Genetic interpretation of microsatellite polymorphism in Pacific salmon: case studies in population genetics and kinship analysis
I conducted five independent studies focusing on development and application of microsatellite DNA for intra-specific genetic analyses of Pacific salmon (Oncorhynchus spp.). I developed techniques for multiplex analysis of microsatellite loci for chinook, coho, sockeye and pink salmon using a semi-automated 4-color fluorescent detection system. I cloned seven novel microsatellite loci from pink salmon that also amplify in other species of Pacific salmon. I examined genetic variation at five microsatellite loci in 12 odd-year populations and one even-year population of pink salmon from six geographic regions of North America. The results suggest that the statistic theta is a better estimator of intra-lineage (odd-year x odd-year) population structure, whereas PST is best suited for estimating inter-lineage (odd-year x even-year) population structure. The difference in performance of theta and rho ST for estimating intra-lineage and inter-lineage population structure suggests high migration rates and short divergence times are dominant influences on genetic population structure in odd-year pink salmon. I compared microsatellites and allozymes for estimating population origin of individual pink salmon in a supportive breeding program. Both marker types reveal similarly low estimates of relative genetic differentiation (theta = 0.02) between two fall-run and summer-run populations but microsatellites provided a more accurate estimate of population origin. The difference in assignment success was best predicted by the statistic delta, which estimates cumulative allele frequency differences among populations. Finally, I used computer simulation and actual microsatellite data from a known chinook salmon pedigree to determine how number of loci, heterozygosity, parent population size and full sibs in the parent population affect pedigree reconstruction. The results indicate that parentage assignment success is highly sensitive to mean locus heterozygosity while moderate increases in parent population size have a minor affect on assignment success. The presence of closely related individuals in the parent population confounded pedigree reconstruction but the use of parent pair-offspring likelihood analysis improved resolution.
- Fisheries