INFORMING CONSERVATION ACTIONS : GENETIC APPROACHES TO CHINOOK SALMON MANAGEMENT IN THE SACRAMENTO RIVER OF CALIFORNIA

Biocomplexity provides many benefits to ecosystems, chief among them allowing for species persistence and resilience. Genetic diversity is the fundamental building block that allows for intraspecific diversity. Unfortunately, anthropogenic changes to the environment have led to a sharp decrease in the abundance of many species, therefore reducing genetic diversity within and among populations. This increases the need for ways to monitor this complexity, and genetic methods are a very promising tool. In this dissertation, I explore biocomplexity through the lens of life history diversity in Chinook salmon (Oncorhynchus tshawytscha), a culturally, ecologically, and economically important species. The Sacramento River of California is the only place throughout the entire range where fish return at four different times during the year to spawn (Fall, Late Fall, Spring, and Winter), providing them with important adaptive variation to ensure population persistence and resilience. This phenotype, known as their run type or run timing, can be identified using genetics and is important for monitoring, as the run types are morphologically indistinguishable at most life stages and two of the run types are federally listed as threatened and endangered (Spring and Winter, respectively). My research explores broadly how we can use genetic methods to assess and monitor biocomplexity of imperiled species in highly altered environments using genetic tools and methods.In Chapter 1, “Genetic Assessment of Floodplain Habitat Use by Juvenile Chinook salmon”, I explore how biocomplexity in juvenile Chinook salmon in a managed floodplain in California can buffer the effects of climate change. To do this, I genetically identified juvenile Chinook salmon samples from surveys in the Sacramento River and Yolo Bypass to run type using an 80 loci informative Fluidigm panel. I first analyzed how accurate current management methods are at identifying run-type as compared to genetic methods, finding that current methods are often inaccurate. I further found that drought conditions had negative impacts on imperiled populations of juvenile Chinook salmon. Despite this, I found that even during periods of drought, the Yolo Bypass juvenile Chinook salmon attained larger sizes than the adjacent Sacramento River, suggesting that managed floodplain is critical for maintaining diversity in this system. In Chapter 2, “Remnant salmon life history diversity rediscovered in a highly compressed habitat”, I explore how genetic tools can be utilized to understand run timing in the Yuba River of California. I did this by assigning individuals to early or late migrating groups, based on informative genetic markers from the GREB1L region of the Chinook genome and compared that to date of entry in the system. I found that despite large amounts of anthropogenic alteration, the Yuba River supports life history diversity of Fall and Spring run types, and this diversity is correlated with the genetic markers in the GREB1L region of the Chinook genome. This study highlights the incredible resilience of Chinook salmon populations in the Yuba River, as well as validates exciting new genomic regions that can be used for monitoring populations in the Sacramento River. In Chapter 3, “Genetic divergence of recently introduced populations of Chinook salmon (Oncorhynchus tshawytscha) in New Zealand”, I explore how New Zealand populations of Chinook salmon compare genetically to each other, as well as how they have diverged from their source, Chinook salmon from the Sacramento River of California. This research is the first time New Zealand Chinook salmon have been compared to all four run types in the Sacramento River and is a critical first step in understanding those relationships. To do this, I analyzed genomic data obtained from genotyping by sequencing and restriction site associated DNA sequencing data from Chinook salmon sampled in rivers in New Zealand and all major tributaries and run types from the Sacramento River. I found that there is genetic structure between the different rivers in New Zealand, and that although New Zealand fish have diverged from the Sacramento River fish, they appear more genetically similar to contemporary Fall and Spring run populations than to contemporary Winter run. This research highlights the importance of genomic tools to understand genetic relationships and could inform restoration efforts such as genetic rescue. This body of work highlights the importance of using genetic tools for management of imperiled species, especially identifying and monitoring biocomplexity. It also addresses how anthropogenic activities can impact species and systems, which will be important in informing how to mitigate potential impacts on imperiled species.