Diving deep into dolphin DNA

Sunday, 12 July 2026

Brainwaves is a new weekly Post and Sunday Star-Times feature showcasing the best, brightest and most innovative minds in New Zealand. Each week we will bring you four pieces of research from each of the country’s top universities - the articles will cover a broad range of disciplines and topics as both a window into what Kiwis are working on, and a showcase of how we can mould the future through inventive thinking.

Sourcing DNA samples from rare dolphins can be a slippery challenge. Sebastian Alvarez-Costes, of the University of Otago – Ōtākou Whakaihu Waka, helped find an innovative way to create genomes without entering the water.

How do you save an endangered species without going near them? By diving into the archives.

Hector’s and Māui dolphins are only found in Aotearoa New Zealand. For Māori, they are both taonga and tapu – they have important roles as kaiārahi (guides) for the great voyaging waka that travelled to Aotearoa and for wairua (spirits) of those who have passed, returning to the ancestral homeland of Hawaiki.

Sadly, Hector's dolphins are classified as endangered, while the Māui dolphin is among the world’s most critically endangered marine mammals – fewer than 100 remain in the wild.

Of particular concern for both species are their small population sizes, inshore distribution, low reproductive rates, and exposure to human-caused impacts, including fisheries bycatch, pollution, vessel traffic, and emerging pathogens.

Creating genomes from DNA is hugely important for managing threatened species. It helps us understand their evolutionary history, genomic health, and adaptive potential in the face of threats.

However, as the two species are so rare, and getting samples from free-swimming aquatic mammals is tricky, pulling together a quality genome using their DNA is a challenge.

That’s where my PhD studies came in.

Alongside colleagues from Otago, the University of Auckland, Massey University, Oregon State University, and the University of Munich, I co-developed an innovative genome mapping process combining available, but degraded, archived DNA samples of Hector’s and Māui dolphins, with high-quality genomes from closely related whales and dolphins, fitting them together like puzzle pieces.

The assembly process leverages 'synteny' – that is similarities in the order of genes between related species and the structure of their chromosome.

Rather than abandon these valuable but imperfect samples, we looked at how we could work with what we had.

Using high-quality genomes from species, such as the bottlenose dolphin and vaquita, allowed us to create a reference framework to properly assemble and organise the fragmented DNA pieces from Hector's and Māui dolphins.

The technique proved remarkably successful, with more than 99% of the genome mapped to chromosomes.

These now look to be some of the best assembled genomes available for any whale or dolphin in the world.

Analysis of the genomes highlighted the dolphins’ vulnerability but also provided crucial insights to help conservationists better protect them.

Both dolphins have maintained small populations for thousands of years, making them susceptible to environmental changes and genetic drift.

We found Hector's and Māui dolphins split into separate subspecies approximately 20,000 years ago, coinciding with the last major ice age. This likely isolated different populations along New Zealand's coastline, eventually leading to the subspecies we see today.

Things are particularly bad for Māui dolphins as they have 40% lower genetic diversity, indicating they might be at risk of inbreeding and raising serious concerns about their ability to adapt to challenges like climate change.

Globally, the genome mapping technique has created excitement amongst conservationists as it opens up the possibility of generating genomic resources for other endangered species.

Growing concern about the impacts of reduced genetic diversity for endangered species has driven efforts to build more genomes for a range of species across the world.

The Hector’s and Māui dolphins project has become an exemplar genome for these researchers – it demonstrates that valuable genetic insights are possible even from suboptimal DNA samples. That means that our pipeline can potentially be used to generate high-quality genomic resources in other species.

Originally from Puebla, México, I moved to Dunedin to be supervised by world leading researchers Professor Neil Gemmell and Dr Alana Alexander in Otago’s Department of Anatomy.

There are some strong parallels between Hector’s and Māui dolphins and vaquita (a type of porpoise) in my home country.

Beyond advancing knowledge of these endangered subspecies, the research demonstrates how integrative genomic approaches can inform conservation strategies for small, isolated populations facing accelerating environmental change.

This type of work is highly valuable as the genomic maps act as a guidebook to help us take care of these animals for generations to come.

Dr Alana Alexander and Professor Neil Gemmell are Sebastian Alvarez-Costes’ co-supervisors.