Pal Arka, Shipilina Daria, Le Moan Alan, McNairn Adrian J, Grenier Jennifer K, Kucka Marek, Coop Graham, Chan Yingguang Frank, Barton Nicholas H, Field David L, Stankowski Sean
Institute of Science and Technology Austria, Klosterneuburg, Austria.
UMR 7144 AD2M, CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France.
Mol Ecol. 2025 Aug 11:e70067. doi: 10.1111/mec.70067.
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 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.
物种形成研究的一个主要目标是确定构成基因流动障碍的基因座。群体基因组学采用“自下而上”的方法，在基因组中扫描驱动或维持分化过程的分子特征。然而，解释物种形成的“基因组景观”很复杂，因为基因组扫描将多个过程混为一谈，其中大多数过程与基因流动无关。然而，研究重复的种群对比，包括多次二次接触事件，可以加强推断。在本文中，我们使用连锁读取测序（单倍型标记）、F扫描和系谱方法来描述与重复杂交区形成相关的基因组景观。我们研究了常见金鱼草（Antirrhinum majus subspecies majus）的两个花色变种，它们在比利牛斯山脉的多个独立山谷中形成了次生杂交区。与过去的研究一致，我们发现在一个经过充分研究的区域（普拉诺莱斯）分化程度非常低。然而，在第二个区域（阿韦拉内特），我们发现了更强的分化和更大的异质性，我们认为这是由于二次接触后基因渗入量的差异所致。系谱树的拓扑加权确定了单倍型多样性与两个金鱼草变种相关的基因座。两个最强的关联位于先前确定的花色基因座：影响黄色色素沉着的Flavia，以及影响品红色色素沉着的两个连锁基因座Rosea/Eluta。对合并时间的初步分析为这些基因座的选择性清除和基因流动障碍提供了额外的证据。我们的研究强调了种群历史对分化景观的影响，强调了区分历史分歧和近期基因渗入的必要性。
