Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis, whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

物种形成是一个连续的过程。尽管众所周知，即使面对基因流动，差异适应也会引发分化，但我们对驱动完全生殖隔离的机制以及物种形成后期分化和基因渗入的基因组模式知之甚少。刺鱼包含许多对同域物种，它们的生殖隔离和分化历史水平各不相同。尽管如此，以前的大多数研究都集中在年轻的物种对上。在这里，我们调查了两种同域棘鱼，Pungitius pungitius和P. sinensis，其栖息地在北海道东部重叠；这些物种表现出杂交雄性不育，表明它们可能处于物种形成的后期阶段。我们使用全基因组序列数据进行的人口统计分析表明，这些物种分裂 1.73 Ma，并在 37 200 年前经过一段时间的同种异体后再次接触。这段长时间的异种移植可能促进了内在不相容性的演变。尽管我们检测到持续的基因流和基因渗入的特征，但总体基因组差异很大，整个基因组具有相当大的异质性。异质性与重组率的变化显着相关。这对同域对提供了研究棘鱼物种形成连续体后期阶段的新途径。

这篇文章是主题问题“走向物种形成的完成：超越第一道障碍的生殖隔离的进化”的一部分。