Ancestry testing of "Old Tom," a killer whale central to mutualistic interactions with human whalers

Abstract

Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as "Old Tom," washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom's genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.

Keywords: Indigenous knowledge; cetaceans; human-wildlife cooperation; mutualism; phylogenomics; whaling.

Graphical Abstract

Fig. 1.

A) Map of Eden relative to Twofold Bay (see square) in the context of Australia, detailing the location that the whalers and killer whales (Orcinus orca) used to cooperatively hunt baleen whales together. B) Whalers and killer whales of Eden on the chase of a humpback whale (Megaptera novaeangliae) captured between 1910 and 1920. Image by Charles E. Welling provided by Eden Killer Whale Museum.

Fig. 2.

Killer whale (Orcinus orca) mitogenome analysis based on 490 mitogenome sequences (166 unique haplotypes). A) World Map of 490 samples used in the study. B) Maximum likelihood phylogenetic tree of 166 haplotypes, based on an HKY nucleotide substitution model, colored by clade. The two museum samples sequenced for this study are labeled with asterisks. The tip representing the mitogenome sequence of Tom is marked with a light asterisk; the tip representing the Kattegat sample by the dark asterisk. A tree with all tips labeled can be found in Supplementary Material (Fig. S8).

Fig. 3.

Global dataset of Killer whale (Orcinus orca) nuclear genomes based on 1,093,893 transversions, A) displays a map of the sampling localities of the global dataset including Tom, with B) a genetic distance matrix in which increasing genetic distance is indicated by shading from red to blue. Self-comparisons are blacked out. The data displayed here was based on mapping to the mOrcOrc1.1 assembly. Black borders represent Tom and the New Zealand genome’s relationship. Ant, Antarctica; NP, North Pacific.

Fig. 4.

Australasian whole genome dataset of killer whales (Orcinus orca) with A) sample localities displayed of 38 animals, including Tom. A total of 1,087,094 transversions were used to B) assess the genetic clustering of Tom on a regional scale using a PCA based on covariance estimates, and C) estimate pairwise genetic distance between genomes. Increasing genetic distance is indicated by shading from red to blue, with self-comparisons blacked out. The data displayed here were based on mapping to the mOrcOrc1.1 assembly. In front of each sample is the locality of origin, MWA, midwestern Australia; NWA, northwestern Australia; NZ, New Zealand; QLD, Queensland; SWA, southwestern Australia; TAS, Tasmania.