Journal Articles

Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

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    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.
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    Estimating abundance of a small population of Bryde's whales: a comparison between aerial surveys and boat-based platforms of opportunity
    (John Wiley & Sons Ltd., on behalf of Zoological Society of London, 2024-08-01) Hamilton ONP; Fewster RM; Low P; Johnson F; Lea C; Stockin KA; van der Linde K; Constantine R; Boersch-Supan P; Williams R
    Accurate abundance estimates are essential for the development of effective conservation management strategies, yet they are difficult to produce for small populations that are elusive and sparsely distributed throughout their range. For such populations it is challenging to collect a representative dataset sufficient for robust estimation of detectability and abundance. Over a one-year study, we used two methods to estimate abundance of a Nationally Critical, widely dispersed Bryde's whale population in the Hauraki Gulf, Aotearoa/New Zealand; (i) distance sampling from systematic line-transect aerial surveys (n = 22 surveys, 9,944 km, total sightings 21–24 whales), and (ii) mark-recapture (MR) using photo-identification images collected from a platform-of-opportunity and small-boat surveys (218 sampling occasions, 27 whales). From the aerial surveys, we estimated an average of 15 whales (95% CI = 6, 30; CV = 37%) at the sea-surface at any time. For the boat-based surveys, we developed a custom MR model to address seasonal and individual heterogeneity in capture probabilities and obtained an estimate of 72 distinct whales (95% CI = 38, 106; CV = 24%) in the population. These two approaches provide different perspectives on the abundance and dynamics of Bryde's whales. The aerial surveys estimate the average number of individuals present at any one time, whereas the MR model estimates the total number of animals that used the Gulf during the study. Although neither sampling method is optimal for estimating the abundance of this small, dispersed population, the use of two complementary approaches informs conservation managers about patterns of abundance and distribution over different temporal and spatial scales. It is common to have limited resources for marine research where model assumptions cannot be met. Here, we highlight pragmatic strategies showing how models can be customized to the population of interest to assist with monitoring species of conservation concern.
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    Looking Back to Move Forward: Lessons From Three Decades of Research and Management of Cetacean Tourism in New Zealand
    (Frontiers Media S.A., 2021-02-11) Fumagalli M; Guerra M; Brough T; Carome W; Constantine R; Higham J; Rayment W; Slooten E; Stockin K; Dawson S; Pacheco AS
    Cetacean tourism in Aotearoa New Zealand is now over 30 years old and has experienced substantial growth in visitor numbers and operations. The industry is remarkably diverse, targeting several dolphin and whale species, and encompassing varied habitats in coastal waters, fiords and submarine canyons. The knowledge and experience collected over these past 30 years has both advanced the global understanding of cetacean tourism, and influenced scientific practices for its study and management. Here we review the approaches taken in quantifying the impact of cetacean tourism in New Zealand, and critically assess the efficacy of the research and management strategies adopted. We place particular focus on the Bay of Islands, Hauraki Gulf, Kaikoura, Akaroa and Fiordland, areas that include the oldest, and longest studied industries nationally. We propose a set of best research practices, expose the most notable knowledge gaps and identify emerging research questions. Drawing on perspectives from the natural and social sciences, we outline the key determinants of failure and success in protecting cetacean populations from the detrimental impact of tourism. We suggest four golden rules for future management efforts: (1) acknowledge cetacean tourism as a sub-lethal anthropogenic stressor to be managed with precaution, (2) apply integrated and adaptive site- and species-specific approaches, (3) fully conceptualize tourism within its broader social and ecological contexts, and (4) establish authentic collaborations and engagement with the local community. Lastly, we forecast upcoming challenges and opportunities for research and management of this industry in the context of global climate change. Despite New Zealand's early establishment of precautionary legislation and advanced tourism research and management approaches, we detected flaws in current schemes, and emphasize the need for more adaptive and comprehensive strategies. Cetacean tourism remains an ongoing challenge in New Zealand and globally.