DNA floating in seawater is now enough to let scientists monitor the health of America’s dolphin populations
Scientists shows that simply sampling seawater can reveal health of dolphin populations, in a first for conservation
image:
Common bottlenose dolphins off Southern California, USA. Photograph by John Durban / Holly Fearnbach using a drone at 200ft, authorized by NMFS Research Permit # 22306
view moreCredit: John Durban / Holly Fearnbach
DNA is everywhere in the world’s oceans – not only packaged inside cells from skin, scales, mucous, feces, and blood, but also floating freely. Sequencing such ‘environmental DNA’ (eDNA) from open water has long been used as a cost-effective way of gauging the number and identity of species in a region, especially when they are rare and elusive or living at great depths.
But species richness is only the most basic biodiversity measure. Until now, eDNA-based methods could only give limited insight into the variables that are most relevant for conservation: the number of individuals, the evenness of the abundances of co-occurring species, or their within-species genetic diversity. But that may be about to change, shows a new, groundbreaking study in Frontiers in Marine Science.
“Here we show that repeated eDNA sampling can be used to estimate the genetic diversity of dolphins that occur in large schools and have very large populations,” said corresponding author Dr Frederick Archer from the NOAA/NMFS Southwest Fisheries Science Center in La Jolla, California.
“This is important because genetic diversity, its outcome measure, can be used as a measure of population size and how ready a population is to react to changes in its environment.”
Around Santa Catalina Island, located 47 km off Long Beach in California, in October and December 2021, the researchers followed 15 schools of dolphins with small boats. They focused on the most common species locally: long-beaked common dolphins, short-beaked common dolphins, common bottlenose dolphins, and Risso’s dolphins. The project was directed the Marine Mammal Institute of Oregon State University (OSU), with funding from the US Office of Naval Research (ONR).
Whenever they encountered a school, the researchers collected a series of two-liter samples of seawater from the surface within 10 meters from the animals. Back in the laboratory, they sequenced each sample’s mitochondrial eDNA in the laboratory – paying particular attention to quality control – and compared the observed genetic diversity to that in public databases.
The scientists found 836 mitochondrial sequence variants in 126 water samples, of which 76% were from cetaceans and 60% from toothed whales. Overall, 29% were from the species of the school, which had been visually identified. Long-beaked common dolphins had the greatest genetic diversity, followed by short-beaked common dolphins, while Risso's and bottlenose dolphins proved much less diverse around Santa Catalina.
“Our study demonstrates the utility [of eDNA surveys] for efficiently assessing and comparing genetic diversity in social odontocetes,” concluded the authors.
The data indicated that in general, taking as many samples as feasible from multiple schools helps to gain an accurate estimate of the genetic diversity. The researchers calculated that between 60 and 72 liters of seawater would be enough for long-beaked common dolphins, the most diverse around Santa Catalina. But they emphasized that this volume may depend on the species.
“The temperature and salinity of the water are expected to affect the rate of skin shedding. Faster swimming affects shedding as well as respiration, so that DNA will be released through air blows at different rates. Feeding rate and prey should affect the frequency and composition of their defecation. The size of schools and behavior are also likely to be important, as bodies rubbing together or aerial activity such as breaching will promote shedding,” hypothesized Archer.
The authors are eager to put their methods to good use in conservation, now that they have been proven to work.
“It would be good to start eDNA monitoring programs as soon as possible that were not possible before. For example, we will be able to see how species composition in very small areas change over the course of a year – including rarer species that we don’t often detect on visual surveys,” said Archer.
“This can give us a lot of information on habitat use and will also allow us to potentially observe how environmental changes and anthropogenic effects such as pollution or underwater sound affect species distributions.”
Journal
Frontiers in Marine Science
Method of Research
Experimental study
Subject of Research
Animals
Article Title
Estimating genetic diversity of abundant oceanic dolphins through repeated environmental (e)DNA sampling
Article Publication Date
19-May-2026
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