Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item 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 AEscalating 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.Item Population structure and genetic diversity of false killer whales (Pseudorca crassidens) in New Zealand waters: preliminary results(Taylor and Francis Group, 2024-05-30) Tezanos-Pinto G; Bohorquez L; Zaeschmar JR; Stockin K; Carroll EL; Caballero-Gaitan SFalse killer whales (Pseudorca crassidens) are globally distributed cetaceans, often found in deep oceanic waters but occasionally near coastlines. Despite their broad distribution, information on their abundance, genetics, and ecology remains limited. In New Zealand waters, these whales occur year-round, with increased sightings during the warmer months due to the East Auckland Current. This study investigates the genetic diversity and population structure of New Zealand false killer whales using 17 samples collected from 2005 to 2018 in four locations, comparing them to global studies. New Zealand samples revealed four unique haplotypes with low genetic diversity (h = 0.42 ± 0.141; π = 0.29%± 0.002). No genetic differentiation was observed between South Pacific and New Zealand populations (FST= 0.05 p = 0.1602 (Formula presented.) ST= 0.058 p = 0.145). These findings suggest low genetic diversity for New Zealand false killer whales, but within values expected for other cetaceans with matrilineal social structures. The presence of shared haplotypes suggests potential historical or ongoing connections with wider Pacific populations. However, further research is needed due to the short mtDNA-CR fragment analysed and small sample size, which may have resulted in an inability to capture the full extent of the genetic variation. This study contributes to our understanding of this species and its conservation within New Zealand.