Phenotypic trait associations explain existence of genomic islands of divergence on chromosomes
Trait associations with adult body-size metrics and female gonad size (a proxy for maturity) appear to explain the presence of high levels of genomic divergence on two of the four major adaptive chromosomes in Pacific lamprey (i.e., chromosomes 01 and 02). Genotype-phenotype association testing across multiple data sets from the Columbia and Klamath River basins consistently had strong association of body size with chromosome 02. Using samples from the Klamath River in California, Parker et al . (2019) associated the maturity trait (“ocean” and “river-maturing” ecotypes) with markers we have now mapped on chromosome 01. In this study, the association has been extended geographically to include Willamette Falls, in Oregon City, OR. We have evidence, particularly on chromosome 01, that the divergent alleles on these chromosomes are tightly linked across extensive genomic regions because they are captured within inversions that are polymorphic in the species. This concentrated genomic architecture could be key to the landscape genetics and apparent local adaptation for this highly dispersive and near panmictic species. The genotype-by-phenotype associations of candidate markers were exploited for their predictive ability to extrapolate putative distributions of the phenotypes across the species’ range. These predicted phenotypic distributions provide insight into how these traits may be heterogeneously distributed in space: ocean-mature and small-bodied lamprey appear concentrated in coastal streams, whereas stream-mature and large-bodied lamprey are concentrated in interior streams. These phenotypes also appear temporally heterogeneous based on their arrival at Willamette Falls where stream-mature fish return to freshwater long before spawning in contrast to ocean-mature fish that arrive shortly before spawning. This predicted heterogeneity of the spatiotemporal distribution of maturity and body size traits provides a basis for understanding what combinations of traits may be optimally suited for particular freshwater habitats across the species’ range.