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.