--- _id: '8928' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Stéphanie full_name: Arnoux, Stéphanie last_name: Arnoux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Christopher full_name: Sauvage, Christopher last_name: Sauvage citation: 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 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 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. 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. 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. short: S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283. date_created: 2020-12-06T23:01:16Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-04T11:19:26Z day: '01' department: - _id: NiBa doi: 10.1111/jeb.13723 external_id: isi: - '000587769700001' pmid: - '33107098' intvolume: ' 34' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/jeb.13723 month: '02' oa: 1 oa_version: Published Version page: 270-283 pmid: 1 project: - _id: 2662AADE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02463 name: Sex chromosomes and species barriers publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13065' relation: research_data status: public scopus_import: '1' status: public title: Genomic inference of complex domestication histories in three Solanaceae species type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2021' ... --- _id: '9100' abstract: - lang: eng 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.' 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." article_processing_charge: No article_type: original author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski citation: 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' 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.' 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.' 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.' short: R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15. date_created: 2021-02-07T23:01:13Z date_published: 2021-01-18T00:00:00Z date_updated: 2023-08-07T13:42:08Z day: '18' ddc: - '570' department: - _id: NiBa doi: 10.1111/jeb.13756 external_id: isi: - '000608367500001' file: - access_level: open_access checksum: 5755856a5368d4b4cdd6fad5ab27f4d1 content_type: application/pdf creator: dernst date_created: 2021-02-09T09:04:02Z date_updated: 2021-02-09T09:04:02Z file_id: '9108' file_name: 2021_JourEvolBiology_Faria.pdf file_size: 561340 relation: main_file success: 1 file_date_updated: 2021-02-09T09:04:02Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 4-15 publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Speciation in marine environments: Diving under the surface' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2021' ... --- _id: '9168' 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 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)." article_number: iyaa025 article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva 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' 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.' 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.' 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.' 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.' short: C. Fraisse, H. Sachdeva, Genetics 217 (2021). date_created: 2021-02-18T14:41:30Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-07T13:47:01Z day: '01' department: - _id: NiBa doi: 10.1093/genetics/iyaa025 external_id: isi: - '000637218100005' intvolume: ' 217' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/genetics/iyaa025 month: '02' oa: 1 oa_version: Published Version project: - _id: 2662AADE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02463 name: Sex chromosomes and species barriers publication: Genetics publication_identifier: issn: - 1943-2631 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: 'The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 217 year: '2021' ... --- _id: '9119' abstract: - lang: eng 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.' article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Iva full_name: Popovic, Iva last_name: Popovic - first_name: Clément full_name: Mazoyer, Clément last_name: Mazoyer - first_name: Bruno full_name: Spataro, Bruno last_name: Spataro - first_name: Stéphane full_name: Delmotte, Stéphane last_name: Delmotte - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Étienne full_name: Loire, Étienne last_name: Loire - first_name: Alexis full_name: Simon, Alexis last_name: Simon - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Laurent full_name: Duret, Laurent last_name: Duret - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne - first_name: Xavier full_name: Vekemans, Xavier last_name: Vekemans - first_name: Camille full_name: Roux, Camille last_name: Roux citation: 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' 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' 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.' ieee: 'C. Fraisse et al., “DILS: Demographic inferences with linked selection by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644, 2021.' 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.' 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.' 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. date_created: 2021-02-14T23:01:14Z date_published: 2021-01-15T00:00:00Z date_updated: 2023-08-07T13:45:18Z day: '15' department: - _id: NiBa doi: 10.1111/1755-0998.13323 external_id: isi: - '000614183100001' intvolume: ' 21' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2 month: '01' oa: 1 oa_version: Preprint page: 2629-2644 publication: Molecular Ecology Resources publication_identifier: eissn: - '17550998' issn: - 1755098X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'DILS: Demographic inferences with linked selection by using ABC' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2021' ... --- _id: '9375' 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. 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”).' article_number: e2015005118 article_processing_charge: No article_type: original author: - first_name: Joana I. full_name: Meier, Joana I. last_name: Meier - first_name: Patricio A. full_name: Salazar, Patricio A. last_name: Salazar - first_name: Marek full_name: Kučka, Marek last_name: Kučka - first_name: Robert William full_name: Davies, Robert William last_name: Davies - first_name: Andreea full_name: Dréau, Andreea last_name: Dréau - first_name: Ismael full_name: Aldás, Ismael last_name: Aldás - first_name: Olivia Box full_name: Power, Olivia Box last_name: Power - first_name: Nicola J. full_name: Nadeau, Nicola J. last_name: Nadeau - first_name: Jon R. full_name: Bridle, Jon R. last_name: Bridle - first_name: Campbell full_name: Rolian, Campbell last_name: Rolian - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: W. Owen full_name: McMillan, W. Owen last_name: McMillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins - first_name: Yingguang Frank full_name: Chan, Yingguang Frank last_name: Chan citation: 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 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. 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. 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). date_created: 2021-05-07T17:10:21Z date_published: 2021-06-21T00:00:00Z date_updated: 2023-08-08T13:33:09Z day: '21' ddc: - '570' department: - _id: NiBa doi: 10.1073/pnas.2015005118 external_id: isi: - '000671755600001' pmid: - '34155138' file: - access_level: open_access checksum: cb30c6166b2132ee60d616b31a1a7c29 content_type: application/pdf creator: dernst date_created: 2022-03-08T08:18:16Z date_updated: 2022-03-08T08:18:16Z file_id: '10835' file_name: 2021_PNAS_Meier.pdf file_size: 20592929 relation: main_file success: 1 file_date_updated: 2022-03-08T08:18:16Z has_accepted_license: '1' intvolume: ' 118' isi: 1 issue: '25' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: PNAS publication_identifier: eissn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '9394' 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.' 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. ' article_processing_charge: No article_type: original 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 full_name: Larsson, Jenny last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: 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 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. 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. date_created: 2021-05-16T22:01:47Z date_published: 2021-05-07T00:00:00Z date_updated: 2023-08-08T13:34:08Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1002/evl3.227 ec_funded: 1 external_id: isi: - '000647846200001' file: - access_level: open_access checksum: 023b1608e311f0fda30593ba3d0a4e0b content_type: application/pdf creator: cchlebak date_created: 2021-10-15T08:26:02Z date_updated: 2021-10-15T08:26:02Z file_id: '10142' file_name: 2021_EvolutionLetters_Koch.pdf file_size: 3021108 relation: main_file success: 1 file_date_updated: 2021-10-15T08:26:02Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 196-213 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Evolution Letters publication_identifier: eissn: - 2056-3744 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '12987' relation: research_data status: public scopus_import: '1' status: public title: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2021' ... --- _id: '9392' 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.' 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. article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet 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 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. ieee: S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021. 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. short: S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429. date_created: 2021-05-16T22:01:46Z date_published: 2021-05-10T00:00:00Z date_updated: 2023-08-08T13:34:38Z day: '10' department: - _id: NiBa doi: 10.1016/j.cub.2021.03.060 external_id: isi: - '000654741200004' pmid: - '33974865' intvolume: ' 31' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2021.03.060 month: '05' oa: 1 oa_version: Published Version page: R428-R429 pmid: 1 publication: Current Biology publication_identifier: eissn: - '18790445' issn: - '09609822' publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Quantifying the use of species concepts type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 31 year: '2021' ... --- _id: '12987' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Eva full_name: Koch, Eva last_name: Koch - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Jenny full_name: Larsson, Jenny last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin 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' 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.' ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.' 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.' 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.' 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). date_created: 2023-05-16T12:34:09Z date_published: 2021-04-10T00:00:00Z date_updated: 2023-08-08T13:34:07Z day: '10' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.ZGMSBCCB4 has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.zgmsbccb4 month: '04' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9394' relation: used_in_publication status: public status: public title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis' 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 user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9410' 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. 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. article_number: '20200913' article_processing_charge: No author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Paul full_name: Neve, Paul last_name: Neve citation: 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 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. 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. ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913. 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. short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021). date_created: 2021-05-23T22:01:43Z date_published: 2021-05-12T00:00:00Z date_updated: 2023-08-08T13:44:35Z day: '12' ddc: - '570' department: - _id: NiBa doi: 10.1098/rsbl.2020.0913 ec_funded: 1 external_id: isi: - '000651501400001' pmid: - ' 33975485' file: - access_level: open_access checksum: 9c13c1f5af7609c97c741f11d293188a content_type: application/pdf creator: kschuh date_created: 2021-05-25T14:09:03Z date_updated: 2021-05-25T14:09:03Z file_id: '9425' file_name: 2021_BiologyLetters_Lagator.pdf file_size: 726759 relation: main_file success: 1 file_date_updated: 2021-05-25T14:09:03Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Biology letters publication_identifier: eissn: - 1744957X publication_status: published publisher: Royal Society of London quality_controlled: '1' scopus_import: '1' status: public title: Adaptation at different points along antibiotic concentration gradients tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2021' ... --- _id: '9470' 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. 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). article_processing_charge: No author: - first_name: Emma L. full_name: Berdan, Emma L. last_name: Berdan - first_name: Alexandre full_name: Blanckaert, Alexandre last_name: Blanckaert - first_name: Tanja full_name: Slotte, Tanja last_name: Slotte - first_name: Alexander full_name: Suh, Alexander last_name: Suh - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Inês full_name: Fragata, Inês last_name: Fragata citation: 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' 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' 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.' 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.' 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.' 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.' short: E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723. date_created: 2021-06-06T22:01:31Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-08T13:59:18Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.15936 ec_funded: 1 external_id: isi: - '000652056400001' file: - access_level: open_access checksum: e6f4731365bde2614b333040a08265d8 content_type: application/pdf creator: kschuh date_created: 2021-06-11T15:34:53Z date_updated: 2021-06-11T15:34:53Z file_id: '9545' file_name: 2021_MolecularEcology_Berdan.pdf file_size: 1031978 relation: main_file success: 1 file_date_updated: 2021-06-11T15:34:53Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '06' oa: 1 oa_version: Published Version page: 2710-2723 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Molecular Ecology publication_identifier: eissn: - 1365294X issn: - '09621083' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Unboxing mutations: Connecting mutation types with evolutionary consequences' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 30 year: '2021' ... --- _id: '9816' abstract: - lang: eng text: "Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test." acknowledgement: We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used. article_number: e0255267 article_processing_charge: Yes article_type: original author: - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Mathias full_name: Beiglböck, Mathias last_name: Beiglböck - first_name: Anna Nele full_name: Herdina, Anna Nele last_name: Herdina - first_name: Robert full_name: Strassl, Robert last_name: Strassl - first_name: Martin full_name: Posch, Martin last_name: Posch citation: ama: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267 apa: Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267 chicago: Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267. ieee: M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021. ista: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267. mla: Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267. short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021). date_created: 2021-08-08T22:01:26Z date_published: 2021-07-29T00:00:00Z date_updated: 2023-08-10T14:26:32Z day: '29' ddc: - '610' department: - _id: NiBa doi: 10.1371/journal.pone.0255267 external_id: isi: - '000685248200095' pmid: - '34324553' file: - access_level: open_access checksum: ae4df60eb62f4491278588548d0c1f93 content_type: application/pdf creator: asandaue date_created: 2021-08-09T11:52:14Z date_updated: 2021-08-09T11:52:14Z file_id: '9835' file_name: 2021_PLoSONE_Hledík.pdf file_size: 773921 relation: main_file success: 1 file_date_updated: 2021-08-09T11:52:14Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS ONE publication_identifier: eissn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2021' ... --- _id: '9252' abstract: - lang: eng text: 'This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.' acknowledgement: We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Eniko full_name: Szep, Eniko id: 485BB5A4-F248-11E8-B48F-1D18A9856A87 last_name: Szep - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210' apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley. https://doi.org/10.1111/evo.14210' chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14210.' ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.' ista: 'Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.' mla: 'Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:10.1111/evo.14210.' short: E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045. date_created: 2021-03-20T08:22:10Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-09-05T15:44:06Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.14210 external_id: isi: - '000636966300001' file: - access_level: open_access checksum: b90fb5767d623602046fed03725e16ca content_type: application/pdf creator: kschuh date_created: 2021-08-11T13:39:19Z date_updated: 2021-08-11T13:39:19Z file_id: '9886' file_name: 2021_Evolution_Szep.pdf file_size: 734102 relation: main_file success: 1 file_date_updated: 2021-08-11T13:39:19Z has_accepted_license: '1' intvolume: ' 75' isi: 1 issue: '5' keyword: - Genetics - Ecology - Evolution - Behavior and Systematics - General Agricultural and Biological Sciences language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1030-1045 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13062' relation: research_data status: public scopus_import: '1' status: public title: 'Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 75 year: '2021' ... --- _id: '9374' abstract: - lang: eng text: If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since. acknowledgement: RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290). article_processing_charge: No article_type: original author: - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Maria R. full_name: Servedio, Maria R. last_name: Servedio - first_name: Carole M. full_name: Smadja, Carole M. last_name: Smadja - first_name: Claudia full_name: Bank, Claudia last_name: Bank - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Samuel M. full_name: Flaxman, Samuel M. last_name: Flaxman - first_name: Tatiana full_name: Giraud, Tatiana last_name: Giraud - first_name: Robin full_name: Hopkins, Robin last_name: Hopkins - first_name: Erica L. full_name: Larson, Erica L. last_name: Larson - first_name: Martine E. full_name: Maan, Martine E. last_name: Maan - first_name: Joana full_name: Meier, Joana last_name: Meier - first_name: Richard full_name: Merrill, Richard last_name: Merrill - first_name: Mohamed A. F. full_name: Noor, Mohamed A. F. last_name: Noor - first_name: Daniel full_name: Ortiz‐Barrientos, Daniel last_name: Ortiz‐Barrientos - first_name: Anna full_name: Qvarnström, Anna last_name: Qvarnström citation: ama: Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235 apa: Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235 chicago: Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235. ieee: R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021. ista: Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988. mla: Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235. short: R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988. date_created: 2021-05-06T04:34:47Z date_published: 2021-04-19T00:00:00Z date_updated: 2023-09-05T15:44:33Z day: '19' department: - _id: NiBa doi: 10.1111/evo.14235 external_id: isi: - '000647224000001' intvolume: ' 75' isi: 1 issue: '5' keyword: - Genetics - Ecology - Evolution - Behavior and Systematics - General Agricultural and Biological Sciences language: - iso: eng main_file_link: - open_access: '1' url: https://onlinelibrary.wiley.com/doi/10.1111/evo.14235 month: '04' oa: 1 oa_version: Published Version page: 978-988 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Homage to Felsenstein 1981, or why are there so few/many species? tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 75 year: '2021' ... --- _id: '13062' abstract: - lang: eng text: 'This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.' article_processing_charge: No author: - first_name: Eniko full_name: Szep, Eniko id: 485BB5A4-F248-11E8-B48F-1D18A9856A87 last_name: Szep - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1' apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1' chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.' ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.' ista: 'Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.' mla: 'Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.' short: E. Szep, H. Sachdeva, N.H. Barton, (2021). date_created: 2023-05-23T16:17:02Z date_published: 2021-03-02T00:00:00Z date_updated: 2023-09-05T15:44:05Z day: '02' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.8GTHT76P1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.8gtht76p1 month: '03' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9252' relation: used_in_publication status: public status: public title: 'Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model' 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 user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9383' abstract: - lang: eng text: A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us. acknowledgement: We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft. article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet citation: ama: Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215 apa: Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215 chicago: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215. ieee: S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021. ista: Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273. mla: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215. short: S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273. date_created: 2021-05-09T22:01:39Z date_published: 2021-03-22T00:00:00Z date_updated: 2023-10-18T08:16:01Z day: '22' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.14215 external_id: isi: - '000647226400001' file: - access_level: open_access checksum: 96f6ccf15d95a4e9f7c0b27eee570fa6 content_type: application/pdf creator: kschuh date_created: 2022-03-25T12:02:04Z date_updated: 2022-03-25T12:02:04Z file_id: '10921' file_name: 2021_Evolution_Stankowski.pdf file_size: 719991 relation: main_file success: 1 file_date_updated: 2022-03-25T12:02:04Z has_accepted_license: '1' intvolume: ' 75' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1256-1273 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Defining the speciation continuum tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 75 year: '2021' ... --- _id: '14984' abstract: - lang: eng text: Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them. article_processing_charge: No author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 citation: ama: 'Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355' apa: Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355 chicago: Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355. ieee: S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021. ista: 'Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.' mla: Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355. short: S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021. date_created: 2024-02-14T12:05:50Z date_published: 2021-05-28T00:00:00Z date_updated: 2024-02-19T09:54:18Z day: '28' department: - _id: NiBa doi: 10.1002/9780470015902.a0029355 intvolume: ' 2' language: - iso: eng month: '05' oa_version: None publication: Encyclopedia of Life Sciences publication_identifier: eisbn: - '9780470015902' isbn: - '9780470016176' publication_status: published publisher: Wiley quality_controlled: '1' series_title: eLS status: public title: Hybrid Zones type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2021' ... --- _id: '9192' abstract: - lang: eng text: Here are the research data underlying the publication " Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus)." Further information are summed up in the README document. article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: 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. 2021. doi:10.15479/AT:ISTA:9192 apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2021). 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:9192 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, 2021. https://doi.org/10.15479/AT:ISTA:9192. 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, 2021. ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. 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:9192. 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, 2021, doi:10.15479/AT:ISTA:9192. short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021). contributor: - contributor_type: project_member first_name: Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - contributor_type: project_member first_name: Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon - contributor_type: project_member first_name: Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett - contributor_type: project_member first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - contributor_type: project_member first_name: Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - contributor_type: project_leader first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 date_created: 2021-02-24T17:49:21Z date_published: 2021-02-26T00:00:00Z date_updated: 2024-02-21T12:41:09Z day: '26' ddc: - '576' department: - _id: GradSch - _id: NiBa doi: 10.15479/AT:ISTA:9192 file: - access_level: open_access checksum: f85537815809a8a4b7da9d01163f88c0 content_type: application/x-zip-compressed creator: larathoo date_created: 2021-02-24T17:45:13Z date_updated: 2021-02-24T17:45:13Z file_id: '9193' file_name: Data_Code.zip file_size: 5934452 relation: main_file success: 1 file_date_updated: 2021-02-24T17:45:13Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: used_in_publication status: public - id: '11321' relation: later_version status: public - id: '8254' relation: earlier_version status: public status: public title: Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '7651' abstract: - lang: eng text: The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods. article_number: '20190721' article_processing_charge: No article_type: original author: - first_name: J. full_name: Larsson, J. last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: S. full_name: Bengmark, S. last_name: Bengmark - first_name: T. full_name: Lundh, T. last_name: Lundh - first_name: R. K. full_name: Butlin, R. K. last_name: Butlin citation: ama: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 2020;17(163). doi:10.1098/rsif.2019.0721 apa: Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0721 chicago: Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721. ieee: J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” Journal of The Royal Society Interface, vol. 17, no. 163. The Royal Society, 2020. ista: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 17(163), 20190721. mla: Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface, vol. 17, no. 163, 20190721, The Royal Society, 2020, doi:10.1098/rsif.2019.0721. short: J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of The Royal Society Interface 17 (2020). date_created: 2020-04-08T15:19:17Z date_published: 2020-02-01T00:00:00Z date_updated: 2021-01-12T08:14:41Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1098/rsif.2019.0721 file: - access_level: open_access checksum: 4eb102304402f5c56432516b84df86d6 content_type: application/pdf creator: dernst date_created: 2020-04-14T12:31:16Z date_updated: 2020-07-14T12:48:01Z file_id: '7660' file_name: 2020_JournRoyalSociety_Larsson.pdf file_size: 1556190 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 17' issue: '163' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Journal of The Royal Society Interface publication_identifier: eissn: - 1742-5662 issn: - 1742-5689 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: 1 status: public title: A developmentally descriptive method for quantifying shape in gastropod shells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2020' ... --- _id: '9123' abstract: - lang: eng text: 'Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution.' article_processing_charge: No author: - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Roger full_name: Butlin, Roger last_name: Butlin - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson citation: ama: 'Westram AM, Faria R, Butlin R, Johannesson K. Inversions and Evolution. In: ELS. Wiley; 2020. doi:10.1002/9780470015902.a0029007' apa: Westram, A. M., Faria, R., Butlin, R., & Johannesson, K. (2020). Inversions and Evolution. In eLS. Wiley. https://doi.org/10.1002/9780470015902.a0029007 chicago: Westram, Anja M, Rui Faria, Roger Butlin, and Kerstin Johannesson. “Inversions and Evolution.” In ELS. Wiley, 2020. https://doi.org/10.1002/9780470015902.a0029007. ieee: A. M. Westram, R. Faria, R. Butlin, and K. Johannesson, “Inversions and Evolution,” in eLS, Wiley, 2020. ista: 'Westram AM, Faria R, Butlin R, Johannesson K. 2020.Inversions and Evolution. In: eLS. .' mla: Westram, Anja M., et al. “Inversions and Evolution.” ELS, Wiley, 2020, doi:10.1002/9780470015902.a0029007. short: A.M. Westram, R. Faria, R. Butlin, K. Johannesson, in:, ELS, Wiley, 2020. date_created: 2021-02-15T12:39:04Z date_published: 2020-05-16T00:00:00Z date_updated: 2021-02-15T13:18:16Z day: '16' department: - _id: NiBa doi: 10.1002/9780470015902.a0029007 language: - iso: eng month: '05' oa_version: None publication: eLS publication_identifier: isbn: - '9780470016176' - '9780470015902' publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Inversions and Evolution type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '13073' 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. article_processing_charge: No author: - first_name: Alexis full_name: Simon, Alexis last_name: Simon - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Tahani full_name: El Ayari, Tahani last_name: El Ayari - first_name: Cathy full_name: Liautard-Haag, Cathy last_name: Liautard-Haag - first_name: Petr full_name: Strelkov, Petr last_name: Strelkov - first_name: John full_name: Welch, John last_name: Welch - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: 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. 2020. doi:10.5061/DRYAD.R4XGXD29N apa: Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N chicago: Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N. ieee: A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020. ista: Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N. mla: Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N. short: A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020). date_created: 2023-05-23T16:48:27Z date_published: 2020-09-22T00:00:00Z date_updated: 2023-08-04T11:04:11Z day: '22' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.R4XGXD29N main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.r4xgxd29n month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '8708' relation: used_in_publication status: public status: public title: How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels 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 user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ...