New Clues Reveal Genetic Diversity among Alaska's Harbor Porpoises

Harbor porpoises are shy, elusive creatures that live in Alaska's coastal waters and are vital parts of the marine ecosystem. But how these animals are distributed and connected across the vast Alaskan waters remains a mystery. A new studypublished in the scientific journal Molecular Ecologysheds light on the hidden structure of Alaska's harbor porpoise populations, using the powerful tools of environmental DNA (eDNA) and molecular genetic analyses.

Research Challenges

Studying harbor porpoises can be tricky. Their shy nature and preference for nearshore habitats make them difficult to approach and collect tissue samples from directly. Previous research relied on samples gathered opportunistically from beach strandings and fisheries bycatch, which limited the complete picture.

This new NOAA Fisheries-led study tackled these challenges with a two-pronged approach. First, researchers utilized the existing collection of tissue samples, spanning decades of dedicated effort. Second, they harnessed the power of eDNA, a revolutionary approach that detects tiny traces of genetic material left in the water behind passing animals. By strategically collecting eDNA samples from key areas where harbor porpoises occur, scientists were able to glean valuable genetic information from these elusive creatures without needing to collect tissue samples from every individual.

Two Harbor Porpoises swimming in Southeastern Alaskan waters. Credit: NOAA Fisheries

Unveiling Hidden Populations with eDNA

Traditionally, information on the genetic structure of animal populations was based on the analysis of tissue samples. The need for large numbers of tissue samples is incredibly time-consuming and can be very challenging for elusive species like harbor porpoises. Thankfully, science has a new tool in its toolbox: environmental DNA (eDNA).

eDNA consists of tiny fragments of genetic material shed by animals in their environment, like skin flakes or bits of scat. By collecting and analyzing eDNA from water samples, scientists can indirectly detect the presence of species, even in areas where direct tissue sampling is difficult.

This study harnessed the power of eDNA alongside traditional tissue samples collected over decades from beach strandings and fisheries bycatch. This innovative approach allowed researchers to gather genetic data from harbor porpoises across a wider range of areas than ever before.

"The use of eDNA alongside traditional tissue samples allowed us to gain a much more comprehensive picture of harbor porpoise population structure in Alaska," notes Kim Parsons, a research geneticist at NOAA's Northwest Fisheries Science Center and lead author of the paper. "These findings highlight the importance of considering genetic data when managing this species and paves the way for more effective conservation strategies."

Dorsal fin of a harbor porpoise. Credit: NOAA Fisheries.

Limited Dispersal Shapes Population Structure

The analysis of both mitochondrial DNA (mtDNA) and nuclear DNA markers revealed a fascinating story. The data indicate limited movement between harbor porpoise populations in different regions of the Gulf of Alaska and the Bering Sea. This finding mirrors what's been observed in coastal harbor porpoise populations along the West Coast from California to Washington.

While some nuclear markers didn't show strong evidence for separation, patterns in mtDNA and overall relatedness suggest that harbor porpoises exhibit a degree of "site fidelity." This means they tend to stay in specific areas and don't stray far from their birthplace, even if they make daily or seasonal movements. This limited dispersal between regions can lead to distinct genetic signatures in different populations.

Two Harbor Porpoises swimming. Credit: NOAA Fisheries

Southeast Alaska's Hidden Diversity

The study also revealed intriguing details within Southeast Alaska. Genetic analysis, including data from targeted eDNA sampling, uncovered significant genetic differentiation within the previously recognized management unit for harbor porpoises. This suggested the presence of multiple, demographically independent populations within this region.

These findings built upon past workand align with previous observations that hinted at distinct populations. For instance, studies noted contrasting abundance trends and distributional gaps within Southeast Alaska. Together, these studies support recent revisions to the stock assessment report for harbor porpoises in Southeast Alaska that better reflect the population structure.

Dorsal fin of a harbor porpoise. Credit: NOAA Fisheries.

Why Population Structure Matters

"Understanding population structure is critical for harbor porpoises because it allows us to identify distinct groups with potentially different vulnerabilities," explained Anne Marie Eich, who leads NOAA Fisheries Alaska Regional Office Protected Resources Division. "By treating these groups as separate entities, we can develop more targeted conservation strategies."

This study's successful use of eDNA paves the way for future research on cryptic marine species like harbor porpoises. This innovative approach, along with conventional methods, promises to unlock even deeper secrets about these fascinating creatures and the vital role they play in Alaska's marine ecosystems.

This innovative study, utilizing the power of eDNA, provides a wealth of new information about Alaska's harbor porpoises. It reveals a population structure more complex than previously understood, highlighting the importance of considering genetic data for effective conservation. By acknowledging these hidden differences, we can ensure a brighter future for these captivating creatures who grace the icy waters of Alaska.

NOAA Fisheries is continuing to work closely with Alaska Department of Fish and Game to further our collective understanding of harbor porpoise stock structure in Southeast Alaska and the extent and significance of interactions between porpoise and salmon gillnet fisheries.

Research is needed to further refine our knowledge of abundance and distribution throughout southeast Alaska. Additional data are also needed on the level of fishery bycatch, where and when bycatch is occurring, for the Yakutat/Southeast Alaska offshore waters stock.

Based on 2007-2008 observer data the Yakutat salmon set gillnet fishery had an estimated bycatch of 22 harbor porpoises per year. Because we have no current abundance estimate and thus cannot calculate a Potential Biological Removal(PBR) level, we do not know whether this level of bycatch is sustainable.

To gather updated estimates of rates of bycatch of harbor porpoise in the Southeast Alaska salmon gillnet fisheries, We are implementing the Alaska Marine Mammal Observer Program. The last observer observations of these fisheries is from 2012-13.

Initial results of this research were used in 2022 to designate new stocks of harbor porpoise in 2022. Given the new stock structure, a potential conservation problem for the Southern Southeast Alaska Inland Waters stock was highlighted because the estimated mortality and serious injury (7.4 individuals/year) from the Southeast Alaska salmon drift gillnet commercial fishery exceeds the stock's PBR level (6.1 individuals/year). This level of estimated mortality and serious injury is based on the 2012-13 observations of the fishery and is the best estimate currently available. New observations via the Alaska Marine Mammal Observer Program will enable us to refine that estimate.

We are exploring ways to reduce bycatch of this stock to below the PBR level. For instance, Alaska Fisheries Science Center is also conducting research on gear modifications (specifically, pingers) as a potential tool to reduce harbor porpoise bycatch in Southeast Alaska salmon gillnet fisheries.

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