Evaluation of population structure in Pacific Lepeophtheirus salmonis (Krøyer) using polymorphic single nucleotide and microsatellite genetic markers: evidence for high gene flow among host species and habitats

Supervisory Committee Dr. Ben F. Koop, Supervisor (Department of Biology) Dr. R. John Nelson, Departmental Member (Department of Biology) Dr. Geraldine Allen, Departmental Member (Department of Biology) Parasitic copepods including Lepeophtheirus salmonis have been the focus of strong concern for the health of wild and farmed salmonids in the Pacific and Atlantic Oceans. Salmon are highly valuable species from both socioeconomic and ecological perspectives. The host-parasite dynamics of Lepeophtheirus salmonis and the Atlantic and Pacific salmonids have changed over evolutionary time to the point that both Atlantic and Pacific salmon and Atlantic and Pacific Lepeophtheirus salmonis are genetically distinct. Recent human interference with the natural population dynamics of this parasite and its hosts may have altered the population genetic structure of Lepeophtheirus salmonis, particularly because salmon farms may provide more stable conditions for parasite population growth. High abundance of Lepeophtheirus salmonis on salmon farms causes damage to the farmed salmon and leads to increased infection intensities in nearby wild hosts. Some Atlantic Lepeophtheirus salmonis have developed resistance to the anti-parasitic drugs they are repeatedly exposed to. No drug resistance has yet been detected within the Pacific Ocean, where only one drug is available, and heavily relied on, to treat Lepeophtheirus salmonis infections. Control of Lepeophtheirus salmonis abundance on Pacific salmon farms is important to maintain the health of farmed salmon and is also important to protect wild salmonids from increased infections originating from salmon farms. The goal of this thesis was to characterize and employ a large suite of molecular markers to assess the population structure of Lepeophtheirus salmonis in the Pacific Ocean. Until this point, the primary focus of Lepeophtheirus salmonis population iv genetics research has been limited to the Atlantic Ocean and has relied on a small number of available molecular markers. Available expressed sequence tag DNA libraries were screened to identify putative polymorphic loci, which were then experimentally evaluated. We characterized 22 novel microsatellite loci and 87 single nucleotide polymorphisms within 25 nuclear loci for Lepeophtheirus salmonis. We used these genetic markers, as well as 5 microsatellite loci previously developed for use in Atlantic Lepeophtheirus salmonis population studies, to genotype 562 Lepeophtheirus salmonis that were collected from12 Pacific Ocean sampling locations. We compared Lepeophtheirus salmonis genotypes among: (1) seven wild host populations and five farmed host populations within the Pacific Ocean; (2) geographically separated wild host populations, ranging from the Bering Sea to the southwest end of Vancouver Island, British Columbia; and (3) temporally separated cohorts of farmed Atlantic salmon from two geographically distant farm locations on the northwest coast of Vancouver Island and the Campbell River area east of central Vancouver Island. Our analyses failed to resolve significant population structure among sampled Pacific Lepeophtheirus salmonis and, therefore, supports a hypothesis of high gene flow throughout the Northeast Pacific Ocean. It is important to understand the biology and population dynamics of Lepeophtheirus salmonis because it is a consequential parasite of wild and farmed salmonids in the Pacific Ocean. Both the molecular tools developed for this study and the population genetics information generated from this study have contributed to our overall understanding of the evolutionary history and population dynamics of Lepeophtheirus salmonis.