[{"file_date_updated":"2020-07-14T12:47:42Z","year":"2019","external_id":{"pmid":["31505037"]},"_id":"6856","date_published":"2019-11-01T00:00:00Z","license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2019-09-07T14:35:40Z","pmid":1,"publication":"New Phytologist","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"file":[{"file_name":"2019_NewPhytologist_Pickup.pdf","relation":"main_file","date_created":"2019-11-13T08:15:05Z","file_size":1511958,"access_level":"open_access","creator":"dernst","file_id":"7011","content_type":"application/pdf","checksum":"21e4c95599bbcaf7c483b89954658672","date_updated":"2020-07-14T12:47:42Z"}],"abstract":[{"text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.","lang":"eng"}],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","quality_controlled":"1","publisher":"Wiley","oa":1,"article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","date_updated":"2026-07-28T13:22:14Z","doi":"10.1111/nph.16180","project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","call_identifier":"FP7"},{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"oa_version":"Published Version","page":"1035-1047","language":[{"iso":"eng"}],"volume":224,"month":"11","author":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Brandvain, Yaniv","last_name":"Brandvain","first_name":"Yaniv"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"last_name":"Yakimowski","full_name":"Yakimowski, Sarah","first_name":"Sarah"},{"full_name":"Dixit, Tanmay","last_name":"Dixit","first_name":"Tanmay"},{"first_name":"Christian","full_name":"Lexer, Christian","last_name":"Lexer"},{"first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","last_name":"Cereghetti","full_name":"Cereghetti, Eva"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","last_name":"Field","orcid":"0000-0002-4014-8478"}],"department":[{"_id":"NiBa"}],"publication_status":"published","scopus_import":"1","ddc":["570"],"intvolume":"       224","OA_type":"hybrid","issue":"3","citation":{"short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. <i>New Phytologist</i>. 2019;224(3):1035-1047. doi:<a href=\"https://doi.org/10.1111/nph.16180\">10.1111/nph.16180</a>","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16180\">https://doi.org/10.1111/nph.16180</a>","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” <i>New Phytologist</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/nph.16180\">https://doi.org/10.1111/nph.16180</a>.","ieee":"M. Pickup <i>et al.</i>, “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” <i>New Phytologist</i>, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” <i>New Phytologist</i>, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:<a href=\"https://doi.org/10.1111/nph.16180\">10.1111/nph.16180</a>."},"ec_funded":1,"has_accepted_license":"1","OA_place":"publisher"},{"publication":"eLife","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","day":"06","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:38Z","year":"2019","_id":"6713","external_id":{"isi":["000473588700001"],"pmid":["31169497"]},"date_published":"2019-06-06T00:00:00Z","date_created":"2019-07-28T21:59:17Z","pmid":1,"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","date_updated":"2026-08-28T22:30:09Z","doi":"10.7554/eLife.42014","file":[{"date_updated":"2020-07-14T12:47:38Z","file_id":"6721","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","content_type":"application/pdf","file_size":6748249,"creator":"apreinsp","access_level":"open_access","relation":"main_file","date_created":"2019-07-29T07:41:18Z","file_name":"2019_eLife_Castro.pdf"}],"title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","quality_controlled":"1","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"publisher":"eLife Sciences Publications","month":"06","volume":8,"author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"full_name":"Yancoskie, Michelle N.","last_name":"Yancoskie","first_name":"Michelle N."},{"full_name":"Marchini, Marta","last_name":"Marchini","first_name":"Marta"},{"first_name":"Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","full_name":"Belohlavy, Stefanie","last_name":"Belohlavy","orcid":"0000-0002-9849-498X"},{"first_name":"Layla","full_name":"Hiramatsu, Layla","last_name":"Hiramatsu"},{"last_name":"Kučka","full_name":"Kučka, Marek","first_name":"Marek"},{"first_name":"William H.","full_name":"Beluch, William H.","last_name":"Beluch"},{"first_name":"Ronald","full_name":"Naumann, Ronald","last_name":"Naumann"},{"first_name":"Isabella","full_name":"Skuplik, Isabella","last_name":"Skuplik"},{"first_name":"John","last_name":"Cobb","full_name":"Cobb, John"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"}],"department":[{"_id":"NiBa"}],"isi":1,"publication_status":"published","scopus_import":"1","intvolume":"         8","ddc":["576"],"oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42014\">10.7554/eLife.42014</a>","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42014\">https://doi.org/10.7554/eLife.42014</a>","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42014\">https://doi.org/10.7554/eLife.42014</a>.","ieee":"J. P. Castro <i>et al.</i>, “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>, vol. 8, e42014, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42014\">10.7554/eLife.42014</a>.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014."},"article_number":"e42014","related_material":{"record":[{"id":"9804","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"11388","status":"public"}]},"has_accepted_license":"1"},{"date_published":"2018-08-01T00:00:00Z","_id":"282","external_id":{"isi":["000440014100020"]},"date_created":"2018-12-11T11:45:36Z","year":"2018","publist_id":"7617","article_processing_charge":"No","day":"01","publication":"Genetics","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Genetics Society of America","title":"Introgression of a block of genome under infinitesimal selection","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"doi":"10.1534/genetics.118.301018","status":"public","date_updated":"2023-09-13T08:22:32Z","oa":1,"page":"1279 - 1303","oa_version":"Submitted Version","language":[{"iso":"eng"}],"intvolume":"       209","scopus_import":"1","volume":209,"month":"08","isi":1,"publication_status":"published","department":[{"_id":"NiBa"}],"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"issue":"4","citation":{"ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 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>.","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>.","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.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 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>","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>"}},{"publisher":"Wiley","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","abstract":[{"lang":"eng","text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. "}],"quality_controlled":"1","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_updated":"2025-04-15T07:11:03Z","status":"public","doi":"10.1111/1755-0998.12782","date_created":"2018-12-11T11:45:37Z","date_published":"2018-09-01T00:00:00Z","external_id":{"isi":["000441753000007"]},"_id":"286","year":"2018","article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","publication":"Molecular Ecology Resources","ec_funded":1,"related_material":{"record":[{"relation":"popular_science","id":"5583","status":"public"}]},"citation":{"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>.","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.","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>.","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.","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>","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."},"issue":"5","language":[{"iso":"eng"}],"page":"988 - 999","oa_version":"None","intvolume":"        18","scopus_import":"1","acknowledgement":"ERC, Grant/Award Number: 250152","publication_status":"published","isi":1,"department":[{"_id":"NiBa"}],"author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254"},{"full_name":"Field, David","last_name":"Field","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"volume":18,"month":"09"},{"issue":"7","citation":{"short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., &#38; Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. 2018;2018(7). doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>.","ieee":"C. Fraisse <i>et al.</i>, “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” <i>PeerJ</i>, vol. 2018, no. 7. PeerJ, 2018.","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>."},"article_number":"30083438","has_accepted_license":"1","volume":2018,"month":"07","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"last_name":"Gagnaire","full_name":"Gagnaire, Pierre","first_name":"Pierre"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"last_name":"Faivre","full_name":"Faivre, Nicolas","first_name":"Nicolas"},{"full_name":"Welch, John","last_name":"Welch","first_name":"John"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"publication_status":"published","isi":1,"scopus_import":"1","intvolume":"      2018","ddc":["576"],"oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.7717/peerj.5198","status":"public","date_updated":"2023-10-17T12:25:28Z","file":[{"checksum":"7d55ae22598a1c70759cd671600cff53","content_type":"application/pdf","file_id":"5739","date_updated":"2020-07-14T12:44:48Z","file_name":"2018_PeerJ_Fraisse.pdf","date_created":"2018-12-18T09:42:11Z","relation":"main_file","creator":"dernst","file_size":1480792,"access_level":"open_access"}],"title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","quality_controlled":"1","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"publisher":"PeerJ","publication":"PeerJ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"30","article_processing_charge":"No","file_date_updated":"2020-07-14T12:44:48Z","publist_id":"7784","year":"2018","_id":"139","external_id":{"isi":["000440484800002"]},"date_published":"2018-07-30T00:00:00Z","date_created":"2018-12-11T11:44:50Z"},{"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","author":[{"orcid":"0000-0002-8511-0254","last_name":"Ellis","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"}],"department":[{"_id":"NiBa"}],"contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"article_processing_charge":"No","day":"12","file_date_updated":"2020-07-14T12:47:07Z","oa_version":"Published Version","year":"2018","date_published":"2018-02-12T00:00:00Z","_id":"5583","datarep_id":"95","date_created":"2018-12-12T12:31:39Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","oa":1,"tmp":{"image":"/images/cc_0.png","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"doi":"10.15479/AT:ISTA:95","status":"public","date_updated":"2025-04-15T07:11:03Z","citation":{"apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>","short":"T. Ellis, (2018).","mla":"Ellis, Thomas. <i>Data and Python Scripts Supporting Python Package FAPS</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>.","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>.","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>."},"related_material":{"record":[{"relation":"research_paper","status":"public","id":"286"}]},"file":[{"file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","access_level":"open_access","file_size":122048,"creator":"system","date_created":"2018-12-12T13:02:41Z","relation":"main_file","checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_id":"5606","content_type":"text/csv","date_updated":"2020-07-14T12:47:07Z"},{"date_updated":"2020-07-14T12:47:07Z","checksum":"92347586ae4f8a6eb7c04354797bf314","file_id":"5607","content_type":"text/csv","relation":"main_file","date_created":"2018-12-12T13:02:42Z","file_size":235980,"access_level":"open_access","creator":"system","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv"},{"date_updated":"2020-07-14T12:47:07Z","content_type":"text/csv","checksum":"3300813645a54e6c5c39f41917228354","file_id":"5608","access_level":"open_access","file_size":311712,"creator":"system","date_created":"2018-12-12T13:02:43Z","relation":"main_file","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv"},{"date_created":"2018-12-12T13:02:44Z","relation":"main_file","file_size":342090,"access_level":"open_access","creator":"system","file_name":"IST-2018-95-v1+4_faps_scripts.zip","date_updated":"2020-07-14T12:47:07Z","file_id":"5609","checksum":"e739fc473567fd8f39438b445fc46147","content_type":"application/zip"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","title":"Data and Python scripts supporting Python package FAPS","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}]},{"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Genetics","day":"01","article_processing_charge":"No","publist_id":"7251","year":"2018","date_created":"2018-12-11T11:47:12Z","_id":"563","external_id":{"isi":["000426219600025"]},"date_published":"2018-03-01T00:00:00Z","oa":1,"date_updated":"2026-04-08T14:06:35Z","doi":"10.1534/genetics.117.300638","status":"public","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}],"abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"quality_controlled":"1","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","publisher":"Genetics Society of America","author":[{"first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","last_name":"Ringbauer"},{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov"},{"last_name":"Field","full_name":"Field, David","first_name":"David"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"department":[{"_id":"NiBa"},{"_id":"ChLa"}],"publication_status":"published","isi":1,"volume":208,"month":"03","scopus_import":"1","intvolume":"       208","language":[{"iso":"eng"}],"oa_version":"Preprint","page":"1231-1245","citation":{"ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. <i>Genetics</i>. 2018;208(3):1231-1245. doi:<a href=\"https://doi.org/10.1534/genetics.117.300638\">10.1534/genetics.117.300638</a>","apa":"Ringbauer, H., Kolesnikov, A., Field, D., &#38; Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300638\">https://doi.org/10.1534/genetics.117.300638</a>","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300638\">https://doi.org/10.1534/genetics.117.300638</a>.","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” <i>Genetics</i>, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” <i>Genetics</i>, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:<a href=\"https://doi.org/10.1534/genetics.117.300638\">10.1534/genetics.117.300638</a>.","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245."},"corr_author":"1","issue":"3","related_material":{"record":[{"relation":"dissertation_contains","id":"200","status":"public"}]}},{"citation":{"ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. 2018;122(7):110-127. doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>","apa":"Barton, N. H., &#38; Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” <i>Theoretical Population Biology</i>, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>. Academic Press, 2018. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127."},"issue":"7","has_accepted_license":"1","ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"9842","status":"public"}]},"language":[{"iso":"eng"}],"page":"110-127","oa_version":"Submitted Version","publication_status":"published","isi":1,"department":[{"_id":"NiBa"}],"author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"}],"volume":122,"month":"07","ddc":["519","576"],"intvolume":"       122","scopus_import":"1","publisher":"Academic Press","title":"Establishment in a new habitat by polygenic adaptation","quality_controlled":"1","abstract":[{"text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population.","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:09Z","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_id":"7199","content_type":"application/pdf","relation":"main_file","date_created":"2019-12-21T09:36:39Z","access_level":"open_access","file_size":2287682,"creator":"nbarton","file_name":"bartonetheridge.pdf"}],"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"oa":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"status":"public","doi":"10.1016/j.tpb.2017.11.007","date_updated":"2025-04-15T07:11:04Z","year":"2018","publist_id":"7250","file_date_updated":"2020-07-14T12:47:09Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2018-12-11T11:47:12Z","date_published":"2018-07-01T00:00:00Z","_id":"564","external_id":{"isi":["000440392900014"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","publication":"Theoretical Population Biology","article_processing_charge":"No","day":"01"},{"publisher":"Genetics Society of America","quality_controlled":"1","title":"The spread of an inversion with migration and selection","abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"status":"public","doi":"10.1534/genetics.117.300426","date_updated":"2026-06-18T18:54:42Z","article_type":"original","oa":1,"date_created":"2018-12-11T11:47:12Z","pmid":1,"date_published":"2018-01-01T00:00:00Z","external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"_id":"565","year":"2018","publist_id":"7249","article_processing_charge":"No","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"Genetics","citation":{"short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. <i>Genetics</i>. 2018;208(1):377-382. doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>","apa":"Charlesworth, B., &#38; Barton, N. H. (2018). The spread of an inversion with migration and selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>.","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 377–382, 2018.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 2018, pp. 377–82, doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>."},"issue":"1","language":[{"iso":"eng"}],"page":"377 - 382","oa_version":"Published Version","intvolume":"       208","ddc":["570"],"scopus_import":"1","publication_status":"published","isi":1,"author":[{"last_name":"Charlesworth","full_name":"Charlesworth, Brian","first_name":"Brian"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"department":[{"_id":"NiBa"}],"volume":208,"month":"01"},{"year":"2018","file_date_updated":"2020-07-14T12:47:11Z","oa_version":"Published Version","date_created":"2018-12-19T14:22:35Z","_id":"5757","date_published":"2018-12-19T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","month":"12","day":"19","ddc":["576"],"article_processing_charge":"No","contributor":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"citation":{"short":"C. Fraisse, (2018).","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>."},"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:47:11Z","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758","content_type":"application/zip","access_level":"open_access","creator":"cfraisse","file_size":369837892,"relation":"main_file","date_created":"2018-12-19T14:19:52Z","file_name":"FileS1.zip"},{"date_created":"2018-12-19T14:19:49Z","relation":"main_file","creator":"cfraisse","file_size":84856909,"access_level":"open_access","file_name":"FileS2.zip","date_updated":"2020-07-14T12:47:11Z","content_type":"application/zip","checksum":"3592e467b4d8206650860b612d6e12f3","file_id":"5759"},{"date_updated":"2020-07-14T12:47:11Z","checksum":"c37ac5d5437c457338afc128c1240655","file_id":"5760","content_type":"text/plain","date_created":"2018-12-19T14:19:49Z","relation":"main_file","file_size":881133,"creator":"cfraisse","access_level":"open_access","file_name":"FileS3.txt"},{"checksum":"943dfd14da61817441e33e3e3cb8cdb9","content_type":"text/plain","file_id":"5761","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS4.txt","creator":"cfraisse","file_size":883742,"access_level":"open_access","relation":"main_file","date_created":"2018-12-19T14:19:49Z"},{"date_updated":"2020-07-14T12:47:11Z","file_id":"5762","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","content_type":"text/plain","creator":"cfraisse","access_level":"open_access","file_size":2495437,"relation":"main_file","date_created":"2018-12-19T14:19:49Z","file_name":"FileS5.txt"},{"date_updated":"2020-07-14T12:47:11Z","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763","content_type":"text/plain","access_level":"open_access","file_size":15913457,"creator":"cfraisse","date_created":"2018-12-19T14:19:50Z","relation":"main_file","file_name":"FileS6.txt"},{"date_updated":"2020-07-14T12:47:11Z","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","content_type":"text/plain","file_id":"5764","creator":"cfraisse","file_size":2584120,"access_level":"open_access","date_created":"2018-12-19T14:19:50Z","relation":"main_file","file_name":"FileS7.txt"},{"access_level":"open_access","creator":"cfraisse","file_size":2446059,"date_created":"2018-12-19T14:19:50Z","relation":"main_file","file_name":"FileS8.txt","date_updated":"2020-07-14T12:47:11Z","file_id":"5765","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","content_type":"text/plain"},{"content_type":"text/plain","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","file_id":"5766","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS9.txt","creator":"cfraisse","access_level":"open_access","file_size":100737,"date_created":"2018-12-19T14:19:50Z","relation":"main_file"}],"related_material":{"record":[{"relation":"research_paper","id":"6089","status":"public"}]},"ec_funded":1,"oa":1,"status":"public","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"date_updated":"2025-04-15T08:18:38Z","doi":"10.15479/at:ista:/5757","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"day":"01","article_processing_charge":"No","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Physica D: Nonlinear Phenomena","date_created":"2018-12-11T11:47:28Z","external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"_id":"607","date_published":"2018-08-01T00:00:00Z","publist_id":"7198","year":"2018","arxiv":1,"status":"public","date_updated":"2024-10-09T20:58:45Z","doi":"10.1016/j.physd.2017.10.015","oa":1,"quality_controlled":"1","abstract":[{"text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one.","lang":"eng"}],"title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"scopus_import":"1","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","author":[{"orcid":"0000-0002-7214-0171","last_name":"Bodova","full_name":"Bodova, Katarina","first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Haskovec","full_name":"Haskovec, Jan","first_name":"Jan"},{"full_name":"Markowich, Peter","last_name":"Markowich","first_name":"Peter"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publication_status":"published","isi":1,"volume":"376-377","month":"08","language":[{"iso":"eng"}],"oa_version":"Submitted Version","page":"108-120","citation":{"ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” <i>Physica D: Nonlinear Phenomena</i>, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:<a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">10.1016/j.physd.2017.10.015</a>.","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” <i>Physica D: Nonlinear Phenomena</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">https://doi.org/10.1016/j.physd.2017.10.015</a>.","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” <i>Physica D: Nonlinear Phenomena</i>, vol. 376–377. Elsevier, pp. 108–120, 2018.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","apa":"Bodova, K., Haskovec, J., &#38; Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. <i>Physica D: Nonlinear Phenomena</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">https://doi.org/10.1016/j.physd.2017.10.015</a>","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. <i>Physica D: Nonlinear Phenomena</i>. 2018;376-377:108-120. doi:<a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">10.1016/j.physd.2017.10.015</a>"},"corr_author":"1"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","article_processing_charge":"No","day":"21","year":"2018","publist_id":"7713","file_date_updated":"2020-07-14T12:45:23Z","date_created":"2018-12-11T11:45:10Z","date_published":"2018-02-21T00:00:00Z","_id":"200","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"oa":1,"status":"public","doi":"10.15479/AT:ISTA:th_963","date_updated":"2026-04-08T14:06:37Z","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"title":"Inferring recent demography from spatial genetic structure","file":[{"file_name":"IST-2018-963-v1+1_thesis.pdf","relation":"main_file","date_created":"2018-12-12T10:14:55Z","file_size":5792935,"creator":"system","access_level":"open_access","checksum":"8cc534d2b528ae017acf80874cce48c9","content_type":"application/pdf","file_id":"5111","date_updated":"2020-07-14T12:45:23Z"},{"content_type":"application/zip","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","file_id":"6224","date_updated":"2020-07-14T12:45:23Z","file_name":"2018_thesis_ringbauer_source.zip","relation":"source_file","date_created":"2019-04-05T09:30:12Z","creator":"dernst","access_level":"closed","file_size":113365}],"publication_status":"published","author":[{"full_name":"Ringbauer, Harald","last_name":"Ringbauer","orcid":"0000-0002-4884-9682","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"month":"02","ddc":["576"],"language":[{"iso":"eng"}],"page":"146","oa_version":"Published Version","pubrep_id":"963","OA_place":"publisher","supervisor":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","citation":{"short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>","apa":"Ringbauer, H. (2018). <i>Inferring recent demography from spatial genetic structure</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>.","mla":"Ringbauer, Harald. <i>Inferring Recent Demography from Spatial Genetic Structure</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>."},"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"563"},{"status":"public","id":"1074","relation":"part_of_dissertation"}]},"degree_awarded":"PhD"},{"date_published":"2018-04-30T00:00:00Z","_id":"9813","date_created":"2021-08-06T13:04:32Z","oa_version":"Published Version","year":"2018","article_processing_charge":"No","day":"30","month":"04","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"author":[{"orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","last_name":"Bod'ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína"},{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541"}],"related_material":{"record":[{"status":"public","id":"316","relation":"used_in_publication"}]},"publisher":"Genetics Society of America","title":"Supplemental material for Bodova et al., 2018","abstract":[{"lang":"eng","text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"citation":{"mla":"Bodova, Katarina, et al. <i>Supplemental Material for Bodova et Al., 2018</i>. Genetics Society of America, 2018, doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018)."},"date_updated":"2025-04-15T07:17:08Z","status":"public","doi":"10.25386/genetics.6148304.v1","oa":1},{"year":"2018","oa_version":"Published Version","date_created":"2021-08-09T12:46:39Z","date_published":"2018-10-09T00:00:00Z","_id":"9837","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"department":[{"_id":"NiBa"}],"month":"10","article_processing_charge":"No","day":"09","citation":{"ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, <a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>.","ieee":"R. Faria <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","mla":"Faria, Rui, et al. <i>Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"publisher":"Dryad","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6095"}]},"oa":1,"status":"public","date_updated":"2023-08-24T14:50:26Z","doi":"10.5061/dryad.72cg113"},{"publisher":"Dryad","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"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"423"}]},"citation":{"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>.","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>.","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.","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>.","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>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"status":"public","date_updated":"2025-04-15T08:17:50Z","doi":"10.5061/dryad.42n44","oa":1,"date_created":"2021-08-09T13:10:02Z","date_published":"2018-03-12T00:00:00Z","_id":"9840","year":"2018","oa_version":"Published Version","article_processing_charge":"No","day":"12","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","author":[{"full_name":"Payne, Pavel","last_name":"Payne","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel"},{"last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas","first_name":"Lukas"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"month":"03"},{"citation":{"mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” <i>Algorithmica</i>, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:<a href=\"https://doi.org/10.1007/s00453-017-0369-2\">10.1007/s00453-017-0369-2</a>.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” <i>Algorithmica</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00453-017-0369-2\">https://doi.org/10.1007/s00453-017-0369-2</a>.","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” <i>Algorithmica</i>, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-017-0369-2\">https://doi.org/10.1007/s00453-017-0369-2</a>","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. <i>Algorithmica</i>. 2018;80(5):1604-1633. doi:<a href=\"https://doi.org/10.1007/s00453-017-0369-2\">10.1007/s00453-017-0369-2</a>","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633."},"issue":"5","has_accepted_license":"1","ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"1604 - 1633","pubrep_id":"1014","author":[{"last_name":"Oliveto","full_name":"Oliveto, Pietro","first_name":"Pietro"},{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge","first_name":"Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","isi":1,"month":"05","volume":80,"scopus_import":"1","intvolume":"        80","ddc":["576"],"abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","quality_controlled":"1","publisher":"Springer","file":[{"content_type":"application/pdf","checksum":"7d92f5d7be81e387edeec4f06442791c","file_id":"4674","date_updated":"2020-07-14T12:47:54Z","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","creator":"system","file_size":691245,"access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:08:14Z"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"status":"public","date_updated":"2025-04-15T08:22:22Z","doi":"10.1007/s00453-017-0369-2","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"publist_id":"6957","year":"2018","file_date_updated":"2020-07-14T12:47:54Z","date_created":"2018-12-11T11:48:09Z","external_id":{"isi":["000428239300010"]},"_id":"723","date_published":"2018-05-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","publication":"Algorithmica","day":"01","article_processing_charge":"No"},{"day":"15","article_processing_charge":"No","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"PLoS Biology","date_created":"2018-12-11T11:45:46Z","_id":"315","date_published":"2018-06-15T00:00:00Z","publist_id":"7550","year":"2018","file_date_updated":"2020-07-14T12:46:01Z","status":"public","doi":"10.1371/journal.pbio.2005372","date_updated":"2025-07-10T11:52:27Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"title":"Is the sky the limit? On the expansion threshold of a species’ range","publisher":"Public Library of Science","file":[{"file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","file_size":6968201,"creator":"dernst","relation":"main_file","date_created":"2019-01-22T08:30:03Z","content_type":"application/pdf","checksum":"908c52751bba30c55ed36789e5e4c84d","file_id":"5870","date_updated":"2020-07-14T12:46:01Z"}],"publication_identifier":{"issn":["1544-9173"]},"scopus_import":"1","ddc":["576"],"intvolume":"        16","author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova","full_name":"Polechova, Jitka"}],"department":[{"_id":"NiBa"}],"publication_status":"published","month":"06","volume":16,"language":[{"iso":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"9839"}]},"citation":{"ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","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>.","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.","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>.","short":"J. Polechova, PLoS Biology 16 (2018).","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>","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>"},"article_number":"e2005372","issue":"6"},{"project":[{"call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","doi":"10.1534/genetics.118.300748","date_updated":"2025-04-15T06:50:00Z","oa":1,"article_type":"original","publisher":"Genetics Society of America","quality_controlled":"1","title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","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."}],"main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"article_processing_charge":"No","day":"01","publication":"Genetics","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-01T00:00:00Z","external_id":{"isi":["000437171700017"]},"_id":"316","date_created":"2018-12-11T11:45:47Z","year":"2018","ec_funded":1,"related_material":{"link":[{"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/","relation":"press_release"}],"record":[{"status":"public","id":"9813","relation":"research_data"}]},"issue":"3","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>","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>","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>.","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.","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>."},"intvolume":"       209","scopus_import":"1","volume":209,"month":"07","isi":1,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"author":[{"first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bodova, Katarina","last_name":"Bodova","orcid":"0000-0002-7214-0171"},{"first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"}],"page":"861-883","oa_version":"Preprint","language":[{"iso":"eng"}]},{"doi":"10.7717/peerj.5325","status":"public","date_updated":"2023-10-17T12:24:43Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","quality_controlled":"1","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."}],"publisher":"PeerJ","file":[{"date_updated":"2020-07-14T12:46:06Z","file_id":"5692","checksum":"3334886c4b39678db4c4b74299ca14ba","content_type":"application/pdf","access_level":"open_access","file_size":1328344,"creator":"dernst","relation":"main_file","date_created":"2018-12-17T10:46:06Z","file_name":"2018_PeerJ_Bertl.pdf"}],"day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"PeerJ","date_created":"2018-12-11T11:44:16Z","pmid":1,"_id":"33","external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"date_published":"2018-10-01T00:00:00Z","publist_id":"8022","year":"2018","file_date_updated":"2020-07-14T12:46:06Z","has_accepted_license":"1","citation":{"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>","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>","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","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.","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>.","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>.","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."},"article_number":"e5325","issue":"10","scopus_import":"1","ddc":["576"],"intvolume":"      2018","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","department":[{"_id":"NiBa"}],"author":[{"full_name":"Bertl, Johanna","last_name":"Bertl","first_name":"Johanna"},{"orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","last_name":"Ringbauer","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Blum, Michaël","last_name":"Blum","first_name":"Michaël"}],"publication_status":"published","isi":1,"month":"10","volume":2018,"language":[{"iso":"eng"}],"oa_version":"Published Version"},{"language":[{"iso":"eng"}],"page":"11006 - 11011","oa_version":"Published Version","publication_status":"published","isi":1,"department":[{"_id":"NiBa"}],"author":[{"last_name":"Tavares","full_name":"Tavares, Hugo","first_name":"Hugo"},{"first_name":"Annabel","last_name":"Whitley","full_name":"Whitley, Annabel"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","last_name":"Field","orcid":"0000-0002-4014-8478"},{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"first_name":"Matthew","last_name":"Couchman","full_name":"Couchman, Matthew"},{"first_name":"Lucy","full_name":"Copsey, Lucy","last_name":"Copsey"},{"last_name":"Elleouet","full_name":"Elleouet, Joane","first_name":"Joane"},{"first_name":"Monique","full_name":"Burrus, Monique","last_name":"Burrus"},{"first_name":"Christophe","last_name":"Andalo","full_name":"Andalo, Christophe"},{"first_name":"Miaomiao","last_name":"Li","full_name":"Li, Miaomiao"},{"full_name":"Li, Qun","last_name":"Li","first_name":"Qun"},{"first_name":"Yongbiao","full_name":"Xue, Yongbiao","last_name":"Xue"},{"first_name":"Alexandra B","last_name":"Rebocho","full_name":"Rebocho, Alexandra B"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"full_name":"Coen, Enrico","last_name":"Coen","first_name":"Enrico"}],"volume":115,"month":"10","intvolume":"       115","ddc":["570"],"scopus_import":"1","acknowledgement":" ERC Grant 201252 (to N.H.B.)","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>","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>","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.","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>.","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>.","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."},"issue":"43","has_accepted_license":"1","year":"2018","publist_id":"8017","file_date_updated":"2020-07-14T12:46:16Z","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2018-12-11T11:44:18Z","date_published":"2018-10-23T00:00:00Z","external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"_id":"38","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"PNAS","article_processing_charge":"No","day":"23","publication_identifier":{"issn":["0027-8424"]},"publisher":"National Academy of Sciences","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"}],"title":"Selection and gene flow shape genomic islands that control floral guides","quality_controlled":"1","file":[{"creator":"dernst","access_level":"open_access","file_size":1911302,"relation":"main_file","date_created":"2018-12-17T08:44:03Z","file_name":"11006.full.pdf","date_updated":"2020-07-14T12:46:16Z","file_id":"5683","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","content_type":"application/pdf"}],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa":1,"doi":"10.1073/pnas.1801832115","status":"public","date_updated":"2025-07-10T11:52:32Z"}]