Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype‐resolved whole‐genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in RI between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the two D. labrax lineages.

中文翻译：

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古代混合物对欧洲鲈鱼谱系之间生殖隔离的贡献

通过逐步建立不同种群之间的生殖隔离（RI）障碍来了解新物种的产生是进化生物学的主要目标。物种基因组学研究的一个重要结果是，参与RI的基因组区域经常具有古老的单倍型，这些单倍型早于物种多样性的重建历史。这些旧等位基因的可能起源尚有争议，因为它们与尚未完全了解的物种形成对比机制有关。在欧洲鲈鱼（Dicentrarchus labrax），大西洋和地中海沿袭之间的RI涉及的基因组区域丰富了未知来源的古代发散等位基因。在这里，我们使用单倍型解析的全基因组序列来测试不同的单倍型是否可能起源于密切相关的物种，即斑点鲈鱼（Dicentrarchus punctatus）。我们发现，之间的古老混合物事件D.鲈和D.毛虫负责共享派生等位基因中的两个谱系的存在下偏析在低频D.鲈。在两个D. labrax世系之间的RI涉及区域内发现了一个例外。在那些地区，古道起源于马尾藻局部到达高频甚至固定在大西洋基因组中，但在地中海几乎不存在。我们表明，古老的混合事件最有可能发生在马尾藻和大西洋D. labrax血统之间，而大西洋和地中海D. labrax血统正在经历异源隔离。我们的研究结果表明，局部适应性基因渗入和/或古老混合物引起的基因组冲突的解决可能有助于在两个D. labrax谱系之间建立RI 。