[{"type":"research_data_reference","status":"public","_id":"9856","author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Gordana","full_name":"Rasic, Gordana","last_name":"Rasic"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe","first_name":"Inaki"},{"full_name":"Cook, Peter","last_name":"Cook","first_name":"Peter"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"full_name":"Hoffmann, Ary","last_name":"Hoffmann","first_name":"Ary"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"article_processing_charge":"No","title":"Supporting Information concerning additional likelihood analyses and results","department":[{"_id":"NiBa"}],"date_updated":"2023-09-22T10:02:51Z","citation":{"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.","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","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","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., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","month":"05","oa_version":"Published Version","date_published":"2017-05-30T00:00:00Z","related_material":{"record":[{"id":"951","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.2001894.s014","date_created":"2021-08-10T07:36:04Z","year":"2017","day":"30"},{"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5264","checksum":"f7c32dabf52e6d9e709d9203761e39fd","creator":"system","date_updated":"2020-07-14T12:48:15Z","file_size":494268,"date_created":"2018-12-12T10:17:12Z","file_name":"IST-2018-974-v1+1_manuscript.pdf"}],"language":[{"iso":"eng"}],"issue":"2","volume":207,"ec_funded":1,"abstract":[{"lang":"eng","text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n"}],"oa_version":"Submitted Version","scopus_import":"1","month":"10","intvolume":" 207","date_updated":"2023-09-26T15:49:15Z","ddc":["576"],"file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"NiBa"}],"_id":"910","type":"journal_article","status":"public","pubrep_id":"974","isi":1,"has_accepted_license":"1","year":"2017","day":"01","publication":"Genetics","page":"653 - 668","date_published":"2017-10-01T00:00:00Z","doi":"10.1534/genetics.117.300129","date_created":"2018-12-11T11:49:09Z","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"citation":{"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.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 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.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6533","author":[{"last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"article_processing_charge":"No","external_id":{"isi":["000412232600019"]},"title":"When does frequency-independent selection maintain genetic variation?","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}]},{"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2017","day":"01","publication":"Nature Communications","doi":"10.1038/s41467-017-01663-5","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:47:30Z","article_number":"1486","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"citation":{"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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A","last_name":"Picard","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"publist_id":"7190","article_processing_charge":"No","external_id":{"pmid":["29133797"]},"title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","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","scopus_import":1,"month":"12","intvolume":" 8","publication_identifier":{"issn":["20411723"]},"publication_status":"published","file":[{"date_created":"2020-03-03T15:55:50Z","file_name":"2017_NatureComm_Fraisse.pdf","date_updated":"2020-07-14T12:47:20Z","file_size":1201520,"creator":"dernst","checksum":"4da2651303c8afc2f7fc419be42a2433","file_id":"7562","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":8,"related_material":{"record":[{"relation":"popular_science","id":"7163","status":"public"}]},"issue":"1","_id":"614","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)"},"status":"public","pubrep_id":"910","date_updated":"2024-02-21T13:47:47Z","ddc":["570","576"],"file_date_updated":"2020-07-14T12:47:20Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:47:47Z","citation":{"ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:10.15479/AT:ISTA:7163","apa":"Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7163","ieee":"C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017.","short":"C. Fraisse, (2017).","mla":"Fraisse, Christelle. Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:7163.","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."},"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","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"}],"article_processing_charge":"No","_id":"7163","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","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)"},"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"}],"has_accepted_license":"1","year":"2017","date_published":"2017-12-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"614","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:7163","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"},{"last_name":"Picard","orcid":"0000-0002-8101-2518","first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","abstract":[{"text":"The de novo genome assemblies generated for this study, and the associated metadata.","lang":"eng"}],"month":"12","publisher":"Institute of Science and Technology Austria","oa":1},{"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","publication":"PLoS Computational Biology","day":"18","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:47:58Z","doi":"10.1371/journal.pcbi.1005609","date_published":"2017-07-18T00:00:00Z","article_number":"e1005609","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","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"},"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta","last_name":"Lukacisinova"},{"last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7004","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."}],"intvolume":" 13","month":"07","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a","date_updated":"2020-07-14T12:47:46Z","file_size":3775716,"creator":"system","date_created":"2018-12-12T10:15:01Z","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf"}],"publication_status":"published","publication_identifier":{"issn":["1553734X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"9849","relation":"research_data"},{"id":"9850","status":"public","relation":"research_data"},{"status":"public","id":"9851","relation":"research_data"},{"relation":"research_data","status":"public","id":"9852"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"volume":13,"issue":"7","_id":"696","pubrep_id":"894","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)"},"article_type":"original","type":"journal_article","ddc":["576"],"date_updated":"2024-03-27T23:30:28Z","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:46Z"},{"doi":"10.1038/srep38840","date_published":"2016-12-19T00:00:00Z","date_created":"2018-12-11T11:50:32Z","has_accepted_license":"1","year":"2016","day":"19","publication":"Scientific Reports","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mustansir","last_name":"Barma","full_name":"Barma, Mustansir"},{"last_name":"Rao","full_name":"Rao, Madan","first_name":"Madan"}],"publist_id":"6183","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","citation":{"mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6, 38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.","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.","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.","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"38840","volume":6,"publication_status":"published","file":[{"date_created":"2018-12-12T10:12:56Z","file_name":"IST-2017-737-v1+1_srep38840.pdf","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_size":760967,"checksum":"cb378732da885ea4959ec5b845fb6e52","file_id":"4977","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"12","intvolume":" 6","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","file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:48:50Z","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":"737","_id":"1172"},{"intvolume":" 34","month":"10","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"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. ","lang":"eng"}],"ec_funded":1,"issue":"1","volume":34,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","file_id":"5223","creator":"system","date_updated":"2020-07-14T12:44:38Z","file_size":295274,"date_created":"2018-12-12T10:16:35Z","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf"},{"date_created":"2018-12-12T10:16:36Z","file_name":"IST-2017-770-v1+2_Fig1.pdf","date_updated":"2020-07-14T12:44:38Z","file_size":10902625,"creator":"system","file_id":"5224","checksum":"e13171843283774404c936c581b4543e","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"63bc6e6e61f347594d8c00c37f874a0b","file_id":"5225","date_updated":"2020-07-14T12:44:38Z","file_size":21437,"creator":"system","date_created":"2018-12-12T10:16:37Z","file_name":"IST-2017-770-v1+3_Fig2.pdf"},{"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"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"e47b2a0c32142f423b3100150c0294f8","file_id":"5227","creator":"system","date_updated":"2020-07-14T12:44:38Z","file_size":50045,"date_created":"2018-12-12T10:16:38Z","file_name":"IST-2017-770-v1+5_Fig4.pdf"},{"checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","file_id":"5228","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-770-v1+6_Fig5.pdf","date_created":"2018-12-12T10:16:39Z","creator":"system","file_size":50705,"date_updated":"2020-07-14T12:44:38Z"}],"publication_status":"published","pubrep_id":"770","status":"public","type":"journal_article","_id":"1195","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:38Z","ddc":["576"],"date_updated":"2021-01-12T06:49:00Z","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","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”.","date_created":"2018-12-11T11:50:39Z","date_published":"2016-10-03T00:00:00Z","doi":"10.1093/molbev/msw210","page":"174 - 184","publication":"Molecular Biology and Evolution","day":"03","year":"2016","has_accepted_license":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"title":"Reconstruction of haplotype-blocks selected during experimental evolution.","author":[{"last_name":"Franssen","full_name":"Franssen, Susan","first_name":"Susan"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlötterer","full_name":"Schlötterer, Christian","first_name":"Christian"}],"publist_id":"6155","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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."}},{"publication_status":"published","year":"2016","day":"01","publication":"Plant Biology","language":[{"iso":"eng"}],"page":"98 - 103","issue":"1","doi":"10.1111/plb.12336","date_published":"2016-01-01T00:00:00Z","volume":18,"date_created":"2018-12-11T11:50:48Z","abstract":[{"text":"Sexual dimorphism in resource allocation is expected to change during the life cycle of dioecious plants because of temporal differences between the sexes in reproductive investment. Given the potential for sex-specific differences in reproductive costs, resource availability may contribute to variation in reproductive allocation in females and males. Here, we used Rumex hastatulus, a dioecious, wind-pollinated annual plant, to investigate whether sexual dimorphism varies with life-history stage and nutrient availability, and determine whether allocation patterns differ depending on reproductive commitment. To examine if the costs of reproduction varied between the sexes, reproduction was either allowed or prevented through bud removal, and biomass allocation was measured at maturity. In a second experiment to assess variation in sexual dimorphism across the life cycle, and whether this varied with resource availability, plants were grown in high and low nutrients and allocation to roots, aboveground vegetative growth and reproduction were measured at three developmental stages. Males prevented from reproducing compensated with increased above- and belowground allocation to a much larger degree than females, suggesting that male reproductive costs reduce vegetative growth. The proportional allocation to roots, reproductive structures and aboveground vegetative growth varied between the sexes and among life-cycle stages, but not with nutrient treatment. Females allocated proportionally more resources to roots than males at peak flowering, but this pattern was reversed at reproductive maturity under low-nutrient conditions. Our study illustrates the importance of temporal dynamics in sex-specific resource allocation and provides support for high male reproductive costs in wind-pollinated plants.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"Wiley-Blackwell","scopus_import":1,"month":"01","intvolume":" 18","date_updated":"2021-01-12T06:49:12Z","citation":{"mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” Plant Biology, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:10.1111/plb.12336.","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","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.","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","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","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"publist_id":"6110","department":[{"_id":"NiBa"}],"title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","_id":"1224","type":"journal_article","status":"public"},{"month":"02","intvolume":" 202","scopus_import":1,"main_file_link":[{"url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract","open_access":"1"}],"oa_version":"Preprint","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."}],"issue":"2","volume":202,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1241","department":[{"_id":"NiBa"}],"date_updated":"2023-02-21T10:24:19Z","quality_controlled":"1","publisher":"Genetics Society of America","oa":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).","date_published":"2016-02-01T00:00:00Z","doi":"10.1534/genetics.115.180299","date_created":"2018-12-11T11:50:54Z","page":"721 - 732","day":"01","publication":"Genetics","year":"2016","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"L'OREAL Fellowship","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"title":"The role of recombination in evolutionary rescue","publist_id":"6091","author":[{"orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. 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","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.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","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."}},{"quality_controlled":"1","publisher":"ACM","oa":1,"day":"20","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","has_accepted_license":"1","year":"2016","date_published":"2016-07-20T00:00:00Z","doi":"10.1145/2908812.2908909","date_created":"2018-12-11T11:51:31Z","page":"1163 - 1170","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","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.","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","apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170.","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.","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."},"title":"When non-elitism outperforms elitism for crossing fitness valleys","author":[{"first_name":"Pietro","last_name":"Oliveto","full_name":"Oliveto, Pietro"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"}],"publist_id":"5900","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"07","scopus_import":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5214","checksum":"a1896e39e4113f2711e46b435d5f3e69","creator":"system","file_size":979026,"date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","date_created":"2018-12-12T10:16:27Z"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"_id":"1349","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"},"ddc":["576"],"date_updated":"2021-01-12T06:50:03Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:44:45Z"},{"external_id":{"pmid":["27044080"]},"article_processing_charge":"No","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"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":"5886","title":"The effect of gene interactions on the long-term response to selection","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.","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.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"page":"4422 - 4427","date_created":"2018-12-11T11:51:34Z","date_published":"2016-04-19T00:00:00Z","doi":"10.1073/pnas.1518830113","year":"2016","publication":"PNAS","day":"19","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"date_updated":"2021-01-12T06:50:08Z","article_type":"original","type":"journal_article","status":"public","_id":"1359","ec_funded":1,"volume":113,"issue":"16","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/"}],"scopus_import":1,"intvolume":" 113","month":"04","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."}],"oa_version":"Published Version","pmid":1},{"date_updated":"2021-01-12T06:50:07Z","ddc":["570"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:46Z","_id":"1356","type":"journal_article","pubrep_id":"769","status":"public","publication_status":"published","language":[{"iso":"eng"}],"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"}],"volume":202,"issue":"1","oa_version":"Submitted Version","scopus_import":1,"intvolume":" 202","month":"01","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5889","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","year":"2016","has_accepted_license":"1","publication":"Genetics","day":"05","page":"3 - 4","date_created":"2018-12-11T11:51:33Z","date_published":"2016-01-05T00:00:00Z","doi":"10.1534/genetics.115.184796","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1"},{"ddc":["576"],"date_updated":"2021-01-12T06:50:07Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:46Z","_id":"1357","status":"public","pubrep_id":"768","type":"journal_article","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b2174bab2de1d1142900062a150f35c9","file_id":"5127","creator":"system","file_size":130779,"date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","date_created":"2018-12-12T10:15:09Z"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":202,"oa_version":"Submitted Version","month":"03","intvolume":" 202","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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."},"title":"Richard Hudson and Norman Kaplan on the coalescent process","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"5888","day":"01","publication":"Genetics","has_accepted_license":"1","year":"2016","doi":"10.1534/genetics.116.187542","date_published":"2016-03-01T00:00:00Z","date_created":"2018-12-11T11:51:33Z","page":"865 - 866","publisher":"Genetics Society of America","quality_controlled":"1","oa":1},{"citation":{"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","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","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.","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.","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.","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5798","author":[{"first_name":"Richard","last_name":"Abbott","full_name":"Abbott, Richard"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Good, Jeffrey","last_name":"Good","first_name":"Jeffrey"}],"title":"Genomics of hybridization and its evolutionary consequences","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"has_accepted_license":"1","year":"2016","day":"08","publication":"Molecular Ecology","page":"2325 - 2332","doi":"10.1111/mec.13685","date_published":"2016-06-08T00:00:00Z","date_created":"2018-12-11T11:51:51Z","_id":"1409","type":"journal_article","status":"public","pubrep_id":"772","date_updated":"2021-01-12T06:50:33Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:53Z","oa_version":"Submitted Version","scopus_import":1,"month":"06","intvolume":" 25","publication_status":"published","file":[{"file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","date_created":"2018-12-12T10:10:12Z","file_size":226137,"date_updated":"2020-07-14T12:44:53Z","creator":"system","checksum":"ede7d0b8a471754f71f17e2b20f3135b","file_id":"4797","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"issue":"11","volume":25},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","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.","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","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","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.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548."},"title":"A general approximation for the dynamics of quantitative traits","article_processing_charge":"No","external_id":{"arxiv":["1510.08344"]},"author":[{"last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","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"},{"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":"5787","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"}],"publication":"Genetics","day":"06","year":"2016","date_created":"2018-12-11T11:51:55Z","doi":"10.1534/genetics.115.184127","date_published":"2016-04-06T00:00:00Z","page":"1523 - 1548","oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","date_updated":"2022-08-01T10:49:55Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"_id":"1420","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"4","volume":202,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. "}],"intvolume":" 202","month":"04","main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"scopus_import":"1"},{"article_type":"original","type":"journal_article","pubrep_id":"561","status":"public","_id":"1518","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:00Z","date_updated":"2022-05-24T09:16:22Z","ddc":["570"],"scopus_import":"1","intvolume":" 202","month":"02","abstract":[{"lang":"eng","text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno."}],"pmid":1,"oa_version":"Preprint","ec_funded":1,"volume":202,"issue":"2","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:16:51Z","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":957466,"file_id":"5241","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"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"},{"first_name":"Simon","last_name":"Martin","full_name":"Martin, Simon"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","citation":{"mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:10.1534/genetics.115.183814.","apa":"Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.183814","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","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.","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.","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.).","page":"775 - 786","date_created":"2018-12-11T11:52:29Z","doi":"10.1534/genetics.115.183814","date_published":"2016-02-01T00:00:00Z","year":"2016","has_accepted_license":"1","publication":"Genetics","day":"01"},{"publist_id":"5524","author":[{"first_name":"Jerome","full_name":"Kelleher, Jerome","last_name":"Kelleher"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","citation":{"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.","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","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","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.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008.","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."},"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"}],"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","has_accepted_license":"1","year":"2016","day":"01","publication":"Theoretical Population Biology","quality_controlled":"1","publisher":"Academic Press","oa":1,"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:07Z","date_updated":"2021-01-12T06:52:07Z","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":"465","_id":"1631","volume":108,"ec_funded":1,"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"6a65ba187994d4ad86c1c509e0ff482a","file_id":"4865","creator":"system","file_size":1684043,"date_updated":"2020-07-14T12:45:07Z","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","date_created":"2018-12-12T10:11:12Z"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"04","intvolume":" 108","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"},{"issue":"12","related_material":{"record":[{"relation":"research_data","status":"public","id":"9862"},{"status":"public","id":"9863","relation":"research_data"}]},"volume":14,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:44:36Z","file_size":2494348,"date_created":"2018-12-12T10:15:42Z","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"2bab63b068a9840efd532b9ae583f9bb","file_id":"5164"}],"scopus_import":1,"intvolume":" 14","month":"12","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."}],"oa_version":"Published Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:36Z","date_updated":"2023-02-23T14:11:16Z","ddc":["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":"742","status":"public","_id":"1158","date_created":"2018-12-11T11:50:28Z","date_published":"2016-12-27T00:00:00Z","doi":"10.1371/journal.pbio.2000234","year":"2016","has_accepted_license":"1","publication":"PLoS Biology","day":"27","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","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.","publist_id":"6200","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"last_name":"Anciaux","full_name":"Anciaux, Youann","first_name":"Youann"},{"first_name":"Nicolas","full_name":"Galtier, Nicolas","last_name":"Galtier"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","citation":{"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.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. 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