Hierarchical Phylogeographic Structure of Coho Salmon in California

Abstract

Evaluation of population genetic structure and variation is an important part of planning for the recovery and management of protected species. Data from 18 polymorphic microsatellite DNA markers were used to analyze the phylogeographic structure of protected Coho Salmon Oncorhynchus kisutch from populations throughout California. Fish from 30 locations in two evolutionarily significant units (ESUs) representing most of the extant populations in the state were studied. Multiple analyses indicated a hierarchical pattern of population structure: the greatest divergence was found at the broadest geographic scale (ESU), followed by the divergences between basins and populations within basins. The populations of the large Klamath River basin were consistently identified as a distinct phylogenetic group, nearly as divergent from all other populations as the two ESUs were from each other. All populations in different basins were differentiated from each other and a pattern of isolation by distance was found at a California‐wide scale, but not at smaller spatial scales. Similarly, most individuals were accurately assigned to their population of origin, and almost all misassignments were to an adjacent or geographically proximal basin, indicating that there is substantial gene flow within each region but much less between regions. The number of parents contributing to each population was highly variable and reflected larger patterns of genetic variation, which was found to be generally higher in the southerly, low‐elevation coastal populations than in the northern, interior, higher‐elevation populations. The results strongly support the current boundary between the two ESU regions, and the detailed understanding of phylogeographic structure provided here will help to guide the management and recovery of Coho Salmon at the southern end of their geographic range. Received August 25, 2015; accepted May 4, 2016 Published online August 12, 2016

Long‐distance migration is a major factor driving local adaptation at continental scale in Coho salmon

“…These results indicate that genetic variation mirrors geography for Coho salmon, similar to human populations (Menozzi et al, 1978;Novembre et al, 2008). As previously observed, some Californian samples displayed high genetic diversity while others displayed reduced diversity, strongly suggesting recent population declines in some of these rivers (Rougemont et al, 2020;Gilbert-Horvath et al, 2016;Williams et al, 2011). Accordingly, highest levels of genetic diversity and lower β ST were observed in Cascadia, rather than California, as already noted (Rougemont et al, 2020).…”

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

“…All regions differed significantly in their distribution of singleton (p < 0.0001) except the comparison between Thompson and California ( S3 Fig ) The observed signal in the Thompson was consistent with our above observations of reduced diversity. Similarly, we hypothesized that such reduced number of singletons in a few Californian samples reflects recent and strong population declines in some of these populations [ 44 , 45 ] (see also S1 Text ). The similarity of the singleton distributions for both Cascadia and Alaska further emphasized the need for additional analyses (i.e.…”

Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding

“…The high number of ND2 haplotypes within the Coquille watershed, and the observation of shared haplotypes between the Coquille watershed and the Klamath and Nestucca watersheds agrees with previous studies demonstrating higher within‐population genetic variation than between populations (Ford et al, 2004 ; Olsen et al, 2003 ). In contrast, the Nestucca and Coquille O. kisutch populations belong to a different evolutionarily significant unit than the Klamath population (Lawson et al, 2007 ), and the Klamath population has been shown to belong to a lineage distinct from other California populations (Gilbert‐Horvath et al, 2016 ). The pattern of haplotypes observed here may imply migration from the Coquille watershed to the Klamath and Nestucca watersheds, and the Coquille watershed has been classified as a “functionally independent population” by Lawson et al ( 2007 ), meaning migration from other populations does not substantially affect it and it is a net donor to small populations (Lawson et al, 2007 , p. 10).…”