[{"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"07","publisher":"Public Library of Science","day":"18","year":"2017","date_created":"2021-08-09T14:08:14Z","date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s003","related_material":{"record":[{"relation":"used_in_publication","id":"696","status":"public"}]},"_id":"9851","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","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","ama":"Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003","mla":"Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 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."},"date_updated":"2023-02-23T12:55:39Z","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"title":"Heuristic prediction for multiple stresses","article_processing_charge":"No","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta","last_name":"Lukacisinova"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}]},{"related_material":{"record":[{"id":"696","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pcbi.1005609.s004","date_published":"2017-07-18T00:00:00Z","date_created":"2021-08-09T14:11:40Z","year":"2017","day":"18","publisher":"Public Library of Science","month":"07","abstract":[{"text":"We show how different combination strategies affect the fraction of individuals that are multi-resistant.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova"},{"full_name":"Novak, Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"article_processing_charge":"No","title":"Resistance frequencies for different combination strategies","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"citation":{"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.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 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).","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"},"date_updated":"2023-02-23T12:55:39Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9852"},{"date_published":"2017-02-01T00:00:00Z","date_created":"2019-04-09T15:16:45Z","page":"83","day":"01","file":[{"checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","file_id":"6292","relation":"main_file","access_level":"closed","content_type":"application/pdf","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","date_created":"2019-04-09T15:15:32Z","creator":"dernst","file_size":3025175,"date_updated":"2020-07-14T12:47:27Z"},{"file_id":"9187","checksum":"af531e921a7f64a9e0af4cd8783b2226","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-02-22T13:45:59Z","file_name":"2017_Payne_Thesis.pdf","creator":"dernst","date_updated":"2021-02-22T13:45:59Z","file_size":3111536}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","degree_awarded":"PhD","publication_status":"published","year":"2017","month":"02","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","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"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Bacterial herd and social immunity to phages","file_date_updated":"2021-02-22T13:45:59Z","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","last_name":"Payne","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"supervisor":[{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"citation":{"chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 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.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017."},"date_updated":"2023-09-07T12:00:00Z","status":"public","type":"dissertation","_id":"6291"},{"abstract":[{"text":"Mathematica notebooks used to generate figures.","lang":"eng"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}],"publisher":"Mendeley Data","month":"12","year":"2017","day":"29","date_created":"2021-08-09T13:18:55Z","related_material":{"record":[{"relation":"used_in_publication","id":"564","status":"public"}]},"doi":"10.17632/nw68fxzjpm.1","date_published":"2017-12-29T00:00:00Z","_id":"9842","type":"research_data_reference","status":"public","date_updated":"2023-09-11T13:41:21Z","citation":{"ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 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).","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:10.17632/nw68fxzjpm.1","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","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"title":"Data for: Establishment in a new habitat by polygenic adaptation"},{"page":"765 - 787","doi":"10.1007/s00236-016-0278-x","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:51:32Z","has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"Acta Informatica","quality_controlled":"1","publisher":"Springer","oa":1,"author":[{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5898","external_id":{"isi":["000414343200003"]},"article_processing_charge":"No","title":"Model checking the evolution of gene regulatory networks","citation":{"short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"volume":54,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1835"}]},"issue":"8","ec_funded":1,"publication_identifier":{"issn":["00015903"]},"publication_status":"published","file":[{"date_created":"2019-01-17T15:57:29Z","file_name":"2017_ActaInformatica_Giacobbe.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:46Z","file_size":755241,"checksum":"4e661d9135d7f8c342e8e258dee76f3e","file_id":"5841","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 54","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."}],"oa_version":"Published Version","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:46Z","date_updated":"2023-09-20T11:06:03Z","ddc":["006","576"],"type":"journal_article","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":"649","_id":"1351"},{"day":"01","publication":"Algorithmica","isi":1,"has_accepted_license":"1","year":"2017","date_published":"2017-06-01T00:00:00Z","doi":"10.1007/s00453-016-0212-1","date_created":"2018-12-11T11:51:27Z","page":"681 - 713","quality_controlled":"1","publisher":"Springer","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","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","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."},"title":"Towards a runtime comparison of natural and artificial evolution","publist_id":"5931","author":[{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jorge","full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"external_id":{"isi":["000400379500013"]},"article_processing_charge":"No","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"file":[{"creator":"system","file_size":710206,"date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","date_created":"2018-12-12T10:10:19Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4805","checksum":"7873f665a0c598ac747c908f34cb14b9"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["01784617"]},"publication_status":"published","volume":78,"issue":"2","ec_funded":1,"oa_version":"Published Version","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."}],"month":"06","intvolume":" 78","scopus_import":"1","ddc":["576"],"date_updated":"2023-09-20T11:14:42Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:44:44Z","_id":"1336","status":"public","pubrep_id":"658","type":"journal_article","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)"}},{"date_published":"2017-01-01T00:00:00Z","doi":"10.1038/hdy.2016.109","date_created":"2018-12-11T11:50:40Z","page":"96 - 109","day":"01","publication":"Heredity","isi":1,"year":"2017","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"title":"How does epistasis influence the response to selection?","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publist_id":"6151","article_processing_charge":"No","external_id":{"isi":["000392229100011"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” Heredity, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","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","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.","ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109."},"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"volume":118,"related_material":{"record":[{"status":"public","id":"9710","relation":"research_data"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 118","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/"}],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2023-09-20T11:17:47Z","status":"public","type":"journal_article","_id":"1199"},{"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"article_processing_charge":"No","external_id":{"isi":["000393677300025"]},"publist_id":"6188","author":[{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak"},{"full_name":"Kollár, Richard","last_name":"Kollár","first_name":"Richard"}],"title":"Spatial gene frequency waves under genotype dependent dispersal","citation":{"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.","ista":"Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374.","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.","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","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","page":"367 - 374","date_created":"2018-12-11T11:50:31Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1534/genetics.116.193946","year":"2017","has_accepted_license":"1","isi":1,"publication":"Genetics","day":"01","type":"journal_article","pubrep_id":"727","status":"public","_id":"1169","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:37Z","date_updated":"2023-09-20T11:24:21Z","ddc":["576"],"scopus_import":"1","intvolume":" 205","month":"01","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"volume":205,"issue":"1","publication_status":"published","publication_identifier":{"issn":["00166731"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:44:37Z","file_size":361500,"creator":"system","date_created":"2018-12-12T10:10:43Z","file_name":"IST-2016-727-v1+1_SFC_Genetics_final.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7c8ab79cda1f92760bbbbe0f53175bfc","file_id":"4833"}]},{"date_updated":"2023-09-20T11:35:03Z","department":[{"_id":"NiBa"}],"_id":"1111","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"issn":["00166731"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":205,"issue":"2","ec_funded":1,"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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1534/genetics.116.189340","open_access":"1"}],"month":"02","intvolume":" 205","citation":{"ista":"Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6256","author":[{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["27881471"],"isi":["000394144900025"]},"article_processing_charge":"No","title":"Selection limits to adaptive walks on correlated landscapes","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"isi":1,"year":"2017","day":"01","publication":"Genetics","page":"803 - 825","doi":"10.1534/genetics.116.189340","date_published":"2017-02-01T00:00:00Z","date_created":"2018-12-11T11:50:12Z","quality_controlled":"1","publisher":"Genetics Society of America","oa":1},{"file_date_updated":"2019-01-18T09:14:02Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_updated":"2023-09-20T11:56:34Z","ddc":["570"],"type":"journal_article","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","_id":"1077","issue":"126","volume":14,"related_material":{"record":[{"id":"9864","status":"public","relation":"research_data"}]},"ec_funded":1,"publication_identifier":{"issn":["17425689"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"5843","creator":"dernst","file_size":1092015,"date_updated":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","date_created":"2019-01-18T09:14:02Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 14","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 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."}],"oa_version":"Published Version","author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo"},{"last_name":"Vladar","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold"},{"full_name":"Włodarski, Tomasz","last_name":"Włodarski","first_name":"Tomasz"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6303","external_id":{"isi":["000393380400001"]},"article_processing_charge":"Yes (in subscription journal)","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","citation":{"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.","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.","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","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"20160139","doi":"10.1098/rsif.2016.0139","date_published":"2017-01-04T00:00:00Z","date_created":"2018-12-11T11:50:01Z","isi":1,"has_accepted_license":"1","year":"2017","day":"04","publication":"Journal of the Royal Society Interface","publisher":"Royal Society of London","quality_controlled":"1","oa":1},{"citation":{"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.","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.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Ringbauer","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald"},{"first_name":"Graham","last_name":"Coop","full_name":"Coop, Graham"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publist_id":"6307","article_processing_charge":"No","external_id":{"isi":["000395807200023"]},"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"isi":1,"year":"2017","day":"01","publication":"Genetics","page":"1335 - 1351","date_published":"2017-03-01T00:00:00Z","doi":"10.1534/genetics.116.196220","date_created":"2018-12-11T11:50:00Z","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"date_updated":"2023-09-20T12:00:56Z","department":[{"_id":"NiBa"}],"_id":"1074","type":"journal_article","status":"public","publication_identifier":{"issn":["00166731"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":205,"issue":"3","related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"month":"03","intvolume":" 205"},{"_id":"1063","type":"journal_article","status":"public","date_updated":"2023-09-20T12:10:32Z","department":[{"_id":"NiBa"}],"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."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"http://biorxiv.org/content/early/2016/10/14/081042","open_access":"1"}],"month":"04","intvolume":" 71","publication_identifier":{"issn":["00143820"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":71,"ec_funded":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"citation":{"short":"H. Uecker, Evolution 71 (2017) 845–858.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi: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.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard","last_name":"Uecker","full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813"}],"publist_id":"6327","external_id":{"isi":["000398545200003"]},"article_processing_charge":"No","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"isi":1,"year":"2017","day":"01","publication":"Evolution","page":"845 - 858","date_published":"2017-04-01T00:00:00Z","doi":"10.1111/evo.13191","date_created":"2018-12-11T11:49:57Z"},{"volume":71,"issue":"6","ec_funded":1,"publication_identifier":{"issn":["00143820"]},"publication_status":"published","file":[{"checksum":"6d4c38cb1347fd43620d1736c6df5c79","file_id":"6329","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_Evolution_Sachdeva_supplement.pdf","date_created":"2019-04-17T07:37:04Z","creator":"dernst","file_size":625260,"date_updated":"2020-07-14T12:48:18Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6330","checksum":"f1d90dd8831b44baf49b4dd176f263af","creator":"dernst","date_updated":"2020-07-14T12:48:18Z","file_size":520110,"date_created":"2019-04-17T07:37:04Z","file_name":"2017_Evolution_Sachdeva_article.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 71","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"}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:18Z","date_updated":"2023-09-22T09:55:13Z","ddc":["576"],"type":"journal_article","status":"public","pubrep_id":"977","_id":"990","page":"1478 - 1493 ","date_published":"2017-06-01T00:00:00Z","doi":"10.1111/evo.13252","date_created":"2018-12-11T11:49:34Z","isi":1,"has_accepted_license":"1","year":"2017","day":"01","publication":"Evolution; International Journal of Organic Evolution","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"author":[{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6409","external_id":{"pmid":["28419447"],"isi":["000403014800005"]},"article_processing_charge":"No","title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","citation":{"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.","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.","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.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}]},{"volume":6,"ec_funded":1,"file":[{"checksum":"59cdd4400fb41280122d414fea971546","file_id":"5306","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","date_created":"2018-12-12T10:17:49Z","creator":"system","file_size":2441529,"date_updated":"2020-07-14T12:48:16Z"},{"file_id":"5307","checksum":"b69024880558b858eb8c5d47a92b6377","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:17:50Z","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","creator":"system","date_updated":"2020-07-14T12:48:16Z","file_size":3752660}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050084X"]},"publication_status":"published","month":"05","intvolume":" 6","scopus_import":"1","oa_version":"Published Version","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"}],"department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:48:16Z","ddc":["576"],"date_updated":"2023-09-22T10:01:17Z","status":"public","pubrep_id":"841","type":"journal_article","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)"},"_id":"954","doi":"10.7554/eLife.25192","date_published":"2017-05-18T00:00:00Z","date_created":"2018-12-11T11:49:23Z","day":"18","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2017","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","publist_id":"6460","author":[{"last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"external_id":{"isi":["000404024800001"]},"article_processing_charge":"Yes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","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","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","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.","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."},"project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"article_number":"e25192"},{"_id":"955","status":"public","pubrep_id":"864","type":"journal_article","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)"},"ddc":["539","576"],"date_updated":"2023-09-22T10:00:49Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","oa_version":"Published Version","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"}],"month":"08","intvolume":" 8","scopus_import":"1","file":[{"file_id":"5064","checksum":"29a1b5db458048d3bd5c67e0e2a56818","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:14Z","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","date_updated":"2020-07-14T12:48:16Z","file_size":998157,"creator":"system"},{"file_size":9715993,"date_updated":"2020-07-14T12:48:16Z","creator":"system","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","date_created":"2018-12-12T10:14:15Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5065","checksum":"7b78401e52a576cf3e6bbf8d0abadc17"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","volume":8,"related_material":{"record":[{"relation":"dissertation_contains","id":"6071","status":"public"}]},"issue":"1","ec_funded":1,"article_number":"216","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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).","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.","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","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"},"title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","publist_id":"6459","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"full_name":"Prizak, Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000407198800005"]},"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"09","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2017","doi":"10.1038/s41467-017-00238-8","date_published":"2017-08-09T00:00:00Z","date_created":"2018-12-11T11:49:23Z"},{"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"31","year":"2017","isi":1,"date_created":"2018-12-11T11:49:23Z","date_published":"2017-05-31T00:00:00Z","doi":"10.1098/rspb.2016.2864","oa":1,"publisher":"Royal Society, The","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","short":"D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017).","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","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","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.","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."},"title":"The sources of adaptive evolution","article_processing_charge":"No","external_id":{"isi":["000405148800021"],"pmid":["28566483"]},"publist_id":"6462","author":[{"full_name":"Charlesworth, Deborah","last_name":"Charlesworth","first_name":"Deborah"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Charlesworth","full_name":"Charlesworth, Brian","first_name":"Brian"}],"article_number":"20162864","language":[{"iso":"eng"}],"publication_status":"published","volume":284,"issue":"1855","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","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."}],"intvolume":" 284","month":"05","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/","open_access":"1"}],"scopus_import":"1","date_updated":"2023-09-22T10:01:48Z","department":[{"_id":"NiBa"}],"_id":"953","status":"public","type":"journal_article"},{"author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"6463","external_id":{"pmid":["28411063"]},"article_processing_charge":"No","title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","citation":{"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.","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","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Elsevier","oa":1,"page":"45 - 60","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.tpb.2017.03.003","date_created":"2018-12-11T11:49:22Z","has_accepted_license":"1","year":"2017","day":"01","publication":"Theoretical Population Biology","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"972","_id":"952","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","date_updated":"2023-09-22T10:02:21Z","ddc":["576"],"scopus_import":"1","month":"06","intvolume":" 115","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"}],"pmid":1,"oa_version":"Submitted Version","volume":115,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["00405809"]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:48:16Z","file_size":2073856,"creator":"dernst","date_created":"2019-04-17T06:39:45Z","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","file_id":"6327"}],"language":[{"iso":"eng"}]},{"issue":"5","related_material":{"record":[{"status":"public","id":"9856","relation":"research_data"},{"status":"public","id":"9857","relation":"research_data"},{"id":"9858","status":"public","relation":"research_data"}]},"volume":15,"publication_identifier":{"issn":["15449173"]},"publication_status":"published","file":[{"file_size":5541206,"date_updated":"2020-07-14T12:48:16Z","creator":"system","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","date_created":"2018-12-12T10:08:30Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"107d290bd1159ec77b734eb2824b01c8","file_id":"4691"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 15","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"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:16Z","department":[{"_id":"NiBa"}],"date_updated":"2023-09-22T10:02:52Z","ddc":["576"],"type":"journal_article","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":"843","_id":"951","doi":"10.1371/journal.pbio.2001894","date_published":"2017-05-30T00:00:00Z","date_created":"2018-12-11T11:49:22Z","isi":1,"has_accepted_license":"1","year":"2017","day":"30","publication":"PLoS Biology","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"author":[{"first_name":"Tom","last_name":"Schmidt","full_name":"Schmidt, Tom"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gordana","full_name":"Rasic, Gordana","last_name":"Rasic"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"first_name":"Brian","full_name":"Montgomery, Brian","last_name":"Montgomery"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"first_name":"Peter","full_name":"Cook, Peter","last_name":"Cook"},{"last_name":"Ryan","full_name":"Ryan, Peter","first_name":"Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"publist_id":"6464","external_id":{"isi":["000402520000012"]},"article_processing_charge":"No","title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","citation":{"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","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","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).","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"e2001894"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-22T10:02:51Z","citation":{"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.","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","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","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).","ieee":"T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017.","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.","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."},"title":"Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics","department":[{"_id":"NiBa"}],"author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Rasic","full_name":"Rasic, Gordana","first_name":"Gordana"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"first_name":"Scott","full_name":"Ritchie, Scott","last_name":"Ritchie"},{"last_name":"Hoffmann","full_name":"Hoffmann, Ary","first_name":"Ary"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"article_processing_charge":"No","_id":"9858","status":"public","type":"research_data_reference","day":"30","year":"2017","doi":"10.1371/journal.pbio.2001894.s016","related_material":{"record":[{"relation":"used_in_publication","id":"951","status":"public"}]},"date_published":"2017-05-30T00:00:00Z","date_created":"2021-08-10T07:47:07Z","oa_version":"Published Version","month":"05","publisher":"Public Library of Science"},{"year":"2017","day":"30","date_published":"2017-05-30T00:00:00Z","doi":"10.1371/journal.pbio.2001894.s015","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"date_created":"2021-08-10T07:41:52Z","oa_version":"Published Version","publisher":"Public Library of Science ","month":"05","date_updated":"2023-09-22T10:02:51Z","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 observed wMel frequencies and analyses of habitat variables, Public Library of Science , 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.","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","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","ieee":"T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Gordana","full_name":"Rasic, Gordana","last_name":"Rasic"},{"last_name":"Turley","full_name":"Turley, Andrew","first_name":"Andrew"},{"first_name":"Brian","full_name":"Montgomery, Brian","last_name":"Montgomery"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"last_name":"Cook","full_name":"Cook, Peter","first_name":"Peter"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"first_name":"Scott","last_name":"Ritchie","full_name":"Ritchie, Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","_id":"9857","type":"research_data_reference","status":"public"},{"_id":"9856","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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.","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.","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.","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","ieee":"T. Schmidt et al., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017.","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)."},"date_updated":"2023-09-22T10:02:51Z","department":[{"_id":"NiBa"}],"title":"Supporting Information concerning additional likelihood analyses and results","author":[{"first_name":"Tom","full_name":"Schmidt, Tom","last_name":"Schmidt"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","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"},{"first_name":"Brian","full_name":"Montgomery, Brian","last_name":"Montgomery"},{"first_name":"Inaki","last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"first_name":"Peter","full_name":"Ryan, Peter","last_name":"Ryan"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"first_name":"Ary","full_name":"Hoffmann, Ary","last_name":"Hoffmann"},{"last_name":"O’Neill","full_name":"O’Neill, Scott","first_name":"Scott"},{"last_name":"Turelli","full_name":"Turelli, Michael","first_name":"Michael"}],"article_processing_charge":"No","oa_version":"Published Version","month":"05","publisher":"Public Library of Science","day":"30","year":"2017","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"doi":"10.1371/journal.pbio.2001894.s014","date_published":"2017-05-30T00:00:00Z","date_created":"2021-08-10T07:36:04Z"},{"pubrep_id":"974","status":"public","type":"journal_article","_id":"910","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:15Z","ddc":["576"],"date_updated":"2023-09-26T15:49:15Z","intvolume":" 207","month":"10","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"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","lang":"eng"}],"ec_funded":1,"issue":"2","volume":207,"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":494268,"date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2018-974-v1+1_manuscript.pdf","date_created":"2018-12-12T10:17:12Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"f7c32dabf52e6d9e709d9203761e39fd","file_id":"5264"}],"publication_status":"published","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"When does frequency-independent selection maintain genetic variation?","article_processing_charge":"No","external_id":{"isi":["000412232600019"]},"author":[{"last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publist_id":"6533","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 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","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","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.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","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."},"oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","date_created":"2018-12-11T11:49:09Z","date_published":"2017-10-01T00:00:00Z","doi":"10.1534/genetics.117.300129","page":"653 - 668","publication":"Genetics","day":"01","year":"2017","has_accepted_license":"1","isi":1},{"scopus_import":1,"intvolume":" 8","month":"12","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":8,"related_material":{"record":[{"status":"public","id":"7163","relation":"popular_science"}]},"issue":"1","publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"4da2651303c8afc2f7fc419be42a2433","file_id":"7562","date_updated":"2020-07-14T12:47:20Z","file_size":1201520,"creator":"dernst","date_created":"2020-03-03T15:55:50Z","file_name":"2017_NatureComm_Fraisse.pdf"}],"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)"},"article_type":"original","type":"journal_article","pubrep_id":"910","status":"public","_id":"614","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:20Z","date_updated":"2024-02-21T13:47:47Z","ddc":["570","576"],"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:47:30Z","doi":"10.1038/s41467-017-01663-5","date_published":"2017-12-01T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Nature Communications","day":"01","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"article_number":"1486","article_processing_charge":"No","external_id":{"pmid":["29133797"]},"author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"publist_id":"7190","title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","citation":{"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","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","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"7163","type":"research_data","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)"},"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","date_updated":"2024-02-21T13:47:47Z","citation":{"short":"C. Fraisse, (2017).","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.","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"}],"article_processing_charge":"No","title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"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."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"12","has_accepted_license":"1","year":"2017","day":"01","file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","file_id":"7164","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","date_updated":"2020-07-14T12:47:50Z","file_size":841375478,"creator":"cfraisse","date_created":"2019-12-10T08:46:46Z","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip"}],"doi":"10.15479/AT:ISTA:7163","related_material":{"record":[{"relation":"research_paper","id":"614","status":"public"}]},"date_published":"2017-12-01T00:00:00Z","date_created":"2019-12-09T23:03:03Z","contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","orcid":"0000-0002-8101-2518"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}]},{"volume":13,"issue":"7","related_material":{"record":[{"id":"9849","status":"public","relation":"research_data"},{"status":"public","id":"9850","relation":"research_data"},{"relation":"research_data","id":"9851","status":"public"},{"id":"9852","status":"public","relation":"research_data"},{"status":"public","id":"6263","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"creator":"system","file_size":3775716,"date_updated":"2020-07-14T12:47:46Z","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_created":"2018-12-12T10:15:01Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553734X"]},"publication_status":"published","month":"07","intvolume":" 13","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"ddc":["576"],"date_updated":"2024-03-27T23:30:28Z","status":"public","pubrep_id":"894","type":"journal_article","article_type":"original","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)"},"_id":"696","doi":"10.1371/journal.pcbi.1005609","date_published":"2017-07-18T00:00:00Z","date_created":"2018-12-11T11:47:58Z","day":"18","publication":"PLoS Computational Biology","has_accepted_license":"1","year":"2017","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","author":[{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"}],"publist_id":"7004","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","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.","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."},"project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"article_number":"e1005609"},{"acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"has_accepted_license":"1","year":"2016","day":"19","publication":"Scientific Reports","doi":"10.1038/srep38840","date_published":"2016-12-19T00:00:00Z","date_created":"2018-12-11T11:50:32Z","article_number":"38840","citation":{"ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","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.","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","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","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"first_name":"Mustansir","full_name":"Barma, Mustansir","last_name":"Barma"},{"full_name":"Rao, Madan","last_name":"Rao","first_name":"Madan"}],"publist_id":"6183","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"}],"oa_version":"Published Version","scopus_import":1,"month":"12","intvolume":" 6","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4977","checksum":"cb378732da885ea4959ec5b845fb6e52","date_updated":"2020-07-14T12:44:37Z","file_size":760967,"creator":"system","date_created":"2018-12-12T10:12:56Z","file_name":"IST-2017-737-v1+1_srep38840.pdf"}],"language":[{"iso":"eng"}],"volume":6,"_id":"1172","type":"journal_article","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":"737","date_updated":"2021-01-12T06:48:50Z","ddc":["576"],"file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"NiBa"}]},{"oa_version":"Submitted Version","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. "}],"intvolume":" 34","month":"10","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:44:38Z","file_size":295274,"creator":"system","date_created":"2018-12-12T10:16:35Z","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5223","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0"},{"checksum":"e13171843283774404c936c581b4543e","file_id":"5224","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-770-v1+2_Fig1.pdf","date_created":"2018-12-12T10:16:36Z","file_size":10902625,"date_updated":"2020-07-14T12:44:38Z","creator":"system"},{"creator":"system","file_size":21437,"date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2017-770-v1+3_Fig2.pdf","date_created":"2018-12-12T10:16:37Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5225","checksum":"63bc6e6e61f347594d8c00c37f874a0b"},{"date_created":"2018-12-12T10:16:38Z","file_name":"IST-2017-770-v1+4_Fig3.pdf","creator":"system","date_updated":"2020-07-14T12:44:38Z","file_size":1172194,"file_id":"5226","checksum":"da87cc7c78808837f22a3dae1c8397f9","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"creator":"system","file_size":50045,"date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2017-770-v1+5_Fig4.pdf","date_created":"2018-12-12T10:16:38Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"e47b2a0c32142f423b3100150c0294f8","file_id":"5227"},{"file_name":"IST-2017-770-v1+6_Fig5.pdf","date_created":"2018-12-12T10:16:39Z","file_size":50705,"date_updated":"2020-07-14T12:44:38Z","creator":"system","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","file_id":"5228","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","ec_funded":1,"volume":34,"issue":"1","_id":"1195","pubrep_id":"770","status":"public","type":"journal_article","ddc":["576"],"date_updated":"2021-01-12T06:49:00Z","department":[{"_id":"NiBa"}],"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”.","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","publication":"Molecular Biology and Evolution","day":"03","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:50:39Z","date_published":"2016-10-03T00:00:00Z","doi":"10.1093/molbev/msw210","page":"174 - 184","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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.","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","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.","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.","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","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","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"},"title":"Reconstruction of haplotype-blocks selected during experimental evolution.","author":[{"first_name":"Susan","last_name":"Franssen","full_name":"Franssen, Susan"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Christian","last_name":"Schlötterer","full_name":"Schlötterer, Christian"}],"publist_id":"6155"},{"_id":"1224","type":"journal_article","status":"public","citation":{"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.","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.","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,” Plant Biology, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016.","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","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","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."},"date_updated":"2021-01-12T06:49:12Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6110","author":[{"last_name":"Teitel","full_name":"Teitel, Zachary","first_name":"Zachary"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"full_name":"Barrett, Spencer","last_name":"Barrett","first_name":"Spencer"}],"title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","department":[{"_id":"NiBa"}],"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."}],"oa_version":"None","quality_controlled":"1","publisher":"Wiley-Blackwell","scopus_import":1,"intvolume":" 18","month":"01","publication_status":"published","year":"2016","publication":"Plant Biology","language":[{"iso":"eng"}],"day":"01","page":"98 - 103","date_created":"2018-12-11T11:50:48Z","date_published":"2016-01-01T00:00:00Z","issue":"1","volume":18,"doi":"10.1111/plb.12336"},{"type":"journal_article","status":"public","_id":"1241","department":[{"_id":"NiBa"}],"date_updated":"2023-02-21T10:24:19Z","main_file_link":[{"url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract","open_access":"1"}],"scopus_import":1,"intvolume":" 202","month":"02","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","ec_funded":1,"issue":"2","volume":202,"publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}],"publist_id":"6091","author":[{"full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","last_name":"Uecker","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hermisson, Joachim","last_name":"Hermisson","first_name":"Joachim"}],"title":"The role of recombination in evolutionary rescue","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.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 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.","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","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. doi:10.1534/genetics.115.180299","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","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).","page":"721 - 732","date_created":"2018-12-11T11:50:54Z","date_published":"2016-02-01T00:00:00Z","doi":"10.1534/genetics.115.180299","year":"2016","publication":"Genetics","day":"01"},{"date_published":"2016-07-20T00:00:00Z","doi":"10.1145/2908812.2908909","date_created":"2018-12-11T11:51:31Z","page":"1163 - 1170","day":"20","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","has_accepted_license":"1","year":"2016","quality_controlled":"1","publisher":"ACM","oa":1,"title":"When non-elitism outperforms elitism for crossing fitness valleys","author":[{"first_name":"Pietro","full_name":"Oliveto, Pietro","last_name":"Oliveto"},{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"first_name":"Jorge","full_name":"Heredia, Jorge","last_name":"Heredia"},{"last_name":"Sudholt","full_name":"Sudholt, Dirk","first_name":"Dirk"},{"orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5900","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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 Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 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","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","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.","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.","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."},"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ec_funded":1,"file":[{"file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","date_created":"2018-12-12T10:16:27Z","file_size":979026,"date_updated":"2020-07-14T12:44:45Z","creator":"system","checksum":"a1896e39e4113f2711e46b435d5f3e69","file_id":"5214","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"07","scopus_import":1,"oa_version":"Published Version","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."}],"file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"ddc":["576"],"date_updated":"2021-01-12T06:50:03Z","status":"public","pubrep_id":"650","type":"conference","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)"},"conference":{"location":"Denver, CO, USA","end_date":"2016-07-24","start_date":"2016-07-20","name":"GECCO: Genetic and evolutionary computation conference"},"_id":"1349"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 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.","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","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","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","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."},"title":"The effect of gene interactions on the long-term response to selection","author":[{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publist_id":"5886","article_processing_charge":"No","external_id":{"pmid":["27044080"]},"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"19","publication":"PNAS","year":"2016","date_published":"2016-04-19T00:00:00Z","doi":"10.1073/pnas.1518830113","date_created":"2018-12-11T11:51:34Z","page":"4422 - 4427","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"date_updated":"2021-01-12T06:50:08Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"_id":"1359","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":113,"issue":"16","ec_funded":1,"pmid":1,"oa_version":"Published Version","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."}],"month":"04","intvolume":" 113","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}]},{"file_date_updated":"2020-07-14T12:44:46Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2021-01-12T06:50:07Z","status":"public","pubrep_id":"769","type":"journal_article","_id":"1356","issue":"1","volume":202,"file":[{"file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","date_created":"2018-12-12T10:08:26Z","creator":"system","file_size":112674,"date_updated":"2020-07-14T12:44:46Z","file_id":"4687","checksum":"3562b89c821a4be84edf2b6ebd870cf5","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 202","scopus_import":1,"oa_version":"Submitted Version","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"publist_id":"5889","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","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.","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.","short":"N.H. Barton, Genetics 202 (2016) 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","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","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."},"date_published":"2016-01-05T00:00:00Z","doi":"10.1534/genetics.115.184796","date_created":"2018-12-11T11:51:33Z","page":"3 - 4","day":"05","publication":"Genetics","has_accepted_license":"1","year":"2016","quality_controlled":"1","publisher":"Genetics Society of America","oa":1},{"file_date_updated":"2020-07-14T12:44:46Z","department":[{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2021-01-12T06:50:07Z","status":"public","pubrep_id":"768","type":"journal_article","_id":"1357","volume":202,"issue":"3","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"b2174bab2de1d1142900062a150f35c9","file_id":"5127","date_updated":"2020-07-14T12:44:46Z","file_size":130779,"creator":"system","date_created":"2018-12-12T10:15:09Z","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"03","intvolume":" 202","scopus_import":1,"oa_version":"Submitted Version","title":"Richard Hudson and Norman Kaplan on the coalescent process","publist_id":"5888","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"N.H. Barton, Genetics 202 (2016) 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.","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 2016;202(3):865-866. doi:10.1534/genetics.116.187542","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","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.","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","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."},"doi":"10.1534/genetics.116.187542","date_published":"2016-03-01T00:00:00Z","date_created":"2018-12-11T11:51:33Z","page":"865 - 866","day":"01","publication":"Genetics","has_accepted_license":"1","year":"2016","publisher":"Genetics Society of America","quality_controlled":"1","oa":1},{"author":[{"last_name":"Abbott","full_name":"Abbott, Richard","first_name":"Richard"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Good","full_name":"Good, Jeffrey","first_name":"Jeffrey"}],"publist_id":"5798","title":"Genomics of hybridization and its evolutionary consequences","citation":{"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.","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","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","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.","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.","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.","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"page":"2325 - 2332","doi":"10.1111/mec.13685","date_published":"2016-06-08T00:00:00Z","date_created":"2018-12-11T11:51:51Z","has_accepted_license":"1","year":"2016","day":"08","publication":"Molecular Ecology","type":"journal_article","status":"public","pubrep_id":"772","_id":"1409","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:50:33Z","ddc":["576"],"scopus_import":1,"month":"06","intvolume":" 25","oa_version":"Submitted Version","volume":25,"issue":"11","publication_status":"published","file":[{"date_created":"2018-12-12T10:10:12Z","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","date_updated":"2020-07-14T12:44:53Z","file_size":226137,"creator":"system","checksum":"ede7d0b8a471754f71f17e2b20f3135b","file_id":"4797","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}]},{"_id":"1420","type":"journal_article","status":"public","date_updated":"2022-08-01T10:49:55Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"abstract":[{"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. ","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08344"}],"scopus_import":"1","intvolume":" 202","month":"04","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":202,"issue":"4","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","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","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","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.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1510.08344"]},"author":[{"orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","last_name":"Bod'ová","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publist_id":"5787","title":"A general approximation for the dynamics of quantitative traits","oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","year":"2016","publication":"Genetics","day":"06","page":"1523 - 1548","date_created":"2018-12-11T11:51:55Z","doi":"10.1534/genetics.115.184127","date_published":"2016-04-06T00:00:00Z"},{"ec_funded":1,"volume":202,"issue":"2","publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5241","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":957466,"date_created":"2018-12-12T10:16:51Z","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf"}],"scopus_import":"1","intvolume":" 202","month":"02","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"date_updated":"2022-05-24T09:16:22Z","ddc":["570"],"type":"journal_article","article_type":"original","pubrep_id":"561","status":"public","_id":"1518","page":"775 - 786","date_created":"2018-12-11T11:52:29Z","date_published":"2016-02-01T00:00:00Z","doi":"10.1534/genetics.115.183814","year":"2016","has_accepted_license":"1","publication":"Genetics","day":"01","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","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.).","article_processing_charge":"No","external_id":{"pmid":["26715666"]},"publist_id":"5658","author":[{"first_name":"Konrad","full_name":"Lohse, Konrad","last_name":"Lohse"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Martin","full_name":"Martin, Simon","first_name":"Simon"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","citation":{"ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.","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.","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.","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}]},{"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"}],"oa_version":"Published Version","scopus_import":1,"month":"04","intvolume":" 108","publication_status":"published","file":[{"date_created":"2018-12-12T10:11:12Z","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","creator":"system","date_updated":"2020-07-14T12:45:07Z","file_size":1684043,"file_id":"4865","checksum":"6a65ba187994d4ad86c1c509e0ff482a","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":108,"ec_funded":1,"_id":"1631","type":"journal_article","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":"465","date_updated":"2021-01-12T06:52:07Z","ddc":["576"],"file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"NiBa"}],"publisher":"Academic Press","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2016","day":"01","publication":"Theoretical Population Biology","page":"1 - 12","doi":"10.1016/j.tpb.2015.10.008","date_published":"2016-04-01T00:00:00Z","date_created":"2018-12-11T11:53:08Z","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"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","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","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 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.","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.","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"first_name":"Amandine","full_name":"Véber, Amandine","last_name":"Véber"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5524","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations"},{"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.","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS Biology","day":"27","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:50:28Z","doi":"10.1371/journal.pbio.2000234","date_published":"2016-12-27T00:00:00Z","article_number":"e2000234","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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."},"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"last_name":"Anciaux","full_name":"Anciaux, Youann","first_name":"Youann"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"publist_id":"6200","oa_version":"Published Version","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 "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."}],"intvolume":" 14","month":"12","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":2494348,"date_updated":"2020-07-14T12:44:36Z","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","date_created":"2018-12-12T10:15:42Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5164","checksum":"2bab63b068a9840efd532b9ae583f9bb"}],"publication_status":"published","related_material":{"record":[{"id":"9862","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9863"}]},"volume":14,"issue":"12","_id":"1158","pubrep_id":"742","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)"},"type":"journal_article","ddc":["576"],"date_updated":"2023-02-23T14:11:16Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:36Z"},{"_id":"9862","type":"research_data_reference","status":"public","date_updated":"2023-02-21T16:21:20Z","citation":{"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.","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","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.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","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.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"article_processing_charge":"No","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa_version":"Published Version","publisher":"Public Library of Science","month":"12","year":"2016","day":"27","doi":"10.1371/journal.pbio.2000234.s016","related_material":{"record":[{"relation":"used_in_publication","id":"1158","status":"public"}]},"date_created":"2021-08-10T08:20:17Z"},{"doi":"10.1371/journal.pbio.2000234.s017","related_material":{"record":[{"relation":"used_in_publication","id":"1158","status":"public"}]},"date_created":"2021-08-10T08:22:52Z","day":"27","year":"2016","month":"12","publisher":"Public Library of Science","oa_version":"Published Version","title":"Accessions of surveyed individuals, geographic locations and summary statistics","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"first_name":"Nicolas","full_name":"Galtier, Nicolas","last_name":"Galtier"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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.","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.","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.","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","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","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."},"date_updated":"2023-02-21T16:21:20Z","status":"public","type":"research_data_reference","_id":"9863"},{"title":"Evolutionary proccesses in variable emvironments","publist_id":"6235","author":[{"last_name":"Novak","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Novak, Sebastian. 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.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","ieee":"S. Novak, “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.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2016-07-01T00:00:00Z","date_created":"2018-12-11T11:50:17Z","page":"124","day":"01","has_accepted_license":"1","year":"2016","status":"public","type":"dissertation","_id":"1125","department":[{"_id":"NiBa"}],"file_date_updated":"2021-02-22T13:42:47Z","ddc":["576"],"supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"date_updated":"2023-09-07T11:55:53Z","month":"07","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"status":"public","id":"2023","relation":"part_of_dissertation"}]},"file":[{"date_created":"2019-08-13T09:01:00Z","file_name":"Novak_thesis.pdf","date_updated":"2019-08-13T09:01:00Z","file_size":3564901,"creator":"dernst","file_id":"6811","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","content_type":"application/pdf","access_level":"closed","relation":"main_file"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"30808d2f7ca920e09f63a95cdc49bffd","file_id":"9186","file_size":2814384,"date_updated":"2021-02-22T13:42:47Z","creator":"dernst","file_name":"2016_Novak_Thesis.pdf","date_created":"2021-02-22T13:42:47Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD"},{"ec_funded":1,"volume":7,"related_material":{"record":[{"id":"6071","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-627-v1+1_ncomms12307.pdf","date_created":"2018-12-12T10:12:01Z","creator":"system","file_size":861805,"date_updated":"2020-07-14T12:44:46Z","checksum":"fe3f3a1526d180b29fe691ab11435b78","file_id":"4919","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"checksum":"164864a1a675f3ad80e9917c27aba07f","file_id":"4920","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:12:02Z","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","creator":"system","date_updated":"2020-07-14T12:44:46Z","file_size":1084703}],"publication_status":"published","intvolume":" 7","month":"08","scopus_import":1,"oa_version":"Published Version","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."}],"department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:44:46Z","ddc":["576"],"date_updated":"2023-09-07T12:53:49Z","pubrep_id":"627","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)"},"type":"journal_article","_id":"1358","date_created":"2018-12-11T11:51:34Z","doi":"10.1038/ncomms12307","date_published":"2016-08-04T00:00:00Z","publication":"Nature Communications","day":"04","year":"2016","has_accepted_license":"1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","title":"Intrinsic limits to gene regulation by global crosstalk","publist_id":"5887","author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","full_name":"Prizak, Roshan","last_name":"Prizak"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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.","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.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","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","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","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."},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"12307"},{"date_created":"2021-07-23T11:45:47Z","date_published":"2016-09-23T00:00:00Z","doi":"10.5061/dryad.s5s7r","related_material":{"record":[{"relation":"used_in_publication","id":"1199","status":"public"}]},"year":"2016","day":"23","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.s5s7r","open_access":"1"}],"publisher":"Dryad","month":"09","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"department":[{"_id":"NiBa"}],"title":"Data from: How does epistasis influence the response to selection?","date_updated":"2023-09-20T11:17:47Z","citation":{"ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, 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.","short":"N.H. Barton, (2016).","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:10.5061/dryad.s5s7r","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r","mla":"Barton, Nicholas H. Data from: How Does Epistasis Influence the Response to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9710"},{"status":"public","type":"research_data_reference","_id":"9864","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","article_processing_charge":"No","author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold"},{"first_name":"Tomasz","full_name":"Włodarski, Tomasz","last_name":"Włodarski"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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.","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.","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.","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","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","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.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016)."},"date_updated":"2023-09-20T11:56:33Z","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.4315652.v1"}],"oa":1,"publisher":"The Royal Society","oa_version":"Published Version","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 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.","lang":"eng"}],"date_created":"2021-08-10T08:29:47Z","related_material":{"record":[{"status":"public","id":"1077","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.4315652.v1","date_published":"2016-12-14T00:00:00Z","day":"14","year":"2016"},{"type":"journal_article","status":"public","_id":"1382","author":[{"last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"}],"publist_id":"5828","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","department":[{"_id":"NiBa"}],"citation":{"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.","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.","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","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","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","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.","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."},"date_updated":"2024-02-21T13:49:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":1,"publisher":"Oxford University Press","month":"06","intvolume":" 117","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"}],"oa_version":"None","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.","page":"1133 - 1140","issue":"7","volume":117,"doi":"10.1093/aob/mcw043","date_published":"2016-06-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"5550","relation":"popular_science"}]},"date_created":"2018-12-11T11:51:42Z","publication_status":"published","year":"2016","day":"1","language":[{"iso":"eng"}],"publication":"Annals of Botany"},{"month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","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)"}],"date_created":"2018-12-12T12:31:29Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"status":"public","id":"1382","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:34","file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","file_id":"5594","checksum":"950f85b80427d357bfeff09608ba02e9","date_updated":"2020-07-14T12:47:00Z","file_size":4468543,"creator":"system","date_created":"2018-12-12T13:02:27Z","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip"}],"day":"19","year":"2016","datarep_id":"34","has_accepted_license":"1","status":"public","tmp":{"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)","short":"CC0 (1.0)"},"type":"research_data","_id":"5550","title":"Flower colour data and phylogeny (NEXUS) files","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:00Z","article_processing_charge":"No","publist_id":"5828","author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"date_updated":"2024-02-21T13:49:54Z","citation":{"ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, 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.","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","short":"T. Ellis, D. Field, (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","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34","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."}},{"pubrep_id":"526","status":"public","type":"dissertation","_id":"1398","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:48Z","ddc":["576"],"date_updated":"2024-02-21T13:51:39Z","supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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."}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5553"},{"relation":"popular_science","id":"5551","status":"public"},{"relation":"popular_science","id":"5552","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:14:51Z","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","date_updated":"2020-07-14T12:44:48Z","file_size":11928241,"creator":"system","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","file_id":"5106","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","article_processing_charge":"No","publist_id":"5809","author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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 .","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.","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 .","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.","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.","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 ","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 "},"oa":1,"publisher":"Institute of Science and Technology Austria","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. ","date_created":"2018-12-11T11:51:47Z","doi":"10.15479/AT:ISTA:TH_526 ","date_published":"2016-02-18T00:00:00Z","page":"130","day":"18","year":"2016","has_accepted_license":"1"},{"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-08-13T08:53:52Z","file_name":"Tugrul_thesis_w_signature_page.pdf","date_updated":"2019-08-13T08:53:52Z","file_size":3695257,"creator":"dernst","file_id":"6810","checksum":"66cb61a59943e4fb7447c6a86be5ef51","content_type":"application/pdf","access_level":"closed","relation":"main_file"},{"file_name":"2016_Tugrul_Thesis.pdf","date_created":"2021-02-22T11:45:20Z","file_size":3880811,"date_updated":"2021-02-22T11:45:20Z","creator":"dernst","success":1,"checksum":"293e388d70563760f6b24c3e66283dda","file_id":"9182","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1666","status":"public"},{"id":"5554","status":"public","relation":"research_data"}]},"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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07","date_updated":"2024-02-21T13:50:34Z","supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"ddc":["576"],"file_date_updated":"2021-02-22T11:45:20Z","department":[{"_id":"NiBa"}],"_id":"1131","type":"dissertation","status":"public","year":"2016","has_accepted_license":"1","day":"01","page":"89","date_created":"2018-12-11T11:50:19Z","date_published":"2016-07-01T00:00:00Z","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.","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Tugrul, Murat. “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.","mla":"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.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","apa":"Tugrul, M. (2016). Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul"}],"publist_id":"6229","title":"Evolution of transcriptional regulatory sequences"},{"oa_version":"Published Version","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."}],"month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":132808,"date_created":"2018-12-12T13:03:02Z","file_name":"IST-2016-37-v1+1_paternity_archive.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5620","checksum":"4ae751b1fa4897fa216241f975a57313"}],"day":"19","has_accepted_license":"1","datarep_id":"37","year":"2016","date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:37","related_material":{"record":[{"relation":"research_paper","id":"1398","status":"public"}]},"date_created":"2018-12-12T12:31:30Z","contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","contributor_type":"project_manager","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"_id":"5553","status":"public","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"type":"research_data","tmp":{"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)","short":"CC0 (1.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"date_updated":"2024-02-21T13:51:14Z","citation":{"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.","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","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","short":"D. Field, T. Ellis, (2016).","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.","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.","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."},"file_date_updated":"2020-07-14T12:47:01Z","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","department":[{"_id":"NiBa"}],"author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"},{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis"}],"article_processing_charge":"No"},{"author":[{"orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","last_name":"Ellis","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Data on pollinator observations and offpsring phenotypes","file_date_updated":"2020-07-14T12:47:01Z","date_updated":"2024-02-21T13:51:27Z","citation":{"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.","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:35.","mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","short":"T. Ellis, (2016).","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","tmp":{"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)","short":"CC0 (1.0)"},"status":"public","_id":"5551","related_material":{"record":[{"relation":"research_paper","id":"1398","status":"public"}]},"doi":"10.15479/AT:ISTA:35","date_published":"2016-02-19T00:00:00Z","date_created":"2018-12-12T12:31:29Z","contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"has_accepted_license":"1","year":"2016","datarep_id":"35","day":"19","file":[{"date_created":"2018-12-12T13:05:12Z","file_name":"IST-2016-35-v1+1_array_data.zip","creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":32775,"checksum":"aa3eb85d52b110cd192aa23147c4d4f3","file_id":"5640","access_level":"open_access","relation":"main_file","content_type":"application/zip"}],"publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","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"}],"oa_version":"Published Version"},{"status":"public","type":"research_data","_id":"5552","file_date_updated":"2020-07-14T12:47:01Z","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","department":[{"_id":"NiBa"}],"author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","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","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi: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.","short":"T. Ellis, (2016)."},"date_updated":"2024-02-21T13:51:40Z","month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","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."}],"date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:36","contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-12T12:31:30Z","file":[{"date_created":"2018-12-12T13:03:07Z","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":44905,"file_id":"5625","checksum":"cbc61b523d4d475a04a737d50dc470ef","access_level":"open_access","relation":"main_file","content_type":"application/zip"}],"day":"19","has_accepted_license":"1","year":"2016","datarep_id":"36"},{"file_date_updated":"2020-07-14T12:47:01Z","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"author":[{"last_name":"Tugrul","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"M. Tugrul, (2016).","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","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","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.","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."},"date_updated":"2024-02-21T13:50:34Z","status":"public","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"type":"research_data","tmp":{"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)","short":"CC0 (1.0)"},"_id":"5554","date_published":"2016-05-12T00:00:00Z","doi":"10.15479/AT:ISTA:43","related_material":{"record":[{"relation":"used_in_publication","id":"1131","status":"public"}]},"date_created":"2018-12-12T12:31:30Z","contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Magdalena","last_name":"Steinrück"},{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","first_name":"Fabienne","contributor_type":"researcher","last_name":"Jesse"}],"day":"12","file":[{"creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":1123495,"date_created":"2018-12-12T13:03:08Z","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","file_id":"5626"}],"has_accepted_license":"1","year":"2016","datarep_id":"43","month":"05","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","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"}]},{"month":"07","publisher":"ACM","scopus_import":1,"quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1504.06260","open_access":"1"}],"oa":1,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"date_published":"2015-07-11T00:00:00Z","doi":"10.1145/2739480.2754758","date_created":"2018-12-11T11:51:58Z","ec_funded":1,"page":"1455 - 1462","day":"11","publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","type":"conference","conference":{"location":"Madrid, Spain","end_date":"2015-07-15","start_date":"2015-07-11","name":"GECCO: Genetic and evolutionary computation conference"},"_id":"1430","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"title":"First steps towards a runtime comparison of natural and artificial evolution","publist_id":"5768","author":[{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"first_name":"Jorge","last_name":"Heredia","full_name":"Heredia, Jorge"},{"last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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.","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.","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."},"date_updated":"2021-01-12T06:50:41Z"},{"oa":1,"quality_controlled":"1","publisher":"Wiley","page":"1101 - 1112","date_created":"2018-12-11T11:52:29Z","date_published":"2015-03-19T00:00:00Z","doi":"10.1111/evo.12641","year":"2015","has_accepted_license":"1","publication":"Evolution","day":"19","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"publist_id":"5656","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Maria","full_name":"Servedio, Maria","last_name":"Servedio"}],"title":"The interpretation of selection coefficients","citation":{"ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","apa":"Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641","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.","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 69","month":"03","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"issue":"5","volume":69,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":188872,"date_created":"2018-12-12T10:10:34Z","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4822","checksum":"fd8d23f476bc194419929b72ca265c02"},{"file_size":577415,"date_updated":"2020-07-14T12:45:00Z","creator":"system","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","date_created":"2018-12-12T10:10:35Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b774911e70044641d556e258efcb52ef","file_id":"4823"}],"type":"journal_article","pubrep_id":"560","status":"public","_id":"1519","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:51:20Z","ddc":["570"]},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"21","publication":" Journal of Theoretical Biology","has_accepted_license":"1","year":"2015","date_published":"2015-10-21T00:00:00Z","doi":"10.1016/j.jtbi.2015.07.011","date_created":"2018-12-11T11:52:37Z","page":"28 - 43","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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","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","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.","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.","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."},"title":"Toward a unifying framework for evolutionary processes","author":[{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Golnaz","full_name":"Badkobeh, Golnaz","last_name":"Badkobeh"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Çörüş","full_name":"Çörüş, Doğan","first_name":"Doğan"},{"full_name":"Dang, Duccuong","last_name":"Dang","first_name":"Duccuong"},{"full_name":"Friedrich, Tobias","last_name":"Friedrich","first_name":"Tobias"},{"first_name":"Per","full_name":"Lehre, Per","last_name":"Lehre"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"first_name":"Andrew","last_name":"Sutton","full_name":"Sutton, Andrew"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"}],"publist_id":"5629","oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"month":"10","intvolume":" 383","scopus_import":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5244","checksum":"33b60ecfea60764756a9ee9df5eb65ca","creator":"system","date_updated":"2020-07-14T12:45:01Z","file_size":595307,"date_created":"2018-12-12T10:16:53Z","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":383,"ec_funded":1,"_id":"1542","status":"public","pubrep_id":"483","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"ddc":["570"],"date_updated":"2021-01-12T06:51:29Z","file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}]},{"volume":70,"issue":"7","publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:45:12Z","file_size":1321527,"date_created":"2018-12-12T10:14:27Z","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad","file_id":"5079"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"06","intvolume":" 70","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"}],"oa_version":"Published Version","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:12Z","date_updated":"2023-02-23T10:10:36Z","ddc":["576"],"type":"journal_article","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":"458","_id":"1699","page":"1523 - 1580","doi":"10.1007/s00285-014-0802-y","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:53:32Z","has_accepted_license":"1","year":"2015","day":"01","publication":"Journal of Mathematical Biology","publisher":"Springer","quality_controlled":"1","oa":1,"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).","publist_id":"5442","author":[{"last_name":"Uecker","full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Setter, Derek","last_name":"Setter","first_name":"Derek"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"}],"title":"Adaptive gene introgression after secondary contact","citation":{"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.","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","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.","short":"H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580.","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.","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}]},{"oa_version":"None","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"}],"intvolume":" 63","month":"05","scopus_import":1,"publisher":"CSIRO","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Australian Journal of Botany","day":"26","year":"2015","publication_status":"published","date_created":"2018-12-11T11:53:34Z","volume":63,"doi":"10.1071/BT15023","issue":"5","date_published":"2015-05-26T00:00:00Z","page":"455 - 466","_id":"1703","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:38Z","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.","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.","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.","short":"L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466.","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","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","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."},"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","department":[{"_id":"NiBa"}],"author":[{"first_name":"Linda","last_name":"Broadhurst","full_name":"Broadhurst, Linda"},{"first_name":"Graham","full_name":"Fifield, Graham","last_name":"Fifield"},{"first_name":"Bindi","last_name":"Vanzella","full_name":"Vanzella, Bindi"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"}],"publist_id":"5434"},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":112,"issue":"20","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/"}],"scopus_import":1,"intvolume":" 112","month":"05","date_updated":"2021-01-12T06:53:24Z","department":[{"_id":"NiBa"}],"_id":"1818","type":"journal_article","status":"public","year":"2015","publication":"PNAS","day":"19","page":"6401 - 6406","date_created":"2018-12-11T11:54:11Z","doi":"10.1073/pnas.1421515112","date_published":"2015-05-19T00:00:00Z","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","citation":{"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.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112","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","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.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","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.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25941385"]},"publist_id":"5288","author":[{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"Limits to adaptation along environmental gradients","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","author":[{"full_name":"Novak, Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"publist_id":"5251","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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"},"oa":1,"publisher":"Elsevier","quality_controlled":"1","date_created":"2018-12-11T11:54:21Z","date_published":"2015-05-07T00:00:00Z","doi":"10.1016/j.jtbi.2015.02.018","page":"54 - 64","publication":"Journal of Theoretical Biology","day":"07","year":"2015","has_accepted_license":"1","pubrep_id":"329","status":"public","type":"journal_article","_id":"1850","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"ddc":["576"],"date_updated":"2021-01-12T06:53:37Z","intvolume":" 372","month":"05","scopus_import":1,"oa_version":"Submitted Version","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."}],"ec_funded":1,"volume":372,"issue":"5","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:19Z","file_size":1546914,"creator":"system","date_created":"2018-12-12T10:18:07Z","file_name":"IST-2015-329-v1+1_manuscript.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3c0dcacc900bc45cc65a453dfda4ca43","file_id":"5326"}],"publication_status":"published"},{"ddc":["570"],"date_updated":"2022-06-07T10:52:37Z","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:19Z","_id":"1851","status":"public","article_type":"original","type":"journal_article","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7855","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798","file_size":967214,"date_updated":"2020-07-14T12:45:19Z","creator":"dernst","file_name":"2015_Evolution_Priklopil.pdf","date_created":"2020-05-15T09:05:34Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication_status":"published","volume":69,"issue":"4","ec_funded":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","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."}],"month":"02","intvolume":" 69","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","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","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","short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","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."},"title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","author":[{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kisdi","full_name":"Kisdi, Eva","first_name":"Eva"},{"first_name":"Mats","last_name":"Gyllenberg","full_name":"Gyllenberg, Mats"}],"publist_id":"5249","external_id":{"pmid":["25662095"]},"article_processing_charge":"No","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"09","publication":"Evolution","has_accepted_license":"1","year":"2015","date_published":"2015-02-09T00:00:00Z","doi":"10.1111/evo.12618","date_created":"2018-12-11T11:54:21Z","page":"1015 - 1026","publisher":"Wiley","quality_controlled":"1","oa":1},{"article_number":"022803","title":"Anomalous scaling in an age-dependent branching model","author":[{"first_name":"Stephanie","full_name":"Keller-Schmidt, Stephanie","last_name":"Keller-Schmidt"},{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758"},{"first_name":"Víctor","full_name":"Eguíluz, Víctor","last_name":"Eguíluz"},{"first_name":"Emilio","full_name":"Hernandez Garcia, Emilio","last_name":"Hernandez Garcia"},{"first_name":"Konstantin","full_name":"Klemm, Konstantin","last_name":"Klemm"}],"publist_id":"5213","external_id":{"arxiv":["1012.3298"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.022803","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute of Physics, 2015.","mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803."},"publisher":"American Institute of Physics","quality_controlled":"1","oa":1,"date_published":"2015-02-02T00:00:00Z","doi":"10.1103/PhysRevE.91.022803","date_created":"2018-12-11T11:54:31Z","day":"02","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","year":"2015","status":"public","article_type":"original","type":"journal_article","_id":"1883","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:53:49Z","month":"02","intvolume":" 91","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1012.3298","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n"}],"issue":"2","volume":91,"language":[{"iso":"eng"}],"publication_status":"published"},{"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"NiBa"}],"ddc":["570","576"],"date_updated":"2023-02-23T14:07:48Z","pubrep_id":"453","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)"},"type":"journal_article","_id":"1809","volume":10,"issue":"5","related_material":{"record":[{"relation":"research_data","id":"9715","status":"public"},{"relation":"research_data","id":"9772","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4730","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_size":2748982,"date_updated":"2020-07-14T12:45:17Z","creator":"system","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","date_created":"2018-12-12T10:09:07Z"}],"publication_status":"published","intvolume":" 10","month":"05","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"title":"Indirect genetic effects and the dynamics of social interactions","author":[{"last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}],"publist_id":"5299","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907."},"date_created":"2018-12-11T11:54:07Z","doi":"10.1371/journal.pone.0126907","date_published":"2015-05-18T00:00:00Z","publication":"PLoS One","day":"18","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Public Library of Science"},{"status":"public","type":"research_data_reference","_id":"9772","title":"Description of the agent based simulations","department":[{"_id":"NiBa"}],"author":[{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak"},{"last_name":"Hager","full_name":"Hager, Reinmar","first_name":"Reinmar"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:15:25Z","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003."},"month":"05","publisher":"Public Library of Science","oa_version":"Published Version","date_published":"2015-05-18T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"1809","status":"public"}]},"doi":"10.1371/journal.pone.0126907.s003","date_created":"2021-08-05T12:55:20Z","day":"18","year":"2015"},{"year":"2015","day":"06","doi":"10.1371/journal.pgen.1005639.s001","related_material":{"record":[{"relation":"used_in_publication","id":"1666","status":"public"}]},"date_published":"2015-11-06T00:00:00Z","date_created":"2021-07-23T12:00:37Z","oa_version":"Published Version","publisher":"Public Library of Science","month":"11","citation":{"mla":"Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001."},"date_updated":"2023-02-23T10:09:08Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Tugrul","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Other fitness models for comparison & for interacting TFBSs","_id":"9712","type":"research_data_reference","status":"public"},{"department":[{"_id":"NiBa"}],"title":"Mathematical inference of the results","article_processing_charge":"No","author":[{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","full_name":"Novak, Sebastian"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:15:25Z","citation":{"chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001.","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, 10.1371/journal.pone.0126907.s001.","mla":"Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001.","ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:10.1371/journal.pone.0126907.s001","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","short":"B. Trubenova, S. Novak, R. Hager, (2015)."},"status":"public","type":"research_data_reference","_id":"9715","date_created":"2021-07-23T12:11:30Z","doi":"10.1371/journal.pone.0126907.s001","date_published":"2015-05-18T00:00:00Z","related_material":{"record":[{"status":"public","id":"1809","relation":"used_in_publication"}]},"day":"18","year":"2015","month":"05","publisher":"Public Library of Science","oa_version":"Published Version"},{"_id":"1666","pubrep_id":"463","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)"},"type":"journal_article","ddc":["576"],"date_updated":"2023-09-07T11:53:49Z","file_date_updated":"2020-07-14T12:45:10Z","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"oa_version":"Published Version","abstract":[{"text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.","lang":"eng"}],"intvolume":" 11","month":"11","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4657","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","date_updated":"2020-07-14T12:45:10Z","file_size":2580778,"creator":"system","date_created":"2018-12-12T10:07:58Z","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf"}],"publication_status":"published","ec_funded":1,"volume":11,"issue":"11","related_material":{"record":[{"relation":"research_data","status":"public","id":"9712"},{"relation":"dissertation_contains","status":"public","id":"1131"}]},"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11)."},"title":"Dynamics of transcription factor binding site evolution","author":[{"orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","last_name":"Tugrul","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publist_id":"5483","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","publication":"PLoS Genetics","day":"06","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:53:21Z","date_published":"2015-11-06T00:00:00Z","doi":"10.1371/journal.pgen.1005639"},{"page":"469 - 483","date_published":"2015-04-01T00:00:00Z","doi":"10.1007/978-3-662-46681-0_47","date_created":"2018-12-11T11:54:16Z","year":"2015","day":"01","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","publist_id":"5267","author":[{"last_name":"Giacobbe","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"last_name":"Petrov","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"title":"Model checking gene regulatory networks","citation":{"mla":"Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"related_material":{"record":[{"relation":"later_version","id":"1351","status":"public"}]},"volume":9035,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.7704","open_access":"1"}],"month":"04","intvolume":" 9035","abstract":[{"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 logics. 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.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"date_updated":"2023-09-20T11:06:03Z","type":"conference","conference":{"start_date":"2015-04-11","end_date":"2015-04-18","location":"London, United Kingdom","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"status":"public","_id":"1835","series_title":"Lecture Notes in Computer Science"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.","ieee":"T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp. 413–437, 2015.","ama":"Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413","apa":"Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413","mla":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:10.3390/g6040413.","ista":"Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437.","chicago":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games. MDPI, 2015. https://doi.org/10.3390/g6040413."},"title":"Evolution of decisions in population games with sequentially searching individuals","author":[{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","last_name":"Priklopil","full_name":"Priklopil, Tadeas"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5467","article_processing_charge":"No","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"day":"29","publication":"Games","has_accepted_license":"1","year":"2015","date_published":"2015-09-29T00:00:00Z","doi":"10.3390/g6040413","date_created":"2018-12-11T11:53:26Z","page":"413 - 437","quality_controlled":"1","publisher":"MDPI","oa":1,"ddc":["000"],"date_updated":"2023-10-17T11:42:52Z","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:12Z","_id":"1681","status":"public","pubrep_id":"448","article_type":"original","type":"journal_article","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)"},"file":[{"file_name":"IST-2016-448-v1+1_games-06-00413.pdf","date_created":"2018-12-12T10:12:41Z","creator":"system","file_size":518832,"date_updated":"2020-07-14T12:45:12Z","checksum":"912e1acbaf201100f447a43e4d5958bd","file_id":"4959","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2073-4336"]},"publication_status":"published","volume":6,"issue":"4","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game."}],"month":"09","intvolume":" 6","scopus_import":"1"},{"_id":"1896","type":"journal_article","status":"public","date_updated":"2022-08-01T10:50:10Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0430"}],"month":"03","intvolume":" 89","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":89,"article_number":"032701","citation":{"ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701.","apa":"Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701","ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Richard","full_name":"Kollár, Richard","last_name":"Kollár"},{"first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171"},{"full_name":"Nosek, Jozef","last_name":"Nosek","first_name":"Jozef"},{"first_name":"Ľubomír","last_name":"Tomáška","full_name":"Tomáška, Ľubomír"}],"publist_id":"5198","article_processing_charge":"No","title":"Mathematical model of alternative mechanism of telomere length maintenance","acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","publisher":"American Institute of Physics","oa":1,"year":"2014","day":"04","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","date_published":"2014-03-04T00:00:00Z","doi":"10.1103/PhysRevE.89.032701","date_created":"2018-12-11T11:54:35Z"},{"page":"693 - 701","date_published":"2014-06-01T00:00:00Z","doi":"10.1111/1365-2435.12207","date_created":"2018-12-11T11:54:40Z","has_accepted_license":"1","year":"2014","day":"01","publication":"Functional Ecology","publisher":"Wiley-Blackwell","oa":1,"acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","author":[{"last_name":"Ezard","full_name":"Ezard, Thomas","first_name":"Thomas"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","full_name":"Prizak, Roshan"},{"first_name":"Rebecca","last_name":"Hoyle","full_name":"Hoyle, Rebecca"}],"publist_id":"5186","title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","citation":{"ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.","chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","apa":"Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207","ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207","mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":28,"issue":"3","publication_status":"published","file":[{"checksum":"3cbe8623174709a8ceec2103246f8fe0","file_id":"5167","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:15:45Z","file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf","date_updated":"2020-07-14T12:45:20Z","file_size":536154,"creator":"system"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"06","intvolume":" 28","abstract":[{"text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:20Z","date_updated":"2021-01-12T06:54:00Z","ddc":["570"],"type":"journal_article","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":"419","_id":"1909"},{"abstract":[{"lang":"eng","text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations."}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1307.0737","open_access":"1"}],"scopus_import":1,"intvolume":" 196","month":"04","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":196,"issue":"4","_id":"1908","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:59Z","department":[{"_id":"NiBa"}],"oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","year":"2014","publication":"Genetics","day":"01","page":"1167 - 1183","date_created":"2018-12-11T11:54:39Z","doi":"10.1534/genetics.113.160705","date_published":"2014-04-01T00:00:00Z","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.","apa":"Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.160705","ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014.","chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.160705.","ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5187","author":[{"first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","full_name":"Weissman, Daniel"},{"last_name":"Hallatschek","full_name":"Hallatschek, Oskar","first_name":"Oskar"}],"title":"The rate of adaptation in large sexual populations with linear chromosomes"},{"_id":"1936","type":"journal_article","status":"public","date_updated":"2021-01-12T06:54:11Z","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race's plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures."}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/"}],"month":"02","intvolume":" 25","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":25,"ec_funded":1,"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology. Oxford University Press, 2014. https://doi.org/10.1093/beheco/aru002.","ista":"Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 25(3), 487–495.","mla":"Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology, vol. 25, no. 3, Oxford University Press, 2014, pp. 487–95, doi:10.1093/beheco/aru002.","ama":"Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 2014;25(3):487-495. doi:10.1093/beheco/aru002","apa":"Arbilly, M., Weissman, D., Feldman, M., & Grodzinski, U. (2014). An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/aru002","short":"M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25 (2014) 487–495.","ieee":"M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between producers and scroungers can drive the evolution of social cognition,” Behavioral Ecology, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Michal","last_name":"Arbilly","full_name":"Arbilly, Michal"},{"full_name":"Weissman, Daniel","last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"first_name":"Marcus","full_name":"Feldman, Marcus","last_name":"Feldman"},{"last_name":"Grodzinski","full_name":"Grodzinski, Uri","first_name":"Uri"}],"publist_id":"5157","title":"An arms race between producers and scroungers can drive the evolution of social cognition","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"year":"2014","day":"13","publication":"Behavioral Ecology","page":"487 - 495","doi":"10.1093/beheco/aru002","date_published":"2014-02-13T00:00:00Z","date_created":"2018-12-11T11:54:48Z"},{"oa_version":"Submitted Version","abstract":[{"text":"The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.","lang":"eng"}],"intvolume":" 68","month":"12","main_file_link":[{"url":"http://arxiv.org/abs/1310.6077","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":68,"issue":"12","_id":"1932","status":"public","type":"journal_article","date_updated":"2021-01-12T06:54:10Z","department":[{"_id":"NiBa"}],"acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","publication":"Evolution","day":"01","year":"2014","date_created":"2018-12-11T11:54:47Z","doi":"10.1111/evo.12517","date_published":"2014-12-01T00:00:00Z","page":"3357 - 3367","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution, vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517.","ieee":"M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell, pp. 3357–3367, 2014.","short":"M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 3357–3367.","ama":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517","apa":"Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014). Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.12517","chicago":"Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna Masel. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1111/evo.12517.","ista":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 68(12), 3357–3367."},"title":"Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations","author":[{"last_name":"Trotter","full_name":"Trotter, Meredith","first_name":"Meredith"},{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Weissman, Daniel","last_name":"Weissman"},{"first_name":"Grant","last_name":"Peterson","full_name":"Peterson, Grant"},{"first_name":"Kayla","full_name":"Peck, Kayla","last_name":"Peck"},{"full_name":"Masel, Joanna","last_name":"Masel","first_name":"Joanna"}],"publist_id":"5162"},{"_id":"2168","pubrep_id":"391","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)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:55:44Z","file_date_updated":"2020-07-14T12:45:31Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","abstract":[{"text":"Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail.","lang":"eng"}],"intvolume":" 95","month":"08","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_size":569005,"date_updated":"2020-07-14T12:45:31Z","creator":"system","file_name":"IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf","date_created":"2018-12-12T10:10:49Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"979d7a8034e9df198f068f0d251f31bd","file_id":"4839"}],"publication_status":"published","ec_funded":1,"volume":95,"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Kelleher, J., Etheridge, A., & Barton, N. H. (2014). Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2014.05.001","ama":"Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 2014;95:13-23. doi:10.1016/j.tpb.2014.05.001","ieee":"J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous space: Algorithms for large neighbourhood size,” Theoretical Population Biology, vol. 95. Academic Press, pp. 13–23, 2014.","short":"J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95 (2014) 13–23.","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology, vol. 95, Academic Press, 2014, pp. 13–23, doi:10.1016/j.tpb.2014.05.001.","ista":"Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 95, 13–23.","chicago":"Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology. Academic Press, 2014. https://doi.org/10.1016/j.tpb.2014.05.001."},"title":"Coalescent simulation in continuous space: Algorithms for large neighbourhood size","publist_id":"4816","author":[{"last_name":"Kelleher","full_name":"Kelleher, Jerome","first_name":"Jerome"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"oa":1,"quality_controlled":"1","publisher":"Academic Press","publication":"Theoretical Population Biology","day":"01","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:56:06Z","date_published":"2014-08-01T00:00:00Z","doi":"10.1016/j.tpb.2014.05.001","page":"13 - 23"},{"date_published":"2014-07-22T00:00:00Z","doi":"10.1073/pnas.1410107111","issue":"29","volume":111,"date_created":"2018-12-11T11:56:07Z","page":"10398 - 10399","day":"22","publication":"PNAS","language":[{"iso":"eng"}],"year":"2014","publication_status":"published","month":"07","intvolume":" 111","scopus_import":1,"publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/","open_access":"1"}],"oa_version":"Submitted Version","title":"Diverse forms of selection in evolution and computer science","department":[{"_id":"NiBa"}],"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"}],"publist_id":"4815","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:55:45Z","citation":{"ista":"Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.","chicago":"Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410107111.","ieee":"N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” PNAS, vol. 111, no. 29. National Academy of Sciences, pp. 10398–10399, 2014.","short":"N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.","apa":"Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection in evolution and computer science. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1410107111","ama":"Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111","mla":"Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:10.1073/pnas.1410107111."},"status":"public","type":"journal_article","_id":"2169"},{"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Stability and response of polygenic traits to stabilizing selection and mutation","publist_id":"4809","author":[{"full_name":"De Vladar, Harold","last_name":"De Vladar","first_name":"Harold"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.159111.","ista":"De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 197(2), 749–767.","mla":"De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” Genetics, vol. 197, no. 2, Genetics Society of America, 2014, pp. 749–67, doi:10.1534/genetics.113.159111.","ieee":"H. De Vladar and N. H. Barton, “Stability and response of polygenic traits to stabilizing selection and mutation,” Genetics, vol. 197, no. 2. Genetics Society of America, pp. 749–767, 2014.","short":"H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767.","apa":"De Vladar, H., & Barton, N. H. (2014). Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.159111","ama":"De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 2014;197(2):749-767. doi:10.1534/genetics.113.159111"},"publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"doi":"10.1534/genetics.113.159111","date_published":"2014-06-01T00:00:00Z","date_created":"2018-12-11T11:56:08Z","page":"749 - 767","day":"01","publication":"Genetics","year":"2014","status":"public","type":"journal_article","_id":"2174","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:55:47Z","month":"06","intvolume":" 197","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.1017"}],"oa_version":"Submitted Version","abstract":[{"text":"When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation-selection balance is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by 2μ/S, and on the total mutational effects of alleles that are at intermediate frequency. The inpplayfi between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find p the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value.","lang":"eng"}],"volume":197,"issue":"2","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"_id":"2252","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-08-25T14:45:42Z","citation":{"ista":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135.","chicago":"Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University Press, 2014. https://doi.org/10.1093/jhered/est063.","short":"S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135.","ieee":"S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014.","apa":"Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063","ama":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063","mla":"Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063."},"title":"Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"last_name":"Phadke","full_name":"Phadke, Sujal","first_name":"Sujal"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"first_name":"Tuan","full_name":"Pham, Tuan","last_name":"Pham"},{"full_name":"Pham, Stephanie","last_name":"Pham","first_name":"Stephanie"},{"first_name":"Rebecca","full_name":"Zufall, Rebecca","last_name":"Zufall"}],"publist_id":"4695","oa_version":"None","abstract":[{"text":"The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila.","lang":"eng"}],"intvolume":" 105","month":"01","publisher":"Oxford University Press","scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Journal of Heredity","day":"01","year":"2014","publication_status":"published","publication_identifier":{"issn":["00221503"]},"date_created":"2018-12-11T11:56:35Z","issue":"1","date_published":"2014-01-01T00:00:00Z","volume":105,"doi":"10.1093/jhered/est063","page":"130 - 135"},{"has_accepted_license":"1","year":"2014","day":"19","publication":"Ecology and Evolution","page":"3139 - 3145","doi":"10.1002/ece3.1150","date_published":"2014-07-19T00:00:00Z","date_created":"2018-12-11T11:47:02Z","publisher":"Wiley-Blackwell","oa":1,"citation":{"ista":"Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.","chicago":"Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1150.","ama":"Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150","apa":"Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150","ieee":"R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.","short":"R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.","mla":"Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:10.1002/ece3.1150."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Prizak","full_name":"Prizak, Roshan","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ezard, Thomas","last_name":"Ezard","first_name":"Thomas"},{"full_name":"Hoyle, Rebecca","last_name":"Hoyle","first_name":"Rebecca"}],"publist_id":"7280","title":"Fitness consequences of maternal and grandmaternal effects","publication_status":"published","file":[{"file_name":"IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf","date_created":"2018-12-12T10:11:31Z","creator":"system","file_size":621582,"date_updated":"2020-07-14T12:46:38Z","checksum":"e32abf75a248e7a11811fd7f60858769","file_id":"4886","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":4,"issue":"15","abstract":[{"text":"Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"07","intvolume":" 4","date_updated":"2021-01-12T08:01:30Z","ddc":["530","571"],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:46:38Z","_id":"537","type":"journal_article","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":"934"},{"_id":"2170","type":"journal_article","status":"public","pubrep_id":"559","date_updated":"2023-02-23T14:07:09Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:31Z","department":[{"_id":"NiBa"}],"abstract":[{"text":" Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"01","intvolume":" 23","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"4de1ab255976a8ae77eb0e55ad62ecc9","file_id":"4651","file_size":807444,"date_updated":"2020-07-14T12:45:31Z","creator":"system","file_name":"IST-2016-559-v1+1_Hearn_et_al.pdf","date_created":"2018-12-12T10:07:52Z"},{"date_created":"2018-12-12T10:07:53Z","file_name":"IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf","date_updated":"2020-07-14T12:45:31Z","file_size":1518088,"creator":"system","file_id":"4652","checksum":"01a8073e071c088500425f910b0f1f71","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":23,"issue":"1","related_material":{"record":[{"relation":"research_data","id":"9754","status":"public"}]},"citation":{"short":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular Ecology 23 (2014) 198–211.","ieee":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse, “Likelihood-based inference of population history from low-coverage de novo genome assemblies,” Molecular Ecology, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211, 2014.","apa":"Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., & Lohse, K. (2014). Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12578","ama":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 2014;23(1):198-211. doi:10.1111/mec.12578","mla":"Hearn, Jack, et al. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” Molecular Ecology, vol. 23, no. 1, Wiley-Blackwell, 2014, pp. 198–211, doi:10.1111/mec.12578.","ista":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 23(1), 198–211.","chicago":"Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” Molecular Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/mec.12578."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jack","full_name":"Hearn, Jack","last_name":"Hearn"},{"first_name":"Graham","last_name":"Stone","full_name":"Stone, Graham"},{"first_name":"Lynsey","last_name":"Bunnefeld","full_name":"Bunnefeld, Lynsey"},{"first_name":"James","full_name":"Nicholls, James","last_name":"Nicholls"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"}],"publist_id":"4814","title":"Likelihood-based inference of population history from low-coverage de novo genome assemblies","acknowledgement":"This work was funded by NERC grants to G Stone, J Nicholls, K Lohse and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"has_accepted_license":"1","year":"2014","day":"01","publication":"Molecular Ecology","page":"198 - 211","doi":"10.1111/mec.12578","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:56:07Z"},{"publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2014","day":"27","publication":"Ecology and Evolution","page":"4589 - 4597","date_published":"2014-11-27T00:00:00Z","doi":"10.1002/ece3.1289","date_created":"2018-12-11T11:55:16Z","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"citation":{"chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289.","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.","short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” Ecology and Evolution, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597. doi:10.1002/ece3.1289","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1289"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5049","author":[{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X"}],"title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","abstract":[{"text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"11","intvolume":" 4","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"9ab43db1b0fede7bfe560ed77e177b76","file_id":"4946","date_updated":"2020-07-14T12:45:25Z","file_size":118813,"creator":"system","date_created":"2018-12-12T10:12:28Z","file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf"}],"language":[{"iso":"eng"}],"volume":4,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1125"}]},"issue":"24","ec_funded":1,"_id":"2023","type":"journal_article","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":"462","date_updated":"2023-09-07T11:55:53Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:25Z","department":[{"_id":"NiBa"}]},{"scopus_import":"1","publisher":"Elsevier","quality_controlled":"1","edition":"2","month":"01","oa_version":"None","page":"508-515","doi":"10.1016/b978-0-12-384719-5.00031-9","date_published":"2013-01-01T00:00:00Z","date_created":"2022-03-21T07:46:22Z","publication_identifier":{"isbn":["978-0-12-384720-1"]},"publication_status":"published","year":"2013","day":"01","language":[{"iso":"eng"}],"publication":"Encyclopedia of Biodiversity","type":"book_chapter","status":"public","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"_id":"10899","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"article_processing_charge":"No","title":"Differentiation","department":[{"_id":"NiBa"}],"citation":{"chicago":"Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity, 2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9.","ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","mla":"Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9.","ama":"Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed. Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9","apa":"Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity (2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9","ieee":"N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515."},"date_updated":"2022-06-20T09:18:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"day":"01","publication":"Ecology and Evolution","has_accepted_license":"1","year":"2013","date_published":"2013-03-01T00:00:00Z","doi":"10.1002/ece3.465","date_created":"2018-12-11T11:56:47Z","page":"629 - 639","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465.","ista":"Pickup M, Barrett S. 2013. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3), 629–639.","mla":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465.","apa":"Pickup, M., & Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465","ama":"Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 2013;3(3):629-639. doi:10.1002/ece3.465","ieee":"M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013.","short":"M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639."},"title":"The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant","publist_id":"4644","author":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"first_name":"Spencer","full_name":"Barrett, Spencer","last_name":"Barrett"}],"oa_version":"Published Version","abstract":[{"text":"Negative frequency-dependent selection should result in equal sex ratios in large populations of dioecious flowering plants, but deviations from equality are commonly reported. A variety of ecological and genetic factors can explain biased sex ratios, although the mechanisms involved are not well understood. Most dioecious species are long-lived and/or clonal complicating efforts to identify stages during the life cycle when biases develop. We investigated the demographic correlates of sex-ratio variation in two chromosome races of Rumex hastatulus, an annual, wind-pollinated colonizer of open habitats from the southern USA. We examined sex ratios in 46 populations and evaluated the hypothesis that the proximity of males in the local mating environment, through its influence on gametophytic selection, is the primary cause of female-biased sex ratios. Female-biased sex ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62), with significant female bias in 89% of populations. Large, high-density populations had the highest proportion of females, whereas smaller, low-density populations had sex ratios closer to equality. Progeny sex ratios were more female biased when males were in closer proximity to females, a result consistent with the gametophytic selection hypothesis. Our results suggest that interactions between demographic and genetic factors are probably the main cause of female-biased sex ratios in R. hastatulus. The annual life cycle of this species may limit the scope for selection against males and may account for the weaker degree of bias in comparison with perennial Rumex species.","lang":"eng"}],"month":"03","intvolume":" 3","scopus_import":1,"file":[{"creator":"system","file_size":626949,"date_updated":"2020-07-14T12:45:37Z","file_name":"IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf","date_created":"2018-12-12T10:17:35Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b5531bab4c0dec396bf5c8497fe178bf","file_id":"5290"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":3,"_id":"2287","status":"public","pubrep_id":"416","type":"journal_article","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)"},"ddc":["576"],"date_updated":"2021-01-12T06:56:32Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:37Z"},{"citation":{"apa":"Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2012.12.001","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 2013;87(8):75-89. doi:10.1016/j.tpb.2012.12.001","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” Theoretical Population Biology, vol. 87, no. 8. Elsevier, pp. 75–89, 2013.","mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population Biology, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:10.1016/j.tpb.2012.12.001.","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2012.12.001."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4428","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"first_name":"Amandine","full_name":"Véber, Amandine","last_name":"Véber"}],"title":"Genetic hitch-hiking in spatially extended populations","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"year":"2013","has_accepted_license":"1","publication":"Theoretical Population Biology","day":"03","page":"75 - 89","date_created":"2018-12-11T11:57:52Z","date_published":"2013-01-03T00:00:00Z","doi":"10.1016/j.tpb.2012.12.001","oa":1,"quality_controlled":"1","publisher":"Elsevier","date_updated":"2021-01-12T06:57:42Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:41Z","department":[{"_id":"NiBa"}],"_id":"2473","type":"journal_article","pubrep_id":"118","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:18:54Z","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","creator":"system","date_updated":"2020-07-14T12:45:41Z","file_size":1706282,"checksum":"4274ec1f433b838a7d5b941cc9684ca7","file_id":"5376","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"issue":"8","volume":87,"abstract":[{"lang":"eng","text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift, . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis."}],"oa_version":"Submitted Version","scopus_import":1,"intvolume":" 87","month":"01"},{"date_updated":"2021-01-12T06:59:15Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:45Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"_id":"2718","conference":{"name":"GECCO: Genetic and evolutionary computation conference","start_date":"2013-07-06","location":"Amsterdam, Netherlands","end_date":"2013-07-10"},"type":"conference","pubrep_id":"564","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"9d9be9090ce5c20766e0eb076ace5b98","file_id":"5159","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:15:38Z","file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf","creator":"system","date_updated":"2020-07-14T12:45:45Z","file_size":475844}],"ec_funded":1,"abstract":[{"text":"Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"07","citation":{"chicago":"Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013. https://doi.org/10.1145/2463372.2463568.","ista":"Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.","mla":"Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80, doi:10.1145/2463372.2463568.","ieee":"N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 1573–1580.","short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.","ama":"Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568","apa":"Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463568"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4174","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"}],"title":"Can quantitative and population genetics help us understand evolutionary computation?","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"year":"2013","has_accepted_license":"1","publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","day":"01","page":"1573 - 1580","date_created":"2018-12-11T11:59:14Z","doi":"10.1145/2463372.2463568","date_published":"2013-07-01T00:00:00Z","oa":1,"publisher":"ACM","quality_controlled":"1"},{"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["23934880"]},"article_processing_charge":"No","author":[{"full_name":"Long, Hongan","last_name":"Long","first_name":"Hongan"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao"},{"last_name":"Azevedo","full_name":"Azevedo, Ricardo","first_name":"Ricardo"},{"last_name":"Zufall","full_name":"Zufall, Rebecca","first_name":"Rebecca"}],"publist_id":"4172","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","citation":{"mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.","ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.","short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","apa":"Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.153536","ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540. doi:10.1534/genetics.113.153536","chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics. Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536.","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","page":"527-540","date_created":"2018-12-11T11:59:15Z","date_published":"2013-10-01T00:00:00Z","doi":"10.1534/genetics.113.153536","year":"2013","publication":"Genetics","day":"01","type":"journal_article","status":"public","_id":"2720","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"date_updated":"2021-01-12T06:59:16Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/","open_access":"1"}],"scopus_import":1,"intvolume":" 195","month":"10","abstract":[{"text":"Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","ec_funded":1,"issue":"2","volume":195,"publication_status":"published","language":[{"iso":"eng"}]},{"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"conference","conference":{"name":"GECCO: Genetic and evolutionary computation conference","location":"Amsterdam, Netherlands","end_date":"2013-07-10","start_date":"2013-07-06"},"_id":"2719","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"title":"A variance decomposition approach to the analysis of genetic algorithms","publist_id":"4173","author":[{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.","chicago":"Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.","ama":"Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470","apa":"Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470","short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.","ieee":"T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.","mla":"Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470."},"date_updated":"2021-01-12T06:59:15Z","month":"07","publisher":"ACM","quality_controlled":"1","scopus_import":1,"oa_version":"None","abstract":[{"text":"Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation.","lang":"eng"}],"doi":"10.1145/2463372.2463470","date_published":"2013-07-01T00:00:00Z","date_created":"2018-12-11T11:59:15Z","ec_funded":1,"page":"845 - 852","day":"01","language":[{"iso":"eng"}],"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","publication_status":"published","year":"2013"},{"page":"26 - 34","date_created":"2018-12-11T11:59:45Z","date_published":"2013-10-07T00:00:00Z","doi":"10.1016/j.jtbi.2013.05.029","year":"2013","has_accepted_license":"1","publication":"Journal of Theoretical Biology","day":"07","oa":1,"quality_controlled":"1","publisher":"Elsevier","publist_id":"3984","author":[{"last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"title":"Density games","citation":{"mla":"Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology, vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029.","ieee":"S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical Biology, vol. 334. Elsevier, pp. 26–34, 2013.","short":"S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34.","ama":"Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology. 2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029","apa":"Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029","chicago":"Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029.","ista":"Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"volume":334,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5110","checksum":"3c29059ab03a4b8f97a07646b817ddbb","date_updated":"2020-07-14T12:45:49Z","file_size":834604,"creator":"system","date_created":"2018-12-12T10:14:54Z","file_name":"IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf"}],"scopus_import":1,"intvolume":" 334","month":"10","abstract":[{"lang":"eng","text":"The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle."}],"oa_version":"Published Version","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:49Z","date_updated":"2021-01-12T06:59:55Z","ddc":["000"],"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)"},"type":"journal_article","pubrep_id":"400","status":"public","_id":"2817"},{"intvolume":" 38","month":"05","publisher":"Wiley-Blackwell","quality_controlled":"1","scopus_import":1,"oa_version":"None","abstract":[{"text":"The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (>60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands <10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment.","lang":"eng"}],"date_created":"2018-12-11T11:59:47Z","doi":"10.1111/j.1442-9993.2012.02404.x","volume":38,"date_published":"2013-05-01T00:00:00Z","issue":"3","page":"300 - 312","language":[{"iso":"eng"}],"publication":"Austral Ecology","day":"01","year":"2013","publication_status":"published","status":"public","type":"journal_article","_id":"2823","title":"Post-fire recovery of revegetated woodland communities in south-eastern Australia","department":[{"_id":"NiBa"}],"publist_id":"3978","author":[{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Susie","last_name":"Wilson","full_name":"Wilson, Susie"},{"last_name":"Freudenberger","full_name":"Freudenberger, David","first_name":"David"},{"full_name":"Nicholls, Nick","last_name":"Nicholls","first_name":"Nick"},{"full_name":"Gould, Lori","last_name":"Gould","first_name":"Lori"},{"first_name":"Sarah","last_name":"Hnatiuk","full_name":"Hnatiuk, Sarah"},{"full_name":"Delandre, Jeni","last_name":"Delandre","first_name":"Jeni"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:59:58Z","citation":{"ista":"Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312.","chicago":"Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x.","ama":"Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312. doi:10.1111/j.1442-9993.2012.02404.x","apa":"Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x","ieee":"M. Pickup et al., “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013.","short":"M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312.","mla":"Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x."}},{"ec_funded":1,"issue":"1","volume":87,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"9bf9d9a6fd03dd9df50906891f393bf8","file_id":"5288","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:17:33Z","file_name":"IST-2016-558-v1+1_inference_revised3101NB.pdf","creator":"system","date_updated":"2020-07-14T12:45:50Z","file_size":1554712},{"creator":"system","file_size":822964,"date_updated":"2020-07-14T12:45:50Z","file_name":"IST-2016-558-v1+2_inference_revised3101NBApp.pdf","date_created":"2018-12-12T10:17:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5289","checksum":"2bceddb76edacd0cd5fad73051e2a928"}],"scopus_import":1,"intvolume":" 87","month":"08","abstract":[{"text":"We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a 'local scale', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:50Z","date_updated":"2021-01-12T07:00:09Z","ddc":["570"],"type":"journal_article","pubrep_id":"558","status":"public","_id":"2842","page":"105 - 119","date_created":"2018-12-11T11:59:53Z","date_published":"2013-08-01T00:00:00Z","doi":"10.1016/j.tpb.2013.03.001","year":"2013","has_accepted_license":"1","publication":"Theoretical Population Biology","day":"01","oa":1,"quality_controlled":"1","publisher":"Elsevier","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"first_name":"Amandine","full_name":"Véber, Amandine","last_name":"Véber"}],"publist_id":"3953","title":"Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks","citation":{"ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001","mla":"Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}]},{"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","date_created":"2018-12-11T12:00:17Z","date_published":"2013-02-07T00:00:00Z","doi":"10.1093/bioinformatics/btt067","page":"955 - 956","publication":"Bioinformatics","day":"07","year":"2013","has_accepted_license":"1","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Coalescent simulation in continuous space","author":[{"first_name":"Jerome","full_name":"Kelleher, Jerome","last_name":"Kelleher"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"}],"publist_id":"3833","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067.","ama":"Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067","apa":"Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067","ieee":"J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013.","short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.","chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” Bioinformatics. Oxford University Press, 2013. https://doi.org/10.1093/bioinformatics/btt067.","ista":"Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956."},"intvolume":" 29","month":"02","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module."}],"ec_funded":1,"issue":"7","volume":29,"language":[{"iso":"eng"}],"file":[{"file_size":170197,"date_updated":"2020-07-14T12:45:52Z","creator":"system","file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","date_created":"2018-12-12T10:16:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"a3b54d7477fac923815ac082403d9bd0","file_id":"5189"}],"publication_status":"published","pubrep_id":"556","status":"public","type":"journal_article","_id":"2910","file_date_updated":"2020-07-14T12:45:52Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2021-01-12T07:00:38Z"},{"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Modelling evolution in a spatial continuum","article_processing_charge":"No","publist_id":"3834","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"first_name":"Amandine","full_name":"Véber, Amandine","last_name":"Véber"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1. IOP Publishing Ltd., 2013.","short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002","ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002.","ista":"Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1).","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002."},"oa":1,"publisher":"IOP Publishing Ltd.","quality_controlled":"1","date_created":"2018-12-11T12:00:17Z","doi":"10.1088/1742-5468/2013/01/P01002","date_published":"2013-01-16T00:00:00Z","publication":"Journal of Statistical Mechanics Theory and Experiment","day":"16","year":"2013","has_accepted_license":"1","pubrep_id":"557","status":"public","type":"journal_article","_id":"2909","file_date_updated":"2020-07-14T12:45:52Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2021-01-12T07:00:37Z","intvolume":" 2013","month":"01","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research.","lang":"eng"}],"ec_funded":1,"issue":"1","volume":2013,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5242","checksum":"ce8a4424385b3086138a1e054e16e0e3","file_size":702583,"date_updated":"2020-07-14T12:45:52Z","creator":"system","file_name":"IST-2016-557-v1+1_BEVrevised.pdf","date_created":"2018-12-12T10:16:52Z"}],"publication_status":"published"},{"oa_version":"Submitted Version","abstract":[{"text":"Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence.","lang":"eng"}],"intvolume":" 26","month":"01","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf","date_created":"2018-12-12T10:09:38Z","file_size":13339,"date_updated":"2020-07-14T12:45:52Z","creator":"system","file_id":"4762","checksum":"716e88714c3411cd0bd70928b14ea692","content_type":"text/rtf","relation":"main_file","access_level":"open_access"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"957fd07c71c1b1eac2c65ae3311aca78","file_id":"4763","date_updated":"2020-07-14T12:45:52Z","file_size":103437,"creator":"system","date_created":"2018-12-12T10:09:39Z","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf"}],"publication_status":"published","issue":"2","volume":26,"_id":"2908","pubrep_id":"111","status":"public","type":"journal_article","ddc":["576"],"date_updated":"2021-01-12T07:00:37Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:52Z","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","publication":"Journal of Evolutionary Biology","day":"17","year":"2013","has_accepted_license":"1","date_created":"2018-12-11T12:00:17Z","doi":"10.1111/jeb.12015","date_published":"2013-01-17T00:00:00Z","page":"267 - 269","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary Biology. 26(2), 267–269.","chicago":"Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015.","short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","ieee":"N. H. Barton, “Does hybridisation influence speciation? ,” Journal of Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.","ama":"Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015","apa":"Barton, N. H. (2013). Does hybridisation influence speciation? . Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015","mla":"Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:10.1111/jeb.12015."},"title":"Does hybridisation influence speciation? ","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3835"},{"oa":1,"publisher":"Princeton University Press","quality_controlled":"1","month":"11","abstract":[{"lang":"eng","text":"Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on."}],"oa_version":"Submitted Version","page":"328 - 333","date_created":"2018-12-11T12:00:16Z","date_published":"2013-11-04T00:00:00Z","publication_status":"published","year":"2013","has_accepted_license":"1","publication_identifier":{"isbn":["9780691149776"]},"language":[{"iso":"eng"}],"publication":"The Princeton Guide to Evolution","day":"04","file":[{"file_size":79838,"date_updated":"2020-07-14T12:45:52Z","creator":"system","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx","date_created":"2018-12-12T10:16:47Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"main_file","access_level":"open_access","checksum":"8332ca9cb40f7e66d1006b175ce36b60","file_id":"5237"},{"checksum":"849f418620fb78d6ba23bb4f488ee93f","file_id":"5238","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf","date_created":"2018-12-12T10:16:48Z","file_size":144131,"date_updated":"2020-07-14T12:45:52Z","creator":"system"}],"type":"book_chapter","pubrep_id":"119","status":"public","_id":"2907","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"3839","title":"Recombination and sex","file_date_updated":"2020-07-14T12:45:52Z","department":[{"_id":"NiBa"}],"citation":{"mla":"Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–33.","apa":"Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution (pp. 328–333). Princeton University Press.","ama":"Barton NH. Recombination and sex. In: The Princeton Guide to Evolution. Princeton University Press; 2013:328-333.","short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","ieee":"N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","chicago":"Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide to Evolution, 328–33. Princeton University Press, 2013.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333."},"date_updated":"2021-01-12T07:00:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"]},{"status":"public","type":"journal_article","_id":"450","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:57:25Z","month":"01","intvolume":" 280","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.","lang":"eng"}],"volume":280,"issue":"1750","language":[{"iso":"eng"}],"publication_status":"published","article_number":"2058","title":"Source population characteristics affect heterosis following genetic rescue of fragmented plant populations","author":[{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"full_name":"Rowell, David","last_name":"Rowell","first_name":"David"},{"last_name":"Young","full_name":"Young, Andrew","first_name":"Andrew"}],"publist_id":"7372","external_id":{"pmid":["23173202"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058","ama":"Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 2013;280(1750). doi:10.1098/rspb.2012.2058","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750. Royal Society, The, 2013.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","mla":"Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058.","ista":"Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058."},"quality_controlled":"1","publisher":"Royal Society, The","oa":1,"doi":"10.1098/rspb.2012.2058","date_published":"2013-01-07T00:00:00Z","date_created":"2018-12-11T11:46:32Z","day":"07","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","year":"2013"},{"status":"public","type":"journal_article","_id":"2944","department":[{"_id":"NiBa"}],"date_updated":"2023-02-23T14:07:19Z","intvolume":" 22","month":"02","scopus_import":1,"oa_version":"None","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.","lang":"eng"}],"issue":"4","volume":22,"related_material":{"record":[{"id":"9758","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"publication_status":"published","title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","publist_id":"3788","author":[{"full_name":"Aeschbacher, Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"full_name":"Futschik, Andreas","last_name":"Futschik","first_name":"Andreas"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/mec.12165.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165","apa":"Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002."},"publisher":"Wiley-Blackwell","quality_controlled":"1","acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","date_created":"2018-12-11T12:00:28Z","doi":"10.1111/mec.12165","date_published":"2013-02-01T00:00:00Z","page":"987 - 1002","publication":"Molecular Ecology","day":"01","year":"2013"},{"department":[{"_id":"NiBa"}],"title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","author":[{"first_name":"Jack","full_name":"Hearn, Jack","last_name":"Hearn"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"first_name":"Lynsey","full_name":"Bunnefeld, Lynsey","last_name":"Bunnefeld"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.","ista":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, 10.5061/dryad.r3r60.","mla":"Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.","ama":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:10.5061/dryad.r3r60","apa":"Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60","short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).","ieee":"J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013."},"date_updated":"2023-02-23T10:31:17Z","status":"public","type":"research_data_reference","_id":"9754","date_published":"2013-10-01T00:00:00Z","doi":"10.5061/dryad.r3r60","related_material":{"record":[{"status":"public","id":"2170","relation":"used_in_publication"}]},"date_created":"2021-07-30T08:31:22Z","day":"01","year":"2013","month":"10","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r3r60"}],"oa_version":"Published Version","abstract":[{"text":"Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.","lang":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"de Vladar, Harold. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology, vol. 12, no. 1, Cambridge University Press, 2012, pp. 53–62, doi:10.1017/S1473550412000407.","apa":"de Vladar, H. (2012). The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. Cambridge University Press. https://doi.org/10.1017/S1473550412000407","ama":"de Vladar H. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 2012;12(1):53-62. doi:10.1017/S1473550412000407","short":"H. de Vladar, International Journal of Astrobiology 12 (2012) 53–62.","ieee":"H. de Vladar, “The game of active search for extra terrestrial intelligence Breaking the Great Silence ,” International Journal of Astrobiology, vol. 12, no. 1. Cambridge University Press, pp. 53–62, 2012.","chicago":"Vladar, Harold de. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology. Cambridge University Press, 2012. https://doi.org/10.1017/S1473550412000407.","ista":"de Vladar H. 2012. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 12(1), 53–62."},"date_updated":"2021-01-12T07:00:41Z","department":[{"_id":"NiBa"}],"title":"The game of active search for extra terrestrial intelligence Breaking the Great Silence ","author":[{"last_name":"Vladar","orcid":"0000-0002-5985-7653","full_name":"Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold"}],"publist_id":"3821","_id":"2917","status":"public","type":"journal_article","day":"06","language":[{"iso":"eng"}],"publication":"International Journal of Astrobiology","publication_status":"published","year":"2012","doi":"10.1017/S1473550412000407","date_published":"2012-11-06T00:00:00Z","issue":"1","volume":12,"date_created":"2018-12-11T12:00:19Z","page":"53 - 62","oa_version":"None","abstract":[{"lang":"eng","text":"The search for extra-terrestrial intelligence (SETI) has been performed principally as a one-way survey, listening of radio frequencies across the Milky Way and other galaxies. However, scientists have engaged in an active messaging only rarely. This suggests the simple rationale that if other civilizations exist and take a similar approach to ours, namely listening but not broadcasting, the result is a silent universe. A simple game theoretical model, the prisoner's dilemma, explains this situation: each player (civilization) can passively search (defect), or actively search and broadcast (cooperate). In order to maximize the payoff (or, equivalently, minimize the risks) the best strategy is not to broadcast. In fact, the active search has been opposed on the basis that it might be dangerous to expose ourselves. However, most of these ideas have not been based on objective arguments, and ignore accounting of the possible gains and losses. Thus, the question stands: should we perform an active search? I develop a game-theoretical framework where civilizations can be of different types, and explicitly apply it to a situation where societies are either interested in establishing a two-way communication or belligerent and in urge to exploit ours. The framework gives a quantitative solution (a mixed-strategy), which is how frequent we should perform the active SETI. This frequency is roughly proportional to the inverse of the risk, and can be extremely small. However, given the immense amount of stars being scanned, it supports active SETI. The model is compared with simulations, and the possible actions are evaluated through the San Marino scale, measuring the risks of messaging."}],"month":"11","intvolume":" 12","scopus_import":1,"quality_controlled":"1","publisher":"Cambridge University Press"},{"_id":"2962","type":"journal_article","status":"public","date_updated":"2021-01-12T07:40:05Z","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/","open_access":"1"}],"month":"11","intvolume":" 192","publication_status":"published","language":[{"iso":"eng"}],"volume":192,"issue":"3","citation":{"short":"S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.","ieee":"S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” Genetics, vol. 192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.","apa":"Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.112.143164","ama":"Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047. doi:10.1534/genetics.112.143164","mla":"Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.","ista":"Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.","chicago":"Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics. Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Aeschbacher","full_name":"Aeschbacher, Simon"},{"first_name":"Mark","last_name":"Beaumont","full_name":"Beaumont, Mark"},{"full_name":"Futschik, Andreas","last_name":"Futschik","first_name":"Andreas"}],"publist_id":"3763","external_id":{"pmid":["22960215"]},"title":"A novel approach for choosing summary statistics in approximate Bayesian computation","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"year":"2012","day":"01","publication":"Genetics","page":"1027 - 1047","doi":"10.1534/genetics.112.143164","date_published":"2012-11-01T00:00:00Z","date_created":"2018-12-11T12:00:34Z"},{"oa_version":"None","abstract":[{"text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ","lang":"eng"}],"intvolume":" 21","month":"08","scopus_import":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","publication":"Molecular Ecology","language":[{"iso":"eng"}],"day":"01","year":"2012","publication_status":"published","date_created":"2018-12-11T12:01:31Z","date_published":"2012-08-01T00:00:00Z","volume":21,"doi":"10.1111/j.1365-294X.2012.05643.x","issue":"15","page":"3640 - 3643","_id":"3122","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x","apa":"Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x."},"date_updated":"2021-01-12T07:41:13Z","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","department":[{"_id":"NiBa"}],"publist_id":"3577","author":[{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Spencer","full_name":"Barrett, Spencer","last_name":"Barrett"}]},{"date_created":"2018-12-11T12:01:34Z","date_published":"2012-06-07T00:00:00Z","doi":"10.1371/journal.pgen.1002740","year":"2012","has_accepted_license":"1","publication":"PLoS Genetics","day":"07","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","acknowledgement":"The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions.","publist_id":"3566","author":[{"last_name":"Weissman","full_name":"Weissman, Daniel","first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"title":"Limits to the rate of adaptive substitution in sexual populations","citation":{"mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740.","ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740","apa":"Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740.","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"article_number":"e1002740","ec_funded":1,"volume":8,"issue":"6","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"729a4becda7d786c4c3db8f9a1f77953","file_id":"4659","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:08:00Z","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","creator":"system","date_updated":"2020-07-14T12:46:01Z","file_size":1284801}],"scopus_import":1,"intvolume":" 8","month":"06","abstract":[{"lang":"eng","text":"In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection."}],"oa_version":"Published Version","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:01Z","date_updated":"2021-01-12T07:41:17Z","ddc":["570","576"],"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)"},"type":"journal_article","pubrep_id":"114","status":"public","_id":"3131"}]