Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges

The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, e.g., when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence w...种群历史建模与推断（demographic history modelling and inference）在物种分化研究中的应用，已成为物种形成基因组学（speciation genomics）的核心基石。当前物种形成历史的重构通常通过分析每个物种的单一种群完成，其前提假设为：推断得到的种群历史可代表真实的物种形成历史。然而，当物种分化伴随基因流（gene flow）发生时，例如当二次接触（secondary contact）仅局限于特定地理区域时，这一假设可能不再成立。本研究以两种木蚁——多栉蚁（Formica polyctena）与F. aquilonia——为研究对象，检验了基于异种种群推断得到的分化历史是否会因其地理分布位置而异。我们对采自两个物种欧洲分布范围内多个地点的20个个体进行了全基因组重测序（whole-genome resequencing）。随后，我们采用基于溯祖理论的分析方法，重构了不同异种种群对的演化历史。我们的分析始终支持分化场景为……