[{"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.","oa":1,"publisher":"Wiley","quality_controlled":"1","year":"2021","isi":1,"publication":"Journal of Evolutionary Biology","day":"01","page":"270-283","date_created":"2020-12-06T23:01:16Z","date_published":"2021-02-01T00:00:00Z","doi":"10.1111/jeb.13723","project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463"}],"citation":{"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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["33107098"],"isi":["000587769700001"]},"author":[{"last_name":"Arnoux","full_name":"Arnoux, Stéphanie","first_name":"Stéphanie"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"full_name":"Sauvage, Christopher","last_name":"Sauvage","first_name":"Christopher"}],"title":"Genomic inference of complex domestication histories in three Solanaceae species","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"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"scopus_import":"1","intvolume":" 34","month":"02","publication_status":"published","publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"13065","status":"public","relation":"research_data"}]},"issue":"2","volume":34,"_id":"8928","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-04T11:19:26Z","department":[{"_id":"NiBa"}]},{"title":"Speciation in marine environments: Diving under the surface","author":[{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"}],"article_processing_charge":"No","external_id":{"isi":["000608367500001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.","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.","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.","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","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"},"date_published":"2021-01-18T00:00:00Z","doi":"10.1111/jeb.13756","date_created":"2021-02-07T23:01:13Z","page":"4-15","day":"18","publication":"Journal of Evolutionary Biology","isi":1,"has_accepted_license":"1","year":"2021","quality_controlled":"1","publisher":"Wiley","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.","department":[{"_id":"NiBa"}],"file_date_updated":"2021-02-09T09:04:02Z","ddc":["570"],"date_updated":"2023-08-07T13:42:08Z","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)"},"_id":"9100","issue":"1","volume":34,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9108","checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","creator":"dernst","file_size":561340,"date_updated":"2021-02-09T09:04:02Z","file_name":"2021_JourEvolBiology_Faria.pdf","date_created":"2021-02-09T09:04:02Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"publication_status":"published","month":"01","intvolume":" 34","scopus_import":"1","oa_version":"Published Version","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"}]},{"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).","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"day":"01","publication":"Genetics","isi":1,"year":"2021","doi":"10.1093/genetics/iyaa025","date_published":"2021-02-01T00:00:00Z","date_created":"2021-02-18T14:41:30Z","article_number":"iyaa025","project":[{"call_identifier":"FWF","_id":"2662AADE-B435-11E9-9278-68D0E5697425","name":"Sex chromosomes and species barriers","grant_number":"M02463"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","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.","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.","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.","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."},"title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000637218100005"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"02","intvolume":" 217","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1943-2631"]},"publication_status":"published","volume":217,"issue":"2","_id":"9168","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-07T13:47:01Z","department":[{"_id":"NiBa"}]},{"external_id":{"isi":["000614183100001"]},"article_processing_charge":"No","author":[{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Popovic","full_name":"Popovic, Iva","first_name":"Iva"},{"first_name":"Clément","full_name":"Mazoyer, Clément","last_name":"Mazoyer"},{"first_name":"Bruno","last_name":"Spataro","full_name":"Spataro, Bruno"},{"first_name":"Stéphane","last_name":"Delmotte","full_name":"Delmotte, Stéphane"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"first_name":"Étienne","last_name":"Loire","full_name":"Loire, Étienne"},{"first_name":"Alexis","last_name":"Simon","full_name":"Simon, Alexis"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"full_name":"Duret, Laurent","last_name":"Duret","first_name":"Laurent"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"},{"full_name":"Vekemans, Xavier","last_name":"Vekemans","first_name":"Xavier"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"}],"title":"DILS: Demographic inferences with linked selection by using ABC","citation":{"ieee":"C. Fraisse et al., “DILS: Demographic inferences with linked selection by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644, 2021.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"2629-2644","date_created":"2021-02-14T23:01:14Z","doi":"10.1111/1755-0998.13323","date_published":"2021-01-15T00:00:00Z","year":"2021","isi":1,"publication":"Molecular Ecology Resources","day":"15","oa":1,"publisher":"Wiley","quality_controlled":"1","department":[{"_id":"NiBa"}],"date_updated":"2023-08-07T13:45:18Z","article_type":"original","type":"journal_article","status":"public","_id":"9119","volume":21,"publication_status":"published","publication_identifier":{"issn":["1755098X"],"eissn":["17550998"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2","open_access":"1"}],"scopus_import":"1","intvolume":" 21","month":"01","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"}],"oa_version":"Preprint"},{"publication":"PNAS","day":"21","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-05-07T17:10:21Z","doi":"10.1073/pnas.2015005118","date_published":"2021-06-21T00:00:00Z","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”).","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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).","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","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."},"title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","article_processing_charge":"No","external_id":{"isi":["000671755600001"],"pmid":["34155138"]},"author":[{"first_name":"Joana I.","last_name":"Meier","full_name":"Meier, Joana I."},{"last_name":"Salazar","full_name":"Salazar, Patricio A.","first_name":"Patricio A."},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"full_name":"Davies, Robert William","last_name":"Davies","first_name":"Robert William"},{"first_name":"Andreea","last_name":"Dréau","full_name":"Dréau, Andreea"},{"full_name":"Aldás, Ismael","last_name":"Aldás","first_name":"Ismael"},{"full_name":"Power, Olivia Box","last_name":"Power","first_name":"Olivia Box"},{"last_name":"Nadeau","full_name":"Nadeau, Nicola J.","first_name":"Nicola J."},{"first_name":"Jon R.","full_name":"Bridle, Jon R.","last_name":"Bridle"},{"first_name":"Campbell","full_name":"Rolian, Campbell","last_name":"Rolian"},{"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","full_name":"McMillan, W. Owen","last_name":"McMillan"},{"first_name":"Chris D.","full_name":"Jiggins, Chris D.","last_name":"Jiggins"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"}],"article_number":"e2015005118","language":[{"iso":"eng"}],"file":[{"date_updated":"2022-03-08T08:18:16Z","file_size":20592929,"creator":"dernst","date_created":"2022-03-08T08:18:16Z","file_name":"2021_PNAS_Meier.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"cb30c6166b2132ee60d616b31a1a7c29","file_id":"10835","success":1}],"publication_status":"published","publication_identifier":{"eissn":["0027-8424"]},"issue":"25","volume":118,"oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 118","month":"06","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-08T13:33:09Z","file_date_updated":"2022-03-08T08:18:16Z","department":[{"_id":"NiBa"}],"_id":"9375","status":"public","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"},"type":"journal_article","article_type":"original"},{"author":[{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"last_name":"Larsson","full_name":"Larsson, Jenny","first_name":"Jenny"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"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."}],"article_processing_charge":"No","external_id":{"isi":["000647846200001"]},"title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","citation":{"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.","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.","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.","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.","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.","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","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"},"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"}],"page":"196-213","doi":"10.1002/evl3.227","date_published":"2021-05-07T00:00:00Z","date_created":"2021-05-16T22:01:47Z","has_accepted_license":"1","isi":1,"year":"2021","day":"07","publication":"Evolution Letters","quality_controlled":"1","publisher":"Wiley","oa":1,"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. ","department":[{"_id":"NiBa"}],"file_date_updated":"2021-10-15T08:26:02Z","date_updated":"2023-08-08T13:34:08Z","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":"9394","related_material":{"record":[{"relation":"research_data","status":"public","id":"12987"}]},"volume":5,"issue":"3","ec_funded":1,"publication_identifier":{"eissn":["2056-3744"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"023b1608e311f0fda30593ba3d0a4e0b","file_id":"10142","success":1,"date_updated":"2021-10-15T08:26:02Z","file_size":3021108,"creator":"cchlebak","date_created":"2021-10-15T08:26:02Z","file_name":"2021_EvolutionLetters_Koch.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 5","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"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.","oa":1,"quality_controlled":"1","publisher":"Cell Press","year":"2021","isi":1,"publication":"Current Biology","day":"10","page":"R428-R429","date_created":"2021-05-16T22:01:46Z","doi":"10.1016/j.cub.2021.03.060","date_published":"2021-05-10T00:00:00Z","citation":{"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.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), 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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"article_processing_charge":"No","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"}],"title":"Quantifying the use of species concepts","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."}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2021.03.060"}],"scopus_import":"1","intvolume":" 31","month":"05","publication_status":"published","publication_identifier":{"eissn":["18790445"],"issn":["09609822"]},"language":[{"iso":"eng"}],"volume":31,"issue":"9","_id":"9392","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-08T13:34:38Z","department":[{"_id":"NiBa"}]},{"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-08T13:34:07Z","citation":{"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).","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","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","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."},"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"last_name":"Koch","full_name":"Koch, Eva","first_name":"Eva"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"last_name":"Larsson","full_name":"Larsson, Jenny","first_name":"Jenny"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"full_name":"Lemmon, E. Moriarty","last_name":"Lemmon","first_name":"E. Moriarty"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"_id":"12987","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","day":"10","year":"2021","has_accepted_license":"1","date_created":"2023-05-16T12:34:09Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9394"}]},"date_published":"2021-04-10T00:00:00Z","doi":"10.5061/DRYAD.ZGMSBCCB4","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"}],"month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.zgmsbccb4"}],"oa":1,"publisher":"Dryad"},{"pmid":1,"oa_version":"Published Version","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."}],"intvolume":" 17","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9425","checksum":"9c13c1f5af7609c97c741f11d293188a","creator":"kschuh","file_size":726759,"date_updated":"2021-05-25T14:09:03Z","file_name":"2021_BiologyLetters_Lagator.pdf","date_created":"2021-05-25T14:09:03Z"}],"publication_status":"published","publication_identifier":{"eissn":["1744957X"]},"ec_funded":1,"volume":17,"issue":"5","_id":"9410","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-08-08T13:44:35Z","department":[{"_id":"NiBa"}],"file_date_updated":"2021-05-25T14:09:03Z","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.","oa":1,"publisher":"Royal Society of London","quality_controlled":"1","publication":"Biology letters","day":"12","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-05-23T22:01:43Z","date_published":"2021-05-12T00:00:00Z","doi":"10.1098/rsbl.2020.0913","article_number":"20200913","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","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","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","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.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","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."},"title":"Adaptation at different points along antibiotic concentration gradients","article_processing_charge":"No","external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"author":[{"last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker"},{"last_name":"Neve","full_name":"Neve, Paul","first_name":"Paul"}]},{"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","file":[{"date_updated":"2021-06-11T15:34:53Z","file_size":1031978,"creator":"kschuh","date_created":"2021-06-11T15:34:53Z","file_name":"2021_MolecularEcology_Berdan.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e6f4731365bde2614b333040a08265d8","file_id":"9545","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09621083"],"eissn":["1365294X"]},"publication_status":"published","volume":30,"issue":"12","ec_funded":1,"_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)"},"ddc":["570"],"date_updated":"2023-08-08T13:59:18Z","department":[{"_id":"NiBa"}],"file_date_updated":"2021-06-11T15:34:53Z","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,"day":"01","publication":"Molecular Ecology","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1111/mec.15936","date_published":"2021-06-01T00:00:00Z","date_created":"2021-06-06T22:01:31Z","page":"2710-2723","project":[{"call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747"}],"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","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.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","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":[{"last_name":"Berdan","full_name":"Berdan, Emma L.","first_name":"Emma L."},{"first_name":"Alexandre","full_name":"Blanckaert, Alexandre","last_name":"Blanckaert"},{"first_name":"Tanja","full_name":"Slotte, Tanja","last_name":"Slotte"},{"last_name":"Suh","full_name":"Suh, Alexander","first_name":"Alexander"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Inês","last_name":"Fragata","full_name":"Fragata, Inês"}],"article_processing_charge":"No","external_id":{"isi":["000652056400001"]}}]