Genetic interpretation of broad-scale microsatellite polymorphism in odd-year pink salmon

We examined genetic variation at five microsatellite loci in 12 odd-year populations and one even-year population of pink salmon Oncorhynchus gorbuscha from six geographic regions of North America. The degree of polymorphism varied widely among loci. The total number of alleles in the odd-year samples varied from 4 (Oneμ3) to 53 (Ssa85). A probability test revealed significant heterogeneity in allele frequencies among all odd-year samples and among pooled odd-year samples from six regions. We compared estimates of a standard index of population structure (θ) based on variance in allele frequency with a new index suggested for microsatellites (ρ_ST) based on variance in allele size. Our results suggest is a better estimator of intralineage (odd-year × odd-year) population structure, whereas is best suited for estimating interlineage (odd-year × even-year) population structure. The difference in performance of and for estimating intralineage and interlineage population structure suggests high migration rates and possibly recent low divergence times are dominant influences on genetic population structure in odd-year pink salmon. We showed statistical support for genetic isolation by distance and geographically correlated allele frequency clines, suggesting broad-scale gene flow is best described by a linear stepping-stone model. An analysis of molecular variation showed weak but significant regional structuring under two different population grouping schemes. Our results suggest broad-scale population aggregations of odd-year pink salmon are temporally stable but that differentiation is weak, presumably due to migration.