[{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-11-01T00:00:00Z","has_accepted_license":"1","abstract":[{"text":"Speciation is rarely observable directly. A way forward is to compare pairs of ecotypes that evolved in parallel in similar contexts but have reached different degrees of reproductive isolation. Such comparisons are possible in the marine snail Littorina saxatilis by contrasting barriers to gene flow between parallel ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved to withstand either crab predation or wave action. Here, we explore transects spanning contact zones between the Crab and the Wave ecotypes using low-coverage whole-genome sequencing, morphological and behavioural traits. Despite parallel phenotypic divergence, distinct patterns of differentiation between the ecotypes emerged: a continuous cline in Sweden indicating a weak barrier to gene flow, but two highly genetically and phenotypically divergent, and partly spatially overlapping clusters in Spain suggesting a much stronger barrier to gene flow. The absence of Spanish early-generation hybrids supported strong isolation, but a low level of gene flow is evident from molecular data. In both countries, highly differentiated loci were located in both shared and country-specific chromosomal inversions but were also present in collinear regions. Despite being considered the same species and showing similar levels of phenotypic divergence, the Spanish ecotypes are much closer to full reproductive isolation than the Swedish ones. Barriers to gene flow of very different strengths between ecotypes within the same species might be explained by dissimilarities in the spatial arrangement of habitats, the selection gradients or the ages of the systems.","lang":"eng"}],"citation":{"ista":"Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. Molecular Ecology. 34(21), e70025.","chicago":"Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K. Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>.","ama":"Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. 2025;34(21). doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>","apa":"Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram, A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>","mla":"Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>, vol. 34, no. 21, e70025, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>.","ieee":"F. Raffini <i>et al.</i>, “Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail,” <i>Molecular Ecology</i>, vol. 34, no. 21. Wiley, 2025.","short":"F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram, J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025)."},"intvolume":"        34","date_updated":"2025-12-30T09:25:45Z","status":"public","author":[{"full_name":"Raffini, Francesca","last_name":"Raffini","first_name":"Francesca"},{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Zagrodzka","first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B."},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M"},{"full_name":"Galindo, Juan","first_name":"Juan","last_name":"Galindo"},{"first_name":"Emilio","last_name":"Rolán-Alvarez","full_name":"Rolán-Alvarez, Emilio"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"publication":"Molecular Ecology","issue":"21","acknowledgement":"This study was supported by European Research Council grant 693030-BARRIERS to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021) to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU (ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’ and Norwegian Research Council RCN, project 315287 to AMW.","volume":34,"ddc":["570"],"article_number":"e70025","month":"11","file":[{"file_name":"2025_MolecEcology_Raffini.pdf","success":1,"file_id":"20906","file_size":2767745,"content_type":"application/pdf","date_updated":"2025-12-30T09:25:17Z","creator":"dernst","date_created":"2025-12-30T09:25:17Z","access_level":"open_access","relation":"main_file","checksum":"ec01edda64cfbc6cbc8adf300f719644"}],"article_type":"original","file_date_updated":"2025-12-30T09:25:17Z","language":[{"iso":"eng"}],"OA_place":"publisher","doi":"10.1111/mec.70025","_id":"20102","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","date_created":"2025-08-03T22:01:31Z","isi":1,"OA_type":"hybrid","year":"2025","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"PlanS_conform":"1","type":"journal_article","day":"01","external_id":{"isi":["001538172800001"]},"oa":1,"article_processing_charge":"Yes (in subscription journal)","title":"Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/4.0/"},{"acknowledgement":"We thank a large number of field volunteers for maintaining the population sampling, and Tom White for assistance with seed collection. We thank Sylvia Rebel for plating tissue for DNA extraction, as well as Sean Stankowski and two anonymous reviewers for feedback on the manuscript. ","volume":34,"article_number":"e70051","ddc":["570"],"month":"09","file":[{"date_updated":"2025-12-30T10:12:17Z","creator":"dernst","date_created":"2025-12-30T10:12:17Z","access_level":"open_access","relation":"main_file","checksum":"5059ad4d74e6327b84b5282a39d36774","file_name":"2025_MolecularEcology_Ellis.pdf","success":1,"file_id":"20911","file_size":1698605,"content_type":"application/pdf"}],"status":"public","author":[{"first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas"},{"last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"publication":"Molecular Ecology","issue":"15","intvolume":"        34","date_updated":"2025-12-30T10:12:34Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_published":"2025-09-02T00:00:00Z","has_accepted_license":"1","corr_author":"1","abstract":[{"lang":"eng","text":"Inferring genealogical relationships of wild populations is useful because it gives direct estimates of mating patterns and variance in reproductive success. Inference can be improved by including information about parentage shared between siblings, or by modelling phenotypes or population data related to mating. However, we currently lack a framework to infer parent–offspring relationships, sibships and population parameters in a single analysis. To address this, we here extend a previous method, Fractional Analysis of Paternity and Sibships, to include population data for the case where one parent is known. We illustrate this with the example of pollen dispersal in a natural hybrid zone population of the snapdragon Antirrhinum majus. Pollen dispersal is leptokurtic, with half of mating events occurring within 30 m, but with a long tail of mating events up to 859 m. Using simulations, we find that both sibship and population information substantially improve pedigree reconstruction, and that we can expect to resolve median dispersal distances with high accuracy."}],"citation":{"chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Joint Estimation of Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70051\">https://doi.org/10.1111/mec.70051</a>.","ama":"Ellis T, Field D, Barton NH. Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. <i>Molecular Ecology</i>. 2025;34(15). doi:<a href=\"https://doi.org/10.1111/mec.70051\">10.1111/mec.70051</a>","apa":"Ellis, T., Field, D., &#38; Barton, N. H. (2025). Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70051\">https://doi.org/10.1111/mec.70051</a>","mla":"Ellis, Thomas, et al. “Joint Estimation of Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone.” <i>Molecular Ecology</i>, vol. 34, no. 15, e70051, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70051\">10.1111/mec.70051</a>.","ieee":"T. Ellis, D. Field, and N. H. Barton, “Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone,” <i>Molecular Ecology</i>, vol. 34, no. 15. Wiley, 2025.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology 34 (2025).","ista":"Ellis T, Field D, Barton NH. 2025. Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. Molecular Ecology. 34(15), e70051."},"article_processing_charge":"Yes (via OA deal)","title":"Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","OA_type":"hybrid","publication_status":"published","year":"2025","publisher":"Wiley","department":[{"_id":"NiBa"}],"type":"journal_article","day":"02","external_id":{"isi":["001542913000001"],"pmid":["40751392"]},"pmid":1,"oa":1,"quality_controlled":"1","date_created":"2025-09-10T05:42:23Z","isi":1,"article_type":"original","OA_place":"publisher","language":[{"iso":"eng"}],"file_date_updated":"2025-12-30T10:12:17Z","doi":"10.1111/mec.70051","_id":"20325","scopus_import":"1","oa_version":"Published Version"},{"type":"journal_article","oa":1,"external_id":{"isi":["001546622100001"]},"day":"01","publisher":"Wiley","year":"2025","OA_type":"hybrid","publication_status":"published","department":[{"_id":"NiBa"}],"PlanS_conform":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"title":"Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum","article_processing_charge":"Yes (via OA deal)","doi":"10.1111/mec.70067","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","scopus_import":"1","_id":"20190","article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2026-01-05T13:47:47Z","OA_place":"publisher","date_created":"2025-08-17T22:01:37Z","isi":1,"project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"quality_controlled":"1","publication":"Molecular Ecology","issue":"22","author":[{"first_name":"Arka","last_name":"Pal","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"first_name":"Daria","last_name":"Shipilina","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","full_name":"Shipilina, Daria"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"full_name":"Mcnairn, Adrian J.","first_name":"Adrian J.","last_name":"Mcnairn"},{"last_name":"Grenier","first_name":"Jennifer K.","full_name":"Grenier, Jennifer K."},{"first_name":"Marek","last_name":"Kucka","full_name":"Kucka, Marek"},{"first_name":"Graham","last_name":"Coop","full_name":"Coop, Graham"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"}],"status":"public","file":[{"file_size":9886694,"content_type":"application/pdf","file_name":"2025_MolecEcology_Pal.pdf","success":1,"file_id":"20958","relation":"main_file","checksum":"c586fc674df4e7dd6e43aef87a52c6f6","date_updated":"2026-01-05T13:47:47Z","creator":"dernst","access_level":"open_access","date_created":"2026-01-05T13:47:47Z"}],"ddc":["570"],"article_number":"e70067","acknowledgement":"We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other Barton Group and Coop Lab members for stimulating discussions. We are grateful to all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón Mateu for her assistance in fieldwork logistics at the field station, El Serrat. We are grateful to Enrico Coen and his research group for providing the Antirrhinum molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up with sampling led by D.L.F. in 2017. The study was supported by Austrian Science Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.). Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics and analyses was provided by ISTA High Performance Cluster. ","volume":34,"month":"11","corr_author":"1","has_accepted_license":"1","abstract":[{"text":"A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.","lang":"eng"}],"citation":{"ista":"Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067.","chicago":"Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K. Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>.","ama":"Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. 2025;34(22). doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>","apa":"Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka, M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>","ieee":"A. Pal <i>et al.</i>, “Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum,” <i>Molecular Ecology</i>, vol. 34, no. 22. Wiley, 2025.","short":"A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G. Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025).","mla":"Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>, vol. 34, no. 22, e70067, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>."},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/snapdragon-secrets/","relation":"press_release","description":"News on ISTA website"}],"record":[{"status":"public","relation":"dissertation_contains","id":"20694"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-11-01T00:00:00Z","date_updated":"2026-05-17T22:31:22Z","intvolume":"        34"},{"department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2024","OA_type":"hybrid","publication_status":"published","oa":1,"external_id":{"isi":["001085119000001"],"pmid":["37843465"]},"day":"01","pmid":1,"type":"journal_article","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"file_date_updated":"2025-01-09T07:52:12Z","OA_place":"publisher","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","oa_version":"Published Version","_id":"14463","doi":"10.1111/mec.17160","quality_controlled":"1","isi":1,"date_created":"2023-10-29T23:01:17Z","author":[{"last_name":"Reeve","first_name":"James","full_name":"Reeve, James"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"last_name":"Koch","first_name":"Eva L.","full_name":"Koch, Eva L."},{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"}],"status":"public","issue":"24","publication":"Molecular Ecology","month":"12","article_number":"e17160","ddc":["570"],"volume":33,"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).","file":[{"date_created":"2025-01-09T07:52:12Z","access_level":"open_access","creator":"dernst","date_updated":"2025-01-09T07:52:12Z","checksum":"686576036663f489c2d079df3079d126","relation":"main_file","file_id":"18785","success":1,"file_name":"2024_MolecularEcology_Reeve.pdf","content_type":"application/pdf","file_size":6228700}],"date_published":"2024-12-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2024. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 33(24), e17160.","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, 2024. <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>. 2024;33(24). doi:<a href=\"https://doi.org/10.1111/mec.17160\">10.1111/mec.17160</a>","apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., &#38; Faria, R. (2024). 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>","short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology 33 (2024).","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>, vol. 33, no. 24. Wiley, 2024.","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>, vol. 33, no. 24, e17160, Wiley, 2024, doi:<a href=\"https://doi.org/10.1111/mec.17160\">10.1111/mec.17160</a>."},"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"}],"has_accepted_license":"1","intvolume":"        33","date_updated":"2025-01-09T07:53:18Z"},{"date_published":"2023-01-01T00:00:00Z","abstract":[{"lang":"eng","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."}],"citation":{"ista":"Westram AM, Butlin R. 2023. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","apa":"Westram, A. M., &#38; Butlin, R. (2023). 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>","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, 2023.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2023) 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, 2023, 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, 2023. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>.","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. 2023;32(1):26-29. doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>"},"corr_author":"1","intvolume":"        32","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_updated":"2025-04-23T08:44:33Z","status":"public","author":[{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"}],"publication":"Molecular Ecology","issue":"1","month":"01","volume":32,"page":"26-29","language":[{"iso":"eng"}],"article_type":"editorial","_id":"12166","oa_version":"Published Version","scopus_import":"1","doi":"10.1111/mec.16779","quality_controlled":"1","isi":1,"date_created":"2023-01-12T12:10:28Z","department":[{"_id":"NiBa"}],"main_file_link":[{"url":"https://doi.org/10.1111/mec.16779","open_access":"1"}],"OA_type":"free access","year":"2023","publication_status":"published","publisher":"Wiley","pmid":1,"day":"01","external_id":{"isi":["000892168800001"],"pmid":["36443277"]},"oa":1,"type":"journal_article","article_processing_charge":"No","title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","oa":1,"day":"01","external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"pmid":1,"publisher":"Wiley","publication_status":"published","year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.01.28.478139"}],"department":[{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","article_processing_charge":"No","doi":"10.1111/mec.16849","oa_version":"Preprint","_id":"14787","article_type":"original","language":[{"iso":"eng"}],"date_created":"2024-01-10T10:44:45Z","isi":1,"quality_controlled":"1","publication":"Molecular Ecology","issue":"8","author":[{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"last_name":"Chase","first_name":"Madeline A.","full_name":"Chase, Madeline A."},{"first_name":"Hanna","last_name":"McIntosh","full_name":"McIntosh, Hanna"},{"full_name":"Streisfeld, Matthew A.","first_name":"Matthew A.","last_name":"Streisfeld"}],"status":"public","page":"2041-2054","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.","month":"04","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 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."}],"citation":{"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>.","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>","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,” <i>Molecular Ecology</i>, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","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>.","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."},"date_published":"2023-04-01T00:00:00Z","date_updated":"2024-01-16T10:10:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"intvolume":"        32"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"title":"On the origin and structure of haplotype blocks","article_processing_charge":"Yes (via OA deal)","oa":1,"pmid":1,"day":"01","external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"type":"journal_article","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2023","publication_status":"published","isi":1,"date_created":"2023-01-12T12:09:17Z","quality_controlled":"1","project":[{"name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"scopus_import":"1","oa_version":"Published Version","_id":"12159","doi":"10.1111/mec.16793","language":[{"iso":"eng"}],"file_date_updated":"2023-08-16T08:15:41Z","article_type":"original","file":[{"relation":"main_file","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","date_updated":"2023-08-16T08:15:41Z","creator":"dernst","date_created":"2023-08-16T08:15:41Z","access_level":"open_access","file_size":7144607,"content_type":"application/pdf","file_name":"2023_MolecularEcology_Shipilina.pdf","success":1,"file_id":"14062"}],"page":"1441-1457","month":"03","ddc":["570"],"volume":32,"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).","publication":"Molecular Ecology","issue":"6","author":[{"first_name":"Daria","orcid":"0000-0002-1145-9226","last_name":"Shipilina","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","last_name":"Pal","orcid":"0000-0002-4530-8469"},{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"status":"public","date_updated":"2026-05-17T22:31:21Z","intvolume":"        32","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"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>.","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>","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>","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","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.","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>.","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."},"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"}],"has_accepted_license":"1","corr_author":"1","date_published":"2023-03-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"id":"20694","status":"public","relation":"dissertation_contains"}]}},{"quality_controlled":"1","isi":1,"date_created":"2022-03-08T11:28:32Z","language":[{"iso":"eng"}],"file_date_updated":"2022-03-08T11:31:30Z","article_type":"original","_id":"10838","oa_version":"Published Version","scopus_import":"1","doi":"10.1111/mec.15861","article_processing_charge":"No","title":"Using replicate hybrid zones to understand the genomic basis of adaptive divergence","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BeVi"}],"publication_status":"published","year":"2021","publisher":"Wiley","external_id":{"pmid":["33638231"],"isi":["000669439700001"]},"pmid":1,"day":"01","oa":1,"type":"journal_article","intvolume":"        30","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_updated":"2024-10-09T21:01:47Z","date_published":"2021-08-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"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.","lang":"eng"}],"citation":{"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.","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>","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021) 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>.","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."},"has_accepted_license":"1","corr_author":"1","month":"08","volume":30,"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.","ddc":["570"],"file":[{"file_id":"10839","success":1,"file_name":"2021_MolecularEcology_Westram.pdf","content_type":"application/pdf","file_size":1726548,"access_level":"open_access","date_created":"2022-03-08T11:31:30Z","creator":"dernst","date_updated":"2022-03-08T11:31:30Z","checksum":"d5611f243ceb63a0e091d6662ebd9cda","relation":"main_file"}],"page":"3797-3814","status":"public","author":[{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"publication":"Molecular Ecology","issue":"15"},{"day":"01","external_id":{"isi":["000652056400001"]},"oa":1,"type":"journal_article","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2021","publisher":"Wiley","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","_id":"9470","oa_version":"Published Version","scopus_import":"1","doi":"10.1111/mec.15936","language":[{"iso":"eng"}],"file_date_updated":"2021-06-11T15:34:53Z","isi":1,"date_created":"2021-06-06T22:01:31Z","quality_controlled":"1","project":[{"grant_number":"797747","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"publication":"Molecular Ecology","issue":"12","status":"public","author":[{"full_name":"Berdan, Emma L.","last_name":"Berdan","first_name":"Emma L."},{"full_name":"Blanckaert, Alexandre","first_name":"Alexandre","last_name":"Blanckaert"},{"first_name":"Tanja","last_name":"Slotte","full_name":"Slotte, Tanja"},{"full_name":"Suh, Alexander","last_name":"Suh","first_name":"Alexander"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"last_name":"Fragata","first_name":"Inês","full_name":"Fragata, Inês"}],"file":[{"date_updated":"2021-06-11T15:34:53Z","creator":"kschuh","access_level":"open_access","date_created":"2021-06-11T15:34:53Z","relation":"main_file","checksum":"e6f4731365bde2614b333040a08265d8","file_name":"2021_MolecularEcology_Berdan.pdf","success":1,"file_id":"9545","file_size":1031978,"content_type":"application/pdf"}],"page":"2710-2723","month":"06","volume":30,"ec_funded":1,"acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","ddc":["570"],"citation":{"ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” <i>Molecular Ecology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/mec.15936\">https://doi.org/10.1111/mec.15936</a>.","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. <i>Molecular Ecology</i>. 2021;30(12):2710-2723. doi:<a href=\"https://doi.org/10.1111/mec.15936\">10.1111/mec.15936</a>","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., &#38; Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15936\">https://doi.org/10.1111/mec.15936</a>","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” <i>Molecular Ecology</i>, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” <i>Molecular Ecology</i>, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:<a href=\"https://doi.org/10.1111/mec.15936\">10.1111/mec.15936</a>.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723."},"abstract":[{"lang":"eng","text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance."}],"has_accepted_license":"1","date_published":"2021-06-01T00:00:00Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"date_updated":"2026-04-16T08:19:26Z","intvolume":"        30"},{"quality_controlled":"1","isi":1,"date_created":"2019-03-10T22:59:21Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:19Z","_id":"6095","oa_version":"Published Version","scopus_import":"1","doi":"10.1111/mec.14972","article_processing_charge":"No","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"}],"year":"2019","publication_status":"published","publisher":"Wiley","day":"01","external_id":{"isi":["000465219200013"]},"oa":1,"type":"journal_article","intvolume":"        28","date_updated":"2023-08-24T14:50:27Z","date_published":"2019-03-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"research_data","status":"public","id":"9837"}]},"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"}],"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.","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>","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.","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>.","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.","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>.","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>"},"has_accepted_license":"1","month":"03","volume":28,"ddc":["570"],"file":[{"checksum":"f915885756057ec0ca5912a41f46a887","relation":"main_file","access_level":"open_access","date_created":"2019-03-11T16:12:54Z","creator":"dernst","date_updated":"2020-07-14T12:47:19Z","content_type":"application/pdf","file_size":1510715,"file_id":"6097","file_name":"2019_MolecularEcology_Faria.pdf"}],"page":"1375-1393","status":"public","author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"publication":"Molecular Ecology","issue":"6"},{"quality_controlled":"1","date_created":"2020-01-30T10:33:05Z","isi":1,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1111/mec.14990","_id":"7421","oa_version":"None","article_processing_charge":"No","title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","publication_status":"published","publisher":"Wiley","department":[{"_id":"BeVi"}],"type":"journal_article","pmid":1,"external_id":{"pmid":["30576024"],"isi":["000468200800004"]},"day":"01","intvolume":"        28","date_updated":"2023-09-06T15:00:13Z","date_published":"2019-04-01T00:00:00Z","citation":{"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.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889.","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.","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>.","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>","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>."},"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,"month":"04","page":"1877-1889","status":"public","author":[{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A"},{"first_name":"Nicolas","last_name":"Rodrigues","full_name":"Rodrigues, Nicolas"},{"last_name":"Perrin","first_name":"Nicolas","full_name":"Perrin, Nicolas"},{"full_name":"Kirkpatrick, Mark","last_name":"Kirkpatrick","first_name":"Mark"}],"publication":"Molecular Ecology","issue":"8"},{"file_date_updated":"2020-07-14T12:47:31Z","language":[{"iso":"eng"}],"doi":"10.1111/mec.15048","scopus_import":"1","oa_version":"Published Version","_id":"6466","quality_controlled":"1","date_created":"2019-05-19T21:59:15Z","isi":1,"publisher":"Wiley","year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"type":"journal_article","oa":1,"day":"01","external_id":{"isi":["000474808300001"]},"title":"Breaking down barriers in morning glories","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2019-04-01T00:00:00Z","has_accepted_license":"1","abstract":[{"text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.","lang":"eng"}],"citation":{"ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","apa":"Field, D., &#38; Fraisse, C. (2019). Breaking down barriers in morning glories. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” <i>Molecular ecology</i>, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. <i>Molecular ecology</i>. 2019;28(7):1579-1581. doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>"},"intvolume":"        28","date_updated":"2026-04-16T08:33:17Z","author":[{"first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"}],"status":"public","issue":"7","publication":"Molecular ecology","ddc":["580","576"],"volume":28,"month":"04","page":"1579-1581","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-20T11:49:06Z","access_level":"open_access","relation":"main_file","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","file_name":"2019_MolecularEcology_Field.pdf","file_id":"6472","file_size":367711,"content_type":"application/pdf"}]}]