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Peer-reviewedCC BYPLoS Genetics

Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone

  • David Luke Field1,2,3
  • Sean Stankowski4,5,6
  • Taylor E. Reiter5,7
  • Jitka Polechová8,9
  • Desmond J. Bradley10,11
  • Daniel M. Richardson10,11
  • Annabel C. Whibley10,7
  • Arka Pal5,7
  • Daria Shipilina12,11
  • Louis Boell (24386755)10,13
  • Melinda Pickup1,14,15
  • Yongbiao Xue16,11
2 more authors
  • Enrico Coen10,17
  • Nick Barton5
17 affiliations
  1. 1Applied BioSciences, Macquarie University, Sydney, New South Wales, Australia
  2. 2School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
  3. 3Applied BioSciences, Macquarie University
  4. 4Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
  5. 5Institute of Science and Technology Austria, Klosterneuburg, Austria
  6. 6University of Sussex
  7. 7Institute of Science and Technology Austria
  8. 8University of Vienna, Department of Mathematics, Vienna, Austria
  9. 9University of Vienna
  10. 10John Innes Centre, Norwich Bioscience Institutes, Norwich, United Kingdom
  11. 11John Innes Centre
  12. 12Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
  13. 13Applied Biosciences, Macquarie University
  14. 14Chinese Academy of Sciences, Beijing, China
  15. 15Institute of Genetics and Developmental Biology
  16. 16Institute of Genetics and Developmental Biology; Chinese Academy of Sciences, Beijing, China
  17. 17Institute of Science and Technology
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Abstract

Identification of the genomic regions that contribute to reproductive isolation and how they interact is a major goal of evolutionary genetics. Much effort has focused on locating candidate genes and potential barrier loci by scanning genomes for regions of excess differentiation (FST). An alternative, and perhaps more robust approach, is to scan for genomic regions exhibiting steep clines in allele frequency across a hybrid zone. We develop a computationally efficient method for approximating cline parameters for large number of loci, and apply it to genomic data from across a hybrid zone between flower colour varieties of Antirrhinum majus (A. m. m var. pseudomajus and A. m. m var. striatum). Most steep clines are clustered in seven genomic regions, only four of which were present from FST scans between all pair-wise comparisons. Six of these regions carry previously identified loci that influence flower colour in the hybrid zone. The seventh region harbours a novel locus, RUBIA, modifying magenta intensity. Clines at RUBIA approached fixation on the magenta side of the hybrid zone, whilst remaining polymorphic on the yellow side. This polymorphism on the yellow side may reflect a smaller phenotypic effect of RUBIA in yellow compared to magenta genetic backgrounds. Our findings illustrate how whole-genome cline scans in hybrid zones can robustly detect genomic regions contributing to phenotypic differences and highlight how different reproductive barrier loci interact across the genome.

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Cite

BibTeXRIS
BibTeX
@article{field2026genomewide,
  title = {{Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone}},
  author = {David Luke Field and Sean Stankowski and Taylor E. Reiter and Jitka Polechová and Desmond J. Bradley and Daniel M. Richardson and Annabel C. Whibley and Arka Pal and Daria Shipilina and Louis Boell (24386755) and Melinda Pickup and Yongbiao Xue and Enrico Coen and Nick Barton},
  journal = {PLoS Genetics},
  year = {2026},
  month = jul,
  doi = {10.1371/journal.pgen.1012173},
  url = {https://doi.org/10.1371/journal.pgen.1012173},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone
AU  - David Luke Field
AU  - Sean Stankowski
AU  - Taylor E. Reiter
AU  - Jitka Polechová
AU  - Desmond J. Bradley
AU  - Daniel M. Richardson
AU  - Annabel C. Whibley
AU  - Arka Pal
AU  - Daria Shipilina
AU  - Louis Boell (24386755)
AU  - Melinda Pickup
AU  - Yongbiao Xue
AU  - Enrico Coen
AU  - Nick Barton
PY  - 2026
DA  - 2026/07/13
JO  - PLoS Genetics
DO  - 10.1371/journal.pgen.1012173
UR  - https://doi.org/10.1371/journal.pgen.1012173
AB  - Identification of the genomic regions that contribute to reproductive isolation and how they interact is a major goal of evolutionary genetics. Much effort has focused on locating candidate genes and potential barrier loci by scanning genomes for regions of excess differentiation (FST). An alternative, and perhaps more robust approach, is to scan for genomic regions exhibiting steep clines in allele frequency across a hybrid zone. We develop a computationally efficient method for approximating cline parameters for large number of loci, and apply it to genomic data from across a hybrid zone between flower colour varieties of Antirrhinum majus (A. m. m var. pseudomajus and A. m. m var. striatum). Most steep clines are clustered in seven genomic regions, only four of which were present from FST scans between all pair-wise comparisons. Six of these regions carry previously identified loci that influence flower colour in the hybrid zone. The seventh region harbours a novel locus, RUBIA, modifying magenta intensity. Clines at RUBIA approached fixation on the magenta side of the hybrid zone, whilst remaining polymorphic on the yellow side. This polymorphism on the yellow side may reflect a smaller phenotypic effect of RUBIA in yellow compared to magenta genetic backgrounds. Our findings illustrate how whole-genome cline scans in hybrid zones can robustly detect genomic regions contributing to phenotypic differences and highlight how different reproductive barrier loci interact across the genome.
SN  - 1553-7390
SN  - 1553-7404
ER  -