[{"_id":"11479","date_updated":"2023-08-01T12:25:44Z","type":"journal_article","article_processing_charge":"No","doi":"10.1111/eva.13428","publisher":"Wiley","quality_controlled":"1","page":"542-559","ddc":["576"],"isi":1,"year":"2023","external_id":{"isi":["000815663700001"]},"date_published":"2023-02-01T00:00:00Z","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","publication":"Evolutionary Applications","status":"public","volume":16,"date_created":"2022-07-03T22:01:33Z","article_type":"original","day":"01","scopus_import":"1","author":[{"first_name":"Aurélien","full_name":"De Jode, Aurélien","last_name":"De Jode"},{"last_name":"Le Moan","full_name":"Le Moan, Alan","first_name":"Alan"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle"}],"oa_version":"Published Version","title":"Ten years of demographic modelling of divergence and speciation in the sea","file_date_updated":"2023-02-27T07:10:17Z","publication_identifier":{"eissn":["1752-4571"]},"publication_status":"published","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"intvolume":" 16","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"file":[{"file_id":"12685","file_size":2269822,"date_created":"2023-02-27T07:10:17Z","creator":"dernst","date_updated":"2023-02-27T07:10:17Z","relation":"main_file","checksum":"d4d6fa9ddf36643af994a6a757919afb","success":1,"file_name":"2023_EvolutionaryApplications_DeJode.pdf","access_level":"open_access","content_type":"application/pdf"}],"month":"02","citation":{"ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428."},"issue":"2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., & Faria, R. (2023). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. Wiley. https://doi.org/10.1111/mec.17160","mla":"Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology, Wiley, 2023, doi:10.1111/mec.17160.","ista":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2023. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology.","chicago":"Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.17160.","ieee":"J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana),” Molecular Ecology. Wiley, 2023.","short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology (2023).","ama":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 2023. doi:10.1111/mec.17160"},"month":"10","department":[{"_id":"NiBa"}],"abstract":[{"text":"Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.","lang":"eng"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"publication_status":"epub_ahead","oa_version":"Published Version","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","scopus_import":"1","day":"16","author":[{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"last_name":"Koch","full_name":"Koch, Eva L.","first_name":"Eva L."},{"first_name":"Sean","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"}],"date_created":"2023-10-29T23:01:17Z","article_type":"original","publication":"Molecular Ecology","status":"public","acknowledgement":"We would like to thank members of the Littorina team for their advice and feedback during this project. In particular, we thank Alan Le Moan, who inspired us to look at heterozygosity differences to identify inversions, and Katherine Hearn for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation and sequencing. Sample collections, sequencing and data preparation were supported by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for Science and Technology (Fundación para a Ciência e Tecnologia) through a research project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND).","date_published":"2023-10-16T00:00:00Z","pmid":1,"external_id":{"isi":["001085119000001"],"pmid":["37843465"]},"isi":1,"year":"2023","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1111/mec.17160","open_access":"1"}],"publisher":"Wiley","article_processing_charge":"Yes (in subscription journal)","doi":"10.1111/mec.17160","type":"journal_article","_id":"14463","date_updated":"2023-12-13T13:05:27Z"},{"pmid":1,"date_published":"2023-04-01T00:00:00Z","acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","publication":"Molecular Ecology","status":"public","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"year":"2023","isi":1,"external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.01.28.478139"}],"quality_controlled":"1","page":"2041-2054","date_updated":"2024-01-16T10:10:00Z","_id":"14787","type":"journal_article","doi":"10.1111/mec.16849","article_processing_charge":"No","publisher":"Wiley","issue":"8","citation":{"ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.","chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16849.","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.","apa":"Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16849"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"month":"04","publication_status":"published","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"intvolume":" 32","abstract":[{"lang":"eng","text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system."}],"volume":32,"article_type":"original","date_created":"2024-01-10T10:44:45Z","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"first_name":"Madeline A.","full_name":"Chase, Madeline A.","last_name":"Chase"},{"first_name":"Hanna","last_name":"McIntosh","full_name":"McIntosh, Hanna"},{"full_name":"Streisfeld, Matthew A.","last_name":"Streisfeld","first_name":"Matthew A."}],"day":"01","title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","oa_version":"Preprint"},{"department":[{"_id":"NiBa"}],"year":"2023","month":"09","related_material":{"record":[{"id":"14796","relation":"used_in_publication","status":"for_moderation"}]},"citation":{"short":"S. Stankowski, (2023).","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","ama":"Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995","mla":"Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.","apa":"Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995","chicago":"Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.","ista":"Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-09-05T00:00:00Z","oa":1,"status":"public","_id":"14812","date_updated":"2025-08-12T09:04:30Z","date_created":"2024-01-16T10:23:01Z","type":"research_data_reference","article_processing_charge":"No","day":"05","contributor":[{"first_name":"Zusanna","last_name":"Zagrodzka"},{"last_name":"Garlovsky","first_name":"Martin"},{"last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","orcid":"0000-0002-4530-8469"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","first_name":"Daria","orcid":"0000-0002-1145-9226"},{"first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo"},{"id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","last_name":"Lifchitz","first_name":"Hila"},{"first_name":"Alan","last_name":"Le Moan"},{"first_name":"Erica","last_name":"Leder"},{"last_name":"Reeve","first_name":"James"},{"first_name":"Kerstin","last_name":"Johannesson"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"last_name":"Butlin","first_name":"Roger"}],"doi":"10.5281/ZENODO.8318995","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"}],"oa_version":"Published Version","publisher":"Zenodo","title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8318995"}],"has_accepted_license":"1","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode"}]},{"year":"2023","publication":"Evolutionary Journal of the Linnean Society","status":"public","acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","date_published":"2023-08-17T00:00:00Z","publisher":"Oxford University Press","article_processing_charge":"Yes (via OA deal)","doi":"10.1093/evolinnean/kzad002","type":"journal_article","_id":"14833","date_updated":"2024-01-23T08:13:43Z","ddc":["570"],"quality_controlled":"1","month":"08","article_number":"kzad002","file":[{"date_created":"2024-01-23T08:10:00Z","file_size":3408944,"date_updated":"2024-01-23T08:10:00Z","creator":"dernst","file_id":"14875","success":1,"file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"ba6f9102d3a9fe6631c4fa398c5e4313"}],"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2023;2(1). doi:10.1093/evolinnean/kzad002","ieee":"S. Stankowski et al., “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society, vol. 2, no. 1. Oxford University Press, 2023.","short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023).","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002.","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002","mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002."},"issue":"1","title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","oa_version":"Published Version","day":"17","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Zagrodzka, Zuzanna B","last_name":"Zagrodzka","first_name":"Zuzanna B"},{"first_name":"Juan","full_name":"Galindo, Juan","last_name":"Galindo"},{"first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio","last_name":"Montaño-Rendón"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Natalia","last_name":"Mikhailova","full_name":"Mikhailova, Natalia"},{"first_name":"April M H","full_name":"Blakeslee, April M H","last_name":"Blakeslee"},{"full_name":"Arnason, Einar","last_name":"Arnason","first_name":"Einar"},{"last_name":"Broquet","full_name":"Broquet, Thomas","first_name":"Thomas"},{"first_name":"Hernán E","full_name":"Morales, Hernán E","last_name":"Morales"},{"first_name":"John W","full_name":"Grahame, John W","last_name":"Grahame"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger K","first_name":"Roger K"}],"date_created":"2024-01-18T07:54:10Z","article_type":"original","volume":2,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"intvolume":" 2","abstract":[{"text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2024-01-23T08:10:00Z","publication_identifier":{"eissn":["2752-938X"]},"publication_status":"published"},{"doi":"10.1111/mec.16793","article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","date_updated":"2023-08-16T08:18:47Z","_id":"12159","type":"journal_article","page":"1441-1457","ddc":["570"],"quality_controlled":"1","isi":1,"year":"2023","external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"project":[{"grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"status":"public","publication":"Molecular Ecology","pmid":1,"acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","date_published":"2023-03-01T00:00:00Z","author":[{"full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","orcid":"0000-0002-1145-9226","first_name":"Daria"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka","last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","day":"01","oa_version":"Published Version","title":"On the origin and structure of haplotype blocks","volume":32,"article_type":"original","date_created":"2023-01-12T12:09:17Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 32","abstract":[{"text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.","lang":"eng"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"publication_status":"published","file_date_updated":"2023-08-16T08:15:41Z","month":"03","department":[{"_id":"NiBa"}],"file":[{"file_id":"14062","file_size":7144607,"date_created":"2023-08-16T08:15:41Z","date_updated":"2023-08-16T08:15:41Z","creator":"dernst","relation":"main_file","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_name":"2023_MolecularEcology_Shipilina.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"oa":1,"language":[{"iso":"eng"}],"issue":"6","citation":{"ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"pmid":1,"acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","date_published":"2023-01-01T00:00:00Z","publication":"Evolution: International journal of organic evolution","status":"public","isi":1,"year":"2023","external_id":{"pmid":["36622661"],"isi":["001021686300024"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evolut/qpac004"}],"quality_controlled":"1","page":"318-328","_id":"12514","date_updated":"2023-08-01T12:58:30Z","type":"journal_article","article_processing_charge":"No","doi":"10.1093/evolut/qpac004","publisher":"Oxford University Press","citation":{"ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004.","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023."},"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"month":"01","publication_identifier":{"eissn":["1558-5646"]},"publication_status":"published","abstract":[{"lang":"eng","text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model."}],"intvolume":" 77","volume":77,"date_created":"2023-02-05T23:00:59Z","article_type":"original","day":"01","scopus_import":"1","author":[{"last_name":"Bolnick","full_name":"Bolnick, Daniel I.","first_name":"Daniel I."},{"first_name":"Amanda K.","last_name":"Hund","full_name":"Hund, Amanda K."},{"last_name":"Nosil","full_name":"Nosil, Patrik","first_name":"Patrik"},{"last_name":"Peng","full_name":"Peng, Foen","first_name":"Foen"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"first_name":"Swapna","last_name":"Subramanian","full_name":"Subramanian, Swapna"},{"full_name":"Wolf, Jochen B.W.","last_name":"Wolf","first_name":"Jochen B.W."},{"first_name":"Roman","full_name":"Yukilevich, Roman","last_name":"Yukilevich"}],"oa_version":"Published Version","title":"A multivariate view of the speciation continuum"},{"ddc":["570"],"page":"358-374","quality_controlled":"1","publisher":"Oxford Academic","doi":"10.1002/evl3.295","article_processing_charge":"Yes","type":"journal_article","date_updated":"2023-08-03T13:18:17Z","_id":"12001","publication":"Evolution Letters","status":"public","date_published":"2022-10-01T00:00:00Z","acknowledgement":"We thank A. Wright and four anonymous reviewers for valuable comments on an earlier draft of this manuscript and all members of the Littorina group for helpful discussions. This work was supported by a European Research Council grant to RKB and by a Natural Environment Research Council studentship to KEH through the ACCE doctoral training program. KJ acknowledges support from the Swedish Science Research Council VR (Vetenskaprådet) (2017-03798). RF was supported by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao Emprego Científico) contract (2020.00275.CEECIND).","external_id":{"isi":["000839621100001"]},"isi":1,"year":"2022","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex-determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex-determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex-determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment-dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well-studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female-heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion-sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex-determining region between ecotypes. Such sex chromosome-environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex-specific selection and divergent natural selection is required to explain these highly unusual patterns.","lang":"eng"}],"intvolume":" 6","has_accepted_license":"1","publication_identifier":{"eissn":["2056-3744"]},"publication_status":"published","file_date_updated":"2023-02-27T07:17:42Z","title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis","oa_version":"Published Version","author":[{"first_name":"Katherine E.","last_name":"Hearn","full_name":"Hearn, Katherine E."},{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M"}],"day":"01","scopus_import":"1","article_type":"original","date_created":"2022-08-28T22:02:02Z","volume":6,"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"5","citation":{"short":"K.E. Hearn, E.L. Koch, S. Stankowski, R.K. Butlin, R. Faria, K. Johannesson, A.M. Westram, Evolution Letters 6 (2022) 358–374.","ieee":"K. E. Hearn et al., “Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis,” Evolution Letters, vol. 6, no. 5. Oxford Academic, pp. 358–374, 2022.","ama":"Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 2022;6(5):358-374. doi:10.1002/evl3.295","mla":"Hearn, Katherine E., et al. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters, vol. 6, no. 5, Oxford Academic, 2022, pp. 358–74, doi:10.1002/evl3.295.","apa":"Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson, K., & Westram, A. M. (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. Oxford Academic. https://doi.org/10.1002/evl3.295","ista":"Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. 2022. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 6(5), 358–374.","chicago":"Hearn, Katherine E., Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui Faria, Kerstin Johannesson, and Anja M Westram. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters. Oxford Academic, 2022. https://doi.org/10.1002/evl3.295."},"month":"10","file":[{"file_id":"12686","date_created":"2023-02-27T07:17:42Z","file_size":2368965,"date_updated":"2023-02-27T07:17:42Z","creator":"dernst","relation":"main_file","checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","file_name":"2022_EvolutionLetters_Hearn.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"department":[{"_id":"NiBa"}]},{"ddc":["570"],"page":"2784-2785","quality_controlled":"1","publisher":"Wiley","doi":"10.1111/evo.14632","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2023-08-04T09:35:48Z","_id":"12234","status":"public","publication":"Evolution","date_published":"2022-11-01T00:00:00Z","external_id":{"isi":["000855751600001"]},"isi":1,"year":"2022","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","text":"Hybrid speciation—the origin of new species resulting from the hybridization of genetically divergent lineages—was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego found genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a broader range of host plants than either of its putative parents."}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":" 76","has_accepted_license":"1","publication_status":"published","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"file_date_updated":"2023-01-27T11:28:38Z","title":"Digest: On the origin of a possible hybrid species","oa_version":"Published Version","author":[{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"day":"01","scopus_import":"1","article_type":"original","date_created":"2023-01-16T09:50:48Z","volume":76,"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"11","citation":{"chicago":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.","ista":"Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution. 76(11), 2784–2785.","mla":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution, vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632.","apa":"Stankowski, S. (2022). Digest: On the origin of a possible hybrid species. Evolution. Wiley. https://doi.org/10.1111/evo.14632","ama":"Stankowski S. Digest: On the origin of a possible hybrid species. Evolution. 2022;76(11):2784-2785. doi:10.1111/evo.14632","short":"S. Stankowski, Evolution 76 (2022) 2784–2785.","ieee":"S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution, vol. 76, no. 11. Wiley, pp. 2784–2785, 2022."},"month":"11","file":[{"creator":"dernst","date_updated":"2023-01-27T11:28:38Z","date_created":"2023-01-27T11:28:38Z","file_size":287282,"file_id":"12425","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_Evolution_Stankowski.pdf","checksum":"4c0f05083b414ac0323a1b9ee1abc275","relation":"main_file"}],"department":[{"_id":"NiBa"}]},{"article_type":"review","date_created":"2023-01-16T09:59:24Z","volume":35,"oa_version":"Published Version","title":"What is reproductive isolation?","author":[{"orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"scopus_import":"1","day":"01","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"publication_status":"published","file_date_updated":"2023-01-30T10:05:31Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 35","abstract":[{"lang":"eng","text":"Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches."}],"has_accepted_license":"1","file":[{"checksum":"f08de57112330a7ee88d2e1b20576a1e","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2022_JourEvoBiology_Westram.pdf","success":1,"file_id":"12448","date_updated":"2023-01-30T10:05:31Z","creator":"dernst","file_size":3146793,"date_created":"2023-01-30T10:05:31Z"}],"department":[{"_id":"NiBa"}],"month":"09","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","citation":{"ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1143–1164, 2022.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1143–1164.","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation? Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). What is reproductive isolation? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14005","mla":"Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14005."},"language":[{"iso":"eng"}],"oa":1,"type":"journal_article","date_updated":"2023-08-04T09:53:40Z","_id":"12264","publisher":"Wiley","doi":"10.1111/jeb.14005","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","ddc":["570"],"page":"1143-1164","keyword":["Ecology","Evolution","Behavior and Systematics"],"external_id":{"isi":["000849851100002"],"pmid":["36063156"]},"related_material":{"record":[{"relation":"other","status":"public","id":"12265"}]},"isi":1,"year":"2022","date_published":"2022-09-01T00:00:00Z","acknowledgement":"We are grateful to the participants of the ESEB satellite symposium ‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments on this manuscript. We are also very grateful to Roger Butlin and the Barton Group for the continued conversa-tions about RI. In addition, we thank all participants of the speciation survey. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166)","pmid":1,"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"publication":"Journal of Evolutionary Biology","status":"public"},{"article_processing_charge":"Yes (via OA deal)","doi":"10.1111/jeb.14082","publisher":"Wiley","_id":"12265","date_updated":"2023-08-04T09:53:41Z","type":"journal_article","page":"1200-1205","ddc":["570"],"quality_controlled":"1","isi":1,"year":"2022","related_material":{"record":[{"id":"12264","relation":"other","status":"public"}]},"external_id":{"isi":["000849851100009"]},"keyword":["Ecology","Evolution","Behavior and Systematics"],"publication":"Journal of Evolutionary Biology","status":"public","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166"}],"date_published":"2022-09-01T00:00:00Z","acknowledgement":"We are very grateful to the authors of the commentaries for the interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166).","day":"01","scopus_import":"1","author":[{"first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"first_name":"Parvathy","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","oa_version":"Published Version","volume":35,"date_created":"2023-01-16T09:59:37Z","article_type":"letter_note","has_accepted_license":"1","intvolume":" 35","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-01-30T10:14:09Z","publication_status":"published","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"month":"09","department":[{"_id":"NiBa"}],"file":[{"file_id":"12449","date_updated":"2023-01-30T10:14:09Z","creator":"dernst","date_created":"2023-01-30T10:14:09Z","file_size":349603,"checksum":"27268009e5eec030bc10667a4ac5ed4c","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_JourEvoBiology_Westram_Response.pdf"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.","mla":"Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:10.1111/jeb.14082.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14082","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205. doi:10.1111/jeb.14082","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205.","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022."},"issue":"9","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication_status":"published","intvolume":" 75","abstract":[{"lang":"eng","text":"Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change."}],"volume":75,"date_created":"2020-11-08T23:01:26Z","article_type":"original","day":"01","scopus_import":"1","author":[{"full_name":"Salces-Castellano, Antonia","last_name":"Salces-Castellano","first_name":"Antonia"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"first_name":"Paula","last_name":"Arribas","full_name":"Arribas, Paula"},{"first_name":"Jairo","full_name":"Patino, Jairo","last_name":"Patino"},{"last_name":"Karger","full_name":"Karger, Dirk N. ","first_name":"Dirk N. "},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"full_name":"Emerson, Brent C.","last_name":"Emerson","first_name":"Brent C."}],"title":"Long-term cloud forest response to climate warming revealed by insect speciation history","oa_version":"Submitted Version","citation":{"ieee":"A. Salces-Castellano et al., “Long-term cloud forest response to climate warming revealed by insect speciation history,” Evolution, vol. 75, no. 2. Wiley, pp. 231–244, 2021.","short":"A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger, R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244.","ama":"Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 2021;75(2):231-244. doi:10.1111/evo.14111","apa":"Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D. N., Butlin, R., & Emerson, B. C. (2021). Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. Wiley. https://doi.org/10.1111/evo.14111","mla":"Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution, vol. 75, no. 2, Wiley, 2021, pp. 231–44, doi:10.1111/evo.14111.","chicago":"Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino, Dirk N. Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14111.","ista":"Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 75(2), 231–244."},"issue":"2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"month":"02","main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/10261/223937"}],"quality_controlled":"1","page":"231-244","_id":"8743","date_updated":"2023-08-04T11:09:49Z","type":"journal_article","article_processing_charge":"No","doi":"10.1111/evo.14111","publisher":"Wiley","pmid":1,"date_published":"2021-02-01T00:00:00Z","acknowledgement":"This work was financed by the Spanish Agencia Estatal de Investigación (CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P), awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the Cabildo of Tenerife. The authors wish to thank the following for field work and sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar. We also thank V. García‐Olivares for assistance with laboratory and bioinformatic work.","status":"public","publication":"Evolution","year":"2021","isi":1,"related_material":{"link":[{"url":"https://doi.org/10.1111/evo.14225","relation":"erratum"}]},"external_id":{"isi":["000583190600001"],"pmid":["33078844"]}},{"day":"28","article_processing_charge":"No","doi":"10.1002/9780470015902.a0029355","author":[{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"last_name":"Shipilina","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","orcid":"0000-0002-1145-9226"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Wiley","oa_version":"None","title":"Hybrid Zones","_id":"14984","volume":2,"date_updated":"2024-02-19T09:54:18Z","series_title":"eLS","date_created":"2024-02-14T12:05:50Z","type":"book_chapter","abstract":[{"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.","lang":"eng"}],"intvolume":" 2","publication_identifier":{"eisbn":["9780470015902"],"isbn":["9780470016176"]},"publication_status":"published","quality_controlled":"1","year":"2021","month":"05","department":[{"_id":"NiBa"}],"publication":"Encyclopedia of Life Sciences","language":[{"iso":"eng"}],"status":"public","citation":{"short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021.","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021.","ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355","mla":"Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, 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.","ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-05-28T00:00:00Z"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","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","short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15.","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.","chicago":"Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13756.","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.","mla":"Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:10.1111/jeb.13756.","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"},"month":"01","file":[{"relation":"main_file","checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","success":1,"file_name":"2021_JourEvolBiology_Faria.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"9108","date_created":"2021-02-09T09:04:02Z","file_size":561340,"date_updated":"2021-02-09T09:04:02Z","creator":"dernst"}],"department":[{"_id":"NiBa"}],"intvolume":" 34","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"file_date_updated":"2021-02-09T09:04:02Z","title":"Speciation in marine environments: Diving under the surface","oa_version":"Published Version","author":[{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"}],"day":"18","scopus_import":"1","article_type":"original","date_created":"2021-02-07T23:01:13Z","volume":34,"status":"public","publication":"Journal of Evolutionary Biology","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.","date_published":"2021-01-18T00:00:00Z","external_id":{"isi":["000608367500001"]},"year":"2021","isi":1,"ddc":["570"],"page":"4-15","quality_controlled":"1","publisher":"Wiley","doi":"10.1111/jeb.13756","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-07T13:42:08Z","_id":"9100"},{"month":"03","file":[{"file_size":719991,"date_created":"2022-03-25T12:02:04Z","date_updated":"2022-03-25T12:02:04Z","creator":"kschuh","file_id":"10921","success":1,"file_name":"2021_Evolution_Stankowski.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6"}],"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","citation":{"ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","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","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.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273."},"title":"Defining the speciation continuum","oa_version":"Published Version","author":[{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"scopus_import":"1","day":"22","article_type":"original","date_created":"2021-05-09T22:01:39Z","volume":75,"abstract":[{"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.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"intvolume":" 75","has_accepted_license":"1","publication_status":"published","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"file_date_updated":"2022-03-25T12:02:04Z","external_id":{"isi":["000647226400001"]},"year":"2021","isi":1,"publication":"Evolution","status":"public","date_published":"2021-03-22T00:00:00Z","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.","publisher":"Oxford University Press","doi":"10.1111/evo.14215","article_processing_charge":"No","type":"journal_article","date_updated":"2023-10-18T08:16:01Z","_id":"9383","ddc":["570"],"page":"1256-1273","quality_controlled":"1"},{"oa":1,"language":[{"iso":"eng"}],"issue":"9","citation":{"short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","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","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060.","apa":"Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"05","department":[{"_id":"NiBa"}],"intvolume":" 31","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."}],"publication_status":"published","publication_identifier":{"issn":["09609822"],"eissn":["18790445"]},"author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"}],"day":"10","scopus_import":"1","oa_version":"Published Version","title":"Quantifying the use of species concepts","volume":31,"article_type":"original","date_created":"2021-05-16T22:01:46Z","status":"public","publication":"Current Biology","pmid":1,"date_published":"2021-05-10T00:00:00Z","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.","isi":1,"year":"2021","external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"page":"R428-R429","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"quality_controlled":"1","doi":"10.1016/j.cub.2021.03.060","article_processing_charge":"No","publisher":"Cell Press","date_updated":"2023-08-08T13:34:38Z","_id":"9392","type":"journal_article"},{"volume":375,"date_created":"2020-07-26T22:01:01Z","article_type":"original","scopus_import":"1","day":"12","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka"},{"full_name":"Eyres, Isobel","last_name":"Eyres","first_name":"Isobel"},{"first_name":"Thomas","full_name":"Broquet, Thomas","last_name":"Broquet"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"title":"The evolution of strong reproductive isolation between sympatric intertidal snails","oa_version":"Published Version","publication_status":"published","publication_identifier":{"eissn":["1471-2970"]},"intvolume":" 375","abstract":[{"text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.","lang":"eng"}],"department":[{"_id":"NiBa"}],"article_number":"20190545","month":"07","citation":{"ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ieee":"S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545"},"issue":"1806","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"_id":"8167","date_updated":"2023-08-22T08:22:13Z","type":"journal_article","article_processing_charge":"No","doi":"10.1098/rstb.2019.0545","publisher":"The Royal Society","main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0545","open_access":"1"}],"quality_controlled":"1","year":"2020","isi":1,"external_id":{"isi":["000552662100014"],"pmid":["32654639"]},"pmid":1,"acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","date_published":"2020-07-12T00:00:00Z","status":"public","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences"}]