Extrapolation of spatiotemporal phenotypic distributions
We characterized candidate SNP genotypic distributions across time and
space to better understand the ecological niche of life history traits.
These spatiotemporal distributions were characterized using the
candidate SNPs with the most robust associations with body size
(chromosome 02) and sexual maturity (chromosome 01). Distributions of
representative SNPs of the other adaptive chromosomes (Chromosomes 04
and 22) were also characterized (Fig. S1, S2).
We used two independent datasets to characterize spatial and temporal
distributions of genetic variation (Table S1). These datasets were
independent of each other and separate from the association testing
samples, and they were optimally suited for these characterizations. For
the spatial dataset, we primarily used collections of larvae and
juveniles (95% of dataset of N=3,435) but included some adult
collections that were distributed widely across the species’ range.
Larvae and juveniles were the ideal life stage to represent genotypic
distributions of individuals that successfully spawned at discrete
locations throughout the range. Adult collections were used to fill in
portions of the range where larval samples were not available.
Genotyping was partially conducted with a TaqMan assay panel (Hesset al. 2015), which overlapped the GT-seq panel by 85 SNPs they
had in common. COLONY v. 2.0.6.5 (Jones and Wang 2010) was used to
reconstruct full-sibling families (Wang 2004) using the 85 shared SNPs
on each of the 70 collections. We analyzed all collections together as
one using the following parameter settings: polygamous mating for males
and females without inbreeding, full-likelihood, medium length of run,
no allele updating, and no sibship priors. Only 1 collection out of the
7 adult collections had full siblings (N=13, Stamp River, B.C.) which
were maintained to accurately represent this small spawning segment. We
excluded duplicate genotypes, 797 full siblings, and collections with
fewer than 5 individuals, resulting in a final set of 57 collections
consisting of a total of 2,581 individuals each representing a unique
family (Table S2). This dataset was then used to calculate allele
frequencies across collections for the representative candidate SNPs
Etr_464 and Etr_5713 within the adaptive regions on chromosomes 01 and
02, respectively.
For the temporal dataset, we used individuals collected from two
successive spawning runs at Willamette Falls (2014 – 2015; N of 868 and
581, respectively) over which it was possible to randomly sample the
majority of the annual adult migration of Pacific lamprey (typically Feb
– August) in weekly strata. A daily abundance estimate (Whitlocket al. 2019) was used to expand candidate SNP allelic proportions
in the weekly strata. One biological complexity was that a portion of
the adults encountered before May probably overwintered and experienced
shrinkage in body size due to advanced maturation (Beamish 1980).
Therefore, in addition to characterizing allele frequencies of candidate
SNPs Etr_464 and Etr_5713, we categorized fish by body length to
provide insight into the transition between overwintered fish and
newly-arrived migrants.