[{"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (https://www.ukri.org/councils/bbsrc/) (grants BB/S009256/1, BB/G009325/1, BBS/E/JI/230002C, and BBS/E/J/000PR9773 to EC, and Norwich Research Park Biosciences Doctoral Training Partnership grant (https://www.jic.ac.uk/training-careers/postgraduate-opportunities/nrp-doctoral-training-partnership/) (BB/M011216/1 to DR) and European Research Council (https://erc.europa.eu/homepage) ERC Advanced Grant HaplotypeStructure (101055327 to NB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We are grateful to Monique Burrus, Christophe Andalo, Tom Ellis, Parvathy Surendranadh and members of the Barton group for interesting discussion. We are also grateful for numerous undergraduate volunteers who assisted with collecting of flowers and leaf samples in the field. Melinda Pickup passed away before the submission of the final version of this manuscript. David L Field accepts responsibility for the integrity and validity of the data collected and analyzed.","external_id":{"pmid":["42441626"],"biorxivid":["10.1101/2025.02.17.638607"]},"oa":1,"article_type":"original","supplementarymaterial":"yes","tmp":{"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","short":"CC BY (4.0)"},"article_processing_charge":"Yes","year":"2026","date_created":"2026-08-11T06:19:05Z","title":"Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone","date_updated":"2026-08-11T07:55:22Z","author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478"},{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Reiter, Taylor","last_name":"Reiter","first_name":"Taylor"},{"last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"},{"first_name":"Desmond","last_name":"Bradley","full_name":"Bradley, Desmond"},{"last_name":"Richardson","first_name":"Daniel M.","full_name":"Richardson, Daniel M."},{"last_name":"Whibley","first_name":"Annabel","full_name":"Whibley, Annabel"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","first_name":"Daria","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"last_name":"Boell","first_name":"Louis","full_name":"Boell, Louis"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541"},{"full_name":"Xue, Yongbiao","last_name":"Xue","first_name":"Yongbiao"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"abstract":[{"text":"Identification of the genomic regions that contribute to reproductive isolation and how\r\nthey interact is a major goal of evolutionary genetics. Much effort has focused on\r\nlocating candidate genes and potential barrier loci by scanning genomes for regions\r\nof excess differentiation (FST). An alternative, and perhaps more robust approach, is\r\nto scan for genomic regions exhibiting steep clines in allele frequency across a hybrid\r\nzone. We develop a computationally efficient method for approximating cline parameters\r\nfor large number of loci, and apply it to genomic data from across a hybrid zone\r\nbetween flower colour varieties of Antirrhinum majus (A. m. m var. pseudomajus and\r\nA. m. m var. striatum). Most steep clines are clustered in seven genomic regions,\r\nonly four of which were present from FST scans between all pair-wise comparisons.\r\nSix of these regions carry previously identified loci that influence flower colour in the\r\nhybrid zone. The seventh region harbours a novel locus, RUBIA, modifying magenta\r\nintensity. Clines at RUBIA approached fixation on the magenta side of the hybrid\r\nzone, whilst remaining polymorphic on the yellow side. This polymorphism on the\r\nyellow side may reflect a smaller phenotypic effect of RUBIA in yellow compared\r\nto magenta genetic backgrounds. Our findings illustrate how whole-genome cline\r\nscans in hybrid zones can robustly detect genomic regions contributing to phenotypic\r\ndifferences and highlight how different reproductive barrier loci interact across the\r\ngenome.","lang":"eng"}],"researchdata_availability":"yes","article_number":"e1012173","day":"13","volume":22,"intvolume":"        22","project":[{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"citation":{"ista":"Field D, Stankowski S, Reiter T, Polechova J, Bradley D, Richardson DM, Whibley A, Pal A, Shipilina D, Boell L, Pickup M, Xue Y, Coen E, Barton NH. 2026. Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone. PLOS Genetics. 22(7), e1012173.","ieee":"D. Field <i>et al.</i>, “Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone,” <i>PLOS Genetics</i>, vol. 22, no. 7. Public Library of Science, 2026.","apa":"Field, D., Stankowski, S., Reiter, T., Polechova, J., Bradley, D., Richardson, D. M., … Barton, N. H. (2026). Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone. <i>PLOS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1012173\">https://doi.org/10.1371/journal.pgen.1012173</a>","mla":"Field, David, et al. “Genome-Wide Cline Analysis Identifies New Locus Contributing to a Barrier to Gene Flow across an Antirrhinum Hybrid Zone.” <i>PLOS Genetics</i>, vol. 22, no. 7, e1012173, Public Library of Science, 2026, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1012173\">10.1371/journal.pgen.1012173</a>.","short":"D. Field, S. Stankowski, T. Reiter, J. Polechova, D. Bradley, D.M. Richardson, A. Whibley, A. Pal, D. Shipilina, L. Boell, M. Pickup, Y. Xue, E. Coen, N.H. Barton, PLOS Genetics 22 (2026).","chicago":"Field, David, Sean Stankowski, Taylor Reiter, Jitka Polechova, Desmond Bradley, Daniel M. Richardson, Annabel Whibley, et al. “Genome-Wide Cline Analysis Identifies New Locus Contributing to a Barrier to Gene Flow across an Antirrhinum Hybrid Zone.” <i>PLOS Genetics</i>. Public Library of Science, 2026. <a href=\"https://doi.org/10.1371/journal.pgen.1012173\">https://doi.org/10.1371/journal.pgen.1012173</a>.","ama":"Field D, Stankowski S, Reiter T, et al. Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone. <i>PLOS Genetics</i>. 2026;22(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1012173\">10.1371/journal.pgen.1012173</a>"},"date_published":"2026-07-13T00:00:00Z","has_accepted_license":"1","das_tickbox":"1","pmid":1,"status":"public","file_date_updated":"2026-08-11T07:53:14Z","issue":"7","quality_controlled":"1","corr_author":"1","doi":"10.1371/journal.pgen.1012173","publication_identifier":{"eissn":["1553-7404"]},"file":[{"content_type":"application/pdf","date_created":"2026-08-11T07:53:14Z","relation":"main_file","success":1,"file_name":"2026_PloSGenetics_Field.pdf","file_size":2462781,"checksum":"3e2d3acc179f4672c49217ae4a6e237c","file_id":"22683","access_level":"open_access","creator":"dernst","date_updated":"2026-08-11T07:53:14Z"}],"fulldoi":"https://doi.org/10.1371/journal.pgen.1012173","OA_type":"gold","department":[{"_id":"NiBa"}],"OA_place":"publisher","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"PLOS Genetics","language":[{"iso":"eng"}],"biorxivid":1,"dataavailabilitystatement":"The raw DNA poolSeq data and RNA data have been uploaded to SRA under accession number PRJNA1232105. The A. m. m. var. pseudo majus assembly and GFF annotations have been uploaded to NCBI WGS under accession number PRJNA1232105. The A. majus reference genome V3.0 is available at the NGDC Genome Warehouse under accession number GWHBJVT00000000. The SNP KASP data and flower colour phenotyping is available on Dryad at DOI: https://doi.org/10.5061/dryad.3bk3j9kx2. The FastClines script is available at https://github.com/dfield007/fastClines, slidingWindow genome scans at https://github.com/dfield007/slidingWindows, and all other scripts for analyses and generating figures available at https://github.com/dfield007/genome_wide_clines].","type":"journal_article","publisher":"Public Library of Science","PlanS_conform":"1","ddc":["570"],"month":"07","_id":"22674","scopus_import":"1","oa_version":"Published Version","DOAJ_listed":"1"},{"article_number":"e70067","day":"01","citation":{"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>","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.","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>","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>.","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>."},"project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"intvolume":"        34","volume":34,"title":"Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum","date_updated":"2026-10-14T22:30:40Z","author":[{"first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469"},{"first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","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"},{"first_name":"Jennifer K.","last_name":"Grenier","full_name":"Grenier, Jennifer K."},{"first_name":"Marek","last_name":"Kucka","full_name":"Kucka, Marek"},{"last_name":"Coop","first_name":"Graham","full_name":"Coop, Graham"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"}],"abstract":[{"lang":"eng","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."}],"article_processing_charge":"Yes (via OA deal)","date_created":"2025-08-17T22:01:37Z","year":"2025","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. ","oa":1,"external_id":{"isi":["001546622100001"]},"article_type":"original","tmp":{"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","short":"CC BY (4.0)"},"ddc":["570"],"month":"11","PlanS_conform":"1","isi":1,"_id":"20190","scopus_import":"1","oa_version":"Published Version","publication":"Molecular Ecology","language":[{"iso":"eng"}],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"link":[{"url":"https://ista.ac.at/en/news/snapdragon-secrets/","description":"News on ISTA website","relation":"press_release"}],"record":[{"status":"public","relation":"dissertation_contains","id":"20694"}]},"publisher":"Wiley","type":"journal_article","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"quality_controlled":"1","file":[{"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2026-01-05T13:47:47Z","file_id":"20958","access_level":"open_access","creator":"dernst","date_updated":"2026-01-05T13:47:47Z","file_name":"2025_MolecEcology_Pal.pdf","file_size":9886694,"checksum":"c586fc674df4e7dd6e43aef87a52c6f6"}],"doi":"10.1111/mec.70067","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"OA_type":"hybrid","fulldoi":"https://doi.org/10.1111/mec.70067","department":[{"_id":"NiBa"}],"OA_place":"publisher","has_accepted_license":"1","date_published":"2025-11-01T00:00:00Z","status":"public","issue":"22","file_date_updated":"2026-01-05T13:47:47Z"},{"acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","oa":1,"external_id":{"isi":["001138156400003"],"pmid":["38175895"]},"article_type":"original","article_processing_charge":"No","date_created":"2024-01-14T23:00:56Z","year":"2024","title":"The genetic basis of a recent transition to live-bearing in marine snails","date_updated":"2026-10-14T22:30:40Z","abstract":[{"text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.","lang":"eng"}],"author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"last_name":"Zagrodzka","first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B."},{"full_name":"Garlovsky, Martin D.","last_name":"Garlovsky","first_name":"Martin D."},{"full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka"},{"first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo","first_name":"Diego Fernando"},{"last_name":"Lifchitz","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","first_name":"Hila","full_name":"Lifchitz, Hila"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"full_name":"Leder, Erica","last_name":"Leder","first_name":"Erica"},{"last_name":"Reeve","first_name":"James","full_name":"Reeve, James"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"day":"05","citation":{"ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. 2024;383(6678):114-119. doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>","ieee":"S. Stankowski <i>et al.</i>, “The genetic basis of a recent transition to live-bearing in marine snails,” <i>Science</i>, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024."},"intvolume":"       383","volume":383,"date_published":"2024-01-05T00:00:00Z","pmid":1,"status":"public","issue":"6678","corr_author":"1","quality_controlled":"1","doi":"10.1126/science.adi2982","publication_identifier":{"eissn":["1095-9203"]},"OA_type":"green","fulldoi":"https://doi.org/10.1126/science.adi2982","OA_place":"repository","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"publication":"Science","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/"}],"record":[{"status":"public","id":"14812","relation":"research_data"},{"status":"public","id":"22905","relation":"research_data"},{"status":"public","id":"20694","relation":"dissertation_contains"}]},"main_file_link":[{"url":"https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241","open_access":"1"}],"publisher":"American Association for the Advancement of Science","type":"journal_article","month":"01","isi":1,"_id":"14796","oa_version":"Submitted Version","scopus_import":"1","page":"114-119"},{"language":[{"iso":"eng"}],"publication":"Molecular Ecology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"20694","status":"public"}]},"publisher":"Wiley","type":"journal_article","ddc":["570"],"month":"03","isi":1,"scopus_import":"1","_id":"12159","oa_version":"Published Version","page":"1441-1457","has_accepted_license":"1","date_published":"2023-03-01T00:00:00Z","pmid":1,"issue":"6","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"file_date_updated":"2023-08-16T08:15:41Z","status":"public","corr_author":"1","quality_controlled":"1","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"file":[{"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2023-08-16T08:15:41Z","file_id":"14062","creator":"dernst","date_updated":"2023-08-16T08:15:41Z","access_level":"open_access","file_name":"2023_MolecularEcology_Shipilina.pdf","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_size":7144607}],"doi":"10.1111/mec.16793","fulldoi":"https://doi.org/10.1111/mec.16793","department":[{"_id":"NiBa"}],"title":"On the origin and structure of haplotype blocks","date_updated":"2026-10-14T22:30:40Z","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"}],"author":[{"orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469"},{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"day":"01","intvolume":"        32","citation":{"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>","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>.","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>.","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.","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>"},"project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"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).","oa":1,"external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"article_type":"original","tmp":{"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","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","year":"2023","date_created":"2023-01-12T12:09:17Z"},{"publisher":"Wiley","series_title":"eLS","type":"book_chapter","abstract":[{"text":"Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them.","lang":"eng"}],"author":[{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","first_name":"Daria","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"}],"date_updated":"2024-10-09T21:08:11Z","publication":"Encyclopedia of Life Sciences","title":"Hybrid Zones","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: <i>Encyclopedia of Life Sciences</i>. Vol 2. eLS. Wiley; 2021. doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029355\">10.1002/9780470015902.a0029355</a>","apa":"Stankowski, S., Shipilina, D., &#38; Westram, A. M. (2021). Hybrid Zones. In <i>Encyclopedia of Life Sciences</i> (Vol. 2). Wiley. <a href=\"https://doi.org/10.1002/9780470015902.a0029355\">https://doi.org/10.1002/9780470015902.a0029355</a>","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in <i>Encyclopedia of Life Sciences</i>, vol. 2, Wiley, 2021.","ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","chicago":"Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In <i>Encyclopedia of Life Sciences</i>, Vol. 2. ELS. Wiley, 2021. <a href=\"https://doi.org/10.1002/9780470015902.a0029355\">https://doi.org/10.1002/9780470015902.a0029355</a>.","mla":"Stankowski, Sean, et al. “Hybrid Zones.” <i>Encyclopedia of Life Sciences</i>, vol. 2, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029355\">10.1002/9780470015902.a0029355</a>.","short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021."},"intvolume":"         2","volume":2,"day":"28","oa_version":"None","_id":"14984","month":"05","status":"public","date_published":"2021-05-28T00:00:00Z","department":[{"_id":"NiBa"}],"year":"2021","date_created":"2024-02-14T12:05:50Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1002/9780470015902.a0029355","publication_identifier":{"eisbn":["9780470015902"],"isbn":["9780470016176"]},"doi":"10.1002/9780470015902.a0029355","corr_author":"1","quality_controlled":"1"}]