Assessing genetic diversity of protected coho salmon (Oncorhynchus kisutch) populations in California

California coho salmon (Oncorhynchus kisutch) are under legal protection owing to significant declines in abundance over the last decades. Previously, California coho salmon were characterized as having low genetic diversity and weak population subdivision, attributable potentially to homogenization by out-of-basin hatchery releases. Here, diversity at seven highly polymorphic microsatellite DNA markers is assessed within and among 32 collections of coho salmon from 16 California watersheds. In 71% of local populations, genotypic composition deviates significantly from that expected under the assumption of random mating. We develop and apply methods to adjust for two potential causes of deviation from random mating expectations: (i) Wahlund effects, owing to heterogeneous collections of individuals, and (ii) the Allendorf-Phelps effect, owing to closely related juveniles in samples. Such population-level adjustments reduce within-region and increase among-region variance; after adjustment, we find strong concordance of genetic and geographic distances. We conclude that stock transfers have had minimal impact on population structure and that California coho salmon populations likely comprise small numbers of endemic breeders, potentially experiencing high levels of genetic drift and inbreeding.