Scientists have successfully assembled the first high-quality reference genomes for New Zealand’s Hector’s and critically endangered Māui dolphins, despite working with degraded DNA samples. The new study reveals these dolphins have maintained small populations for thousands of years, with Māui dolphins showing 40% lower genetic diversity than their Hector’s cousins. The innovative genome assembly approach could become a valuable tool for conservation efforts worldwide.
The research provides crucial insights into these rare marine mammals – particularly the Māui dolphin, which is one of the world’s most endangered cetaceans with fewer than 100 individuals remaining in the wild.
A new approach to conservation genomics
Scientists studying endangered species often face a significant challenge: obtaining high-quality DNA samples. For many rare animals, like the Māui dolphin, most available tissues come from archived collections stored in less-than-optimal conditions – typically in ethanol at temperatures ranging from -20°C to 4°C – leading to DNA degradation over time.
Rather than abandon these valuable but imperfect samples, researchers developed an innovative genome assembly pipeline that leverages “synteny” – the similarity in chromosome structure and gene order between related species.
By using high-quality genomes from closely related cetaceans, particularly the bottlenose dolphin and vaquita, they created a reference framework that allowed them to properly assemble and organize the fragmented DNA pieces from Hector’s and Māui dolphins.
The technique proved remarkably successful, with more than 99% of the genome successfully mapped to chromosomes, meeting the rigorous standards of the Vertebrate Genomes Project. This achievement demonstrates that valuable genetic insights can be obtained even from suboptimal DNA samples.
Small populations and diminished genetic diversity
The newly assembled genomes revealed several important insights about these endemic New Zealand dolphins. Both dolphin subspecies have naturally maintained relatively small populations throughout the last thousands of years, making them inherently vulnerable to environmental changes and genetic drift.
The genetic analyses also revealed that Hector’s and Māui dolphins split into separate subspecies approximately 20,000 years ago, coinciding with the Last Glacial Maximum – a period when Earth experienced its last major ice age. This climate event likely isolated different populations along New Zealand’s coastline, eventually leading to the subspecies we see today.
Lastly, the analyses revealed some concerns for Māui dolphins. These dolphins showed 40% lower genetic diversity than Hector’s dolphins. This reduced diversity is comparable to other cetacean species known for reduced genetic diversity (such as river dolphins and some baleen whales), raising serious concerns about their ability to adapt to new environmental challenges.
Conservation implications
The genetic insights from this research extend far beyond scientific curiosity, offering practical guidance for protecting these vulnerable marine mammals. Conservation managers can now make better-informed decisions about protection measures, armed with a deeper understanding of each population’s genetic health and evolutionary history.
Continuous genetic monitoring becomes possible with these reference genomes, allowing scientists to detect concerning changes in the genetic diversity of Māui and all of Hector’s dolphin populations over time. But beyond New Zealand’s dolphins, the innovative methodology represents a significant advancement for conservation genomics. Researchers working with other endangered species can now apply similar techniques to extract valuable information from suboptimal samples that would previously have been considered inadequate for high-quality genome assembly.
A race against time
For Māui dolphins, these genomic insights come at a critical moment. Threats from fishing gear entanglement, vessel strikes, disease, and habitat degradation continue to pressure this tiny population.
The study serves as both a methodological breakthrough and a sobering reminder of human impacts on marine ecosystems. While Hector’s and Māui dolphins have naturally maintained small populations throughout their evolutionary history, human activities have pushed Māui dolphins to the brink of extinction – and their reduced genetic diversity may hamper their ability to adapt to emerging threats like climate change.
As genomic technologies continue to advance, integrating these genetic insights into conservation planning will be essential for preserving biodiversity in marine ecosystems under increasing pressure from human activities and climate change.
Sources and further readings
Alvarez-Costes, S., Baker, C.S., Constantine, R., Carroll, E.L., Guhlin, J., Dutoit, L., Ferreira, S., Heimeier, D., Gemmell, N.J., Gillum, J., Hamner, R.M., Rayment, W., Roe, W., Te Aikā, B., Urban, L. and Alexander, A. (2025), Leveraging Synteny to Generate Reference Genomes for Conservation: Assembling the Genomes of Hector’s and Māui Dolphins. Molecular Ecology Resources, e14109. https://doi.org/10.1111/1755-0998.14109
Did you enjoy reading about Hector’s and Māui dolphins? Check out our other posts about New Zealand’s amazing marine mammals:
Sebastian Alvarez-Costes
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