UC Santa Cruz

Coho salmon (Oncorhynchus kisutch) is a species of Pacific salmon comprising an important component of the commercial and recreational fishing industry. However, over much of its native range, coho salmon population numbers have declined drastically and, as such, the species is facing extinction. For this reason, strides must be made to better manage and conserve remaining populations in order to ensure that this species will be present for future generations. This thesis provides an in depth evaluation of a population of coho salmon using pedigree inference combined with novel molecular techniques, in order to address several biological questions pertaining to the conservation of this species. In Chapter one, I describe the discovery, characterization and development of a large number of single nucleotide polymorphisms (SNPs) specific to coho salmon for the purpose of future biological inference. In Chapter two, I use these SNPs to reconstruct pedigrees, by way of intergenerational genetic tagging, in an ESA–listed hatchery population of coho salmon located in the Klamath River. Intergenerational genetic tagging involves genotyping parental individuals and using their genotypes as genetic tags that are recovered when the offspring of the parental generation are genotyped with the same markers. In this study, nine consecutive years of broodstock samples were genotyped with 96 SNPs, and tag retrieval was possible for three full cohorts in the offspring generations, revealing large proportions of age–two males returning to spawn at the hatchery, as well as the presence of large families distributed across relatively few parent pairs. Additionally, I performed an in depth evaluation of relatedness (Rxy) in this population by comparing SNP–generated pairwise Rxy values to those generated by microsatellites, in order to test and validate SNP utility for estimates of relatedness. The results of this analysis showed that mean relatedness values generated from both marker types can be skewed by the presence of a large number of half siblings sired by one two–year old male. However, when this individual’s offspring were accounted for, SNPs performed as well or better than microsatellites at estimating relatedness among individuals of known pedigree. The information provided by these tag recoveries will help us to better understand the effects of hatchery practices on hatchery spawned fish as well as the genetic effects of hatcheries on natural populations, which are important matters in regard to an ESA–listed species.