Using eDNA to supplement population genetic analyses for cryptic marine species: identifying population boundaries for alaska harbour porpoises

Authors: PARSONS, KIM - National Oceanic & Atmospheric Administration (NOAA); May, Samuel; GOLD, ZACHARY - National Oceanic & Atmospheric Administration (NOAA); DAHLHEIM, MARILYN - National Oceanic & Atmospheric Administration (NOAA); GABRIELE, CHRISTINE - Glacier Bay National Park And Preserve; STRALEY, JANICE - Southeast Alaska University; MORAN, JOHN - National Oceanic & Atmospheric Administration (NOAA); GOETZ, KIMBERLY - National Oceanic & Atmospheric Administration (NOAA); ZERBINI, ALEXANDRE - University Of Washington; PARK, LINDA - National Oceanic & Atmospheric Administration (NOAA); PHILLIP, MORIN - National Oceanic & Atmospheric Administration (NOAA)

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2024
Publication Date: 10/25/2024
Citation: Parsons, K.M., May, S.A., Gold, Z., Dahlheim, M., Gabriele, C.M., Straley, J.M., Moran, J.R., Goetz, K.T., Zerbini, A.N., Park, L., Phillip, M. 2024. Using eDNA to supplement population genetic analyses for cryptic marine species: identifying population boundaries for alaska harbour porpoises. Molecular Ecology. Article e17563. https://doi.org/10.1111/mec.17563.
DOI: https://doi.org/10.1111/mec.17563

Interpretive Summary: Characterizing population genetic structure is one important way in which stock boundaries are defined for management purposes. In species where tissue samples are difficult to obtain, efforts to characterize structure may generate coarse results and therefore less accurate stock boundaries and less efficient management. Harbor porpoises in the North East Pacific are one such species where tissue samples are difficult to obtain. Here, we used a dataset of tissue samples collected over decades from porpoises that washed up on beaches or were accidentally caught by fisheries throughout Alaska. Still, this dataset was small. We supplemented this data with environmental DNA samples, collected by taking water samples from areas where live porpoises had recently swam. These sampling methods produce different kinds of DNA (genomic vs. mitochondrial), and their combined use increased our statistical power to identify genetic structure. Our study revealed finer-scale genetic structure than had previously been identified in the state. Results also provided support for a population/management boundary within Southeastern Alaska, which was previously recognized as a single stock for management purposes.

Technical 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 characterize population genetic structure throughout the coastal waters of Alaska. Here, tissue samples from beach cast 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 neighboring strata within coastal and inland waters. These results provide evidence supporting a population boundary within the currently recognized 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.