Genetic assessment of a summer chum salmon metapopulation in recovery

Abstract

Programs to rebuild imperiled wild fish populations often include hatchery-born fish derived from wild populations to supplement natural spawner abundance. These programs require monitoring to determine their demographic, biological, and genetic effects. In 1990s in Washington State, the Summer Chum Salmon Conservation Initiative developed a recovery program for the threatened Hood Canal summer chum salmon Evolutionarily Significant Unit (ESU) (the metapopulation) that used in-river spawners (wild fish) for each respective supplementation broodstock in six tributaries. Returning spawners (wild-born and hatchery-born) composed subsequent broodstocks, and tributary-specific supplementation was limited to three generations. We assessed impacts of the programs on neutral genetic diversity in this metapopulation using 16 microsatellite loci and a thirty-year dataset spanning before and after supplementation, roughly eight generations. Following supplementation, differentiation among subpopulations decreased (but not significantly) and isolation by distance patterns remained unchanged. There was no decline in genetic diversity in wild-born fish, but hatchery-born fish sampled in the same spawning areas had significantly lower genetic diversity and unequal family representation. Despite potential for negative effects from supplementation programs, few were detected in wild-born fish. We hypothesize that chum salmon natural history makes them less vulnerable to negative impacts from hatchery supplementation.

Congruent population structure across paralogous and nonparalogous loci in Salish Sea chum salmon (Oncorhynchus keta)

“…The estimated effective population sizes () based on nonparalogous loci were all above 100 and generally larger than previous studies (e.g., Small et al., ). We note that Small et al.…”

“…The estimated effective population sizes ( c N e ) based on nonparalogous loci were all above 100 and generally larger than previous studies (e.g., Small et al, 2014). We note that Small et al (2014) estimated N e over a different time period and also did not use a linkage map to exclude loci colocated on chromosomes, a source of downward bias (Waples, Larson, & Waples, 2016).…”

“…We note that Small et al. () estimated N e over a different time period and also did not use a linkage map to exclude loci colocated on chromosomes, a source of downward bias (Waples, Larson, & Waples, ). There were two collections with infinite estimates of N e ; Hoodsport Hatchery and Squakum Creek.…”

“…We also investigate the genetic associations with life history variation in both paralogous and nonparalogous loci. Our analysis focuses on chum salmon ( Oncorhynchus keta ) from a portion of the Salish Sea in the Pacific Northwest region of North America; populations of this anadromous species are characterized by distinct life history variation in time of spawning including summer, fall and winter runs (Small, Johnson, Bowman, & Martinez, ; Small et al., ). Time of spawning is an ecologically important trait in salmon that contributes to reproductive isolation and resilience (Schindler et al., ).…”

Chum Salmon Genetic Diversity in the Northeastern Pacific Ocean Assessed with Single Nucleotide Polymorphisms (SNPs): Applications to Fishery Management

“…Chum Salmon have a metapopulation structure (Small et al 2009) in which spawning aggregates are connected genetically through straying. Their genetic structure also suggests that strays choose tributaries with similar ecological conditions as their home tributary (Sands et al 2009;Small et al 2013). Across the range, the genetic structure in all salmonids in the northeastern Pacific Ocean has been shaped by geologic forces, most profoundly by Pleistocene events; nearly all tributaries in southern British Columbia and the Pacific Northwest were under continental glaciers, and their populations were founded at most »14,000 years before present, after ice sheets receded (Shafer et al 2010).…”