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

Historical DNA analysis of archival samples has added new dimensions to
population genetic studies, enabling spatiotemporal approaches for
reconstructing population histories and informing conservation management.
Here we tested the efficacy of Genotyping-in-Thousands by sequencing
(GT-seq) for collecting targeted single nucleotide polymorphism (SNP)
genotypic data from archival scale samples, and demonstrate its
application to a study of kokanee salmon (Oncorhynchus nerka) in Kluane
National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe
12-year population decline followed by a rapid rebound. 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.