Data from: Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon

We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (>90% average genotyping across all individuals) and low genotyping error (<0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction.

Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrate GT-seq as a valuable tool for genome-wide data collection from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.

Usage notes onco_223ind_271snp.vcf: genotypic data for 23 individuals at 271 SNPs generated via GT-seq. metadata.xlsx: individual metadata including sample identifiers, location, year sampled, fork length, weight, age and sex (if known).