Abstract
Pacific lamprey (Entosphenus tridentatus) is a culturally important and
imperiled anadromous fish with a parasitic ocean phase. Biological
uncertainties challenge restoration efforts and life-history research is
needed to explain observed trait variation and inform management
actions. Using two new whole genome assemblies and genotypes from 7,716
single nucleotide polymorphism (SNP) loci in 518 individuals from across
the species range, we identified four large regions of high genomic
divergence (on chromosomes 01, 02, 04, and 22). We genotyped a subset of
302 broadly distributed SNPs in 2,145 individuals for
genotype-by-phenotype trait associations for adult body size, sexual
maturity, migration distance and timing, adult swimming ability, and
larval growth. Body size traits were strongly associated with SNPs on
chromosomes 02 and 04. Moderate associations also implicated SNPs on
chromosome 01 as being associated with variation in female maturity.
Using genotypic frequencies of candidate SNPs for female maturity and
body size, we extrapolated a heterogeneous spatiotemporal distribution
of these traits based on independent datasets of larval and adult
collections. These maturity and body size results guide future studies
to validate these predicted phenotypic distributions across the
geographic range and elucidate factors driving regional optimization of
these traits for fitness.