DNA permeates the world's oceans, both packaged inside cells shed as skin, scales, mucous, feces, and blood, and floating freely in the water. Sequencing such environmental DNA (eDNA) from open water has long served as a cost-effective way to assess the number and identity of species in a region, particularly those that are rare, elusive, or living at great depths.
Until now, eDNA-based methods have largely been limited to counting species. The variables most relevant to conservation—the number of individuals, the evenness of abundances among co-occurring species, and within-species genetic diversity—have remained out of reach. A new study in Frontiers in Marine Science suggests that picture is shifting.
"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
Frederick Archer. "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."
The team worked near Santa Catalina Island, located 47 km off Long Beach, California, in October and December 2021. From small boats, they followed 15 schools made up of long-beaked common dolphins, short-beaked common dolphins, common bottlenose dolphins, and Risso's dolphins.
Whenever the researchers encountered a school, they collected a series of two-liter seawater samples from the surface within 10 meters of the animals. Mitochondrial eDNA from each sample was sequenced in the laboratory, and the resulting genetic diversity was compared with public databases.
Across 126 water samples, the scientists identified 836 mitochondrial sequence variants—76% from cetaceans and 60% from toothed whales. Long-beaked common dolphins showed the greatest genetic diversity, followed by short-beaked common dolphins, while Risso's and bottlenose dolphins proved much less diverse around Santa Catalina. The team estimated that between 60 and 72 liters of seawater would be enough to characterize long-beaked common dolphins, though the required volume may vary by species, behavior, and environment.
The authors are now eager to apply the method to conservation. "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," Archer said.
Until now, eDNA-based methods have largely been limited to counting species. The variables most relevant to conservation—the number of individuals, the evenness of abundances among co-occurring species, and within-species genetic diversity—have remained out of reach. A new study in Frontiers in Marine Science suggests that picture is shifting.
"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
Frederick Archer. "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."
The team worked near Santa Catalina Island, located 47 km off Long Beach, California, in October and December 2021. From small boats, they followed 15 schools made up of long-beaked common dolphins, short-beaked common dolphins, common bottlenose dolphins, and Risso's dolphins.
Whenever the researchers encountered a school, they collected a series of two-liter seawater samples from the surface within 10 meters of the animals. Mitochondrial eDNA from each sample was sequenced in the laboratory, and the resulting genetic diversity was compared with public databases.
Across 126 water samples, the scientists identified 836 mitochondrial sequence variants—76% from cetaceans and 60% from toothed whales. Long-beaked common dolphins showed the greatest genetic diversity, followed by short-beaked common dolphins, while Risso's and bottlenose dolphins proved much less diverse around Santa Catalina. The team estimated that between 60 and 72 liters of seawater would be enough to characterize long-beaked common dolphins, though the required volume may vary by species, behavior, and environment.
The authors are now eager to apply the method to conservation. "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," Archer said.