Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries for Alaska Harbour Porpoises

Kim M Parsons; Samuel A May; Zachary Gold; Marilyn Dahlheim; Christine Gabriele; Janice M Straley; John R Moran; Kimberly Goetz; Alexandre N Zerbini; Linda Park; Phillip A Morin

doi:10.1111/mec.17563

Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries for Alaska Harbour Porpoises

Mol Ecol. 2024 Oct 25:e17563. doi: 10.1111/mec.17563. Online ahead of print.

Authors

Kim M Parsons¹, Samuel A May², Zachary Gold³, Marilyn Dahlheim^{4

5}, Christine Gabriele⁶, Janice M Straley^{5

7}, John R Moran⁸, Kimberly Goetz⁴, Alexandre N Zerbini^{9

10

11}, Linda Park^{1

5}, Phillip A Morin¹²

Affiliations

¹ Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA.
² College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA.
³ Ocean Molecular Ecology Group, Pacific Marine Environmental Laboratory, Oceanic and Atmospheric Research, National Oceanic and Atmospheric Administration, Seattle, Washington, USA.
⁴ Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA.
⁵ Retired.
⁶ Glacier Bay National Park and Preserve, Gustavus, Alaska, USA.
⁷ Applied Fisheries, University of Alaska Southeast, Sitka, Alaska, USA.
⁸ Auke Bay Laboratories, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, Alaska, USA.
⁹ Cooperative Institute for Climate, Ocean and Ecosystem Studies (CICOES), University of Washington, Seattle, Washington, USA.
¹⁰ Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA, Seattle, Washington, USA.
¹¹ Marine Ecology and Telemetry Research, Seabeck, Washington, USA.
¹² Marine Mammal Genetics Program, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California, USA.

PMID: 39450613
DOI: 10.1111/mec.17563

Abstract

Isolation by distance and biogeographical boundaries define patterns of population genetic structure for harbour porpoise along the Pacific coast from California to British Columbia. Until recently, inadequate sample sizes in many regions constrained efforts to characterise population genetic structure throughout the coastal waters of Alaska. Here, tissue samples from beachcast strandings and fisheries bycatch were supplemented with targeted environmental DNA (eDNA) samples in key regions of Alaska coastal and inland waters. Using a geographically explicit, hierarchical approach, we examined the genetic structure of Alaska harbour porpoises, using both mitochondrial DNA (mtDNA) sequence data and multilocus SNP genotypes. Despite a lack of evidence of genetic differentiation from nuclear SNP loci, patterns of relatedness and genetic differentiation from mtDNA suggest natal philopatry at multiple geographic scales, with limited gene flow among sites possibly mediated by male dispersal. A priori clustering of sampled areas at an intermediate scale (eastern and western Bering Sea, Gulf of Alaska and Southeast Alaska) best explained the genetic variance (12.37%) among regions. In addition, mtDNA differentiation between the Gulf of Alaska and eastern Bering Sea, and among regions within the Gulf of Alaska, indicated significant genetic structuring of harbour porpoise populations in Southeast Alaska. The targeted collection of eDNA samples from strata within Southeast Alaska was key for elevating the statistical power of our mtDNA dataset, and findings indicate limited dispersal between neighbouring strata within coastal and inland waters. These results provide evidence supporting a population boundary within the currently recognised Southeast Alaska Stock. Together, these findings will prove useful for ongoing management efforts to reduce fisheries conflict and conserve genetic diversity in this iconic coastal species.

Keywords: cetacean; eDNA; management; population structure.

Molecular Ecology© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Grants and funding

Office of Protected Resources, NOAA Fisheries