Globe Institute, University of Copenhagen, Copenhagen, Denmark.
Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
Mol Ecol. 2023 Sep;32(17):4829-4843. doi: 10.1111/mec.17069. Epub 2023 Jul 13.
The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.
近年来，在许多分类群中都记录到了分歧后基因流在物种形成中的影响，而在高度移动、分布广泛的海洋物种（如鲸目动物）中，这种影响可能更为广泛。在这里，我们研究了来自齿鲸超科的三个科的九种物种的个体基因组（海豚科、鼠海豚科和独角鲸科）。为了研究分歧后基因流在物种形成过程中的作用，我们采用了多方面的方法，包括（i）系统基因组学，（ii）共享衍生等位基因的分布和（iii）种群推断。我们发现齿鲸超科内的谱系分歧并没有遵循纯粹的分歧过程，而是要复杂得多。滑动窗口系统基因组学揭示了超科内高度流行的拓扑分歧，进一步的分析表明这些分歧是由于不完全谱系分选和基因流引起的。D 统计量和 f 枝分析支持齿鲸超科成员之间存在基因流，而绝大多数基因流是古老的种间事件。种群动态分析提供的证据表明，尽管有报道称存在当代种间杂种，但在测试的所有物种对之间，基因渗透可能已经停止。我们的研究为解决齿鲸超科内的大复杂性迈出了第一步；我们揭示了在每个科分化之前普遍存在古老的种间基因流事件，并表明当代杂交事件可能是不利的，因为杂交个体似乎没有为亲代物种的基因库做出贡献。
