[{"acknowledgement":"We are very grateful to the authors of the commentaries for the interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166).","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Evolutionary Biology","has_accepted_license":"1","isi":1,"year":"2022","date_published":"2022-09-01T00:00:00Z","doi":"10.1111/jeb.14082","date_created":"2023-01-16T09:59:37Z","page":"1200-1205","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.","mla":"Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:10.1111/jeb.14082.","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205. doi:10.1111/jeb.14082","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14082","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205."},"title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","author":[{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"external_id":{"isi":["000849851100009"]},"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","month":"09","intvolume":" 35","scopus_import":"1","file":[{"success":1,"file_id":"12449","checksum":"27268009e5eec030bc10667a4ac5ed4c","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2022_JourEvoBiology_Westram_Response.pdf","date_created":"2023-01-30T10:14:09Z","file_size":349603,"date_updated":"2023-01-30T10:14:09Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"12264","relation":"other"}]},"issue":"9","volume":35,"_id":"12265","status":"public","keyword":["Ecology","Evolution","Behavior and Systematics"],"article_type":"letter_note","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-04T09:53:41Z","department":[{"_id":"NiBa"}],"file_date_updated":"2023-01-30T10:14:09Z"},{"project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896","name":"Causes and consequences of population fragmentation"}],"title":"The response of a metapopulation to a changing environment","article_processing_charge":"No","external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","last_name":"Olusanya"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1848). doi:10.1098/rstb.2021.0009","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848. The Royal Society, 2022.","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009."},"oa":1,"publisher":"The Royal Society","quality_controlled":"1","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","date_created":"2022-02-21T16:08:10Z","date_published":"2022-04-11T00:00:00Z","doi":"10.1098/rstb.2021.0009","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","day":"11","year":"2022","has_accepted_license":"1","isi":1,"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"10787","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2022-08-02T06:14:32Z","ddc":["570"],"date_updated":"2024-01-26T12:00:53Z","intvolume":" 377","month":"04","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.","lang":"eng"}],"volume":377,"issue":"1848","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14711"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2022-08-02T06:14:32Z","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","creator":"dernst","date_updated":"2022-08-02T06:14:32Z","file_size":1349672,"file_id":"11719","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]}},{"ddc":["576"],"date_updated":"2024-01-26T12:00:53Z","file_date_updated":"2022-01-24T10:34:45Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"_id":"10658","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"rstb.2021.0010.pdf","date_created":"2022-01-24T10:34:45Z","file_size":1845792,"date_updated":"2022-01-24T10:34:45Z","creator":"oolusany","file_id":"10659","checksum":"04ca9e2f0e344d680b947f2457df8d0a","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14711"}],"link":[{"url":"https://doi.org/10.1101/2021.08.05.455207","relation":"earlier_version"}]},"issue":"1846","volume":377,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.","lang":"eng"}],"month":"01","intvolume":" 377","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 2022;377(1846). doi:10.1098/rstb.2021.0010","apa":"Sachdeva, H., Olusanya, O. O., & Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. The Royal Society. https://doi.org/10.1098/rstb.2021.0010","short":"H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022).","ieee":"H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity,” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846. The Royal Society, 2022.","mla":"Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:10.1098/rstb.2021.0010.","ista":"Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 377(1846), 20210010.","chicago":"Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0010."},"title":"Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity","author":[{"first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"first_name":"Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","last_name":"Olusanya"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["35067097"],"isi":["000745854300008"]},"article_processing_charge":"No","article_number":"20210010","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"day":"24","publication":"Philosophical Transactions of the Royal Society B","isi":1,"has_accepted_license":"1","year":"2022","date_published":"2022-01-24T00:00:00Z","doi":"10.1098/rstb.2021.0010","date_created":"2022-01-24T10:34:53Z","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B).","publisher":"The Royal Society","quality_controlled":"1","oa":1},{"intvolume":" 221","month":"07","scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"issue":"3","related_material":{"record":[{"relation":"dissertation_contains","id":"14651","status":"public"},{"status":"public","id":"11321","relation":"research_data"},{"id":"9192","status":"public","relation":"research_data"}]},"volume":221,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"11412","checksum":"cc2d56deb608bd53c5cc02f03a875107","file_size":885374,"date_updated":"2022-05-26T12:48:15Z","creator":"larathoo","file_name":"Manuscript.pdf","date_created":"2022-05-26T12:48:15Z"},{"checksum":"693742595b6c7ed809423be01460d083","file_id":"11413","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-05-26T12:48:21Z","file_name":"SupplementalMaterial.pdf","date_updated":"2022-05-26T12:48:21Z","file_size":1401704,"creator":"larathoo"}],"publication_status":"published","publication_identifier":{"eissn":["1943-2631"]},"status":"public","article_type":"original","type":"journal_article","_id":"11411","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2022-05-26T12:48:21Z","ddc":["576"],"date_updated":"2024-02-21T12:38:33Z","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","date_created":"2022-05-26T13:44:50Z","doi":"10.1093/genetics/iyac083","date_published":"2022-07-01T00:00:00Z","publication":"Genetics","day":"01","year":"2022","isi":1,"has_accepted_license":"1","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"article_number":"iyac083","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","article_processing_charge":"No","external_id":{"isi":["000803735800001"],"pmid":["35639938"]},"author":[{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"last_name":"Arathoon","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","last_name":"Baskett"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","last_name":"Pickup"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac083","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3. Oxford University Press, 2022.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083."}},{"contributor":[{"last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","orcid":"0000-0002-7354-8574"},{"last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","contributor_type":"project_member","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-04-22T09:42:24Z","doi":"10.15479/at:ista:11321","date_published":"2022-04-28T00:00:00Z","related_material":{"record":[{"status":"public","id":"11411","relation":"used_in_publication"},{"status":"public","id":"9192","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"8254"}]},"day":"28","file":[{"date_created":"2022-04-22T09:39:03Z","file_name":"Data_Code.zip","date_updated":"2022-04-22T09:39:03Z","file_size":13260571,"creator":"larathoo","checksum":"96c1b86cdf25481f2a52972fcc45ca7f","file_id":"11326","success":1,"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file"}],"year":"2022","has_accepted_license":"1","month":"04","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. "}],"file_date_updated":"2022-04-22T09:39:03Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","last_name":"Surendranadh","full_name":"Surendranadh, Parvathy"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","last_name":"Arathoon"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","mla":"Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321."},"date_updated":"2024-02-21T12:41:09Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","_id":"11321"},{"title":"Accumulation and maintenance of information in evolution","author":[{"first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"1","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"article_processing_charge":"No","external_id":{"isi":["000889278400014"],"pmid":["36037343"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119."},"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"}],"article_number":"e2123152119","date_published":"2022-08-29T00:00:00Z","doi":"10.1073/pnas.2123152119","date_created":"2022-09-11T22:01:55Z","day":"29","publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","isi":1,"year":"2022","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2022-09-12T08:08:12Z","ddc":["570"],"date_updated":"2024-03-06T14:22:51Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12081","volume":119,"issue":"36","related_material":{"record":[{"relation":"dissertation_contains","id":"15020","status":"public"}]},"ec_funded":1,"file":[{"success":1,"file_id":"12091","checksum":"6dec51f6567da9039982a571508a8e4d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2022_PNAS_Hledik.pdf","date_created":"2022-09-12T08:08:12Z","file_size":2165752,"date_updated":"2022-09-12T08:08:12Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","month":"08","intvolume":" 119","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.","lang":"eng"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","_id":"11388","file_date_updated":"2023-05-20T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_updated":"2023-08-29T06:41:51Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"ddc":["576"],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"6713","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-018-3"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2023-05-19","checksum":"4d75e6a619df7e8a9d6e840aee182380","file_id":"11398","file_size":8247240,"date_updated":"2023-05-20T22:30:03Z","creator":"sbelohla","file_name":"thesis_sb_final_pdfa.pdf","date_created":"2022-05-19T13:03:13Z"},{"creator":"sbelohla","date_updated":"2023-05-20T22:30:03Z","file_size":7094,"date_created":"2022-05-19T13:07:47Z","file_name":"thesis_sb_final.zip","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","embargo_to":"open_access","file_id":"11399","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0"}],"article_processing_charge":"No","author":[{"last_name":"Belohlavy","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie"}],"title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","citation":{"chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publisher":"Institute of Science and Technology Austria","page":"98","date_created":"2022-05-16T16:49:18Z","doi":"10.15479/at:ista:11388","date_published":"2022-05-18T00:00:00Z","year":"2022","has_accepted_license":"1","day":"18"},{"publication":"PLoS Computational Biology","day":"01","year":"2021","has_accepted_license":"1","date_created":"2021-12-12T23:01:27Z","doi":"10.1371/journal.pcbi.1009661","date_published":"2021-12-01T00:00:00Z","acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 2021;17(12). doi:10.1371/journal.pcbi.1009661","ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” PLoS Computational Biology, vol. 17, no. 12. Public Library of Science, 2021.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661."},"title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","article_processing_charge":"No","external_id":{"arxiv":["2102.03669"],"pmid":["34851948"]},"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","last_name":"Bod'ová"},{"first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko","last_name":"Szep"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"article_number":"e1009661","language":[{"iso":"eng"}],"file":[{"date_created":"2022-05-16T08:53:11Z","file_name":"2021_PLOsComBio_Bodova.pdf","date_updated":"2022-05-16T08:53:11Z","file_size":2299486,"creator":"dernst","checksum":"dcd185d4f7e0acee25edf1d6537f447e","file_id":"11383","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"volume":17,"issue":"12","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment."}],"intvolume":" 17","month":"12","scopus_import":"1","ddc":["570"],"date_updated":"2022-08-01T10:48:04Z","file_date_updated":"2022-05-16T08:53:11Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"_id":"10535","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original"},{"issue":"1","volume":34,"related_material":{"record":[{"status":"public","id":"13073","relation":"research_data"}]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"publication_status":"published","month":"01","intvolume":" 34","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/818559","open_access":"1"}],"pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2023-08-04T11:04:11Z","status":"public","type":"journal_article","article_type":"original","_id":"8708","date_published":"2021-01-01T00:00:00Z","doi":"10.1111/jeb.13709","date_created":"2020-10-25T23:01:20Z","page":"208-223","day":"01","publication":"Journal of Evolutionary Biology","isi":1,"year":"2021","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.","title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","author":[{"last_name":"Simon","full_name":"Simon, Alexis","first_name":"Alexis"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"full_name":"El Ayari, Tahani","last_name":"El Ayari","first_name":"Tahani"},{"first_name":"Cathy","last_name":"Liautard‐Haag","full_name":"Liautard‐Haag, Cathy"},{"first_name":"Petr","full_name":"Strelkov, Petr","last_name":"Strelkov"},{"first_name":"John J","last_name":"Welch","full_name":"Welch, John J"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"external_id":{"pmid":["33045123"],"isi":["000579599700001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:10.1111/jeb.13709.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch, J. J., & Bierne, N. (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13709","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 2021;34(1):208-223. doi:10.1111/jeb.13709","ieee":"A. Simon et al., “How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 208–223, 2021.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch, N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag, Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13709.","ista":"Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne N. 2021. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223."}},{"article_processing_charge":"No","external_id":{"isi":["000583190600001"],"pmid":["33078844"]},"author":[{"full_name":"Salces-Castellano, Antonia","last_name":"Salces-Castellano","first_name":"Antonia"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"last_name":"Arribas","full_name":"Arribas, Paula","first_name":"Paula"},{"full_name":"Patino, Jairo","last_name":"Patino","first_name":"Jairo"},{"full_name":"Karger, Dirk N. ","last_name":"Karger","first_name":"Dirk N. "},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"first_name":"Brent C.","last_name":"Emerson","full_name":"Emerson, Brent C."}],"title":"Long-term cloud forest response to climate warming revealed by insect speciation history","citation":{"short":"A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger, R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244.","ieee":"A. Salces-Castellano et al., “Long-term cloud forest response to climate warming revealed by insect speciation history,” Evolution, vol. 75, no. 2. Wiley, pp. 231–244, 2021.","apa":"Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D. N., Butlin, R., & Emerson, B. C. (2021). Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. Wiley. https://doi.org/10.1111/evo.14111","ama":"Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 2021;75(2):231-244. doi:10.1111/evo.14111","mla":"Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution, vol. 75, no. 2, Wiley, 2021, pp. 231–44, doi:10.1111/evo.14111.","ista":"Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 75(2), 231–244.","chicago":"Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino, Dirk N. Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14111."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"This work was financed by the Spanish Agencia Estatal de Investigación (CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P), awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the Cabildo of Tenerife. The authors wish to thank the following for field work and sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar. We also thank V. García‐Olivares for assistance with laboratory and bioinformatic work.","page":"231-244","date_created":"2020-11-08T23:01:26Z","doi":"10.1111/evo.14111","date_published":"2021-02-01T00:00:00Z","year":"2021","isi":1,"publication":"Evolution","day":"01","type":"journal_article","article_type":"original","status":"public","_id":"8743","department":[{"_id":"NiBa"}],"date_updated":"2023-08-04T11:09:49Z","main_file_link":[{"url":"http://hdl.handle.net/10261/223937","open_access":"1"}],"scopus_import":"1","intvolume":" 75","month":"02","abstract":[{"text":"Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1111/evo.14225"}]},"issue":"2","volume":75,"publication_status":"published","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"language":[{"iso":"eng"}]},{"quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","doi":"10.1111/jeb.13723","date_published":"2021-02-01T00:00:00Z","date_created":"2020-12-06T23:01:16Z","page":"270-283","day":"01","publication":"Journal of Evolutionary Biology","isi":1,"year":"2021","project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463"}],"title":"Genomic inference of complex domestication histories in three Solanaceae species","author":[{"first_name":"Stéphanie","full_name":"Arnoux, Stéphanie","last_name":"Arnoux"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christopher","last_name":"Sauvage","full_name":"Sauvage, Christopher"}],"article_processing_charge":"No","external_id":{"isi":["000587769700001"],"pmid":["33107098"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13723","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 2021;34(2):270-283. doi:10.1111/jeb.13723","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” Journal of Evolutionary Biology, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723.","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283."},"month":"02","intvolume":" 34","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available.","lang":"eng"}],"issue":"2","related_material":{"record":[{"id":"13065","status":"public","relation":"research_data"}]},"volume":34,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"8928","department":[{"_id":"NiBa"}],"date_updated":"2023-08-04T11:19:26Z"},{"file_date_updated":"2021-02-09T09:04:02Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-07T13:42:08Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9100","issue":"1","volume":34,"publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","file_id":"9108","success":1,"creator":"dernst","date_updated":"2021-02-09T09:04:02Z","file_size":561340,"date_created":"2021-02-09T09:04:02Z","file_name":"2021_JourEvolBiology_Faria.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 34","abstract":[{"text":"Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"}],"external_id":{"isi":["000608367500001"]},"article_processing_charge":"No","title":"Speciation in marine environments: Diving under the surface","citation":{"ieee":"R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 4–15, 2021.","short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15.","apa":"Faria, R., Johannesson, K., & Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13756","ama":"Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 2021;34(1):4-15. doi:10.1111/jeb.13756","mla":"Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:10.1111/jeb.13756.","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.","chicago":"Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13756."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"4-15","doi":"10.1111/jeb.13756","date_published":"2021-01-18T00:00:00Z","date_created":"2021-02-07T23:01:13Z","has_accepted_license":"1","isi":1,"year":"2021","day":"18","publication":"Journal of Evolutionary Biology","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin."},{"citation":{"mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:10.1093/genetics/iyaa025.","apa":"Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 2021;217(2). doi:10.1093/genetics/iyaa025","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics, vol. 217, no. 2. Genetics Society of America, 2021.","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000637218100005"]},"author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"}],"title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","article_number":"iyaa025","project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463"}],"year":"2021","isi":1,"publication":"Genetics","day":"01","date_created":"2021-02-18T14:41:30Z","date_published":"2021-02-01T00:00:00Z","doi":"10.1093/genetics/iyaa025","acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","date_updated":"2023-08-07T13:47:01Z","department":[{"_id":"NiBa"}],"_id":"9168","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["1943-2631"]},"language":[{"iso":"eng"}],"issue":"2","volume":217,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"intvolume":" 217","month":"02"},{"volume":21,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["17550998"],"issn":["1755098X"]},"intvolume":" 21","month":"01","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.","lang":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2023-08-07T13:45:18Z","status":"public","type":"journal_article","article_type":"original","_id":"9119","date_created":"2021-02-14T23:01:14Z","date_published":"2021-01-15T00:00:00Z","doi":"10.1111/1755-0998.13323","page":"2629-2644","publication":"Molecular Ecology Resources","day":"15","year":"2021","isi":1,"oa":1,"quality_controlled":"1","publisher":"Wiley","title":"DILS: Demographic inferences with linked selection by using ABC","external_id":{"isi":["000614183100001"]},"article_processing_charge":"No","author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"full_name":"Popovic, Iva","last_name":"Popovic","first_name":"Iva"},{"last_name":"Mazoyer","full_name":"Mazoyer, Clément","first_name":"Clément"},{"first_name":"Bruno","full_name":"Spataro, Bruno","last_name":"Spataro"},{"first_name":"Stéphane","full_name":"Delmotte, Stéphane","last_name":"Delmotte"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Loire, Étienne","last_name":"Loire","first_name":"Étienne"},{"last_name":"Simon","full_name":"Simon, Alexis","first_name":"Alexis"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"first_name":"Laurent","last_name":"Duret","full_name":"Duret, Laurent"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"},{"first_name":"Xavier","last_name":"Vekemans","full_name":"Vekemans, Xavier"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644.","ieee":"C. Fraisse et al., “DILS: Demographic inferences with linked selection by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644, 2021.","apa":"Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13323","ama":"Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 2021;21:2629-2644. doi:10.1111/1755-0998.13323","mla":"Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources, vol. 21, Wiley, 2021, pp. 2629–44, doi:10.1111/1755-0998.13323.","ista":"Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644.","chicago":"Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources. Wiley, 2021. https://doi.org/10.1111/1755-0998.13323."}},{"scopus_import":"1","month":"06","intvolume":" 118","abstract":[{"lang":"eng","text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations."}],"pmid":1,"oa_version":"Published Version","issue":"25","volume":118,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"eissn":["0027-8424"]},"publication_status":"published","file":[{"date_created":"2022-03-08T08:18:16Z","file_name":"2021_PNAS_Meier.pdf","creator":"dernst","date_updated":"2022-03-08T08:18:16Z","file_size":20592929,"file_id":"10835","checksum":"cb30c6166b2132ee60d616b31a1a7c29","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9375","department":[{"_id":"NiBa"}],"file_date_updated":"2022-03-08T08:18:16Z","date_updated":"2023-08-08T13:33:09Z","ddc":["570"],"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","oa":1,"acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).","date_published":"2021-06-21T00:00:00Z","doi":"10.1073/pnas.2015005118","date_created":"2021-05-07T17:10:21Z","isi":1,"has_accepted_license":"1","year":"2021","day":"21","publication":"PNAS","article_number":"e2015005118","author":[{"last_name":"Meier","full_name":"Meier, Joana I.","first_name":"Joana I."},{"first_name":"Patricio A.","full_name":"Salazar, Patricio A.","last_name":"Salazar"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"last_name":"Davies","full_name":"Davies, Robert William","first_name":"Robert William"},{"full_name":"Dréau, Andreea","last_name":"Dréau","first_name":"Andreea"},{"first_name":"Ismael","last_name":"Aldás","full_name":"Aldás, Ismael"},{"first_name":"Olivia Box","full_name":"Power, Olivia Box","last_name":"Power"},{"first_name":"Nicola J.","full_name":"Nadeau, Nicola J.","last_name":"Nadeau"},{"last_name":"Bridle","full_name":"Bridle, Jon R.","first_name":"Jon R."},{"first_name":"Campbell","last_name":"Rolian","full_name":"Rolian, Campbell"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"W. Owen","last_name":"McMillan","full_name":"McMillan, W. Owen"},{"first_name":"Chris D.","full_name":"Jiggins, Chris D.","last_name":"Jiggins"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"article_processing_charge":"No","external_id":{"pmid":["34155138"],"isi":["000671755600001"]},"title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","citation":{"chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118.","ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 118(25), e2015005118.","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118.","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2015005118","ieee":"J. I. Meier et al., “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021.","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"ec_funded":1,"issue":"3","related_material":{"record":[{"status":"public","id":"12987","relation":"research_data"}]},"volume":5,"publication_status":"published","publication_identifier":{"eissn":["2056-3744"]},"language":[{"iso":"eng"}],"file":[{"file_id":"10142","checksum":"023b1608e311f0fda30593ba3d0a4e0b","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-15T08:26:02Z","file_name":"2021_EvolutionLetters_Koch.pdf","date_updated":"2021-10-15T08:26:02Z","file_size":3021108,"creator":"cchlebak"}],"scopus_import":"1","intvolume":" 5","month":"05","abstract":[{"lang":"eng","text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow."}],"oa_version":"Published Version","file_date_updated":"2021-10-15T08:26:02Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-08T13:34:08Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"9394","page":"196-213","date_created":"2021-05-16T22:01:47Z","date_published":"2021-05-07T00:00:00Z","doi":"10.1002/evl3.227","year":"2021","isi":1,"has_accepted_license":"1","publication":"Evolution Letters","day":"07","oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. ","external_id":{"isi":["000647846200001"]},"article_processing_charge":"No","author":[{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"first_name":"E. Moriarty","full_name":"Lemmon, E. Moriarty","last_name":"Lemmon"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","citation":{"ista":"Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.","chicago":"Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227.","ieee":"E. L. Koch et al., “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” Evolution Letters, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","short":"E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213.","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 2021;5(3):196-213. doi:10.1002/evl3.227","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.227","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}]},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not."}],"month":"05","intvolume":" 31","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2021.03.060"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["18790445"],"issn":["09609822"]},"publication_status":"published","issue":"9","volume":31,"_id":"9392","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-08T13:34:38Z","department":[{"_id":"NiBa"}],"acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","quality_controlled":"1","publisher":"Cell Press","oa":1,"day":"10","publication":"Current Biology","isi":1,"year":"2021","doi":"10.1016/j.cub.2021.03.060","date_published":"2021-05-10T00:00:00Z","date_created":"2021-05-16T22:01:46Z","page":"R428-R429","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. Current Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060","apa":"Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060."},"title":"Quantifying the use of species concepts","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"external_id":{"pmid":["33974865"],"isi":["000654741200004"]},"article_processing_charge":"No"},{"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"Eva","full_name":"Koch, Eva","last_name":"Koch"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Alan R.","full_name":"Lemmon, Alan R.","last_name":"Lemmon"},{"first_name":"E. Moriarty","last_name":"Lemmon","full_name":"Lemmon, E. Moriarty"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-08T13:34:07Z","citation":{"ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4","ieee":"E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021).","mla":"Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.","ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4."},"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","_id":"12987","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-16T12:34:09Z","date_published":"2021-04-10T00:00:00Z","doi":"10.5061/DRYAD.ZGMSBCCB4","related_material":{"record":[{"relation":"used_in_publication","id":"9394","status":"public"}]},"day":"10","year":"2021","has_accepted_license":"1","month":"04","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.zgmsbccb4"}],"publisher":"Dryad","oa_version":"Published Version","abstract":[{"text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.","lang":"eng"}]},{"quality_controlled":"1","publisher":"Royal Society of London","oa":1,"acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","date_published":"2021-05-12T00:00:00Z","doi":"10.1098/rsbl.2020.0913","date_created":"2021-05-23T22:01:43Z","has_accepted_license":"1","isi":1,"year":"2021","day":"12","publication":"Biology letters","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"20200913","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","last_name":"Uecker","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard"},{"last_name":"Neve","full_name":"Neve, Paul","first_name":"Paul"}],"external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"article_processing_charge":"No","title":"Adaptation at different points along antibiotic concentration gradients","citation":{"mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913.","apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021.","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"05","intvolume":" 17","abstract":[{"lang":"eng","text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains."}],"oa_version":"Published Version","pmid":1,"volume":17,"issue":"5","ec_funded":1,"publication_identifier":{"eissn":["1744957X"]},"publication_status":"published","file":[{"checksum":"9c13c1f5af7609c97c741f11d293188a","file_id":"9425","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-05-25T14:09:03Z","file_name":"2021_BiologyLetters_Lagator.pdf","creator":"kschuh","date_updated":"2021-05-25T14:09:03Z","file_size":726759}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9410","file_date_updated":"2021-05-25T14:09:03Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-08T13:44:35Z","ddc":["570"]},{"ddc":["570"],"date_updated":"2023-08-08T13:59:18Z","file_date_updated":"2021-06-11T15:34:53Z","department":[{"_id":"NiBa"}],"_id":"9470","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"e6f4731365bde2614b333040a08265d8","file_id":"9545","creator":"kschuh","file_size":1031978,"date_updated":"2021-06-11T15:34:53Z","file_name":"2021_MolecularEcology_Berdan.pdf","date_created":"2021-06-11T15:34:53Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365294X"],"issn":["09621083"]},"publication_status":"published","volume":30,"issue":"12","license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance."}],"month":"06","intvolume":" 30","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.","ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723."},"title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","author":[{"full_name":"Berdan, Emma L.","last_name":"Berdan","first_name":"Emma L."},{"full_name":"Blanckaert, Alexandre","last_name":"Blanckaert","first_name":"Alexandre"},{"first_name":"Tanja","full_name":"Slotte, Tanja","last_name":"Slotte"},{"first_name":"Alexander","last_name":"Suh","full_name":"Suh, Alexander"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Inês","last_name":"Fragata","full_name":"Fragata, Inês"}],"article_processing_charge":"No","external_id":{"isi":["000652056400001"]},"project":[{"grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"01","publication":"Molecular Ecology","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-06-01T00:00:00Z","doi":"10.1111/mec.15936","date_created":"2021-06-06T22:01:31Z","page":"2710-2723","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","publisher":"Wiley","quality_controlled":"1","oa":1}]