The Pacific lamprey genomic divergence, association mapping, temporal Willamette Falls, spatial rangewide datasets

High rates of dispersal can breakdown coadapted gene complexes. However,
concentrated genomic architecture (i.e., genomic islands of divergence)
can suppress recombination to allow evolution of local adaptations despite
high gene flow.  Pacific lamprey (Entosphenus tridentatus) is a
highly dispersive anadromous fish.  Observed trait diversity and
evidence for genetic basis of traits suggests it may be locally adapted.
We addressed whether concentrated genomic architecture could influence
local adaptation for Pacific lamprey. 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
genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We
determined robust phenotype-by-genotype relationships by testing multiple
traits across geographic sites. These trait associations likely explain
genomic divergence across the species’ range. We genotyped a subset of 302
broadly distributed SNPs in 2,145 individuals for association testing 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. Finally, we used candidate SNPs to
extrapolate a heterogeneous spatiotemporal distribution of these predicted
phenotypes based on independent datasets of larval and adult collections.
These maturity and body size results guide future elucidation of factors
driving regional optimization of these traits for fitness. Pacific lamprey
is culturally important and imperiled.  This research addresses
biological uncertainties that challenge restoration efforts.