Data from: Genome-wide SNP data suggests complex ancestry of sympatric North Pacific killer whale ecotypes

Three ecotypes of killer whale occur in partial sympatry in the North Pacific. Individuals assortatively mate within the same ecotype, resulting in correlated ecological and genetic differentiation. A key question is whether this pattern of evolutionary divergence is an example of incipient sympatric speciation from a single panmictic ancestral population, or whether sympatry could have resulted from multiple colonisations of the North Pacific and secondary contact between ecotypes. Here, we infer multilocus coalescent trees from >1000 nuclear single-nucleotide polymorphisms (SNPs) and find evidence of incomplete lineage sorting so that the genealogies of SNPs do not all conform to a single topology. To disentangle whether uncertainty in the phylogenetic inference of the relationships among ecotypes could also result from ancestral admixture events we reconstructed the relationship among the ecotypes as an admixture graph and estimated f4-statistics using TreeMix. The results were consistent with episodes of admixture between two of the North Pacific ecotypes and the two outgroups (populations from the Southern Ocean and the North Atlantic). Gene flow may have occurred via unsampled ‘ghost’ populations rather than directly between the populations sampled here. Our results indicate that because of ancestral admixture events and incomplete lineage sorting, a single bifurcating tree does not fully describe the relationship among these populations. The data are therefore most consistent with the genomic variation among North Pacific killer whale ecotypes resulting from multiple colonisation events, and secondary contact may have facilitated evolutionary divergence. Thus, the present-day populations of North Pacific killer whale ecotypes have a complex ancestry, confounding the tree-based inference of ancestral geography.

北太平洋海域存在三种虎鲸生态型（ecotype），它们呈部分同域分布（sympatry）。同一生态型内的个体发生选型交配（assortative mating），进而引发了相关性的生态分化与遗传分化。一个核心科学问题在于，这种进化分化模式究竟是源自单一随机交配（panmictic）的祖先种群的初期同域物种形成（incipient sympatric speciation）实例，还是该同域分布格局源于多次北太平洋定殖（colonisation）事件以及生态型间的次级接触（secondary contact）。本研究基于超过1000个核基因组单核苷酸多态性（SNPs）构建多位点溯祖树（multilocus coalescent trees），发现存在不完全谱系分选（incomplete lineage sorting）的证据，即单核苷酸多态性的基因谱系并非全部符合单一拓扑结构。为厘清生态型间系统发育推断（phylogenetic inference）的不确定性是否也源于祖先基因交流事件，我们以基因交流图（admixture graph）重构了各生态型间的演化关系，并借助TreeMix软件估算f4统计量（f4-statistics）。研究结果显示，北太平洋的两种生态型与两个外类群（outgroups，分别来自南大洋与北大西洋的种群）之间曾发生过多轮基因交流。基因交流可能通过未被采样的‘幽灵’种群（ghost populations）实现，而非直接发生在本次采样的种群之间。本研究结果表明，由于祖先基因交流事件与不完全谱系分选的存在，单一分叉系统树（bifurcating tree）无法完整描述这些种群间的演化关系。因此，现有数据最支持北太平洋虎鲸生态型间的基因组变异源于多次定殖事件，且次级接触可能推动了其进化分化。由此可见，现今北太平洋虎鲸各生态型的种群拥有复杂的祖先起源，这给基于系统树的祖先地理分布推断带来了干扰。