[{"day":"16","doi":"10.1111/mec.17160","abstract":[{"lang":"eng","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."}],"citation":{"apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., &#38; Faria, R. (2023). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.17160\">https://doi.org/10.1111/mec.17160</a>","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). <i>Molecular Ecology</i>. 2023. doi:<a href=\"https://doi.org/10.1111/mec.17160\">10.1111/mec.17160</a>","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),” <i>Molecular Ecology</i>. Wiley, 2023.","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).” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.17160\">https://doi.org/10.1111/mec.17160</a>.","short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology (2023).","mla":"Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” <i>Molecular Ecology</i>, Wiley, 2023, doi:<a href=\"https://doi.org/10.1111/mec.17160\">10.1111/mec.17160</a>.","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."},"year":"2023","date_updated":"2023-12-13T13:05:27Z","external_id":{"pmid":["37843465"],"isi":["001085119000001"]},"isi":1,"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).","department":[{"_id":"NiBa"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2023-10-29T23:01:17Z","publication_status":"epub_ahead","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","scopus_import":"1","_id":"14463","pmid":1,"author":[{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"}],"publisher":"Wiley","article_type":"original","quality_controlled":"1","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"oa":1,"type":"journal_article","date_published":"2023-10-16T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1111/mec.17160","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Published Version","month":"10","publication":"Molecular Ecology","language":[{"iso":"eng"}]},{"main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2023-04-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"oa":1,"language":[{"iso":"eng"}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"publication":"Molecular Ecology","oa_version":"Preprint","month":"04","volume":32,"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.","date_updated":"2024-01-16T10:10:00Z","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. <i>Molecular Ecology</i>. 2023;32(8):2041-2054. doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>","apa":"Stankowski, S., Chase, M. A., McIntosh, H., &#38; Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>","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,” <i>Molecular Ecology</i>, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","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.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>.","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","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."},"year":"2023","isi":1,"external_id":{"pmid":["36651268"],"isi":["000919244600001"]},"doi":"10.1111/mec.16849","day":"01","abstract":[{"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 of<jats:italic>Mimulus aurantiacus</jats:italic>. 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.","lang":"eng"}],"page":"2041-2054","quality_controlled":"1","publisher":"Wiley","article_type":"original","pmid":1,"_id":"14787","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski"},{"last_name":"Chase","first_name":"Madeline A.","full_name":"Chase, Madeline A."},{"full_name":"McIntosh, Hanna","first_name":"Hanna","last_name":"McIntosh"},{"full_name":"Streisfeld, Matthew A.","first_name":"Matthew A.","last_name":"Streisfeld"}],"issue":"8","publication_status":"published","article_processing_charge":"No","date_created":"2024-01-10T10:44:45Z","department":[{"_id":"NiBa"}],"title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","intvolume":"        32"},{"publication":"Molecular Ecology","has_accepted_license":"1","month":"03","oa_version":"Published Version","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"language":[{"iso":"eng"}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_published":"2023-03-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"14062","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_size":7144607,"date_created":"2023-08-16T08:15:41Z","file_name":"2023_MolecularEcology_Shipilina.pdf","content_type":"application/pdf","date_updated":"2023-08-16T08:15:41Z"}],"author":[{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226","last_name":"Shipilina","first_name":"Daria"},{"last_name":"Pal","first_name":"Arka","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"issue":"6","_id":"12159","pmid":1,"license":"https://creativecommons.org/licenses/by/4.0/","scopus_import":"1","title":"On the origin and structure of haplotype blocks","intvolume":"        32","publication_status":"published","date_created":"2023-01-12T12:09:17Z","department":[{"_id":"NiBa"}],"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2023-08-16T08:15:41Z","page":"1441-1457","quality_controlled":"1","article_type":"original","publisher":"Wiley","isi":1,"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"date_updated":"2023-08-16T08:18:47Z","citation":{"chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” <i>Molecular Ecology</i>, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., &#38; Barton, N. H. (2023). On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. 2023;32(6):1441-1457. doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>","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.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>."},"year":"2023","abstract":[{"lang":"eng","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."}],"doi":"10.1111/mec.16793","day":"01","ddc":["570"],"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).","volume":32},{"citation":{"ista":"Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.","mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>, vol. 32, no. 1, Wiley, 2022, pp. 26–29, doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>.","chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>.","ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” <i>Molecular Ecology</i>, vol. 32, no. 1. Wiley, pp. 26–29, 2022.","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. 2022;32(1):26-29. doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>","apa":"Westram, A. M., &#38; Butlin, R. (2022). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>"},"year":"2022","date_updated":"2023-08-04T09:09:15Z","external_id":{"isi":["000892168800001"]},"isi":1,"day":"28","doi":"10.1111/mec.16779","abstract":[{"text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings.","lang":"eng"}],"volume":32,"scopus_import":"1","_id":"12166","issue":"1","author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"date_created":"2023-01-12T12:10:28Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        32","title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","quality_controlled":"1","page":"26-29","publisher":"Wiley","article_type":"letter_note","type":"journal_article","date_published":"2022-11-28T00:00:00Z","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.16779"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Molecular Ecology","oa_version":"Published Version","month":"11","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}]},{"file":[{"date_created":"2022-03-08T11:31:30Z","checksum":"d5611f243ceb63a0e091d6662ebd9cda","file_size":1726548,"date_updated":"2022-03-08T11:31:30Z","content_type":"application/pdf","file_name":"2021_MolecularEcology_Westram.pdf","access_level":"open_access","relation":"main_file","success":1,"file_id":"10839","creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2021-08-01T00:00:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"08","has_accepted_license":"1","publication":"Molecular Ecology","acknowledgement":"We thank everyone who helped with fieldwork, snail processing and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark Ravinet for helpful discussions, and to three anonymous reviewers for their constructive comments. This work was supported by the Natural Environment Research Council (NE/K014021/1), the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628), and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017). A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno. 754411/797747 and no. 706376, respectively.","volume":30,"ddc":["570"],"day":"01","doi":"10.1111/mec.15861","abstract":[{"lang":"eng","text":"Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder–rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones."}],"year":"2021","citation":{"ieee":"A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid zones to understand the genomic basis of adaptive divergence,” <i>Molecular Ecology</i>, vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>.","ama":"Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. 2021;30(15):3797-3814. doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>","apa":"Westram, A. M., Faria, R., Johannesson, K., &#38; Butlin, R. (2021). Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>","ista":"Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 30(15), 3797–3814.","mla":"Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>, vol. 30, no. 15, Wiley, 2021, pp. 3797–814, doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021) 3797–3814."},"date_updated":"2023-09-05T16:02:19Z","external_id":{"pmid":["33638231"],"isi":["000669439700001"]},"isi":1,"publisher":"Wiley","article_type":"original","quality_controlled":"1","page":"3797-3814","file_date_updated":"2022-03-08T11:31:30Z","article_processing_charge":"No","date_created":"2022-03-08T11:28:32Z","department":[{"_id":"BeVi"}],"publication_status":"published","intvolume":"        30","title":"Using replicate hybrid zones to understand the genomic basis of adaptive divergence","scopus_import":"1","_id":"10838","pmid":1,"issue":"15","author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}]},{"citation":{"ieee":"M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog,” <i>Molecular Ecology</i>, vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.","chicago":"Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.14990\">https://doi.org/10.1111/mec.14990</a>.","apa":"Toups, M. A., Rodrigues, N., Perrin, N., &#38; Kirkpatrick, M. (2019). A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14990\">https://doi.org/10.1111/mec.14990</a>","ama":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>. 2019;28(8):1877-1889. doi:<a href=\"https://doi.org/10.1111/mec.14990\">10.1111/mec.14990</a>","ista":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 28(8), 1877–1889.","mla":"Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” <i>Molecular Ecology</i>, vol. 28, no. 8, Wiley, 2019, pp. 1877–89, doi:<a href=\"https://doi.org/10.1111/mec.14990\">10.1111/mec.14990</a>.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889."},"year":"2019","date_updated":"2023-09-06T15:00:13Z","external_id":{"isi":["000468200800004"],"pmid":["30576024"]},"isi":1,"day":"01","doi":"10.1111/mec.14990","abstract":[{"text":"X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes.","lang":"eng"}],"volume":28,"pmid":1,"_id":"7421","issue":"8","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"first_name":"Nicolas","last_name":"Rodrigues","full_name":"Rodrigues, Nicolas"},{"first_name":"Nicolas","last_name":"Perrin","full_name":"Perrin, Nicolas"},{"full_name":"Kirkpatrick, Mark","last_name":"Kirkpatrick","first_name":"Mark"}],"date_created":"2020-01-30T10:33:05Z","department":[{"_id":"BeVi"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        28","title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","quality_controlled":"1","page":"1877-1889","publisher":"Wiley","article_type":"original","type":"journal_article","date_published":"2019-04-01T00:00:00Z","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Molecular Ecology","oa_version":"None","month":"04","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"03","has_accepted_license":"1","publication":"Molecular Ecology","file":[{"file_id":"6097","creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:19Z","file_name":"2019_MolecularEcology_Faria.pdf","content_type":"application/pdf","date_created":"2019-03-11T16:12:54Z","file_size":1510715,"checksum":"f915885756057ec0ca5912a41f46a887"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","related_material":{"record":[{"relation":"research_data","id":"9837","status":"public"}]},"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2019-03-01T00:00:00Z","publisher":"Wiley","quality_controlled":"1","page":"1375-1393","file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2019-03-10T22:59:21Z","publication_status":"published","intvolume":"        28","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","scopus_import":"1","_id":"6095","issue":"6","author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"last_name":"Lemmon","first_name":"Emily M.","full_name":"Lemmon, Emily M."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"volume":28,"ddc":["570"],"day":"01","doi":"10.1111/mec.14972","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"year":"2019","citation":{"ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393.","mla":"Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” <i>Molecular Ecology</i>, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:<a href=\"https://doi.org/10.1111/mec.14972\">10.1111/mec.14972</a>.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.14972\">https://doi.org/10.1111/mec.14972</a>.","ieee":"R. Faria <i>et al.</i>, “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” <i>Molecular Ecology</i>, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14972\">https://doi.org/10.1111/mec.14972</a>","ama":"Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. <i>Molecular Ecology</i>. 2019;28(6):1375-1393. doi:<a href=\"https://doi.org/10.1111/mec.14972\">10.1111/mec.14972</a>"},"date_updated":"2023-08-24T14:50:27Z","external_id":{"isi":["000465219200013"]},"isi":1}]