Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)
Article first published online: 2 JAN 2014
© 2013 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Volume 7, Issue 3, pages 355–369, March 2014
How to Cite
Larson, W. A., Seeb, L. W., Everett, M. V., Waples, R. K., Templin, W. D. and Seeb, J. E. (2014), Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evolutionary Applications, 7: 355–369. doi: 10.1111/eva.12128
- Issue published online: 17 MAR 2014
- Article first published online: 2 JAN 2014
- Manuscript Accepted: 2 OCT 2013
- Manuscript Received: 19 JUN 2013
- NOAA. Grant Number: # 44515
- Gordon and Betty Moore Foundation
- H. Mason Keeler Endowment for Excellence
- National Science Foundation. Grant Number: # DGE-0718124
- Chinook salmon;
- effective population size;
- genetic stock identification;
- population genomics;
- RAD sequencing;
- western Alaska
Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.