Data from: Use of genotyping-by-sequencing data to develop a high-throughput and multi-functional SNP panel for conservation applications in Pacific lamprey

Next generation sequencing data can be mined for highly informative single
nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays
for non-model organisms. However, choosing a set of SNPs to address a
variety of objectives can be difficult because SNPs are often not equally
informative. We developed an optimal combination of 96 high-throughput SNP
assays from a total of 4,439 SNPs identified in a previous study of
Pacific lamprey (Entosphenus tridentatus), and used them to address four
disparate objectives: parentage analysis, species identification, and
characterization of neutral and adaptive variation. Nine of these SNPs are
FST outliers, and five of these outliers are localized within genes and
significantly associated with geography, run-timing, and dwarf life
history. Two of the 96 SNPs were diagnostic for two other lamprey species
which are morphologically indistinguishable at early larval stages and are
sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel
were highly informative for parentage analysis- i.e. putatively neutral
with high minor allele frequency across the species’ range. Results from
three case studies are presented to demonstrate the broad utility of this
panel of SNP markers in this species. As Pacific lamprey populations are
undergoing rapid decline, these SNPs provide an important resource to
address critical uncertainties associated with the conservation and
recovery of this imperiled species.