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