[{"das_tickbox":"1","article_number":"e1012173","_id":"22674","quality_controlled":"1","date_published":"2026-07-13T00:00:00Z","publisher":"Public Library of Science","file":[{"file_id":"22683","file_name":"2026_PloSGenetics_Field.pdf","date_updated":"2026-08-11T07:53:14Z","checksum":"3e2d3acc179f4672c49217ae4a6e237c","success":1,"file_size":2462781,"content_type":"application/pdf","date_created":"2026-08-11T07:53:14Z","access_level":"open_access","creator":"dernst","relation":"main_file"}],"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.","doi":"10.1371/journal.pgen.1012173","PlanS_conform":"1","publication_identifier":{"eissn":["1553-7404"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","oa":1,"title":"Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"day":"13","researchdata_availability":"yes","abstract":[{"lang":"eng","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."}],"external_id":{"pmid":["42441626"],"biorxivid":["10.1101/2025.02.17.638607"]},"has_accepted_license":"1","status":"public","oa_version":"Published Version","publication":"PLOS Genetics","scopus_import":"1","date_created":"2026-08-11T06:19:05Z","corr_author":"1","type":"journal_article","article_type":"original","citation":{"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>.","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.","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>","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>","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).","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>."},"DOAJ_listed":"1","language":[{"iso":"eng"}],"supplementarymaterial":"yes","date_updated":"2026-08-11T07:55:22Z","ddc":["570"],"OA_place":"publisher","intvolume":"        22","OA_type":"gold","project":[{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"biorxivid":1,"author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"last_name":"Reiter","first_name":"Taylor","full_name":"Reiter, Taylor"},{"last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"},{"full_name":"Bradley, Desmond","first_name":"Desmond","last_name":"Bradley"},{"first_name":"Daniel M.","last_name":"Richardson","full_name":"Richardson, Daniel M."},{"full_name":"Whibley, Annabel","first_name":"Annabel","last_name":"Whibley"},{"last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka"},{"orcid":"0000-0002-1145-9226","first_name":"Daria","last_name":"Shipilina","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Louis","last_name":"Boell","full_name":"Boell, Louis"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541"},{"full_name":"Xue, Yongbiao","first_name":"Yongbiao","last_name":"Xue"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"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].","pmid":1,"file_date_updated":"2026-08-11T07:53:14Z","publication_status":"published","year":"2026","month":"07","issue":"7","volume":22}]