Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka)

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (N b ). Third, estimates of N b were bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.