[{"citation":{"short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, <a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"article_processing_charge":"No","day":"12","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"status":"public","date_updated":"2023-09-11T12:49:17Z","date_created":"2021-08-09T13:10:02Z","year":"2018","author":[{"orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","full_name":"Payne, Pavel","first_name":"Pavel","last_name":"Payne"},{"last_name":"Geyrhofer","first_name":"Lukas","full_name":"Geyrhofer, Lukas"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"}],"date_published":"2018-03-12T00:00:00Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"oa_version":"Published Version","type":"research_data_reference","oa":1,"related_material":{"record":[{"id":"423","status":"public","relation":"used_in_publication"}]},"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"03","_id":"9840","doi":"10.5061/dryad.42n44"},{"status":"public","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"intvolume":"       209","citation":{"ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. 2018;209(4):1279-1303. doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>.","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” <i>Genetics</i>, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>"},"day":"01","title":"Introgression of a block of genome under infinitesimal selection","oa":1,"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"282","month":"08","department":[{"_id":"NiBa"}],"volume":209,"isi":1,"quality_controlled":"1","page":"1279 - 1303","date_created":"2018-12-11T11:45:36Z","year":"2018","date_updated":"2023-09-13T08:22:32Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1534/genetics.118.301018","publisher":"Genetics Society of America","issue":"4","publist_id":"7617","publication":"Genetics","author":[{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"oa_version":"Submitted Version","external_id":{"isi":["000440014100020"]},"date_published":"2018-08-01T00:00:00Z"},{"doi":"10.1111/1755-0998.12782","publisher":"Wiley","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","external_id":{"isi":["000441753000007"]},"date_published":"2018-09-01T00:00:00Z","issue":"5","publication":"Molecular Ecology Resources","author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"},{"first_name":"David","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"date_created":"2018-12-11T11:45:37Z","year":"2018","quality_controlled":"1","page":"988 - 999","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"date_updated":"2025-05-28T11:42:43Z","isi":1,"volume":18,"article_processing_charge":"No","scopus_import":"1","month":"09","_id":"286","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","related_material":{"record":[{"id":"5583","status":"public","relation":"popular_science"}]},"acknowledgement":"ERC, Grant/Award Number: 250152","department":[{"_id":"NiBa"}],"ec_funded":1,"status":"public","abstract":[{"text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ","lang":"eng"}],"day":"01","intvolume":"        18","citation":{"ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” <i>Molecular Ecology Resources</i>, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” <i>Molecular Ecology Resources</i>, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:<a href=\"https://doi.org/10.1111/1755-0998.12782\">10.1111/1755-0998.12782</a>.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” <i>Molecular Ecology Resources</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/1755-0998.12782\">https://doi.org/10.1111/1755-0998.12782</a>.","apa":"Ellis, T., Field, D., &#38; Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.12782\">https://doi.org/10.1111/1755-0998.12782</a>","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. <i>Molecular Ecology Resources</i>. 2018;18(5):988-999. doi:<a href=\"https://doi.org/10.1111/1755-0998.12782\">10.1111/1755-0998.12782</a>","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999."}},{"date_published":"2018-06-15T00:00:00Z","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","last_name":"Polechova","full_name":"Polechova, Jitka","first_name":"Jitka"}],"ddc":["576"],"publist_id":"7550","issue":"6","publication":"PLoS Biology","publisher":"Public Library of Science","doi":"10.1371/journal.pbio.2005372","type":"journal_article","file_date_updated":"2020-07-14T12:46:01Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"publication_identifier":{"issn":["15449173"]},"date_updated":"2023-02-23T14:10:16Z","date_created":"2018-12-11T11:45:46Z","year":"2018","quality_controlled":"1","file":[{"relation":"main_file","checksum":"908c52751bba30c55ed36789e5e4c84d","file_size":6968201,"creator":"dernst","file_name":"2017_PLOS_Polechova.pdf","content_type":"application/pdf","date_created":"2019-01-22T08:30:03Z","file_id":"5870","date_updated":"2020-07-14T12:46:01Z","access_level":"open_access"}],"volume":16,"department":[{"_id":"NiBa"}],"month":"06","_id":"315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"title":"Is the sky the limit? On the expansion threshold of a species’ range","related_material":{"record":[{"id":"9839","status":"public","relation":"research_data"}]},"has_accepted_license":"1","day":"15","intvolume":"        16","citation":{"apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005372\">https://doi.org/10.1371/journal.pbio.2005372</a>","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005372\">https://doi.org/10.1371/journal.pbio.2005372</a>.","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” <i>PLoS Biology</i>, vol. 16, no. 6. Public Library of Science, 2018.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” <i>PLoS Biology</i>, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005372\">10.1371/journal.pbio.2005372</a>.","short":"J. Polechova, PLoS Biology 16 (2018).","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. <i>PLoS Biology</i>. 2018;16(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005372\">10.1371/journal.pbio.2005372</a>"},"abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"status":"public","article_number":"e2005372"},{"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"month":"07","_id":"316","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","oa":1,"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/"}],"record":[{"relation":"research_data","status":"public","id":"9813"}]},"article_type":"original","day":"01","citation":{"short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. <i>Genetics</i>. 2018;209(3):861-883. doi:<a href=\"https://doi.org/10.1534/genetics.118.300748\">10.1534/genetics.118.300748</a>","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300748\">https://doi.org/10.1534/genetics.118.300748</a>.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300748\">https://doi.org/10.1534/genetics.118.300748</a>","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” <i>Genetics</i>, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:<a href=\"https://doi.org/10.1534/genetics.118.300748\">10.1534/genetics.118.300748</a>.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” <i>Genetics</i>, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018."},"intvolume":"       209","ec_funded":1,"status":"public","abstract":[{"lang":"eng","text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants."}],"external_id":{"isi":["000437171700017"]},"oa_version":"Preprint","date_published":"2018-07-01T00:00:00Z","publication":"Genetics","issue":"3","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","last_name":"Bodova","first_name":"Katarina","full_name":"Bodova, Katarina"},{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas","first_name":"Tadeas","last_name":"Priklopil"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David","full_name":"Field, David"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","full_name":"Pickup, Melinda","first_name":"Melinda"}],"doi":"10.1534/genetics.118.300748","publisher":"Genetics Society of America","language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/node/80098.abstract"}],"scopus_import":"1","year":"2018","date_created":"2018-12-11T11:45:47Z","page":"861-883","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","_id":"25B36484-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"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_updated":"2025-05-28T11:42:44Z","isi":1,"volume":209},{"type":"journal_article","file_date_updated":"2020-07-14T12:46:06Z","language":[{"iso":"eng"}],"publisher":"PeerJ","doi":"10.7717/peerj.5325","author":[{"full_name":"Bertl, Johanna","first_name":"Johanna","last_name":"Bertl"},{"last_name":"Ringbauer","full_name":"Ringbauer, Harald","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682"},{"full_name":"Blum, Michaël","first_name":"Michaël","last_name":"Blum"}],"ddc":["576"],"issue":"10","publist_id":"8022","publication":"PeerJ","date_published":"2018-10-01T00:00:00Z","external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"oa_version":"Published Version","isi":1,"file":[{"file_size":1328344,"creator":"dernst","relation":"main_file","checksum":"3334886c4b39678db4c4b74299ca14ba","content_type":"application/pdf","date_created":"2018-12-17T10:46:06Z","file_id":"5692","access_level":"open_access","date_updated":"2020-07-14T12:46:06Z","file_name":"2018_PeerJ_Bertl.pdf"}],"volume":2018,"date_updated":"2023-10-17T12:24:43Z","date_created":"2018-12-11T11:44:16Z","year":"2018","quality_controlled":"1","pmid":1,"scopus_import":"1","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","oa":1,"_id":"33","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species."}],"status":"public","article_number":"e5325","intvolume":"      2018","citation":{"short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? <i>PeerJ</i>. 2018;2018(10). doi:<a href=\"https://doi.org/10.7717/peerj.5325\">10.7717/peerj.5325</a>","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5325\">https://doi.org/10.7717/peerj.5325</a>.","apa":"Bertl, J., Ringbauer, H., &#38; Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5325\">https://doi.org/10.7717/peerj.5325</a>","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” <i>PeerJ</i>, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5325\">10.7717/peerj.5325</a>.","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” <i>PeerJ</i>, vol. 2018, no. 10. PeerJ, 2018."},"has_accepted_license":"1","day":"01"},{"scopus_import":"1","pmid":1,"publication_identifier":{"issn":["00278424"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"No","volume":115,"isi":1,"file":[{"date_updated":"2020-07-14T12:46:16Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-17T08:44:03Z","file_id":"5683","file_name":"11006.full.pdf","creator":"dernst","file_size":1911302,"checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","relation":"main_file"}],"date_updated":"2023-09-18T08:36:49Z","quality_controlled":"1","page":"11006 - 11011","year":"2018","date_created":"2018-12-11T11:44:18Z","ddc":["570"],"author":[{"last_name":"Tavares","full_name":"Tavares, Hugo","first_name":"Hugo"},{"last_name":"Whitley","full_name":"Whitley, Annabel","first_name":"Annabel"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"first_name":"Desmond","full_name":"Bradley, Desmond","last_name":"Bradley"},{"last_name":"Couchman","first_name":"Matthew","full_name":"Couchman, Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"first_name":"Joane","full_name":"Elleouet, Joane","last_name":"Elleouet"},{"last_name":"Burrus","first_name":"Monique","full_name":"Burrus, Monique"},{"last_name":"Andalo","full_name":"Andalo, Christophe","first_name":"Christophe"},{"last_name":"Li","first_name":"Miaomiao","full_name":"Li, Miaomiao"},{"last_name":"Li","full_name":"Li, Qun","first_name":"Qun"},{"first_name":"Yongbiao","full_name":"Xue, Yongbiao","last_name":"Xue"},{"first_name":"Alexandra B","full_name":"Rebocho, Alexandra B","last_name":"Rebocho"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"publist_id":"8017","publication":"PNAS","issue":"43","date_published":"2018-10-23T00:00:00Z","external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:16Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","doi":"10.1073/pnas.1801832115","citation":{"ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. 2018;115(43):11006-11011. doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","ieee":"H. Tavares <i>et al.</i>, “Selection and gene flow shape genomic islands that control floral guides,” <i>PNAS</i>, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>."},"intvolume":"       115","has_accepted_license":"1","day":"23","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"status":"public","acknowledgement":" ERC Grant 201252 (to N.H.B.)","department":[{"_id":"NiBa"}],"title":"Selection and gene flow shape genomic islands that control floral guides","oa":1,"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"38","month":"10"},{"_id":"39","month":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","title":"Replicability of introgression under linked, polygenic selection","oa":1,"article_type":"original","department":[{"_id":"NiBa"}],"status":"public","abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"day":"04","intvolume":"       210","citation":{"mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” <i>Genetics</i>, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:<a href=\"https://doi.org/10.1534/genetics.118.301429\">10.1534/genetics.118.301429</a>.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” <i>Genetics</i>, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301429\">https://doi.org/10.1534/genetics.118.301429</a>.","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301429\">https://doi.org/10.1534/genetics.118.301429</a>","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. <i>Genetics</i>. 2018;210(4):1411-1427. doi:<a href=\"https://doi.org/10.1534/genetics.118.301429\">10.1534/genetics.118.301429</a>","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427."},"doi":"10.1534/genetics.118.301429","publisher":"Genetics Society of America","language":[{"iso":"eng"}],"type":"journal_article","external_id":{"isi":["000452315900021"]},"oa_version":"Preprint","date_published":"2018-12-04T00:00:00Z","publication":"Genetics","issue":"4","author":[{"first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"year":"2018","date_created":"2018-12-11T11:44:18Z","page":"1411-1427","quality_controlled":"1","date_updated":"2023-09-18T08:10:29Z","isi":1,"volume":210,"article_processing_charge":"No","publication_identifier":{"issn":["00166731"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}],"scopus_import":"1"},{"department":[{"_id":"NiBa"}],"month":"12","_id":"40","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"letter_note","publication_status":"published","related_material":{"record":[{"id":"9805","status":"public","relation":"research_data"}]},"title":"The consequences of an introgression event","oa":1,"has_accepted_license":"1","day":"31","intvolume":"        27","citation":{"short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","ama":"Barton NH. The consequences of an introgression event. <i>Molecular Ecology</i>. 2018;27(24):4973-4975. doi:<a href=\"https://doi.org/10.1111/mec.14950\">10.1111/mec.14950</a>","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","apa":"Barton, N. H. (2018). The consequences of an introgression event. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14950\">https://doi.org/10.1111/mec.14950</a>","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” <i>Molecular Ecology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/mec.14950\">https://doi.org/10.1111/mec.14950</a>.","ieee":"N. H. Barton, “The consequences of an introgression event,” <i>Molecular Ecology</i>, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” <i>Molecular Ecology</i>, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:<a href=\"https://doi.org/10.1111/mec.14950\">10.1111/mec.14950</a>."},"abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"status":"public","date_published":"2018-12-31T00:00:00Z","oa_version":"Published Version","external_id":{"pmid":["30599087"],"isi":["000454600500001"]},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"ddc":["576"],"issue":"24","publist_id":"8014","publication":"Molecular Ecology","publisher":"Wiley","doi":"10.1111/mec.14950","type":"journal_article","file_date_updated":"2020-07-14T12:46:22Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","pmid":1,"scopus_import":"1","publication_identifier":{"issn":["1365294X"]},"date_updated":"2023-09-19T10:06:08Z","year":"2018","date_created":"2018-12-11T11:44:18Z","page":"4973-4975","quality_controlled":"1","file":[{"creator":"apreinsp","file_size":295452,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:22Z","content_type":"application/pdf","date_created":"2019-07-19T06:54:46Z","file_id":"6652","file_name":"2018_MolecularEcology_BartonNick.pdf"}],"isi":1,"volume":27},{"article_number":"e32035","status":"public","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"ec_funded":1,"citation":{"ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>, vol. 7, e32035, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>"},"intvolume":"         7","day":"09","has_accepted_license":"1","related_material":{"record":[{"id":"9840","relation":"research_data","status":"public"}]},"oa":1,"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"03","_id":"423","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"volume":7,"isi":1,"file":[{"file_name":"2018_eLife_Payne.pdf","date_updated":"2020-07-14T12:46:25Z","access_level":"open_access","content_type":"application/pdf","file_id":"5689","date_created":"2018-12-17T10:36:07Z","checksum":"447cf6e680bdc3c01062a8737d876569","relation":"main_file","creator":"dernst","file_size":3533881}],"quality_controlled":"1","year":"2018","date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-11T12:49:17Z","project":[{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440"}],"scopus_import":"1","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:25Z","type":"journal_article","doi":"10.7554/eLife.32035","publisher":"eLife Sciences Publications","publication":"eLife","publist_id":"7400","ddc":["576"],"author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","last_name":"Payne","full_name":"Payne, Pavel","first_name":"Pavel"},{"last_name":"Geyrhofer","first_name":"Lukas","full_name":"Geyrhofer, Lukas"},{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"}],"external_id":{"isi":["000431035800001"]},"oa_version":"Published Version","date_published":"2018-03-09T00:00:00Z"},{"date_published":"2018-04-01T00:00:00Z","oa_version":"Published Version","external_id":{"isi":["000429094400005"]},"ddc":["576"],"author":[{"last_name":"Novembre","full_name":"Novembre, John","first_name":"John"},{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7393","issue":"4","publication":"Genetics","publisher":"Genetics Society of America","doi":"10.1534/genetics.118.300786","file_date_updated":"2020-07-14T12:46:26Z","type":"journal_article","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-19T10:17:30Z","page":"1351 - 1355","quality_controlled":"1","year":"2018","date_created":"2018-12-11T11:46:26Z","volume":208,"file":[{"relation":"main_file","checksum":"3d838dc285df394376555b794b6a5ad1","file_size":500129,"creator":"system","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","content_type":"application/pdf","file_id":"4958","date_created":"2018-12-12T10:12:40Z","access_level":"open_access","date_updated":"2020-07-14T12:46:26Z"}],"isi":1,"department":[{"_id":"NiBa"}],"pubrep_id":"1012","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"04","_id":"430","oa":1,"title":"Tread lightly interpreting polygenic tests of selection","publication_status":"published","has_accepted_license":"1","day":"01","citation":{"ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>.","apa":"Novembre, J., &#38; Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” <i>Genetics</i>, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. 2018;208(4):1351-1355. doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>"},"intvolume":"       208","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"status":"public"},{"department":[{"_id":"NiBa"}],"pubrep_id":"974","_id":"910","month":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","oa":1,"title":"When does frequency-independent selection maintain genetic variation?","day":"01","has_accepted_license":"1","intvolume":"       207","citation":{"short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. 2017;207(2):653-668. doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>","apa":"Novak, S., &#38; Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>","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?” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” <i>Genetics</i>, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>."},"ec_funded":1,"status":"public","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"}],"external_id":{"isi":["000412232600019"]},"oa_version":"Submitted Version","date_published":"2017-10-01T00:00:00Z","publist_id":"6533","issue":"2","publication":"Genetics","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"ddc":["576"],"doi":"10.1534/genetics.117.300129","publisher":"Genetics Society of America","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:15Z","article_processing_charge":"No","scopus_import":"1","year":"2017","date_created":"2018-12-11T11:49:09Z","quality_controlled":"1","page":"653 - 668","project":[{"call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"date_updated":"2023-09-26T15:49:15Z","file":[{"relation":"main_file","checksum":"f7c32dabf52e6d9e709d9203761e39fd","file_size":494268,"creator":"system","file_name":"IST-2018-974-v1+1_manuscript.pdf","date_created":"2018-12-12T10:17:12Z","content_type":"application/pdf","file_id":"5264","access_level":"open_access","date_updated":"2020-07-14T12:48:15Z"}],"isi":1,"volume":207},{"publication":"PLoS Computational Biology","publist_id":"7004","issue":"7","ddc":["576"],"author":[{"orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","full_name":"Lukacisinova, Marta","last_name":"Lukacisinova"},{"first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","full_name":"Paixao, Tiago","first_name":"Tiago"}],"oa_version":"Published Version","date_published":"2017-07-18T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:46Z","type":"journal_article","doi":"10.1371/journal.pcbi.1005609","publisher":"Public Library of Science","publication_identifier":{"issn":["1553734X"]},"scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":13,"file":[{"file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_created":"2018-12-12T10:15:01Z","content_type":"application/pdf","file_id":"5117","access_level":"open_access","date_updated":"2020-07-14T12:47:46Z","relation":"main_file","checksum":"9143c290fa6458ed2563bff4b295554a","file_size":3775716,"creator":"system"}],"quality_controlled":"1","date_created":"2018-12-11T11:47:58Z","year":"2017","date_updated":"2024-03-25T23:30:14Z","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"pubrep_id":"894","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","related_material":{"record":[{"relation":"research_data","status":"public","id":"9849"},{"id":"9850","relation":"research_data","status":"public"},{"id":"9851","relation":"research_data","status":"public"},{"id":"9852","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"6263"}]},"oa":1,"publication_status":"published","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","_id":"696","intvolume":"        13","citation":{"ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","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.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>"},"day":"18","has_accepted_license":"1","article_number":"e1005609","status":"public","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."}],"ec_funded":1},{"abstract":[{"text":"The de novo genome assemblies generated for this study, and the associated metadata.","lang":"eng"}],"contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Picard","first_name":"Marion A L","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"file":[{"date_updated":"2020-07-14T12:47:50Z","access_level":"open_access","date_created":"2019-12-10T08:46:46Z","file_id":"7164","content_type":"application/zip","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","creator":"cfraisse","file_size":841375478,"checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","relation":"main_file"}],"status":"public","date_updated":"2024-02-21T13:47:47Z","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2019-12-09T23:03:03Z","year":"2017","citation":{"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, <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","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. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>.","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. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>","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.","mla":"Fraisse, Christelle. <i>Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","short":"C. Fraisse, (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:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>"},"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"01","file_date_updated":"2020-07-14T12:47:50Z","type":"research_data","title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","oa":1,"related_material":{"record":[{"id":"614","status":"public","relation":"research_paper"}]},"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","_id":"7163","doi":"10.15479/AT:ISTA:7163","ddc":["576"],"author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"}],"date_published":"2017-12-01T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa_version":"Published Version"},{"date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000400379500013"]},"oa_version":"Published Version","author":[{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"last_name":"Pérez Heredia","first_name":"Jorge","full_name":"Pérez Heredia, Jorge"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova"}],"ddc":["576"],"publist_id":"5931","publication":"Algorithmica","issue":"2","publisher":"Springer","doi":"10.1007/s00453-016-0212-1","type":"journal_article","file_date_updated":"2020-07-14T12:44:44Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","scopus_import":"1","publication_identifier":{"issn":["01784617"]},"project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"date_updated":"2023-09-20T11:14:42Z","date_created":"2018-12-11T11:51:27Z","year":"2017","page":"681 - 713","quality_controlled":"1","isi":1,"file":[{"creator":"system","file_size":710206,"checksum":"7873f665a0c598ac747c908f34cb14b9","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:10:19Z","content_type":"application/pdf","file_id":"4805","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf"}],"volume":78,"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"pubrep_id":"658","_id":"1336","month":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","title":"Towards a runtime comparison of natural and artificial evolution","oa":1,"has_accepted_license":"1","day":"01","citation":{"ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","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.","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713."},"intvolume":"        78","ec_funded":1,"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."}],"status":"public"},{"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:46Z","type":"journal_article","doi":"10.1007/s00236-016-0278-x","publisher":"Springer","issue":"8","publist_id":"5898","publication":"Acta Informatica","ddc":["006","576"],"author":[{"last_name":"Giacobbe","full_name":"Giacobbe, Mirco","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","last_name":"Petrov","full_name":"Petrov, Tatjana","first_name":"Tatjana"}],"external_id":{"isi":["000414343200003"]},"oa_version":"Published Version","date_published":"2017-12-01T00:00:00Z","volume":54,"isi":1,"file":[{"creator":"dernst","file_size":755241,"checksum":"4e661d9135d7f8c342e8e258dee76f3e","relation":"main_file","date_updated":"2020-07-14T12:44:46Z","access_level":"open_access","date_created":"2019-01-17T15:57:29Z","file_id":"5841","content_type":"application/pdf","file_name":"2017_ActaInformatica_Giacobbe.pdf"}],"page":"765 - 787","quality_controlled":"1","date_created":"2018-12-11T11:51:32Z","year":"2017","date_updated":"2025-05-28T11:57:04Z","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"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","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"publication_identifier":{"issn":["00015903"]},"scopus_import":"1","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"title":"Model checking the evolution of gene regulatory networks","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1835"}]},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1351","month":"12","pubrep_id":"649","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"status":"public","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."}],"ec_funded":1,"citation":{"ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. 2017;54(8):765-787. doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>","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,” <i>Acta Informatica</i>, vol. 54, no. 8. Springer, pp. 765–787, 2017.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>.","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.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2017). Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>"},"intvolume":"        54","day":"01","has_accepted_license":"1"},{"article_number":"e28921","status":"public","abstract":[{"lang":"eng","text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. "}],"ec_funded":1,"intvolume":"         6","citation":{"ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” <i>ELife</i>, vol. 6, e28921, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.28921\">10.7554/eLife.28921</a>.","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., &#38; Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.28921\">https://doi.org/10.7554/eLife.28921</a>","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.28921\">https://doi.org/10.7554/eLife.28921</a>.","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921.","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.28921\">10.7554/eLife.28921</a>","short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017)."},"day":"13","has_accepted_license":"1","title":"Regulatory network structure determines patterns of intermolecular epistasis","oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","_id":"570","pubrep_id":"918","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"volume":6,"file":[{"date_updated":"2020-07-14T12:47:10Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:14:42Z","file_id":"5096","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","creator":"system","file_size":8453470,"checksum":"273ab17f33305e4eaafd911ff88e7c5b","relation":"main_file"},{"file_size":1953221,"creator":"system","relation":"main_file","checksum":"b433f90576c7be597cd43367946f8e7f","date_created":"2018-12-12T10:14:43Z","content_type":"application/pdf","file_id":"5097","date_updated":"2020-07-14T12:47:10Z","access_level":"open_access","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf"}],"quality_controlled":"1","year":"2017","date_created":"2018-12-11T11:47:14Z","date_updated":"2021-01-12T08:03:15Z","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"publication_identifier":{"issn":["2050084X"]},"scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:10Z","type":"journal_article","doi":"10.7554/eLife.28921","publisher":"eLife Sciences Publications","publication":"eLife","publist_id":"7244","ddc":["576"],"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan","first_name":"Srdjan","last_name":"Sarikas"},{"id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","last_name":"Acar","full_name":"Acar, Hande","first_name":"Hande"},{"first_name":"Jonathan P","full_name":"Bollback, Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"}],"oa_version":"Published Version","date_published":"2017-11-13T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"611","doi":"10.1126/science.aao3526","month":"11","publisher":"American Association for the Advancement of Science","title":"Evolution of flower color pattern through selection on regulatory small RNAs","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","date_published":"2017-11-17T00:00:00Z","department":[{"_id":"NiBa"}],"publication":"Science","publist_id":"7193","issue":"6365","author":[{"first_name":"Desmond","full_name":"Bradley, Desmond","last_name":"Bradley"},{"last_name":"Xu","first_name":"Ping","full_name":"Xu, Ping"},{"first_name":"Irina","full_name":"Mohorianu, Irina","last_name":"Mohorianu"},{"last_name":"Whibley","full_name":"Whibley, Annabel","first_name":"Annabel"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"first_name":"Hugo","full_name":"Tavares, Hugo","last_name":"Tavares"},{"last_name":"Couchman","first_name":"Matthew","full_name":"Couchman, Matthew"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"last_name":"Carpenter","full_name":"Carpenter, Rosemary","first_name":"Rosemary"},{"last_name":"Li","first_name":"Miaomiao","full_name":"Li, Miaomiao"},{"first_name":"Qun","full_name":"Li, Qun","last_name":"Li"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"last_name":"Dalmay","full_name":"Dalmay, Tamas","first_name":"Tamas"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"page":"925 - 928","quality_controlled":"1","date_created":"2018-12-11T11:47:29Z","year":"2017","date_updated":"2021-01-12T08:06:10Z","status":"public","abstract":[{"lang":"eng","text":"Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity."}],"volume":358,"day":"17","publication_identifier":{"issn":["00368075"]},"scopus_import":1,"intvolume":"       358","citation":{"mla":"Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” <i>Science</i>, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:<a href=\"https://doi.org/10.1126/science.aao3526\">10.1126/science.aao3526</a>.","ieee":"D. Bradley <i>et al.</i>, “Evolution of flower color pattern through selection on regulatory small RNAs,” <i>Science</i>, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017.","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aao3526\">https://doi.org/10.1126/science.aao3526</a>","ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","chicago":"Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aao3526\">https://doi.org/10.1126/science.aao3526</a>.","ama":"Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. <i>Science</i>. 2017;358(6365):925-928. doi:<a href=\"https://doi.org/10.1126/science.aao3526\">10.1126/science.aao3526</a>","short":"D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928."}},{"publication_identifier":{"issn":["20411723"]},"scopus_import":1,"pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","volume":8,"file":[{"creator":"dernst","file_size":1201520,"checksum":"4da2651303c8afc2f7fc419be42a2433","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","file_id":"7562","date_created":"2020-03-03T15:55:50Z","content_type":"application/pdf","file_name":"2017_NatureComm_Fraisse.pdf"}],"quality_controlled":"1","year":"2017","date_created":"2018-12-11T11:47:30Z","date_updated":"2024-02-21T13:47:47Z","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"publication":"Nature Communications","issue":"1","publist_id":"7190","ddc":["570","576"],"author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","full_name":"Picard, Marion A","last_name":"Picard"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"oa_version":"Published Version","external_id":{"pmid":["29133797"]},"date_published":"2017-12-01T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:20Z","type":"journal_article","doi":"10.1038/s41467-017-01663-5","publisher":"Nature Publishing Group","intvolume":"         8","citation":{"apa":"Fraisse, C., Picard, M. A. L., &#38; Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>","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.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>.","mla":"Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>.","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,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>"},"day":"01","has_accepted_license":"1","article_number":"1486","status":"public","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"}],"pubrep_id":"910","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","oa":1,"related_material":{"record":[{"id":"7163","status":"public","relation":"popular_science"}]},"publication_status":"published","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"614","month":"12"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"626","month":"12","oa":1,"title":"The infinitesimal model: Definition derivation and implications","publication_status":"published","department":[{"_id":"NiBa"}],"pubrep_id":"908","ec_funded":1,"abstract":[{"text":"Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.","lang":"eng"}],"status":"public","has_accepted_license":"1","day":"01","intvolume":"       118","citation":{"chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal Model: Definition Derivation and Implications.” <i>Theoretical Population Biology</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.tpb.2017.06.001\">https://doi.org/10.1016/j.tpb.2017.06.001</a>.","ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","apa":"Barton, N. H., Etheridge, A., &#38; Véber, A. (2017). The infinitesimal model: Definition derivation and implications. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2017.06.001\">https://doi.org/10.1016/j.tpb.2017.06.001</a>","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” <i>Theoretical Population Biology</i>, vol. 118. Academic Press, pp. 50–73, 2017.","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” <i>Theoretical Population Biology</i>, vol. 118, Academic Press, 2017, pp. 50–73, doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.06.001\">10.1016/j.tpb.2017.06.001</a>.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73.","ama":"Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation and implications. <i>Theoretical Population Biology</i>. 2017;118:50-73. doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.06.001\">10.1016/j.tpb.2017.06.001</a>"},"publisher":"Academic Press","doi":"10.1016/j.tpb.2017.06.001","file_date_updated":"2020-07-14T12:47:25Z","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2017-12-01T00:00:00Z","oa_version":"Published Version","ddc":["576"],"author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"last_name":"Véber","full_name":"Véber, Amandine","first_name":"Amandine"}],"publist_id":"7169","publication":"Theoretical Population Biology","date_updated":"2021-01-12T08:06:50Z","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","page":"50 - 73","year":"2017","date_created":"2018-12-11T11:47:34Z","volume":118,"file":[{"file_size":1133924,"creator":"system","relation":"main_file","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8","date_created":"2018-12-12T10:12:45Z","content_type":"application/pdf","file_id":"4964","access_level":"open_access","date_updated":"2020-07-14T12:47:25Z","file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"publication_identifier":{"issn":["00405809"]}}]