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

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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 ) and candidates for diversifying selection were not more likely to show significant temporal changes than small- 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.

Document Type: Research Article


Affiliations: 1: School of Aquatic and Fishery Sciences, 1122 NE Boat Street, Box 355020, Seattle, WA 98195-5020, USA. 2: Division of Commercial Fisheries, Alaska Department of Fish and Game, 333 Raspberry Road, Anchorage, AK 99518, USA.

Publication date: May 26, 2012

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  • Published continuously since 1901 (under various titles), this monthly journal is the primary publishing vehicle for the multidisciplinary field of aquatic sciences. It publishes perspectives (syntheses, critiques, and re-evaluations), discussions (comments and replies), articles, and rapid communications, relating to current research on cells, organisms, populations, ecosystems, or processes that affect aquatic systems. The journal seeks to amplify, modify, question, or redirect accumulated knowledge in the field of fisheries and aquatic science. Occasional supplements are dedicated to single topics or to proceedings of international symposia.
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