Published Version","_id":"626","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["576"],"title":"The infinitesimal model: Definition derivation and implications","intvolume":" 118","abstract":[{"text":"Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.","lang":"eng"}],"type":"journal_article","date_published":"2017-12-01T00:00:00Z","publication":"Theoretical Population Biology","citation":{"chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology. Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73.","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology, vol. 118, Academic Press, 2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” Theoretical Population Biology, vol. 118. Academic Press, pp. 50–73, 2017.","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001","ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","ama":"Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001"},"page":"50 - 73","day":"01","has_accepted_license":"1","scopus_import":1},{"article_processing_charge":"No","day":"18","month":"07","citation":{"ista":"Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, 10.1371/journal.pcbi.1005609.s001.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:10.1371/journal.pcbi.1005609.s001","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001.","mla":"Lukacisinova, Marta, et al. Modelling and Simulation Details. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017)."},"date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s001","type":"research_data_reference","abstract":[{"lang":"eng","text":"This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set."}],"publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"title":"Modelling and simulation details","status":"public","_id":"9849","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-02-23T12:55:39Z","date_created":"2021-08-09T14:02:34Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"696"}]},"author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"}]},{"doi":"10.1371/journal.pcbi.1005609.s002","date_published":"2017-07-18T00:00:00Z","citation":{"ista":"Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, 10.1371/journal.pcbi.1005609.s002.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002","ama":"Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002.","mla":"Lukacisinova, Marta, et al. Extensions of the Model. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017)."},"day":"18","month":"07","article_processing_charge":"No","author":[{"orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"related_material":{"record":[{"id":"696","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-09T14:05:24Z","date_updated":"2023-02-23T12:55:39Z","oa_version":"Published Version","_id":"9850","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2017","status":"public","title":"Extensions of the model","publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"abstract":[{"text":"In this text, we discuss how a cost of resistance and the possibility of lethal mutations impact our model.","lang":"eng"}],"type":"research_data_reference"},{"article_processing_charge":"No","month":"07","day":"18","citation":{"apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.","ama":"Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","mla":"Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003."},"doi":"10.1371/journal.pcbi.1005609.s003","date_published":"2017-07-18T00:00:00Z","type":"research_data_reference","abstract":[{"text":"Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations.","lang":"eng"}],"department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"publisher":"Public Library of Science","title":"Heuristic prediction for multiple stresses","status":"public","year":"2017","_id":"9851","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-02-23T12:55:39Z","date_created":"2021-08-09T14:08:14Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"696"}]},"author":[{"full_name":"Lukacisinova, Marta","first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"}]},{"abstract":[{"lang":"eng","text":"We show how different combination strategies affect the fraction of individuals that are multi-resistant."}],"type":"research_data_reference","date_created":"2021-08-09T14:11:40Z","date_updated":"2023-02-23T12:55:39Z","oa_version":"Published Version","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta"},{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"}],"related_material":{"record":[{"id":"696","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Resistance frequencies for different combination strategies","publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"_id":"9852","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"07","day":"18","article_processing_charge":"No","date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s004","citation":{"ista":"Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004","ama":"Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004.","mla":"Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017)."}},{"abstract":[{"text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population.","lang":"eng"}],"file_date_updated":"2021-02-22T13:45:59Z","type":"dissertation","alternative_title":["ISTA Thesis"],"author":[{"full_name":"Payne, Pavel","last_name":"Payne","first_name":"Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"dernst","content_type":"application/pdf","file_size":3025175,"access_level":"closed","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","date_updated":"2020-07-14T12:47:27Z","date_created":"2019-04-09T15:15:32Z","file_id":"6292","relation":"main_file"},{"file_size":3111536,"content_type":"application/pdf","creator":"dernst","file_name":"2017_Payne_Thesis.pdf","access_level":"open_access","date_updated":"2021-02-22T13:45:59Z","date_created":"2021-02-22T13:45:59Z","checksum":"af531e921a7f64a9e0af4cd8783b2226","success":1,"relation":"main_file","file_id":"9187"}],"oa_version":"Published Version","date_created":"2019-04-09T15:16:45Z","date_updated":"2023-09-07T12:00:00Z","_id":"6291","year":"2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Bacterial herd and social immunity to phages","publication_status":"published","status":"public","ddc":["570"],"article_processing_charge":"No","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"day":"01","month":"02","date_published":"2017-02-01T00:00:00Z","language":[{"iso":"eng"}],"supervisor":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"degree_awarded":"PhD","oa":1,"citation":{"short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017.","mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","apa":"Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria."},"page":"83"},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}],"citation":{"apa":"Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:10.17632/nw68fxzjpm.1","chicago":"Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.","short":"A. Etheridge, N.H. Barton, (2017).","mla":"Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1."},"doi":"10.17632/nw68fxzjpm.1","date_published":"2017-12-29T00:00:00Z","article_processing_charge":"No","month":"12","day":"29","_id":"9842","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2017","department":[{"_id":"NiBa"}],"publisher":"Mendeley Data","title":"Data for: Establishment in a new habitat by polygenic adaptation","status":"public","related_material":{"record":[{"id":"564","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","date_updated":"2023-09-11T13:41:21Z","date_created":"2021-08-09T13:18:55Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Mathematica notebooks used to generate figures."}]},{"publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"publication_status":"published","year":"2017","volume":54,"date_created":"2018-12-11T11:51:32Z","date_updated":"2023-09-20T11:06:03Z","related_material":{"record":[{"id":"1835","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","first_name":"Mirco"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana","full_name":"Petrov, Tatjana"}],"ec_funded":1,"publist_id":"5898","file_date_updated":"2020-07-14T12:44:46Z","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000414343200003"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00236-016-0278-x","publication_identifier":{"issn":["00015903"]},"month":"12","intvolume":" 54","title":"Model checking the evolution of gene regulatory networks","status":"public","ddc":["006","576"],"_id":"1351","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"dernst","content_type":"application/pdf","file_size":755241,"access_level":"open_access","file_name":"2017_ActaInformatica_Giacobbe.pdf","checksum":"4e661d9135d7f8c342e8e258dee76f3e","date_updated":"2020-07-14T12:44:46Z","date_created":"2019-01-17T15:57:29Z","file_id":"5841","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"649","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"page":"765 - 787","citation":{"chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8. Springer, pp. 765–787, 2017.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer. https://doi.org/10.1007/s00236-016-0278-x","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x"},"publication":"Acta Informatica","date_published":"2017-12-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5931","ec_funded":1,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Springer","year":"2017","date_created":"2018-12-11T11:51:27Z","date_updated":"2023-09-20T11:14:42Z","volume":78,"author":[{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"full_name":"Pérez Heredia, Jorge","first_name":"Jorge","last_name":"Pérez Heredia"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"}],"month":"06","publication_identifier":{"issn":["01784617"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000400379500013"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00453-016-0212-1","type":"journal_article","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"issue":"2","status":"public","ddc":["576"],"title":"Towards a runtime comparison of natural and artificial evolution","intvolume":" 78","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1336","file":[{"creator":"system","content_type":"application/pdf","file_size":710206,"file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:10:19Z","checksum":"7873f665a0c598ac747c908f34cb14b9","file_id":"4805","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"658","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","page":"681 - 713","publication":"Algorithmica","citation":{"chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica. Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2. Springer, pp. 681–713, 2017.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica. Springer. https://doi.org/10.1007/s00453-016-0212-1","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1"},"date_published":"2017-06-01T00:00:00Z"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2017-01-01T00:00:00Z","page":"96 - 109","citation":{"ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109.","apa":"Barton, N. H. (2017). How does epistasis influence the response to selection? Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” Heredity, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","ama":"Barton NH. How does epistasis influence the response to selection? Heredity. 2017;118:96-109. doi:10.1038/hdy.2016.109","chicago":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.","mla":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.","short":"N.H. Barton, Heredity 118 (2017) 96–109."},"publication":"Heredity","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 118","status":"public","title":"How does epistasis influence the response to selection?","_id":"1199","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"01","language":[{"iso":"eng"}],"doi":"10.1038/hdy.2016.109","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/","open_access":"1"}],"oa":1,"external_id":{"isi":["000392229100011"]},"publist_id":"6151","ec_funded":1,"volume":118,"date_updated":"2023-09-20T11:17:47Z","date_created":"2018-12-11T11:50:40Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9710"}]},"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Nature Publishing Group","publication_status":"published","year":"2017"},{"month":"01","publication_identifier":{"issn":["00166731"]},"oa":1,"external_id":{"isi":["000393677300025"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"doi":"10.1534/genetics.116.193946","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:37Z","publist_id":"6188","ec_funded":1,"year":"2017","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","author":[{"orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian"},{"first_name":"Richard","last_name":"Kollár","full_name":"Kollár, Richard"}],"date_created":"2018-12-11T11:50:31Z","date_updated":"2023-09-20T11:24:21Z","volume":205,"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Genetics","citation":{"ama":"Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946","ista":"Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374.","ieee":"S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp. 367–374, 2017.","apa":"Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946","mla":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America, 2017, pp. 367–74, doi:10.1534/genetics.116.193946.","short":"S. Novak, R. Kollár, Genetics 205 (2017) 367–374.","chicago":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193946."},"page":"367 - 374","date_published":"2017-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies."}],"issue":"1","_id":"1169","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576"],"status":"public","title":"Spatial gene frequency waves under genotype dependent dispersal","intvolume":" 205","pubrep_id":"727","file":[{"creator":"system","content_type":"application/pdf","file_size":361500,"access_level":"open_access","file_name":"IST-2016-727-v1+1_SFC_Genetics_final.pdf","checksum":"7c8ab79cda1f92760bbbbe0f53175bfc","date_created":"2018-12-12T10:10:43Z","date_updated":"2020-07-14T12:44:37Z","file_id":"4833","relation":"main_file"}],"oa_version":"Submitted Version"},{"publication_identifier":{"issn":["00166731"]},"month":"02","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1534/genetics.116.189340","open_access":"1"}],"external_id":{"isi":["000394144900025"],"pmid":["27881471"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.116.189340","ec_funded":1,"publist_id":"6256","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2017","volume":205,"date_updated":"2023-09-20T11:35:03Z","date_created":"2018-12-11T11:50:12Z","author":[{"full_name":"Heredia, Jorge","first_name":"Jorge","last_name":"Heredia"},{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"803 - 825","article_type":"original","citation":{"ama":"Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340","apa":"Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection limits to adaptive walks on correlated landscapes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.189340","ieee":"J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics Society of America, pp. 803–825, 2017.","ista":"Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825.","short":"J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.","mla":"Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25, doi:10.1534/genetics.116.189340.","chicago":"Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.189340."},"publication":"Genetics","date_published":"2017-02-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Adaptation depends critically on the effects of new mutations and their dependency on the genetic background in which they occur. These two factors can be summarized by the fitness landscape. However, it would require testing all mutations in all backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible. Instead of postulating a particular fitness landscape, we address this problem by considering general classes of landscapes and calculating an upper limit for the time it takes for a population to reach a fitness peak, circumventing the need to have full knowledge about the fitness landscape. We analyze populations in the weak-mutation regime and characterize the conditions that enable them to quickly reach the fitness peak as a function of the number of sites under selection. We show that for additive landscapes there is a critical selection strength enabling populations to reach high-fitness genotypes, regardless of the distribution of effects. This threshold scales with the number of sites under selection, effectively setting a limit to adaptation, and results from the inevitable increase in deleterious mutational pressure as the population adapts in a space of discrete genotypes. Furthermore, we show that for the class of all unimodal landscapes this condition is sufficient but not necessary for rapid adaptation, as in some highly epistatic landscapes the critical strength does not depend on the number of sites under selection; effectively removing this barrier to adaptation."}],"intvolume":" 205","status":"public","title":"Selection limits to adaptive walks on correlated landscapes","_id":"1111","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version"},{"author":[{"full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","last_name":"Fernandes Redondo"},{"orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","first_name":"Harold","full_name":"Vladar, Harold"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9864"}]},"date_created":"2018-12-11T11:50:01Z","date_updated":"2023-09-20T11:56:34Z","volume":14,"year":"2017","publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2019-01-18T09:14:02Z","ec_funded":1,"publist_id":"6303","article_number":"20160139","doi":"10.1098/rsif.2016.0139","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000393380400001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"month":"01","publication_identifier":{"issn":["17425689"]},"file":[{"relation":"main_file","file_id":"5843","success":1,"date_updated":"2019-01-18T09:14:02Z","date_created":"2019-01-18T09:14:02Z","access_level":"open_access","file_name":"2017_JRSI_Redondo.pdf","content_type":"application/pdf","file_size":1092015,"creator":"dernst"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1077","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","ddc":["570"],"status":"public","intvolume":" 14","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"issue":"126","type":"journal_article","date_published":"2017-01-04T00:00:00Z","publication":"Journal of the Royal Society Interface","citation":{"chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139"},"day":"04","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1"},{"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2017","date_updated":"2023-09-20T12:00:56Z","date_created":"2018-12-11T11:50:00Z","volume":205,"author":[{"orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","first_name":"Harald","full_name":"Ringbauer, Harald"},{"full_name":"Coop, Graham","last_name":"Coop","first_name":"Graham"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"id":"200","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"publist_id":"6307","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000395807200023"]},"main_file_link":[{"url":"http://www.biorxiv.org/content/early/2016/09/23/076810","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.116.196220","month":"03","publication_identifier":{"issn":["00166731"]},"status":"public","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","intvolume":" 205","_id":"1074","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.","lang":"eng"}],"issue":"3","page":"1335 - 1351","publication":"Genetics","citation":{"ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","apa":"Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351."},"date_published":"2017-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"date_published":"2017-04-01T00:00:00Z","citation":{"chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191.","short":"H. Uecker, Evolution 71 (2017) 845–858.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191"},"publication":"Evolution","page":"845 - 858","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1063","intvolume":" 71","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","status":"public","issue":"4","abstract":[{"lang":"eng","text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations."}],"type":"journal_article","doi":"10.1111/evo.13191","language":[{"iso":"eng"}],"external_id":{"isi":["000398545200003"]},"main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2016/10/14/081042"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00143820"]},"month":"04","author":[{"full_name":"Uecker, Hildegard","last_name":"Uecker","first_name":"Hildegard","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"}],"volume":71,"date_created":"2018-12-11T11:49:57Z","date_updated":"2023-09-20T12:10:32Z","year":"2017","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","ec_funded":1,"publist_id":"6327"},{"external_id":{"isi":["000403014800005"],"pmid":["28419447"]},"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1111/evo.13252","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00143820"]},"month":"06","pmid":1,"year":"2017","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"volume":71,"date_created":"2018-12-11T11:49:34Z","date_updated":"2023-09-22T09:55:13Z","ec_funded":1,"publist_id":"6409","file_date_updated":"2020-07-14T12:48:18Z","citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell, 2017, pp. 1478–93, doi:10.1111/evo.13252.","ieee":"H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow,” Evolution; International Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493, 2017.","apa":"Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252","ista":"Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 71(6), 1478–1493.","ama":"Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252"},"publication":"Evolution; International Journal of Organic Evolution","page":"1478 - 1493 ","date_published":"2017-06-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"990","intvolume":" 71","ddc":["576"],"title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","status":"public","pubrep_id":"977","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2017_Evolution_Sachdeva_supplement.pdf","content_type":"application/pdf","file_size":625260,"creator":"dernst","relation":"main_file","file_id":"6329","checksum":"6d4c38cb1347fd43620d1736c6df5c79","date_updated":"2020-07-14T12:48:18Z","date_created":"2019-04-17T07:37:04Z"},{"file_name":"2017_Evolution_Sachdeva_article.pdf","access_level":"open_access","content_type":"application/pdf","file_size":520110,"creator":"dernst","relation":"main_file","file_id":"6330","date_created":"2019-04-17T07:37:04Z","date_updated":"2020-07-14T12:48:18Z","checksum":"f1d90dd8831b44baf49b4dd176f263af"}],"type":"journal_article","issue":"6","abstract":[{"text":"Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.","lang":"eng"}]},{"file_date_updated":"2020-07-14T12:48:16Z","ec_funded":1,"publist_id":"6460","article_number":"e25192","date_created":"2018-12-11T11:49:23Z","date_updated":"2023-09-22T10:01:17Z","volume":6,"author":[{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"eLife Sciences Publications","year":"2017","month":"05","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.25192","quality_controlled":"1","isi":1,"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000404024800001"]},"abstract":[{"text":"Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","content_type":"application/pdf","file_size":2441529,"creator":"system","relation":"main_file","file_id":"5306","checksum":"59cdd4400fb41280122d414fea971546","date_created":"2018-12-12T10:17:49Z","date_updated":"2020-07-14T12:48:16Z"},{"checksum":"b69024880558b858eb8c5d47a92b6377","date_created":"2018-12-12T10:17:50Z","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","file_id":"5307","file_size":3752660,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf"}],"pubrep_id":"841","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","ddc":["576"],"status":"public","intvolume":" 6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"954","day":"18","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2017-05-18T00:00:00Z","publication":"eLife","citation":{"ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192","ieee":"M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.","chicago":"Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192."}},{"publication_identifier":{"issn":["20411723"]},"month":"08","doi":"10.1038/s41467-017-00238-8","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000407198800005"]},"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"ec_funded":1,"publist_id":"6459","file_date_updated":"2020-07-14T12:48:16Z","article_number":"216","related_material":{"record":[{"id":"6071","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"volume":8,"date_created":"2018-12-11T11:49:23Z","date_updated":"2023-09-22T10:00:49Z","year":"2017","publisher":"Nature Publishing Group","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"09","scopus_import":"1","date_published":"2017-08-09T00:00:00Z","citation":{"ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8."},"publication":"Nature Communications","issue":"1","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"type":"journal_article","pubrep_id":"864","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5064","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:14:14Z","checksum":"29a1b5db458048d3bd5c67e0e2a56818","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","access_level":"open_access","file_size":998157,"content_type":"application/pdf","creator":"system"},{"file_size":9715993,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","date_created":"2018-12-12T10:14:15Z","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","file_id":"5065"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"955","intvolume":" 8","status":"public","ddc":["539","576"],"title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes"},{"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/"}],"external_id":{"isi":["000405148800021"],"pmid":["28566483"]},"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2016.2864","month":"05","publisher":"Royal Society, The","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2017","volume":284,"date_created":"2018-12-11T11:49:23Z","date_updated":"2023-09-22T10:01:48Z","author":[{"full_name":"Charlesworth, Deborah","last_name":"Charlesworth","first_name":"Deborah"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Charlesworth, Brian","first_name":"Brian","last_name":"Charlesworth"}],"article_number":"20162864","publist_id":"6462","citation":{"apa":"Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864","ieee":"D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855. Royal Society, The, 2017.","ista":"Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855), 20162864.","ama":"Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 2017;284(1855). doi:10.1098/rspb.2016.2864","chicago":"Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.","short":"D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017).","mla":"Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864."},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","date_published":"2017-05-31T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"31","intvolume":" 284","status":"public","title":"The sources of adaptive evolution","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"953","oa_version":"Submitted Version","type":"journal_article","issue":"1855","abstract":[{"text":"The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.","lang":"eng"}]},{"status":"public","ddc":["576"],"title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"952","file":[{"date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-17T06:39:45Z","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","file_id":"6327","relation":"main_file","creator":"dernst","file_size":2073856,"content_type":"application/pdf","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"972","type":"journal_article","abstract":[{"text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area.","lang":"eng"}],"page":"45 - 60","publication":"Theoretical Population Biology","citation":{"ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003","ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.","ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.","apa":"Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003."},"date_published":"2017-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"}],"year":"2017","pmid":1,"date_created":"2018-12-11T11:49:22Z","date_updated":"2023-09-22T10:02:21Z","volume":115,"author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"file_date_updated":"2020-07-14T12:48:16Z","publist_id":"6463","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["28411063"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.03.003","month":"06","publication_identifier":{"issn":["00405809"]}},{"ddc":["576"],"title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","status":"public","intvolume":" 15","_id":"951","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_size":5541206,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","checksum":"107d290bd1159ec77b734eb2824b01c8","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:08:30Z","relation":"main_file","file_id":"4691"}],"pubrep_id":"843","type":"journal_article","abstract":[{"lang":"eng","text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo"}],"issue":"5","publication":"PLoS Biology","citation":{"short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017).","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.","ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894","ieee":"T. Schmidt et al., “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894."},"date_published":"2017-05-30T00:00:00Z","scopus_import":"1","day":"30","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"year":"2017","date_updated":"2023-09-22T10:02:52Z","date_created":"2018-12-11T11:49:22Z","volume":15,"author":[{"last_name":"Schmidt","first_name":"Tom","full_name":"Schmidt, Tom"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Rasic, Gordana","first_name":"Gordana","last_name":"Rasic"},{"full_name":"Turley, Andrew","first_name":"Andrew","last_name":"Turley"},{"last_name":"Montgomery","first_name":"Brian","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki","last_name":"Iturbe Ormaetxe"},{"full_name":"Cook, Peter","first_name":"Peter","last_name":"Cook"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"full_name":"Hoffmann, Ary","first_name":"Ary","last_name":"Hoffmann"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9856"},{"status":"public","relation":"research_data","id":"9857"},{"id":"9858","relation":"research_data","status":"public"}]},"article_number":"e2001894","file_date_updated":"2020-07-14T12:48:16Z","publist_id":"6464","isi":1,"quality_controlled":"1","external_id":{"isi":["000402520000012"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2001894","month":"05","publication_identifier":{"issn":["15449173"]}},{"status":"public","title":"Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","year":"2017","_id":"9858","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-22T10:02:51Z","date_created":"2021-08-10T07:47:07Z","oa_version":"Published Version","author":[{"last_name":"Schmidt","first_name":"Tom","full_name":"Schmidt, Tom"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Rasic, Gordana","last_name":"Rasic","first_name":"Gordana"},{"full_name":"Turley, Andrew","first_name":"Andrew","last_name":"Turley"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki","last_name":"Iturbe Ormaetxe"},{"full_name":"Cook, Peter","first_name":"Peter","last_name":"Cook"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"first_name":"Scott","last_name":"Ritchie","full_name":"Ritchie, Scott"},{"full_name":"Hoffmann, Ary","first_name":"Ary","last_name":"Hoffmann"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"related_material":{"record":[{"id":"951","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","citation":{"chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s016.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","mla":"Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s016.","ieee":"T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016.","ama":"Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016"},"date_published":"2017-05-30T00:00:00Z","doi":"10.1371/journal.pbio.2001894.s016","day":"30","month":"05","article_processing_charge":"No"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9857","year":"2017","publisher":"Public Library of Science ","department":[{"_id":"NiBa"}],"title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","status":"public","related_material":{"record":[{"id":"951","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Rasic, Gordana","first_name":"Gordana","last_name":"Rasic"},{"full_name":"Turley, Andrew","first_name":"Andrew","last_name":"Turley"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki","last_name":"Iturbe Ormaetxe"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"first_name":"Scott","last_name":"Ritchie","full_name":"Ritchie, Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"oa_version":"Published Version","date_created":"2021-08-10T07:41:52Z","date_updated":"2023-09-22T10:02:51Z","type":"research_data_reference","citation":{"ieee":"T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , 10.1371/journal.pbio.2001894.s015.","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","mla":"Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015."},"date_published":"2017-05-30T00:00:00Z","doi":"10.1371/journal.pbio.2001894.s015","article_processing_charge":"No","month":"05","day":"30"},{"article_processing_charge":"No","month":"05","day":"30","citation":{"ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting Information concerning additional likelihood analyses and results, Public Library of Science, 10.1371/journal.pbio.2001894.s014.","ieee":"T. Schmidt et al., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting Information concerning additional likelihood analyses and results. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s014","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional likelihood analyses and results. 2017. doi:10.1371/journal.pbio.2001894.s014","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional Likelihood Analyses and Results.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s014.","mla":"Schmidt, Tom, et al. Supporting Information Concerning Additional Likelihood Analyses and Results. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s014.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017)."},"doi":"10.1371/journal.pbio.2001894.s014","date_published":"2017-05-30T00:00:00Z","type":"research_data_reference","_id":"9856","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"status":"public","title":"Supporting Information concerning additional likelihood analyses and results","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"author":[{"last_name":"Schmidt","first_name":"Tom","full_name":"Schmidt, Tom"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Gordana","last_name":"Rasic","full_name":"Rasic, Gordana"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"last_name":"Iturbe Ormaetxe","first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki"},{"full_name":"Cook, Peter","first_name":"Peter","last_name":"Cook"},{"full_name":"Ryan, Peter","first_name":"Peter","last_name":"Ryan"},{"full_name":"Ritchie, Scott","first_name":"Scott","last_name":"Ritchie"},{"full_name":"Hoffmann, Ary","first_name":"Ary","last_name":"Hoffmann"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"oa_version":"Published Version","date_updated":"2023-09-22T10:02:51Z","date_created":"2021-08-10T07:36:04Z"},{"doi":"10.1534/genetics.117.300129","language":[{"iso":"eng"}],"external_id":{"isi":["000412232600019"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"month":"10","author":[{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","first_name":"Sebastian","last_name":"Novak"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"date_updated":"2023-09-26T15:49:15Z","date_created":"2018-12-11T11:49:09Z","volume":207,"year":"2017","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","file_date_updated":"2020-07-14T12:48:15Z","ec_funded":1,"publist_id":"6533","date_published":"2017-10-01T00:00:00Z","publication":"Genetics","citation":{"mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.117.300129.","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","apa":"Novak, S., & Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129"},"page":"653 - 668","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","pubrep_id":"974","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":494268,"file_name":"IST-2018-974-v1+1_manuscript.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-12T10:17:12Z","checksum":"f7c32dabf52e6d9e709d9203761e39fd","file_id":"5264","relation":"main_file"}],"_id":"910","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576"],"status":"public","title":"When does frequency-independent selection maintain genetic variation?","intvolume":" 207","abstract":[{"lang":"eng","text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n"}],"issue":"2","type":"journal_article"},{"doi":"10.1038/s41467-017-01663-5","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["29133797"]},"oa":1,"quality_controlled":"1","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"month":"12","publication_identifier":{"issn":["20411723"]},"author":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Picard, Marion A","first_name":"Marion A","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"related_material":{"record":[{"id":"7163","relation":"popular_science","status":"public"}]},"date_updated":"2024-02-21T13:47:47Z","date_created":"2018-12-11T11:47:30Z","volume":8,"year":"2017","pmid":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:20Z","publist_id":"7190","article_number":"1486","date_published":"2017-12-01T00:00:00Z","publication":"Nature Communications","citation":{"short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","mla":"Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5.","chicago":"Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5.","ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01663-5","ieee":"C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","apa":"Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5","ista":"Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486."},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"pubrep_id":"910","oa_version":"Published Version","file":[{"file_name":"2017_NatureComm_Fraisse.pdf","access_level":"open_access","file_size":1201520,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7562","date_updated":"2020-07-14T12:47:20Z","date_created":"2020-03-03T15:55:50Z","checksum":"4da2651303c8afc2f7fc419be42a2433"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"614","ddc":["570","576"],"title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","status":"public","intvolume":" 8","abstract":[{"lang":"eng","text":"Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes."}],"issue":"1","type":"journal_article"},{"contributor":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"related_material":{"record":[{"id":"614","relation":"research_paper","status":"public"}]},"author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"}],"file":[{"access_level":"open_access","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","file_size":841375478,"content_type":"application/zip","creator":"cfraisse","relation":"main_file","file_id":"7164","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-10T08:46:46Z"}],"oa_version":"Published Version","date_created":"2019-12-09T23:03:03Z","date_updated":"2024-02-21T13:47:47Z","_id":"7163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["576"],"title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","file_date_updated":"2020-07-14T12:47:50Z","abstract":[{"lang":"eng","text":"The de novo genome assemblies generated for this study, and the associated metadata."}],"type":"research_data","doi":"10.15479/AT:ISTA:7163","date_published":"2017-12-01T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"C. Fraisse, (2017).","mla":"Fraisse, Christelle. Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:7163.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:7163.","ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:10.15479/AT:ISTA:7163","apa":"Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7163","ieee":"C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017.","ista":"Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7163."},"project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"article_processing_charge":"No","has_accepted_license":"1","month":"12","day":"01"},{"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1005609","publication_identifier":{"issn":["1553734X"]},"month":"07","publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","year":"2017","volume":13,"date_created":"2018-12-11T11:47:58Z","date_updated":"2024-03-28T23:30:28Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9849"},{"relation":"research_data","status":"public","id":"9850"},{"id":"9851","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9852"},{"id":"6263","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova"},{"last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"article_number":"e1005609","publist_id":"7004","ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","article_type":"original","citation":{"ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609."},"publication":"PLoS Computational Biology","date_published":"2017-07-18T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"18","intvolume":" 13","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","status":"public","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"696","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3775716,"creator":"system","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","access_level":"open_access","date_created":"2018-12-12T10:15:01Z","date_updated":"2020-07-14T12:47:46Z","checksum":"9143c290fa6458ed2563bff4b295554a","relation":"main_file","file_id":"5117"}],"pubrep_id":"894","type":"journal_article","issue":"7","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}]},{"has_accepted_license":"1","day":"19","scopus_import":1,"date_published":"2016-12-19T00:00:00Z","citation":{"mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6, 38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 2016;6. doi:10.1038/srep38840","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","apa":"Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38840","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” Scientific Reports, vol. 6. Nature Publishing Group, 2016."},"publication":"Scientific Reports","abstract":[{"lang":"eng","text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging."}],"type":"journal_article","pubrep_id":"737","file":[{"relation":"main_file","file_id":"4977","checksum":"cb378732da885ea4959ec5b845fb6e52","date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-12T10:12:56Z","access_level":"open_access","file_name":"IST-2017-737-v1+1_srep38840.pdf","file_size":760967,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1172","intvolume":" 6","ddc":["576"],"title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","status":"public","month":"12","doi":"10.1038/srep38840","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","publist_id":"6183","file_date_updated":"2020-07-14T12:44:37Z","article_number":"38840","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"full_name":"Barma, Mustansir","first_name":"Mustansir","last_name":"Barma"},{"first_name":"Madan","last_name":"Rao","full_name":"Rao, Madan"}],"volume":6,"date_updated":"2021-01-12T06:48:50Z","date_created":"2018-12-11T11:50:32Z","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","year":"2016","publisher":"Nature Publishing Group","department":[{"_id":"NiBa"}],"publication_status":"published"},{"month":"10","oa":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.1093/molbev/msw210","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"6155","file_date_updated":"2020-07-14T12:44:38Z","acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe manuscript. This work was supported by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","year":"2016","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","author":[{"first_name":"Susan","last_name":"Franssen","full_name":"Franssen, Susan"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Christian","last_name":"Schlötterer","full_name":"Schlötterer, Christian"}],"volume":34,"date_updated":"2021-01-12T06:49:00Z","date_created":"2018-12-11T11:50:39Z","scopus_import":1,"has_accepted_license":"1","day":"03","citation":{"chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.","mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","apa":"Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210"},"publication":"Molecular Biology and Evolution","page":"174 - 184","date_published":"2016-10-03T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. "}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1195","intvolume":" 34","status":"public","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","ddc":["576"],"pubrep_id":"770","oa_version":"Submitted Version","file":[{"file_id":"5223","relation":"main_file","date_created":"2018-12-12T10:16:35Z","date_updated":"2020-07-14T12:44:38Z","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","access_level":"open_access","creator":"system","file_size":295274,"content_type":"application/pdf"},{"relation":"main_file","file_id":"5224","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:36Z","checksum":"e13171843283774404c936c581b4543e","file_name":"IST-2017-770-v1+2_Fig1.pdf","access_level":"open_access","content_type":"application/pdf","file_size":10902625,"creator":"system"},{"checksum":"63bc6e6e61f347594d8c00c37f874a0b","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:37Z","file_id":"5225","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":21437,"access_level":"open_access","file_name":"IST-2017-770-v1+3_Fig2.pdf"},{"file_id":"5226","relation":"main_file","checksum":"da87cc7c78808837f22a3dae1c8397f9","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:38Z","access_level":"open_access","file_name":"IST-2017-770-v1+4_Fig3.pdf","creator":"system","content_type":"application/pdf","file_size":1172194},{"file_size":50045,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-770-v1+5_Fig4.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:38Z","checksum":"e47b2a0c32142f423b3100150c0294f8","relation":"main_file","file_id":"5227"},{"access_level":"open_access","file_name":"IST-2017-770-v1+6_Fig5.pdf","file_size":50705,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5228","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","date_created":"2018-12-12T10:16:39Z","date_updated":"2020-07-14T12:44:38Z"}]},{"intvolume":" 18","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","status":"public","title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","publication_status":"published","year":"2016","_id":"1224","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":18,"oa_version":"None","date_updated":"2021-01-12T06:49:12Z","date_created":"2018-12-11T11:50:48Z","author":[{"first_name":"Zachary","last_name":"Teitel","full_name":"Teitel, Zachary"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"type":"journal_article","issue":"1","publist_id":"6110","abstract":[{"text":"Sexual dimorphism in resource allocation is expected to change during the life cycle of dioecious plants because of temporal differences between the sexes in reproductive investment. Given the potential for sex-specific differences in reproductive costs, resource availability may contribute to variation in reproductive allocation in females and males. Here, we used Rumex hastatulus, a dioecious, wind-pollinated annual plant, to investigate whether sexual dimorphism varies with life-history stage and nutrient availability, and determine whether allocation patterns differ depending on reproductive commitment. To examine if the costs of reproduction varied between the sexes, reproduction was either allowed or prevented through bud removal, and biomass allocation was measured at maturity. In a second experiment to assess variation in sexual dimorphism across the life cycle, and whether this varied with resource availability, plants were grown in high and low nutrients and allocation to roots, aboveground vegetative growth and reproduction were measured at three developmental stages. Males prevented from reproducing compensated with increased above- and belowground allocation to a much larger degree than females, suggesting that male reproductive costs reduce vegetative growth. The proportional allocation to roots, reproductive structures and aboveground vegetative growth varied between the sexes and among life-cycle stages, but not with nutrient treatment. Females allocated proportionally more resources to roots than males at peak flowering, but this pattern was reversed at reproductive maturity under low-nutrient conditions. Our study illustrates the importance of temporal dynamics in sex-specific resource allocation and provides support for high male reproductive costs in wind-pollinated plants.","lang":"eng"}],"page":"98 - 103","quality_controlled":"1","citation":{"mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” Plant Biology, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:10.1111/plb.12336.","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","chicago":"Teitel, Zachary, Melinda Pickup, David Field, and Spencer Barrett. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” Plant Biology. Wiley-Blackwell, 2016. https://doi.org/10.1111/plb.12336.","ama":"Teitel Z, Pickup M, Field D, Barrett S. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. 2016;18(1):98-103. doi:10.1111/plb.12336","ista":"Teitel Z, Pickup M, Field D, Barrett S. 2016. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. 18(1), 98–103.","apa":"Teitel, Z., Pickup, M., Field, D., & Barrett, S. (2016). The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. Wiley-Blackwell. https://doi.org/10.1111/plb.12336","ieee":"Z. Teitel, M. Pickup, D. Field, and S. Barrett, “The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant,” Plant Biology, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016."},"publication":"Plant Biology","language":[{"iso":"eng"}],"doi":"10.1111/plb.12336","date_published":"2016-01-01T00:00:00Z","scopus_import":1,"month":"01","day":"01"},{"ec_funded":1,"publist_id":"6091","volume":202,"date_created":"2018-12-11T11:50:54Z","date_updated":"2023-02-21T10:24:19Z","author":[{"full_name":"Uecker, Hildegard","first_name":"Hildegard","last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813"},{"full_name":"Hermisson, Joachim","last_name":"Hermisson","first_name":"Joachim"}],"publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","year":"2016","month":"02","language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.180299","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"name":"L'OREAL Fellowship","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract","open_access":"1"}],"oa":1,"issue":"2","abstract":[{"text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 202","title":"The role of recombination in evolutionary rescue","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1241","day":"01","scopus_import":1,"date_published":"2016-02-01T00:00:00Z","page":"721 - 732","citation":{"chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:10.1534/genetics.115.180299.","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","apa":"Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. doi:10.1534/genetics.115.180299"},"publication":"Genetics"},{"language":[{"iso":"eng"}],"doi":"10.1145/2908812.2908909","conference":{"name":"GECCO: Genetic and evolutionary computation conference","end_date":"2016-07-24","start_date":"2016-07-20","location":"Denver, CO, USA"},"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"07","date_created":"2018-12-11T11:51:31Z","date_updated":"2021-01-12T06:50:03Z","author":[{"first_name":"Pietro","last_name":"Oliveto","full_name":"Oliveto, Pietro"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"first_name":"Jorge","last_name":"Heredia","full_name":"Heredia, Jorge"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","publication_status":"published","year":"2016","ec_funded":1,"publist_id":"5900","file_date_updated":"2020-07-14T12:44:45Z","date_published":"2016-07-20T00:00:00Z","page":"1163 - 1170","citation":{"ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170.","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.","mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909.","short":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170."},"publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","has_accepted_license":"1","day":"20","scopus_import":1,"file":[{"file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":979026,"file_id":"5214","relation":"main_file","date_created":"2018-12-12T10:16:27Z","date_updated":"2020-07-14T12:44:45Z","checksum":"a1896e39e4113f2711e46b435d5f3e69"}],"oa_version":"Published Version","pubrep_id":"650","ddc":["576"],"status":"public","title":"When non-elitism outperforms elitism for crossing fitness valleys","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1349","abstract":[{"lang":"eng","text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys."}],"type":"conference"},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1518830113","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"quality_controlled":"1","oa":1,"external_id":{"pmid":["27044080"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}],"month":"04","volume":113,"date_updated":"2021-01-12T06:50:08Z","date_created":"2018-12-11T11:51:34Z","author":[{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"publisher":"National Academy of Sciences","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","pmid":1,"year":"2016","publist_id":"5886","ec_funded":1,"date_published":"2016-04-19T00:00:00Z","page":"4422 - 4427","article_type":"original","citation":{"ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","apa":"Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1518830113","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1518830113.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113."},"publication":"PNAS","article_processing_charge":"No","day":"19","scopus_import":1,"oa_version":"Published Version","intvolume":" 113","title":"The effect of gene interactions on the long-term response to selection","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1359","issue":"16","abstract":[{"lang":"eng","text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population."}],"type":"journal_article"},{"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"volume":202,"date_updated":"2021-01-12T06:50:07Z","date_created":"2018-12-11T11:51:33Z","year":"2016","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","publist_id":"5889","file_date_updated":"2020-07-14T12:44:46Z","doi":"10.1534/genetics.115.184796","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"01","pubrep_id":"769","file":[{"file_id":"4687","relation":"main_file","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:08:26Z","checksum":"3562b89c821a4be84edf2b6ebd870cf5","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","access_level":"open_access","creator":"system","file_size":112674,"content_type":"application/pdf"}],"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1356","intvolume":" 202","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","ddc":["570"],"status":"public","issue":"1","type":"journal_article","date_published":"2016-01-05T00:00:00Z","citation":{"ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016.","ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796","chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184796.","mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796.","short":"N.H. Barton, Genetics 202 (2016) 3–4."},"publication":"Genetics","page":"3 - 4","has_accepted_license":"1","day":"05","scopus_import":1},{"date_published":"2016-03-01T00:00:00Z","publication":"Genetics","citation":{"ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.","apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 2016;202(3):865-866. doi:10.1534/genetics.116.187542","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542.","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:10.1534/genetics.116.187542.","short":"N.H. Barton, Genetics 202 (2016) 865–866."},"page":"865 - 866","day":"01","has_accepted_license":"1","scopus_import":1,"pubrep_id":"768","oa_version":"Submitted Version","file":[{"file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","access_level":"open_access","file_size":130779,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5127","date_created":"2018-12-12T10:15:09Z","date_updated":"2020-07-14T12:44:46Z","checksum":"b2174bab2de1d1142900062a150f35c9"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1357","status":"public","title":"Richard Hudson and Norman Kaplan on the coalescent process","ddc":["576"],"intvolume":" 202","issue":"3","type":"journal_article","doi":"10.1534/genetics.116.187542","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"03","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"date_updated":"2021-01-12T06:50:07Z","date_created":"2018-12-11T11:51:33Z","volume":202,"year":"2016","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:46Z","publist_id":"5888"},{"_id":"1409","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Genomics of hybridization and its evolutionary consequences","ddc":["576"],"intvolume":" 25","pubrep_id":"772","file":[{"date_created":"2018-12-12T10:10:12Z","date_updated":"2020-07-14T12:44:53Z","checksum":"ede7d0b8a471754f71f17e2b20f3135b","relation":"main_file","file_id":"4797","file_size":226137,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","type":"journal_article","issue":"11","publication":"Molecular Ecology","citation":{"ieee":"R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016.","apa":"Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.13685","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332.","ama":"Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685","chicago":"Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell, 2016. https://doi.org/10.1111/mec.13685.","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.","mla":"Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:10.1111/mec.13685."},"page":"2325 - 2332","date_published":"2016-06-08T00:00:00Z","scopus_import":1,"day":"08","has_accepted_license":"1","year":"2016","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"author":[{"full_name":"Abbott, Richard","last_name":"Abbott","first_name":"Richard"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Good","first_name":"Jeffrey","full_name":"Good, Jeffrey"}],"date_created":"2018-12-11T11:51:51Z","date_updated":"2021-01-12T06:50:33Z","volume":25,"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5798","oa":1,"quality_controlled":"1","doi":"10.1111/mec.13685","language":[{"iso":"eng"}],"month":"06"},{"ec_funded":1,"publist_id":"5787","date_created":"2018-12-11T11:51:55Z","date_updated":"2022-08-01T10:49:55Z","volume":202,"author":[{"first_name":"Katarína","last_name":"Bod'ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publication_status":"published","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2016","month":"04","language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.184127","quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"external_id":{"arxiv":["1510.08344"]},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"abstract":[{"lang":"eng","text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. "}],"issue":"4","type":"journal_article","oa_version":"Preprint","status":"public","title":"A general approximation for the dynamics of quantitative traits","intvolume":" 202","_id":"1420","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"06","article_processing_charge":"No","scopus_import":"1","date_published":"2016-04-06T00:00:00Z","page":"1523 - 1548","publication":"Genetics","citation":{"mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016."}},{"publication":"Genetics","citation":{"chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814.","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:10.1534/genetics.115.183814.","apa":"Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.183814","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016.","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.","ama":"Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786. doi:10.1534/genetics.115.183814"},"article_type":"original","page":"775 - 786","date_published":"2016-02-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1518","status":"public","ddc":["570"],"title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","intvolume":" 202","pubrep_id":"561","file":[{"file_id":"5241","relation":"main_file","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:16:51Z","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":957466}],"oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno."}],"issue":"2","oa":1,"external_id":{"pmid":["26715666"]},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"doi":"10.1534/genetics.115.183814","language":[{"iso":"eng"}],"month":"02","year":"2016","acknowledgement":"We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.).","pmid":1,"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"publisher":"Genetics Society of America","author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"full_name":"Martin, Simon","last_name":"Martin","first_name":"Simon"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"date_updated":"2022-05-24T09:16:22Z","date_created":"2018-12-11T11:52:29Z","volume":202,"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5658","ec_funded":1},{"month":"04","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2015.10.008","ec_funded":1,"publist_id":"5524","file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"NiBa"}],"publisher":"Academic Press","publication_status":"published","year":"2016","volume":108,"date_updated":"2021-01-12T06:52:07Z","date_created":"2018-12-11T11:53:08Z","author":[{"last_name":"Kelleher","first_name":"Jerome","full_name":"Kelleher, Jerome"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"scopus_import":1,"has_accepted_license":"1","day":"01","page":"1 - 12","citation":{"ama":"Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 2016;108:1-12. doi:10.1016/j.tpb.2015.10.008","ista":"Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12.","ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” Theoretical Population Biology, vol. 108. Academic Press, pp. 1–12, 2016.","apa":"Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008","mla":"Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology, vol. 108, Academic Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008."},"publication":"Theoretical Population Biology","date_published":"2016-04-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models."}],"intvolume":" 108","status":"public","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","ddc":["576"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1631","file":[{"access_level":"open_access","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","creator":"system","file_size":1684043,"content_type":"application/pdf","file_id":"4865","relation":"main_file","checksum":"6a65ba187994d4ad86c1c509e0ff482a","date_created":"2018-12-12T10:11:12Z","date_updated":"2020-07-14T12:45:07Z"}],"oa_version":"Published Version","pubrep_id":"465"},{"date_published":"2016-12-27T00:00:00Z","publication":"PLoS Biology","citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234."},"day":"27","has_accepted_license":"1","scopus_import":1,"file":[{"file_size":2494348,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:36Z","date_created":"2018-12-12T10:15:42Z","checksum":"2bab63b068a9840efd532b9ae583f9bb","relation":"main_file","file_id":"5164"}],"oa_version":"Published Version","pubrep_id":"742","ddc":["576"],"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","status":"public","intvolume":" 14","_id":"1158","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.","lang":"eng"}],"issue":"12","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2000234","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"12","date_created":"2018-12-11T11:50:28Z","date_updated":"2023-02-23T14:11:16Z","volume":14,"author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"related_material":{"record":[{"id":"9862","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9863"}]},"publication_status":"published","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","year":"2016","acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","file_date_updated":"2020-07-14T12:44:36Z","publist_id":"6200","article_number":"e2000234"},{"month":"12","day":"27","article_processing_charge":"No","doi":"10.1371/journal.pbio.2000234.s016","citation":{"ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, 10.1371/journal.pbio.2000234.s016.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:10.1371/journal.pbio.2000234.s016","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s016.","mla":"Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016)."},"type":"research_data_reference","author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1158"}]},"date_updated":"2023-02-21T16:21:20Z","date_created":"2021-08-10T08:20:17Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9862","year":"2016","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","status":"public","publisher":"Public Library of Science","department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"doi":"10.1371/journal.pbio.2000234.s017","citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, 10.1371/journal.pbio.2000234.s017.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","mla":"Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017."},"article_processing_charge":"No","month":"12","day":"27","oa_version":"Published Version","date_created":"2021-08-10T08:22:52Z","date_updated":"2023-02-21T16:21:20Z","related_material":{"record":[{"id":"1158","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","title":"Accessions of surveyed individuals, geographic locations and summary statistics","status":"public","_id":"9863","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","type":"research_data_reference"},{"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2016","date_created":"2018-12-11T11:50:17Z","date_updated":"2023-09-07T11:55:53Z","author":[{"last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"}],"related_material":{"record":[{"id":"2023","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2021-02-22T13:42:47Z","publist_id":"6235","oa":1,"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["2663-337X"]},"title":"Evolutionary proccesses in variable emvironments","status":"public","ddc":["576"],"_id":"1125","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","date_created":"2019-08-13T09:01:00Z","date_updated":"2019-08-13T09:01:00Z","file_id":"6811","relation":"main_file","creator":"dernst","file_size":3564901,"content_type":"application/pdf","access_level":"closed","file_name":"Novak_thesis.pdf"},{"file_id":"9186","relation":"main_file","success":1,"checksum":"30808d2f7ca920e09f63a95cdc49bffd","date_created":"2021-02-22T13:42:47Z","date_updated":"2021-02-22T13:42:47Z","access_level":"open_access","file_name":"2016_Novak_Thesis.pdf","creator":"dernst","file_size":2814384,"content_type":"application/pdf"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"page":"124","citation":{"mla":"Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments. Institute of Science and Technology Austria, 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria."},"date_published":"2016-07-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"scopus_import":1,"has_accepted_license":"1","day":"04","citation":{"chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12307","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307"},"publication":"Nature Communications","date_published":"2016-08-04T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1358","intvolume":" 7","status":"public","ddc":["576"],"title":"Intrinsic limits to gene regulation by global crosstalk","pubrep_id":"627","file":[{"creator":"system","file_size":861805,"content_type":"application/pdf","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:12:01Z","checksum":"fe3f3a1526d180b29fe691ab11435b78","file_id":"4919","relation":"main_file"},{"file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1084703,"file_id":"4920","relation":"main_file","date_created":"2018-12-12T10:12:02Z","date_updated":"2020-07-14T12:44:46Z","checksum":"164864a1a675f3ad80e9917c27aba07f"}],"oa_version":"Published Version","month":"08","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1038/ncomms12307","language":[{"iso":"eng"}],"article_number":"12307","ec_funded":1,"publist_id":"5887","file_date_updated":"2020-07-14T12:44:46Z","year":"2016","publisher":"Nature Publishing Group","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar"},{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"}],"volume":7,"date_updated":"2023-09-07T12:53:49Z","date_created":"2018-12-11T11:51:34Z"},{"month":"09","day":"23","article_processing_charge":"No","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"citation":{"ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:10.5061/dryad.s5s7r","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, 10.5061/dryad.s5s7r.","short":"N.H. Barton, (2016).","mla":"Barton, Nicholas H. Data from: How Does Epistasis Influence the Response to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r."},"doi":"10.5061/dryad.s5s7r","date_published":"2016-09-23T00:00:00Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}],"year":"2016","_id":"9710","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: How does epistasis influence the response to selection?","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"id":"1199","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-09-20T11:17:47Z","date_created":"2021-07-23T11:45:47Z","oa_version":"Published Version"},{"date_published":"2016-12-14T00:00:00Z","doi":"10.6084/m9.figshare.4315652.v1","citation":{"ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1","mla":"Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family. The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.4315652.v1"}],"oa":1,"day":"14","month":"12","article_processing_charge":"No","date_updated":"2023-09-20T11:56:33Z","date_created":"2021-08-10T08:29:47Z","oa_version":"Published Version","author":[{"orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A"},{"orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"de Vladar","first_name":"Harold","full_name":"de Vladar, Harold"},{"full_name":"Włodarski, Tomasz","last_name":"Włodarski","first_name":"Tomasz"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"related_material":{"record":[{"id":"1077","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"The Royal Society","_id":"9864","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"type":"research_data_reference"},{"type":"journal_article","publist_id":"5828","issue":"7","abstract":[{"text":"Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.","lang":"eng"}],"year":"2016","_id":"1382","acknowledgement":"We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for her efforts in tracking down the more obscure references.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","intvolume":" 117","publication_status":"published","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","status":"public","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5550"}]},"author":[{"full_name":"Ellis, Thomas","last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"}],"volume":117,"oa_version":"None","date_updated":"2024-02-21T13:49:53Z","date_created":"2018-12-11T11:51:42Z","scopus_import":1,"month":"06","day":"1","citation":{"chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany. Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.","apa":"Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcw043","ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” Annals of Botany, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016.","ista":"Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.","ama":"Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140. doi:10.1093/aob/mcw043"},"publication":"Annals of Botany","page":"1133 - 1140","quality_controlled":"1","date_published":"2016-06-01T00:00:00Z","doi":"10.1093/aob/mcw043","language":[{"iso":"eng"}]},{"_id":"5550","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"status":"public","title":"Flower colour data and phylogeny (NEXUS) files","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"author":[{"full_name":"Ellis, Thomas","last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"}],"related_material":{"record":[{"id":"1382","status":"public","relation":"research_paper"}]},"date_updated":"2024-02-21T13:49:54Z","date_created":"2018-12-12T12:31:29Z","file":[{"file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","access_level":"open_access","creator":"system","content_type":"application/zip","file_size":4468543,"file_id":"5594","relation":"main_file","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T13:02:27Z","checksum":"950f85b80427d357bfeff09608ba02e9"}],"oa_version":"Published Version","datarep_id":"34","type":"research_data","file_date_updated":"2020-07-14T12:47:00Z","abstract":[{"text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"publist_id":"5828","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T., & Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:34","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, 10.15479/AT:ISTA:34.","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34.","short":"T. Ellis, D. Field, (2016).","mla":"Ellis, Thomas, and David Field. Flower Colour Data and Phylogeny (NEXUS) Files. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:34."},"doi":"10.15479/AT:ISTA:34","date_published":"2016-02-19T00:00:00Z","day":"19","month":"02","has_accepted_license":"1","article_processing_charge":"No"},{"month":"02","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:TH_526 ","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2020-07-14T12:44:48Z","publist_id":"5809","author":[{"full_name":"Ellis, Thomas","last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"5553","status":"public","relation":"popular_science"},{"id":"5551","relation":"popular_science","status":"public"},{"id":"5552","relation":"popular_science","status":"public"}]},"date_created":"2018-12-11T11:51:47Z","date_updated":"2024-02-21T13:51:39Z","acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","year":"2016","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","day":"18","article_processing_charge":"No","has_accepted_license":"1","date_published":"2016-02-18T00:00:00Z","citation":{"ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526 ","apa":"Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526 ","ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016.","ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria.","short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 .","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 ."},"page":"130","abstract":[{"lang":"eng","text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"526","file":[{"date_created":"2018-12-12T10:14:51Z","date_updated":"2020-07-14T12:44:48Z","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","file_id":"5106","relation":"main_file","creator":"system","file_size":11928241,"content_type":"application/pdf","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"1398","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576"],"title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","status":"public"},{"month":"07","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2021-02-22T11:45:20Z","publist_id":"6229","author":[{"last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1666"},{"status":"public","relation":"research_data","id":"5554"}]},"date_created":"2018-12-11T11:50:19Z","date_updated":"2024-02-21T13:50:34Z","year":"2016","acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2016-07-01T00:00:00Z","citation":{"apa":"Tugrul, M. (2016). Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute of Science and Technology Austria, 2016."},"page":"89","abstract":[{"lang":"eng","text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3695257,"creator":"dernst","access_level":"closed","file_name":"Tugrul_thesis_w_signature_page.pdf","checksum":"66cb61a59943e4fb7447c6a86be5ef51","date_created":"2019-08-13T08:53:52Z","date_updated":"2019-08-13T08:53:52Z","relation":"main_file","file_id":"6810"},{"file_name":"2016_Tugrul_Thesis.pdf","access_level":"open_access","creator":"dernst","file_size":3880811,"content_type":"application/pdf","file_id":"9182","relation":"main_file","date_created":"2021-02-22T11:45:20Z","date_updated":"2021-02-22T11:45:20Z","success":1,"checksum":"293e388d70563760f6b24c3e66283dda"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1131","status":"public","title":"Evolution of transcriptional regulatory sequences","ddc":["576"]},{"author":[{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"}],"contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","contributor_type":"project_manager","last_name":"Barton"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"1398"}]},"date_created":"2018-12-12T12:31:30Z","date_updated":"2024-02-21T13:51:14Z","file":[{"creator":"system","content_type":"application/zip","file_size":132808,"file_name":"IST-2016-37-v1+1_paternity_archive.zip","access_level":"open_access","date_created":"2018-12-12T13:03:02Z","date_updated":"2020-07-14T12:47:01Z","checksum":"4ae751b1fa4897fa216241f975a57313","file_id":"5620","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5553","year":"2016","ddc":["576"],"status":"public","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"lang":"eng","text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org."}],"datarep_id":"37","type":"research_data","date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:37","citation":{"chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.","mla":"Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:37.","short":"D. Field, T. Ellis, (2016).","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, 10.15479/AT:ISTA:37.","apa":"Field, D., & Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:37","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37"},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"day":"19","month":"02","has_accepted_license":"1","article_processing_charge":"No","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"]},{"month":"02","day":"19","has_accepted_license":"1","article_processing_charge":"No","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.","short":"T. Ellis, (2016).","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:35.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35"},"doi":"10.15479/AT:ISTA:35","date_published":"2016-02-19T00:00:00Z","datarep_id":"35","type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}],"status":"public","title":"Data on pollinator observations and offpsring phenotypes","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2016","_id":"5551","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:51:27Z","date_created":"2018-12-12T12:31:29Z","file":[{"file_name":"IST-2016-35-v1+1_array_data.zip","access_level":"open_access","file_size":32775,"content_type":"application/zip","creator":"system","relation":"main_file","file_id":"5640","date_created":"2018-12-12T13:05:12Z","date_updated":"2020-07-14T12:47:01Z","checksum":"aa3eb85d52b110cd192aa23147c4d4f3"}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"19","month":"02","date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:36","oa":1,"citation":{"chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:36.","mla":"Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:36.","short":"T. Ellis, (2016).","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, 10.15479/AT:ISTA:36.","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:36","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36"},"abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"file_date_updated":"2020-07-14T12:47:01Z","type":"research_data","datarep_id":"36","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"author":[{"full_name":"Ellis, Thomas","last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"file":[{"content_type":"application/zip","file_size":44905,"creator":"system","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:07Z","checksum":"cbc61b523d4d475a04a737d50dc470ef","relation":"main_file","file_id":"5625"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:30Z","date_updated":"2024-02-21T13:51:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5552","year":"2016","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data."},{"author":[{"full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","first_name":"Murat"}],"contributor":[{"first_name":"Magdalena","last_name":"Steinrück","contributor_type":"researcher","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","last_name":"Jesse","first_name":"Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1131"}]},"date_updated":"2024-02-21T13:50:34Z","date_created":"2018-12-12T12:31:30Z","file":[{"checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","date_created":"2018-12-12T13:03:08Z","date_updated":"2020-07-14T12:47:01Z","file_id":"5626","relation":"main_file","creator":"system","content_type":"application/zip","file_size":1123495,"access_level":"open_access","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip"}],"oa_version":"Published Version","_id":"5554","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:01Z","datarep_id":"43","type":"research_data","date_published":"2016-05-12T00:00:00Z","doi":"10.15479/AT:ISTA:43","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"short":"M. Tugrul, (2016).","mla":"Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43."},"day":"12","month":"05","article_processing_charge":"No","has_accepted_license":"1","keyword":["RNAP binding","de novo promoter evolution","lac promoter"]},{"quality_controlled":"1","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"page":"1455 - 1462","publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.06260"}],"oa":1,"citation":{"chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.","mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.","apa":"Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758","ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758"},"language":[{"iso":"eng"}],"conference":{"name":"GECCO: Genetic and evolutionary computation conference","location":"Madrid, Spain","start_date":"2015-07-11","end_date":"2015-07-15"},"doi":"10.1145/2739480.2754758","date_published":"2015-07-11T00:00:00Z","scopus_import":1,"month":"07","day":"11","title":"First steps towards a runtime comparison of natural and artificial evolution","status":"public","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","_id":"1430","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:50:41Z","date_created":"2018-12-11T11:51:58Z","oa_version":"Preprint","author":[{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"full_name":"Heredia, Jorge","first_name":"Jorge","last_name":"Heredia"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora"}],"type":"conference","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"ec_funded":1,"publist_id":"5768"},{"day":"19","has_accepted_license":"1","scopus_import":1,"date_published":"2015-03-19T00:00:00Z","publication":"Evolution","citation":{"ama":"Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","apa":"Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641."},"page":"1101 - 1112","abstract":[{"lang":"eng","text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so."}],"issue":"5","type":"journal_article","pubrep_id":"560","oa_version":"Submitted Version","file":[{"checksum":"fd8d23f476bc194419929b72ca265c02","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:34Z","relation":"main_file","file_id":"4822","file_size":188872,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf"},{"file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":577415,"file_id":"4823","relation":"main_file","date_created":"2018-12-12T10:10:35Z","date_updated":"2020-07-14T12:45:00Z","checksum":"b774911e70044641d556e258efcb52ef"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1519","status":"public","ddc":["570"],"title":"The interpretation of selection coefficients","intvolume":" 69","month":"03","doi":"10.1111/evo.12641","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5656","ec_funded":1,"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Servedio, Maria","last_name":"Servedio","first_name":"Maria"}],"date_created":"2018-12-11T11:52:29Z","date_updated":"2021-01-12T06:51:20Z","volume":69,"year":"2015","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley"},{"date_published":"2015-10-21T00:00:00Z","publication":" Journal of Theoretical Biology","citation":{"short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011","ieee":"T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43."},"page":"28 - 43","day":"21","has_accepted_license":"1","scopus_import":1,"pubrep_id":"483","file":[{"access_level":"open_access","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","file_size":595307,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5244","checksum":"33b60ecfea60764756a9ee9df5eb65ca","date_created":"2018-12-12T10:16:53Z","date_updated":"2020-07-14T12:45:01Z"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1542","title":"Toward a unifying framework for evolutionary processes","ddc":["570"],"status":"public","intvolume":" 383","abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"type":"journal_article","doi":"10.1016/j.jtbi.2015.07.011","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"month":"10","author":[{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Badkobeh, Golnaz","last_name":"Badkobeh","first_name":"Golnaz"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Çörüş, Doğan","first_name":"Doğan","last_name":"Çörüş"},{"last_name":"Dang","first_name":"Duccuong","full_name":"Dang, Duccuong"},{"last_name":"Friedrich","first_name":"Tobias","full_name":"Friedrich, Tobias"},{"first_name":"Per","last_name":"Lehre","full_name":"Lehre, Per"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"last_name":"Sutton","first_name":"Andrew","full_name":"Sutton, Andrew"},{"first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"}],"date_updated":"2021-01-12T06:51:29Z","date_created":"2018-12-11T11:52:37Z","volume":383,"year":"2015","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Elsevier","file_date_updated":"2020-07-14T12:45:01Z","ec_funded":1,"publist_id":"5629"},{"month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"L'OREAL Fellowship","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s00285-014-0802-y","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:12Z","publist_id":"5442","acknowledgement":"This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria).","year":"2015","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Springer","author":[{"first_name":"Hildegard","last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard"},{"full_name":"Setter, Derek","last_name":"Setter","first_name":"Derek"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"}],"date_updated":"2023-02-23T10:10:36Z","date_created":"2018-12-11T11:53:32Z","volume":70,"scopus_import":1,"day":"01","has_accepted_license":"1","publication":"Journal of Mathematical Biology","citation":{"short":"H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580.","mla":"Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:10.1007/s00285-014-0802-y.","chicago":"Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology. Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y.","ama":"Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y","ieee":"H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer, pp. 1523–1580, 2015.","apa":"Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580."},"page":"1523 - 1580","date_published":"2015-06-01T00:00:00Z","type":"journal_article","abstract":[{"text":"By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.","lang":"eng"}],"issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1699","title":"Adaptive gene introgression after secondary contact","status":"public","ddc":["576"],"intvolume":" 70","pubrep_id":"458","oa_version":"Published Version","file":[{"file_id":"5079","relation":"main_file","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad","date_created":"2018-12-12T10:14:27Z","date_updated":"2020-07-14T12:45:12Z","access_level":"open_access","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf","creator":"system","file_size":1321527,"content_type":"application/pdf"}]},{"date_published":"2015-05-26T00:00:00Z","doi":"10.1071/BT15023","language":[{"iso":"eng"}],"citation":{"ista":"Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466.","ieee":"L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.","apa":"Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023","ama":"Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023","chicago":"Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023.","mla":"Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023.","short":"L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466."},"publication":"Australian Journal of Botany","page":"455 - 466","quality_controlled":"1","month":"05","day":"26","scopus_import":1,"author":[{"full_name":"Broadhurst, Linda","last_name":"Broadhurst","first_name":"Linda"},{"first_name":"Graham","last_name":"Fifield","full_name":"Fifield, Graham"},{"first_name":"Bindi","last_name":"Vanzella","full_name":"Vanzella, Bindi"},{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"}],"volume":63,"oa_version":"None","date_updated":"2021-01-12T06:52:38Z","date_created":"2018-12-11T11:53:34Z","year":"2015","_id":"1703","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"CSIRO","intvolume":" 63","department":[{"_id":"NiBa"}],"publication_status":"published","status":"public","title":"An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas","issue":"5","publist_id":"5434","abstract":[{"text":"Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.","lang":"eng"}],"type":"journal_article"},{"intvolume":" 112","status":"public","title":"Limits to adaptation along environmental gradients","_id":"1818","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"20","abstract":[{"lang":"eng","text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible."}],"page":"6401 - 6406","citation":{"ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","apa":"Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112."},"publication":"PNAS","date_published":"2015-05-19T00:00:00Z","scopus_import":1,"day":"19","department":[{"_id":"NiBa"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2015","volume":112,"date_updated":"2021-01-12T06:53:24Z","date_created":"2018-12-11T11:54:11Z","author":[{"full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"publist_id":"5288","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"external_id":{"pmid":["25941385"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1421515112","month":"05"},{"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5251","ec_funded":1,"date_updated":"2021-01-12T06:53:37Z","date_created":"2018-12-11T11:54:21Z","volume":372,"author":[{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"publisher":"Elsevier","year":"2015","month":"05","language":[{"iso":"eng"}],"doi":"10.1016/j.jtbi.2015.02.018","quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}],"oa":1,"abstract":[{"lang":"eng","text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels."}],"issue":"5","type":"journal_article","file":[{"file_id":"5326","relation":"main_file","checksum":"3c0dcacc900bc45cc65a453dfda4ca43","date_created":"2018-12-12T10:18:07Z","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access","file_name":"IST-2015-329-v1+1_manuscript.pdf","creator":"system","file_size":1546914,"content_type":"application/pdf"}],"oa_version":"Submitted Version","pubrep_id":"329","ddc":["576"],"title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","status":"public","intvolume":" 372","_id":"1850","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","has_accepted_license":"1","scopus_import":1,"date_published":"2015-05-07T00:00:00Z","page":"54 - 64","publication":"Journal of Theoretical Biology","citation":{"ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64.","ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” Journal of Theoretical Biology, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","apa":"Novak, S., & Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.02.018","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 2015;372(5):54-64. doi:10.1016/j.jtbi.2015.02.018","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.02.018.","mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:10.1016/j.jtbi.2015.02.018.","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64."}},{"citation":{"chicago":"Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12618.","short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:10.1111/evo.12618.","ieee":"T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating,” Evolution, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015.","apa":"Priklopil, T., Kisdi, E., & Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. Wiley. https://doi.org/10.1111/evo.12618","ista":"Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 69(4), 1015–1026.","ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 2015;69(4):1015-1026. doi:10.1111/evo.12618"},"publication":"Evolution","page":"1015 - 1026","article_type":"original","date_published":"2015-02-09T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"09","_id":"1851","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 69","ddc":["570"],"status":"public","title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","file":[{"access_level":"open_access","file_name":"2015_Evolution_Priklopil.pdf","file_size":967214,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7855","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798","date_created":"2020-05-15T09:05:34Z","date_updated":"2020-07-14T12:45:19Z"}],"oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"text":"We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them.","lang":"eng"}],"external_id":{"pmid":["25662095"]},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1111/evo.12618","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"02","pmid":1,"year":"2015","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","first_name":"Tadeas"},{"full_name":"Kisdi, Eva","first_name":"Eva","last_name":"Kisdi"},{"full_name":"Gyllenberg, Mats","last_name":"Gyllenberg","first_name":"Mats"}],"volume":69,"date_created":"2018-12-11T11:54:21Z","date_updated":"2022-06-07T10:52:37Z","publist_id":"5249","ec_funded":1,"file_date_updated":"2020-07-14T12:45:19Z"}]