Population genomics of the basket cockle Clinocardium nuttallii in the southern Salish Sea: Assessing genetic risks of stock enhancement for a culturally important marine bivalve

Coastal Indigenous communities that rely on subsistence harvests are uniquely vulnerable to declines in nearshore species. The basket cockle Clinocardium nuttallii is among the favored foods of Indigenous people along the northwest Pacific coast of North America, yet localized declines in their abundance have led to interest in stock enhancement efforts. We used a population genomics approach to examine potential risks associated with stock enhancement of C. nuttallii in the southern Salish Sea, a large inland estuary that includes Puget Sound. More than 8000 single nucleotide polymorphisms across 349 individuals at 12 locations were assembled de novo using restriction site‐associated DNA sequencing. Results indicated that C. nuttallii within the southern Salish Sea were distinct from those along the outer Pacific coast (F (ST) = 0.021–0.025). Within the southern Salish Sea, C. nuttallii populations appear to be well‐connected despite numerous potential impediments to gene flow; Hood Canal, which experiences the lowest flushing rates of all Puget Sound sub‐basins, was a minor exception to this strong connectivity. We found evidence of isolation by distance within the southern Salish Sea, but the slope of this relationship was shallow, and F (ST) values were low (F (ST) = 0.001–0.004). Meanwhile, outlier analyses did not support the hypothesis that southern Salish Sea sub‐populations are locally adapted. Estimates of effective population size had no upper bound, suggesting potentially very high adaptive capacity in C. nuttallii, but also making it difficult to assess potential reductions in effective population size resulting from stock enhancement. We present several strategies to augment cockle populations for subsistence harvest that would limit risk to the genetic diversity of wild cockle populations.