Browsing by Author "Baker CS"

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Ancestry testing of "Old Tom," a killer whale central to mutualistic interactions with human whalers
(Oxford University Press on behalf of the American Genetic Association, 2023-12) Reeves IM; Totterdell JA; Betty EL; Donnelly DM; George A; Holmes S; Moller L; Stockin KA; Wellard R; White C; Foote AD; Baker CS
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.
Leveraging Synteny to Generate Reference Genomes for Conservation: Assembling the Genomes of Hector's and Māui Dolphins
(John Wiley and Sons Ltd, 2025-04-04) Alvarez-Costes S; Baker CS; Constantine R; Carroll EL; Guhlin J; Dutoit L; Ferreira S; Heimeier D; Gemmell NJ; Gillum J; Hamner RM; Rayment W; Roe W; Te Aikā B; Urban L; Alexander A; DeWoody A
Escalating concern regarding the impacts of reduced genetic diversity on the conservation of endangered species has spurred efforts to obtain chromosome-level genomes through consortia such as the Vertebrate Genomes Project. However, assembling reference genomes for many threatened species remains challenging due to difficulties obtaining optimal input samples (e.g., fresh tissue, cell lines) that can characterise long-term conservation collections. Here, we present a pipeline that leverages genome synteny to construct high-quality genomes for species of conservation concern despite less-than-optimal samples and/or sequencing data, demonstrating its use on Hector's and Māui dolphins. These endemic New Zealand dolphins are threatened by human activities due to their coastal habitat and small population sizes. Hector's dolphins are classified as endangered by the IUCN, while the Māui dolphin is among the most critically endangered marine mammals. To assemble reference genomes for these dolphins, we created a pipeline combining de novo assembly tools with reference-guided techniques, utilising chromosome-level genomes of closely related species. The pipeline assembled highly contiguous chromosome-level genomes (scaffold N50: 110 MB, scaffold L50: 9, miniBUSCO completeness scores > 96.35%), despite non-optimal input tissue samples. We demonstrate that these genomes can provide insights relevant for conservation, including historical demography revealing long-term small population sizes, with subspecies divergence occurring ~20 kya, potentially linked to the Last Glacial Maximum. Māui dolphin heterozygosity was 40% lower than Hector's and comparable to other cetacean species noted for reduced genetic diversity. Through these exemplar genomes, we demonstrate that our pipeline can provide high-quality genomic resources to facilitate ongoing conservation genomics research.