Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

Evolutionary Applications

Wesley A. Larson¹  Lisa W. Seeb¹  Meredith V. Everett¹  Ryan K. Waples¹  William D. Templin² 

[1] School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA;Gene Conservation Laboratory, Alaska Department of Fish and Game, Anchorage, AK, USA

关键词: Chinook salmon;    effective population size;    genetic stock identification;    population genomics;    RAD sequencing;    SNPs;    western Alaska;   

DOI  :  10.1111/eva.12128

来源: Wiley

【 摘 要 】

Abstract

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.

【 授权许可】

CC BY   
© 2013 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.

Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.