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

TLDR

Population genomics now enables detection of hidden structure, more accurate demographic estimates, and adaptive divergence, transforming genetic management of wild populations. The study aimed to use RAD sequencing to identify SNPs and assess population structure, demography, and effective population size in five western Alaskan Chinook salmon populations. RAD sequencing generated 10,944 SNPs, which were used to estimate effective population size (with and without linked loci) and to perform outlier tests that identified 733 loci and three genomic regions under selection. The approach yielded >90 % assignment accuracy, effective population sizes above 1,000 that were underestimated when linked loci were included, and identified 733 loci and three regions under selection that can serve as high‑resolution markers for conservation monitoring.

Abstract

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 (&gt;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.