Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum

作者：Arka Pal, Daria Shipilina, Alan Le Moan, Adrian J. McNairn, Jennifer K. Grenier, Marek Kučka, Graham Coop, Yingguang Frank Chan, Nick Barton, David L. Field, Sean Stankowski · 发表于：Molecular Ecology · 年份：2025 · DOI：10.1111/mec.70067 · 被引用次数：7 · 研究领域：Genetic diversity and population structure、Genetic Mapping and Diversity in Plants and Animals、Plant and animal studies

ABSTRACT 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), F ST 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 lin...