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.

Populations of anadromous Pacific salmon and steelhead are increasingly threatened by degradation and loss of critical freshwater habitat, as well as poor survival at sea. Coho salmon (Oncorhynchus kisutch) populations in California, which represents the southern limit of the species' range, are particularly vulnerable to such environmental disturbances. Accordingly, all California populations are listed under the Endangered Species Act and have been placed into two Evolutionarily Significant Units (ESUs): the Southern Oregon/Northern California Coast (SONCC) ESU, which is listed as threatened; and the Central California Coast (CCC) ESU, which is listed as endangered. Despite these protections, many populations are threatened with extirpation and natural productivity is severely impacted by the lack of natural habitat. In order to facilitate recovery, several integrated recovery and conservation hatchery programs operate within these ESUs. However, how effectively these programs contribute to production in these high-risk populations has yet to be quantified, which prevents the development of evidence-based mitigation strategies that aim to incorporate artificial propagation.

In chapter one, I use pedigree reconstruction tools to understand current reproductive dynamics of coho salmon in the Shasta River, CA. I particularly focus on evaluating the contribution of excess adults released from the nearby Iron Gate Hatchery (IGH) to production within the Shasta to determine the efficacy of directly supplementing the Shasta population with these hatchery releases. Less than 10% of the juveniles sampled in the Shasta each year were assigned to IGH releases, suggesting low reproductive success amongst these individuals within the Shasta River. In chapter two, I assess the efficacy of the current Captive Broodstock program at Kingfisher Flat Hatchery on Scott Creek, CA. I again use pedigree reconstruction methods to perform parentage-based assignment for juveniles collected in Scott Creek, CA against a parental pool of adults that spawned both within the hatchery and the creek. Few Captive Broodstock adults were recovered as parents, again suggesting low reproductive success amongst these individuals.

I ultimately discuss the implication of these results with respect to management, indicating measures that may optimize both ongoing and proposed conservation strategies to ensure long-term stability within these imperiled populations of coho salmon.

Parallel adaptive divergence of migratory and reproductive behavior can occur in multiple populations when similar selection is acting on these traits. Timing of migration, sexual maturity, and reproduction can have major impacts on the dynamics and viability of a population. Life-history variation in steelhead, Oncorhynchus mykiss, including variation in anadromous run timing, reproductive maturity and spawn timing, represents an important aspect of their biology and adaptation to local habitats. Here we present a genetic analysis of naturally spawning steelhead to evaluate the genetic relationships and ancestry of summer- and winter-run reproductive ecotypes from multiple river basins in Oregon and Northern California. We infer the phylogeographic relationships among populations of both summer- and winter-run steelhead ecotypes using 12 microsatellite loci and 90 single nucleotide polymorphisms. Phylogenetic trees and analysis of molecular genetic variance revealed that pairs of phenotypically and genetically distinct reproductive ecotypes within rivers were each other’s closest relatives. Isolation by distance was also observed, confirming that genetic relatedness was strongly associated with geographic distance, and indicating limited migration or gene flow among river basins. These patterns support the hypothesis that the summer-run steelhead ecotype has repeatedly evolved through parallel evolution in multiple river basins. These results, together with further investigation of the underlying molecular basis for the divergence of winter- and summer-run steelhead life-history traits, will inform management and conservation efforts for these ecotypes and improve our understanding of the role of adaptive variation in conservation genetics.

Larval dispersal is consequential for the structure and dynamics of populations and the distribution of species. Most benthic marine species inhabit patchily distributed habitat and larval dispersal is often the primary means of population connectivity. Studies suggest that gene flow is the product of conduits and barriers to dispersal, including oceanic and geographic features and a combination of physical and behavioral mechanisms that effect the relationship between larval supply and settlement. Tracking larval dispersal in the ocean is considered one of the great logistical challenges in marine ecology, with a substantial history of using genetic markers to study dispersal. Although most studies apply indirect methods that integrate information across generations, in highly dispersive populations and across fine spatial scales, genetic parentage analysis has seen increasing use, but with limited examples from temperate environments or along open-coastlines where currents dominate and larvae may be advected offshore. Here, I describe larval dispersal of nearshore rockfishes across a network of marine reserves along the open-coastline of central California, a temper- ate current-driven ecosystem and the site of a network of marine protected areas (MPAs). Rockfishes of the genus Sebastes form a marine species flock of more than 100 species and are a prominent component of the ichthyofauna in temperate ecosystems. Kelp rockfish (S. atrovirens) are part of this species flock and one of >50 species present in the Monterey Bay, California region. In Chapter 1, I describe the development of a novel set of statistically powerful microhaplotype markers for efficiently performing pedigree relationship inference in the kelp rockfish and demonstrate that the false positive rates for single parent-offspring and full-sibling analyses are orders of magnitude lower than relying on the most informative single nucleotide polymorphism (SNP) in the same short-read sequence. In Chapter 2, I apply these new genetic markers to identify eight single parent-offspring pairs and 25 full siblings from thousands of samples of adult and juvenile rockfishes collected inside and outside of marine reserves. Dispersal between reserves and areas where fishing is allowed demonstrates the efficacy of the MPA network. Chapter 3 applies these microhaplotype markers to species identification of >50 rockfishes from the Northeast Pacific. Genetic assignment accuracy exceeds 99% and the species for which accuracy does not reach 100% are gopher (S. carnatus) and black-and-yellow (S. chrysomelas) rockfishes, sister species with evidence of ongoing gene flow. Phylogenetic analyses recovers relationships among species and subgenera concordant with previous studies. Finally, in Chapter 4, I analyze additional species of rockfishes obtained for the larval dispersal study and identify full siblings among juvenile gopher/black-and-yellow and copper rockfishes. Combining these data with results from Chapter 2, I compare the proportions of full sibling pairs among the species, finding the greatest proportion of full siblings sampled in the kelp rockfish. Collectively, these chapters provide valuable new genetic resources for studying rockfishes, describe the first direct observations of dispersal in rockfishes, and provide insight into the efficacy of a network of MPAs along an open-coastline.

Perhaps one of the world's most important groups of fish are the species within the Pacific trout complex, due to their harvest in fisheries and use in aquaculture. This dissertation consists of an in-depth evaluation of this group at different scales, from the assessment of biological traits throughout the reconstruction of pedigrees in two populations to a phylogeographic examination of multiple largely undescribed species. Here, a combination of novel molecular techniques allowed me to address critical ecological questions for the management and conservation of this group.

In chapter one, I describe the discovery, characterization and development of single nucleotide polymorphisms for O. mykiss for the study of ecological interactions, phylogeography, and conservation status. These tools have great power for population genetic analysis, and for individual identification and pedigree reconstruction. The last allows the tracking of families, and an unprecedented level of evaluation of natural and hatchery populations.

Chapter two expands the scope of these molecular tools to provide a powerful means of understanding of biological traits for steelhead hatchery programs in the Russian River, California. Reconstruction of cohort age distributions revealed a strong component of fish that spawn at age two, in contrast to program goals and distinct from naturally spawning steelhead. Correlations between family members in the day of spawning revealed a strongly heritable component to this life history trait and demonstrated the potential for selection to alter life history traits. These results demonstrate the promise of SNP-based pedigree reconstruction for providing biological inference in high-fecundity organisms.

Chapter three describes how the molecular tools developed were applied to population genetics of trout inhabiting northwestern Mexico, to elucidate biodiversity, and evolutionary history, and measure introgression from hatchery rainbow trout. Here, I confirmed the vast genetic diversity present in northwestern Mexican trout and provided evidence that trout inhabiting the Sierra Madre Occidental correspond to independent lineages separated from O. mykiss. Introgression from non-native trout was detected, but the genetic integrity of native trout is still maintained. All the information presented in this document will help to guide effective conservation strategies for this globally important group of fishes.

Steelhead/rainbow trout (Oncorhynchus mykiss) are found in all of the major tributaries of the Sacramento and San Joaquin rivers, which flow through California’s Central Valley and enter the ocean through San Francisco Bay and the Golden Gate. This river system is heavily affected by water development, agriculture, and invasive species, and salmon and trout hatchery propagation has been occurring for over 100 years. We collected genotype data for 18 highly variable microsatellite loci and 95 single nucleotide polymorphisms (SNPs) from more than 1,900 fish from Central Valley drainages to analyze genetic diversity, population structure, differentiation between populations above and below dams, and the relationship of Central Valley O. mykiss populations to coastal California steelhead. In addition, we evaluate introgression by both hatchery rainbow trout strains, which have primarily native Central Valley ancestry, and imported coastal steelhead stocks. In contrast to patterns typical of coastal steelhead, Central Valley O. mykiss above and below dams within the same tributary were not found to be each others’ closest relatives, and we found no relationship between genetic and geographic distance among below-barrier populations. While introgression by hatchery rainbow trout strains does not appear to be widespread among above-barrier populations, steelhead in the American River and some neighboring tributaries have been introgressed by coastal steelhead. Together, these results demonstrate that the ancestral population genetic structure that existed among Central Valley tributaries has been significantly altered in contemporary populations. Future conservation, restoration, and mitigation efforts should take this into account when working to meet recovery planning goals.