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.