Temporal and Geographic Genetic Divergence: Characterizing Sockeye Salmon Populations in the Chignik Watershed, Alaska, Using Single-Nucleotide Polymorphisms

Abstract

The high fidelity of Pacific salmon Oncorhynchus spp. to their natal spawning habitat often results in genetically divergent populations. Management and conservation of the natural variation within species is critical for maintaining robust populations. The Chignik watershed, Alaska, supports highly productive populations of sockeye salmon Oncorhynchus nerka that vary in return timing and spawning locations among breeding populations, presenting challenges to the management of commercially exploited stocks. We describe the genetic structure of the sockeye salmon populations spawning in the Chignik watershed using 45 single-nucleotide polymorphisms from 2,013 individuals representing 19 collections of spawning adults. From these data we estimated within-population statistics and among-population divergence, detected loci in linkage disequilibrium and loci that are F _ST outliers, and tested loci for potential use in mixed-stock assessments. The results indicate significant genetic structure among the sockeye salmon populations in the Chignik watershed at both spatial and temporal scales. This structuring can be largely explained by putative evidence of selection at two markers and the differences in spawn timing between populations. Genetic structure determined at geographic and temporal levels provides a basis for application in the conservation of this resource and the management of commercial and subsistence fisheries.

ACKNOWLEDGMENTS

This project was a collaborative effort of the Alaska Department of Fish and Game (ADFG) Gene Conservation Laboratory and the University of Washington. We are grateful for access to samples of adult spawning collections collected by ADFG and Greg Ruggerone. We especially thank Mark Witteveen and Chris Habicht of ADFG and Jim Seeb, Fred Utter, Carita Pascal, and Eric Grau of the University of Washington School of Aquatic and Fishery Sciences. Helpful comments were provided by Daniel Gomez-Uchida and Molly McGlauflin. Funding for this study was provided by the Alaska Sustainable Salmon Fund under award 63-5096 from the National Oceanic and Atmospheric Administration, administered by ADFG. The statements, findings, conclusions, and recommendations are those of the authors and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, the U.S. Department of Commerce, or ADFG. Support for graduate research was provided by ADFG Cooperative Study 08-150, National Science Foundation grant OCE-0410437, and the Gordon and Betty Moore Foundation. The Gordon and Betty Moore Foundation also funded the establishment of the genetics laboratory at the University of Washington School of Aquatic and Fishery Sciences, where some of the samples used in this study were analyzed.