[{"issue":"7","publication_identifier":{"issn":["1553-734X"]},"doi":"10.1371/journal.pcbi.1005609","publication":"PLoS Computational Biology","year":"2017","date_created":"2018-12-11T11:47:58Z","article_number":"e1005609","has_accepted_license":"1","ddc":["576"],"corr_author":"1","file":[{"access_level":"open_access","relation":"main_file","checksum":"9143c290fa6458ed2563bff4b295554a","file_size":3775716,"date_updated":"2020-07-14T12:47:46Z","file_id":"5117","creator":"system","date_created":"2018-12-12T10:15:01Z","content_type":"application/pdf","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf"}],"quality_controlled":"1","related_material":{"record":[{"id":"9849","relation":"research_data","status":"public"},{"relation":"research_data","id":"9850","status":"public"},{"status":"public","relation":"research_data","id":"9851"},{"status":"public","relation":"research_data","id":"9852"},{"status":"public","relation":"dissertation_contains","id":"6263"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Lukacisinova","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta"},{"orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","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"}],"volume":13,"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","article_processing_charge":"No","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"}],"publication_status":"published","external_id":{"isi":["000406619800014"]},"day":"18","pubrep_id":"894","status":"public","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, 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.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>"},"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"publist_id":"7004","_id":"696","scopus_import":"1","article_type":"original","intvolume":"        13","oa_version":"Published Version","type":"journal_article","month":"07","language":[{"iso":"eng"}],"date_published":"2017-07-18T00:00:00Z","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Public Library of Science","date_updated":"2026-09-04T22:31:10Z","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:47:46Z"},{"pubrep_id":"742","status":"public","day":"27","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","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.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>.","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>.","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,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (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. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>"},"publist_id":"6200","_id":"1158","scopus_import":"1","intvolume":"        14","oa_version":"Published Version","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.","type":"journal_article","language":[{"iso":"eng"}],"month":"12","date_published":"2016-12-27T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","date_updated":"2025-09-22T09:55:10Z","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:44:36Z","issue":"12","doi":"10.1371/journal.pbio.2000234","publication":"PLoS Biology","year":"2016","date_created":"2018-12-11T11:50:28Z","article_number":"e2000234","has_accepted_license":"1","ddc":["576"],"file":[{"date_updated":"2020-07-14T12:44:36Z","file_size":2494348,"access_level":"open_access","checksum":"2bab63b068a9840efd532b9ae583f9bb","relation":"main_file","file_id":"5164","creator":"system","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:15:42Z"}],"quality_controlled":"1","related_material":{"record":[{"id":"9862","relation":"research_data","status":"public"},{"status":"public","id":"9863","relation":"research_data"}]},"author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"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","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":14,"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","article_processing_charge":"No","abstract":[{"lang":"eng","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 &quot;grey zone&quot; 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."}],"external_id":{"isi":["000392120100008"]},"publication_status":"published"},{"publication":"Scientific Reports","doi":"10.1038/srep38840","article_number":"38840","year":"2016","date_created":"2018-12-11T11:50:32Z","ddc":["576"],"has_accepted_license":"1","file":[{"checksum":"cb378732da885ea4959ec5b845fb6e52","relation":"main_file","access_level":"open_access","file_size":760967,"date_updated":"2020-07-14T12:44:37Z","file_id":"4977","creator":"system","date_created":"2018-12-12T10:12:56Z","file_name":"IST-2017-737-v1+1_srep38840.pdf","content_type":"application/pdf"}],"quality_controlled":"1","volume":6,"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"},{"full_name":"Barma, Mustansir","last_name":"Barma","first_name":"Mustansir"},{"full_name":"Rao, Madan","last_name":"Rao","first_name":"Madan"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","abstract":[{"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.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000389885900001"]},"article_processing_charge":"No","pubrep_id":"737","day":"19","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>, vol. 6, 38840, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>.","apa":"Sachdeva, H., Barma, M., &#38; Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>.","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016)."},"_id":"1172","scopus_import":"1","publist_id":"6183","type":"journal_article","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","oa_version":"Published Version","intvolume":"         6","publisher":"Nature Publishing Group","department":[{"_id":"NiBa"}],"date_updated":"2025-09-22T09:49:53Z","month":"12","language":[{"iso":"eng"}],"date_published":"2016-12-19T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:44:37Z","isi":1},{"author":[{"full_name":"Franssen, Susan","first_name":"Susan","last_name":"Franssen"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Schlötterer","first_name":"Christian","full_name":"Schlötterer, Christian"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":34,"article_processing_charge":"No","page":"174 - 184","publication_status":"published","external_id":{"isi":["000396772000009"]},"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. "}],"title":"Reconstruction of haplotype-blocks selected during experimental evolution.","date_created":"2018-12-11T11:50:39Z","year":"2016","doi":"10.1093/molbev/msw210","issue":"1","publication":"Molecular Biology and Evolution","file":[{"creator":"system","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:16:35Z","date_updated":"2020-07-14T12:44:38Z","file_size":295274,"access_level":"open_access","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","relation":"main_file","file_id":"5223"},{"date_created":"2018-12-12T10:16:36Z","file_name":"IST-2017-770-v1+2_Fig1.pdf","content_type":"application/pdf","creator":"system","file_id":"5224","access_level":"open_access","checksum":"e13171843283774404c936c581b4543e","relation":"main_file","file_size":10902625,"date_updated":"2020-07-14T12:44:38Z"},{"file_name":"IST-2017-770-v1+3_Fig2.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:16:37Z","creator":"system","file_id":"5225","date_updated":"2020-07-14T12:44:38Z","file_size":21437,"access_level":"open_access","checksum":"63bc6e6e61f347594d8c00c37f874a0b","relation":"main_file"},{"file_name":"IST-2017-770-v1+4_Fig3.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:16:38Z","creator":"system","file_id":"5226","file_size":1172194,"date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","relation":"main_file","checksum":"da87cc7c78808837f22a3dae1c8397f9"},{"creator":"system","file_name":"IST-2017-770-v1+5_Fig4.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:16:38Z","file_size":50045,"date_updated":"2020-07-14T12:44:38Z","checksum":"e47b2a0c32142f423b3100150c0294f8","relation":"main_file","access_level":"open_access","file_id":"5227"},{"file_id":"5228","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","relation":"main_file","access_level":"open_access","file_size":50705,"date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:39Z","file_name":"IST-2017-770-v1+6_Fig5.pdf","content_type":"application/pdf","creator":"system"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["576"],"intvolume":"        34","oa_version":"Submitted Version","type":"journal_article","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”.","publist_id":"6155","scopus_import":"1","_id":"1195","isi":1,"file_date_updated":"2020-07-14T12:44:38Z","oa":1,"date_published":"2016-10-03T00:00:00Z","month":"10","language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:43:41Z","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","ec_funded":1,"pubrep_id":"770","status":"public","day":"03","citation":{"mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:<a href=\"https://doi.org/10.1093/molbev/msw210\">10.1093/molbev/msw210</a>.","apa":"Franssen, S., Barton, N. H., &#38; Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msw210\">https://doi.org/10.1093/molbev/msw210</a>","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msw210\">https://doi.org/10.1093/molbev/msw210</a>.","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. <i>Molecular Biology and Evolution</i>. 2016;34(1):174-184. doi:<a href=\"https://doi.org/10.1093/molbev/msw210\">10.1093/molbev/msw210</a>","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184."},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}]},{"citation":{"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.” <i>Plant Biology</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>.","apa":"Teitel, Z., Pickup, M., Field, D., &#38; Barrett, S. (2016). The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>","mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>.","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","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,” <i>Plant Biology</i>, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016.","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. <i>Plant Biology</i>. 2016;18(1):98-103. doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>","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."},"day":"01","status":"public","month":"01","language":[{"iso":"eng"}],"date_published":"2016-01-01T00:00:00Z","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"date_updated":"2025-09-22T09:31:49Z","isi":1,"publist_id":"6110","_id":"1224","scopus_import":"1","oa_version":"None","intvolume":"        18","type":"journal_article","quality_controlled":"1","issue":"1","doi":"10.1111/plb.12336","publication":"Plant Biology","year":"2016","date_created":"2018-12-11T11:50:48Z","title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","page":"98 - 103","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"external_id":{"isi":["000369975700011"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Zachary","last_name":"Teitel","full_name":"Teitel, Zachary"},{"first_name":"Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","last_name":"Field"},{"last_name":"Barrett","first_name":"Spencer","full_name":"Barrett, Spencer"}],"volume":18},{"isi":1,"oa":1,"language":[{"iso":"eng"}],"month":"02","date_published":"2016-02-01T00:00:00Z","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","date_updated":"2026-06-22T14:07:01Z","oa_version":"Preprint","intvolume":"       202","type":"journal_article","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).","publist_id":"6091","_id":"1241","scopus_import":"1","citation":{"apa":"Uecker, H., &#38; Hermisson, J. (2016). The role of recombination in evolutionary rescue. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>","chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. <i>Genetics</i>. 2016;202(2):721-732. doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732."},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"Evolutionary rescue"}],"ec_funded":1,"status":"public","day":"01","page":"721 - 732","article_processing_charge":"No","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"}],"publication_status":"published","external_id":{"isi":["000371304600028"],"biorxivid":["10.1101/022020"]},"title":"The role of recombination in evolutionary rescue","author":[{"last_name":"Uecker","first_name":"Hildegard","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","full_name":"Uecker, Hildegard"},{"full_name":"Hermisson, Joachim","last_name":"Hermisson","first_name":"Joachim"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":202,"biorxivid":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1101/022020","open_access":"1"}],"year":"2016","date_created":"2018-12-11T11:50:54Z","issue":"2","doi":"10.1534/genetics.115.180299","publication":"Genetics","das_tickbox":"1"},{"doi":"10.1145/2908812.2908909","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","year":"2016","date_created":"2018-12-11T11:51:31Z","has_accepted_license":"1","ddc":["576"],"conference":{"location":"Denver, CO, USA","end_date":"2016-07-24","name":"GECCO: Genetic and evolutionary computation conference","start_date":"2016-07-20"},"file":[{"file_id":"5214","date_updated":"2020-07-14T12:44:45Z","file_size":979026,"access_level":"open_access","relation":"main_file","checksum":"a1896e39e4113f2711e46b435d5f3e69","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:16:27Z","creator":"system"}],"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Pietro","last_name":"Oliveto","full_name":"Oliveto, Pietro"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"title":"When non-elitism outperforms elitism for crossing fitness valleys","page":"1163 - 1170","article_processing_charge":"No","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."}],"external_id":{"isi":["000382659200147"]},"publication_status":"published","day":"20","status":"public","pubrep_id":"650","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"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.","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, 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: <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>. ACM; 2016:1163-1170. doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>","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., &#38; Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i> (pp. 1163–1170). Denver, CO, USA: ACM. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, 1163–70. ACM, 2016. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>.","mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, ACM, 2016, pp. 1163–70, doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>."},"project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"publist_id":"5900","_id":"1349","scopus_import":"1","oa_version":"Published Version","type":"conference","month":"07","language":[{"iso":"eng"}],"date_published":"2016-07-20T00:00:00Z","publisher":"ACM","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"date_updated":"2025-09-22T08:13:19Z","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:44:45Z"},{"citation":{"chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.184796\">https://doi.org/10.1534/genetics.115.184796</a>.","apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.184796\">https://doi.org/10.1534/genetics.115.184796</a>","mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” <i>Genetics</i>, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>.","short":"N.H. Barton, Genetics 202 (2016) 3–4.","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” <i>Genetics</i>, 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.” <i>Genetics</i>. 2016;202(1):3-4. doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4."},"pubrep_id":"769","day":"05","status":"public","isi":1,"file_date_updated":"2020-07-14T12:44:46Z","oa":1,"date_published":"2016-01-05T00:00:00Z","language":[{"iso":"eng"}],"month":"01","date_updated":"2025-09-22T08:01:07Z","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"oa_version":"Submitted Version","intvolume":"       202","type":"journal_article","publist_id":"5889","scopus_import":"1","_id":"1356","corr_author":"1","file":[{"file_id":"4687","file_size":112674,"date_updated":"2020-07-14T12:44:46Z","access_level":"open_access","checksum":"3562b89c821a4be84edf2b6ebd870cf5","relation":"main_file","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:08:26Z","creator":"system"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["570"],"date_created":"2018-12-11T11:51:33Z","year":"2016","doi":"10.1534/genetics.115.184796","issue":"1","publication":"Genetics","article_processing_charge":"No","page":"3 - 4","external_id":{"isi":["000367718100002"]},"publication_status":"published","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":202},{"status":"public","pubrep_id":"768","day":"01","citation":{"ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. 2016;202(3):865-866. doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” <i>Genetics</i>, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.","short":"N.H. Barton, Genetics 202 (2016) 865–866.","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>.","apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>."},"scopus_import":"1","_id":"1357","publist_id":"5888","type":"journal_article","oa_version":"Submitted Version","intvolume":"       202","date_updated":"2025-09-22T07:56:18Z","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","date_published":"2016-03-01T00:00:00Z","month":"03","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:46Z","oa":1,"isi":1,"publication":"Genetics","doi":"10.1534/genetics.116.187542","issue":"3","date_created":"2018-12-11T11:51:33Z","year":"2016","ddc":["576"],"has_accepted_license":"1","file":[{"file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:15:09Z","creator":"system","file_id":"5127","date_updated":"2020-07-14T12:44:46Z","file_size":130779,"relation":"main_file","checksum":"b2174bab2de1d1142900062a150f35c9","access_level":"open_access"}],"quality_controlled":"1","corr_author":"1","volume":202,"author":[{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Richard Hudson and Norman Kaplan on the coalescent process","external_id":{"isi":["000371596400001"]},"publication_status":"published","article_processing_charge":"No","page":"865 - 866"},{"corr_author":"1","file":[{"file_id":"4919","access_level":"open_access","relation":"main_file","checksum":"fe3f3a1526d180b29fe691ab11435b78","file_size":861805,"date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:12:01Z","content_type":"application/pdf","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","creator":"system"},{"creator":"system","date_created":"2018-12-12T10:12:02Z","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","content_type":"application/pdf","access_level":"open_access","checksum":"164864a1a675f3ad80e9917c27aba07f","relation":"main_file","file_size":1084703,"date_updated":"2020-07-14T12:44:46Z","file_id":"4920"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["576"],"year":"2016","date_created":"2018-12-11T11:51:34Z","article_number":"12307","doi":"10.1038/ncomms12307","publication":"Nature Communications","article_processing_charge":"No","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."}],"external_id":{"isi":["000380858400001"]},"publication_status":"published","title":"Intrinsic limits to gene regulation by global crosstalk","author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar"},{"last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":7,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"citation":{"ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>."},"project":[{"_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"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"627","day":"04","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:44:46Z","language":[{"iso":"eng"}],"month":"08","date_published":"2016-08-04T00:00:00Z","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Nature Publishing Group","date_updated":"2026-04-08T13:54:24Z","intvolume":"         7","oa_version":"Published Version","type":"journal_article","publist_id":"5887","_id":"1358","scopus_import":"1"},{"title":"The effect of gene interactions on the long-term response to selection","page":"4422 - 4427","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"external_id":{"pmid":["27044080"],"isi":["000374393800056"]},"publication_status":"published","pmid":1,"author":[{"last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":113,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}],"ddc":["570"],"corr_author":"1","quality_controlled":"1","issue":"16","doi":"10.1073/pnas.1518830113","publication":"PNAS","year":"2016","date_created":"2018-12-11T11:51:34Z","month":"04","language":[{"iso":"eng"}],"date_published":"2016-04-19T00:00:00Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"National Academy of Sciences","date_updated":"2026-06-18T17:31:02Z","isi":1,"oa":1,"publist_id":"5886","_id":"1359","scopus_import":"1","article_type":"original","oa_version":"Published Version","intvolume":"       113","type":"journal_article","citation":{"ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. 2016;113(16):4422-4427. doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” <i>PNAS</i>, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","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.” <i>PNAS</i>, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>.","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>.","apa":"Paixao, T., &#38; Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>"},"project":[{"_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":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"day":"19","status":"public","ec_funded":1},{"status":"public","day":"01","citation":{"mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>.","apa":"Ellis, T., &#38; Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>","chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>.","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. <i>Annals of Botany</i>. 2016;117(7):1133-1140. doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” <i>Annals of Botany</i>, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016."},"type":"journal_article","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.","intvolume":"       117","oa_version":"None","_id":"1382","scopus_import":"1","publist_id":"5828","isi":1,"publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"date_updated":"2025-09-22T07:32:44Z","month":"06","language":[{"iso":"eng"}],"date_published":"2016-06-01T00:00:00Z","year":"2016","date_created":"2018-12-11T11:51:42Z","publication":"Annals of Botany","issue":"7","doi":"10.1093/aob/mcw043","quality_controlled":"1","corr_author":"1","volume":117,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","last_name":"Ellis","first_name":"Thomas"},{"first_name":"David","last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"}],"related_material":{"record":[{"id":"5550","relation":"popular_science","status":"public"}]},"abstract":[{"lang":"eng","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."}],"external_id":{"isi":["000379733800004"]},"publication_status":"published","page":"1133 - 1140","article_processing_charge":"No","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae"},{"title":"Genomics of hybridization and its evolutionary consequences","external_id":{"isi":["000378941100001"]},"publication_status":"published","page":"2325 - 2332","article_processing_charge":"No","volume":25,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Abbott, Richard","last_name":"Abbott","first_name":"Richard"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Good, Jeffrey","first_name":"Jeffrey","last_name":"Good"}],"ddc":["576"],"has_accepted_license":"1","file":[{"creator":"system","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:10:12Z","date_updated":"2020-07-14T12:44:53Z","file_size":226137,"access_level":"open_access","relation":"main_file","checksum":"ede7d0b8a471754f71f17e2b20f3135b","file_id":"4797"}],"quality_controlled":"1","publication":"Molecular Ecology","issue":"11","doi":"10.1111/mec.13685","year":"2016","date_created":"2018-12-11T11:51:51Z","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","date_updated":"2025-09-18T14:30:06Z","language":[{"iso":"eng"}],"month":"06","date_published":"2016-06-08T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:44:53Z","isi":1,"_id":"1409","scopus_import":"1","publist_id":"5798","type":"journal_article","oa_version":"Submitted Version","intvolume":"        25","citation":{"mla":"Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” <i>Molecular Ecology</i>, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:<a href=\"https://doi.org/10.1111/mec.13685\">10.1111/mec.13685</a>.","chicago":"Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/mec.13685\">https://doi.org/10.1111/mec.13685</a>.","apa":"Abbott, R., Barton, N. H., &#38; Good, J. (2016). Genomics of hybridization and its evolutionary consequences. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.13685\">https://doi.org/10.1111/mec.13685</a>","ama":"Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. <i>Molecular Ecology</i>. 2016;25(11):2325-2332. doi:<a href=\"https://doi.org/10.1111/mec.13685\">10.1111/mec.13685</a>","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332.","ieee":"R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” <i>Molecular Ecology</i>, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016.","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332."},"pubrep_id":"772","status":"public","day":"08"},{"external_id":{"arxiv":["1510.08344"],"isi":["000373959100022"]},"publication_status":"published","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 &lt; 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. "}],"article_processing_charge":"No","page":"1523 - 1548","title":"A general approximation for the dynamics of quantitative traits","volume":202,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Katarína","last_name":"Bod'ová","full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171"},{"last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"quality_controlled":"1","corr_author":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08344"}],"date_created":"2018-12-11T11:51:55Z","year":"2016","publication":"Genetics","doi":"10.1534/genetics.115.184127","issue":"4","oa":1,"isi":1,"date_updated":"2025-09-18T14:22:05Z","publisher":"Genetics Society of America","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"arxiv":1,"date_published":"2016-04-06T00:00:00Z","month":"04","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":"       202","scopus_import":"1","_id":"1420","publist_id":"5787","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"}],"citation":{"mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” <i>Genetics</i>, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:<a href=\"https://doi.org/10.1534/genetics.115.184127\">10.1534/genetics.115.184127</a>.","apa":"Bodova, K., Tkačik, G., &#38; Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.184127\">https://doi.org/10.1534/genetics.115.184127</a>","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.184127\">https://doi.org/10.1534/genetics.115.184127</a>.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. <i>Genetics</i>. 2016;202(4):1523-1548. doi:<a href=\"https://doi.org/10.1534/genetics.115.184127\">10.1534/genetics.115.184127</a>","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” <i>Genetics</i>, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548."},"ec_funded":1,"day":"06","status":"public"},{"day":"01","status":"public","pubrep_id":"561","ec_funded":1,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"citation":{"short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” <i>Genetics</i>, 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. <i>Genetics</i>. 2016;202(2):775-786. doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>","apa":"Lohse, K., Chmelik, M., Martin, S., &#38; Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>","chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>.","mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>."},"_id":"1518","scopus_import":"1","publist_id":"5658","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.).","type":"journal_article","article_type":"original","intvolume":"       202","oa_version":"Preprint","publisher":"Genetics Society of America","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"date_updated":"2025-09-18T11:09:34Z","month":"02","language":[{"iso":"eng"}],"date_published":"2016-02-01T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:45:00Z","isi":1,"publication":"Genetics","issue":"2","doi":"10.1534/genetics.115.183814","year":"2016","date_created":"2018-12-11T11:52:29Z","ddc":["570"],"has_accepted_license":"1","file":[{"file_id":"5241","relation":"main_file","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","access_level":"open_access","date_updated":"2020-07-14T12:45:00Z","file_size":957466,"date_created":"2018-12-12T10:16:51Z","content_type":"application/pdf","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","creator":"system"}],"quality_controlled":"1","pmid":1,"volume":202,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik"},{"last_name":"Martin","first_name":"Simon","full_name":"Martin, Simon"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","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."}],"publication_status":"published","external_id":{"isi":["000371304600032"],"pmid":["26715666"]},"page":"775 - 786","article_processing_charge":"No"},{"day":"01","pubrep_id":"465","status":"public","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"mla":"Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>, vol. 108, Academic Press, 2016, pp. 1–12, doi:<a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">10.1016/j.tpb.2015.10.008</a>.","apa":"Kelleher, J., Etheridge, A., Véber, A., &#38; Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>.","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.","ama":"Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. 2016;108:1-12. doi:<a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">10.1016/j.tpb.2015.10.008</a>","ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” <i>Theoretical Population Biology</i>, vol. 108. Academic Press, pp. 1–12, 2016.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12."},"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"publist_id":"5524","_id":"1631","scopus_import":"1","oa_version":"Published Version","intvolume":"       108","type":"journal_article","month":"04","language":[{"iso":"eng"}],"date_published":"2016-04-01T00:00:00Z","department":[{"_id":"NiBa"}],"publisher":"Academic Press","date_updated":"2025-09-18T10:51:58Z","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:45:07Z","doi":"10.1016/j.tpb.2015.10.008","publication":"Theoretical Population Biology","year":"2016","date_created":"2018-12-11T11:53:08Z","has_accepted_license":"1","ddc":["576"],"corr_author":"1","quality_controlled":"1","file":[{"file_id":"4865","access_level":"open_access","checksum":"6a65ba187994d4ad86c1c509e0ff482a","relation":"main_file","date_updated":"2020-07-14T12:45:07Z","file_size":1684043,"date_created":"2018-12-12T10:11:12Z","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","content_type":"application/pdf","creator":"system"}],"author":[{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":108,"title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","page":"1 - 12","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["000372560000001"]},"publication_status":"published"},{"related_material":{"record":[{"status":"public","id":"1382","relation":"research_paper"}]},"_id":"5550","publist_id":"5828","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","last_name":"Field","first_name":"David"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"date_updated":"2025-09-22T07:32:43Z","month":"02","title":"Flower colour data and phylogeny (NEXUS) files","date_published":"2016-02-19T00:00:00Z","oa":1,"abstract":[{"lang":"eng","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)"}],"file_date_updated":"2020-07-14T12:47:00Z","article_processing_charge":"No","day":"19","status":"public","doi":"10.15479/AT:ISTA:34","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"year":"2016","datarep_id":"34","date_created":"2018-12-12T12:31:29Z","ddc":["576"],"has_accepted_license":"1","file":[{"file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","content_type":"application/zip","date_created":"2018-12-12T13:02:27Z","creator":"system","file_id":"5594","date_updated":"2020-07-14T12:47:00Z","file_size":4468543,"access_level":"open_access","relation":"main_file","checksum":"950f85b80427d357bfeff09608ba02e9"}],"citation":{"ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","short":"T. Ellis, D. Field, (2016).","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>."}},{"doi":"10.5061/dryad.s5s7r","status":"public","day":"23","date_created":"2021-07-23T11:45:47Z","year":"2016","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"citation":{"apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","short":"N.H. Barton, (2016).","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>."},"_id":"9710","related_material":{"record":[{"relation":"used_in_publication","id":"1199","status":"public"}]},"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","type":"research_data_reference","date_published":"2016-09-23T00:00:00Z","title":"Data from: How does epistasis influence the response to selection?","month":"09","date_updated":"2025-04-15T07:11:02Z","department":[{"_id":"NiBa"}],"publisher":"Dryad","article_processing_charge":"No","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."}],"oa":1},{"type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"oa_version":"Published Version","_id":"9862","related_material":{"record":[{"relation":"used_in_publication","id":"1158","status":"public"}]},"article_processing_charge":"No","date_updated":"2025-09-22T09:55:08Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","month":"12","date_created":"2021-08-10T08:20:17Z","year":"2016","day":"27","status":"public","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, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","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:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","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.","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","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. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>"}},{"year":"2016","date_created":"2021-08-10T08:22:52Z","day":"27","status":"public","doi":"10.1371/journal.pbio.2000234.s017","citation":{"short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","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.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","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, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","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. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>.","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>."},"type":"research_data_reference","author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Romiguier","first_name":"Jonathan","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","last_name":"Bierne","first_name":"Nicolas"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"_id":"9863","article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","date_updated":"2025-09-22T09:55:09Z","month":"12","title":"Accessions of surveyed individuals, geographic locations and summary statistics"}]