Genetic history of Chinook and sockeye salmon analyzed using ancient and contemporary mitochondrial DNA
Johnson, Bobbi May
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Pacific salmon (Oncorhynchus spp.) serve an important social and economic role in western North America. Despite historical abundance, native salmonids are now at risk of extinction throughout much of their native range. The accurate characterization of historic range, population size, and gene flow is essential for the development of successful conservation strategies. Therefore, conservation disciplines may look to the past to inform the future. One framework for such investigations is phylogeography, which examines geographical and genealogical connections in an effort to understand the evolutionary history of organisms. Another avenue is the study of genetic data from temporally diverse samples, which facilitates the direct observation of a genetic history. We utilize both methods to examine the history of two salmonid species, Chinook salmon (Oncorhynchus tshawytscha) and sockeye salmon (Oncorhynchus nerka). Additionally, two studies specific to challenges associated with degraded and low copy number (LCN) DNA sources were pursued. Chapter one characterizes the genetic diversity of Chinook salmon in the Columbia River basin using ancient and contemporary samples. The results indicate less genetic diversity in contemporary samples relative to ancient counterparts for both the Snake River and mid/upper-Columbia River subbasins studied. However, there appear to be higher losses of diversity in the mid/upper-Columbia than in the Snake subbasin. Chapters two and three explore specific challenges related to the study of ancient DNA: inhibition and contamination. The investigation of inhibition describes the development of a modified PCR protocol, rescue PCR, which successfully amplifies DNA of low-copy number in the presence of inhibitors. Chapter three, focusing on contamination, summarizes attempts to obtain DNA from formalin-preserved specimens and the resulting identification of non-target DNA from those samples. Finally, chapter four examines the history of sockeye salmon using DNA from contemporary samples in a phylogenetic framework. The genetic marker utilized was directly comparable to previous studies of Chinook salmon and rainbow trout (Oncorhynchus mykiss), allowing for comparisons of the phylogeographic history of three salmonid species with varying life histories. The results revealed limited genetic diversity and a more recent within-species divergence for sockeye salmon.