Extrapolation of spatial and temporal distribution of phenotypic
traits based on candidate SNPs
One general pattern observed consistently across candidate SNPs (e.g.
Etr_464 on chromosome 01 and Etr_5713 on chromosome 02) was a
divergence between coastal and interior collections (Fig. 4). This
pattern was most evident within the Columbia River basin, where both
candidate SNPs increased in one allelic variant with increasing distance
from the river mouth (Fig. S5). The most dramatic increase was with the
frequency of the allelic variant of Etr_5713 associated with large
adult body-size (“A” allele) from ~10% at the river
mouth to near fixation (~98%) upstream of river
kilometer 644. A more moderate increase was observed for the allelic
variation of Etr_464 associated with small gonad size (40% to 95%
shift in “C” allele from the river mouth to river kilometer 644).
Similar clines were observed within the Willamette River subbasin of the
Columbia River (Fig. S5), such that strong linear trends were observed
with a change in frequencies 53% to 77% (Etr_464,
R2=0.42) and 22% to 61% (Etr_5713,
R2=0.87) over the span of 180 river kilometers. We
classified all collections of the spatial dataset into putative
“Mature” and “Premature” forms based on the whether the Etr_464
mature allele frequency was ≥50% or <50%, respectively
(Table 6S). We also classified all collections of the spatial dataset
into putative “Small” and “Large” body-size forms based on the
whether the Etr_5713 large body-size allele frequency was
<50% or ≥50%, respectively (Table 6S).
Intra-annual temporal heterogeneity was observed at Willamette Falls
among the adult Pacific lamprey returning in run years 2014 and 2015.
The abundance of the AA genotype of Etr_464 (chromosome 01) associated
with large gonad size arrived earlier than the CC genotype associated
with small gonad size (Fig. 5a,b). When the abundance of each run year
was divided into equal halves, we estimated that the AA genotype
decreased by 3X and 2X between the first and second halves of the run in
2014 and 2015, respectively (Fig. 5a,b).
For the genotypes at Etr_5317 (chromosome 02) associated with adult
body-size we did not observe consistent intra-annual trends across years
(Fig S6). Genotype proportions at Etr_5317 were similar for both halves
of the runs in 2014 and 2015. However, when we paired phenotypic
body-size with the genotypes at Etr_5317, we observed a relatively
large and consistent trend of a decrease in proportions of AA and AC
genotypes that exhibited phenotypic small body-sizes across the runs in
2014 and 2015 (Fig. 5c,d). We estimated that the AA and AC genotypes
with phenotypic small body-size decreased by >2.5X between
the first and second halves of the run (Fig. 5a,b). On the basis of
multiyear observations of migration patterns, we infer that this
category of AA and AC Etr_5317 genotype with phenotypic small body-size
is a proxy for fish that exhibit advanced maturity. Association testing
conducted on pre-mature adults with genotypes AC and AA at Etr_5317
(e.g. at Bonneville Dam) demonstrated strong association with
intermediate to large adult body-size, respectively. However, Willamette
Falls samples contained mixtures of fish in varying states of maturity.
Since these fish tend to shrink in body size as they reach maturity,
these AC and AA genotypes can also be found at Willamette Falls in
adults with relatively small-body size (i.e., total length in the lower
50% of the length distribution). Our proxy for fish with advanced
maturity (AA and AC Etr_5317 genotype with phenotypic small body-size)
made it possible to demonstrate that these fish arrive shortly before
spawning as compared to premature fish that spend several months in
freshwater prior to spawning (Fig. 5c,d).