Fig. 2: Evolutionary relationships between the ancient individual SP1060 (5,979-5,626 years BP) and the North Atlantic contemporary bottlenose dolphin populations as inferred using qpBrute.

Solid arrows indicate the relationships between populations/samples and the numbers on their right side correspond to the estimated genetic drift represented by the arrow. This graph was the only one of all possible graph combinations presenting no outlier f-statistics (i.e. all |Z| were <3). Populations include eastern North Atlantic coastal (ENAc) and pelagic (ENAp) populations, western North Atlantic coastal (WNAc) and pelagic (WNAp) populations, and the outgroup is the killer whale (KW). Note that the drift value for SP1060 is inflated due to being a single and lower-coverage sample. This inflation is because all alleles found in SP1060 are treated as fixed, therefore singletons and rare alleles in SP1060 that were not shared or were rare in this ancestral population are treated as high frequency or fixed alleles, inflating estimates of drift along the branch to SP1060. Dashed lines are admixture edges and the arrows indicate the inferred direction of admixture, with the numbers reflecting the percentage of ancestry deriving from each lineage. The graph reveals a first split between the lineage that gave rise to the contemporary coastal populations and SP1060, and the lineage that gave rise to the majority of ancestry in contemporary pelagic populations. The WNA coastal and SP1060 are shown as independent lineages. The ENA coastal is depicted as a clade whose ancestry is a mixture of the two ancestral groups leading to SP1060 and WNA coastal. Ancient sample SP1060 is therefore not a direct ancestor of the contemporary ENA coastal dolphins. The ancestry of both North Atlantic contemporary pelagic populations appears to be an admixture of ~30% of the lineage giving rise to the coastal populations, and ~70% from a deeply divergent lineage. Source data are provided in the DataSuds repository.