10.5061/DRYAD.0GB5MKM0C
Ehrlich, Moritz
0000-0002-0774-2037
University of Miami
Wagner, Dominique N.
University of Miami
Oleksiak, Marjorie F.
University of Miami
Crawford, Douglas L.
University of Miami
Polygenic selection within a single generation leads to subtle divergence
among ecological niches
Dryad
dataset
2020
2020-12-30T00:00:00Z
2020-12-30T00:00:00Z
en
https://doi.org/10.1093/gbe/evaa257
2648078796 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Selection on standing genetic variation may be effective enough to allow
for adaptation to distinct niche environments within a single generation.
Minor allele frequency changes at multiple, redundant loci of small effect
can produce remarkable phenotypic shifts. Yet, demonstrating rapid
adaptation via polygenic selection in the wild remains challenging. Here
we harness natural replicate populations that experience similar selection
pressures and harbor high within-, yet negligible among-population genetic
variation. Such populations can be found among the teleost Fundulus
heteroclitus which inhabits marine estuaries characterized by high
environmental heterogeneity. We identify 10,861 single nucleotide
polymorphisms in F. heteroclitus that belong to a single, panmictic
population yet reside in environmentally distinct niches (one coastal
basin and three replicate tidal ponds). By sampling at two time-points
within a single generation we quantify both allele frequency change within
as well as spatial divergence among niche subpopulations. We observe few
individually significant allele frequency changes yet find that the number
of moderate changes exceeds the neutral expectation by 10-100%. We find
allele frequency changes to be significantly concordant in both direction
and magnitude among all niche subpopulations, suggestive of parallel
selection. In addition, within-generation allele frequency changes
generate subtle but significant divergence among niches, indicative of
local adaptation. Although we cannot distinguish between selection and
genotype-dependent migration as drivers of within-generation allele
frequency changes, the trait/s determining fitness and/or migration
likelihood appear to be polygenic. In heterogeneous environments,
polygenic selection and polygenic, genotype-dependent migration offer
conceivable mechanisms for within-generation, local adaptation to distinct
niches.
This dataset includes two variant call format (VCF) files, one
tab-delimited text file containing metadata associated with the genotype
data and one tab-delimited text file containing tag and recapture as well
as morphological data: Ehrlich2020_raw.vcf.gz contains the raw, unfiltered
variant calls attained by genotyping-by-sequencing of 240 Fundulus
heteroclitus individuals collected at four sampling sites around the
Rutgers University Marine Field Station in spring and fall of 2016. It
should be noted that 9 of the 240 genotyped individuals were found to have
been misidentified as F. heteroclitus at the time of sampling. Genetic
analysis later showed significant divergence to the rest of the samples,
with these individuals likely belonging to a different species. These 9
individuals were therefore excluded from the final, filtered variant set
(see Ehrlich2020_meta.txt). Ehrlich2020_filtered.vcf.gz contains the
variant calls used in the analyses presented in the associated
publication. See publication for the specific filtering steps.
Ehrlich2020_meta.txt contains metadata pertaining to each genotyped sample
e.g. sampling site, sampling season. It also shows which samples were
misidentified as F. heteroclitus and therefore removed from further
analysis. Ehrlich2020_taggingData.txt contains data associated with the
tagging and recapturing of F. heteroclitus individuals in spring and fall
2016 respectively. It also contains weight and length data used in the
morphological analysis presented in the associated publication.
Ehrlich2020_filtered.vcf.gz can be used to reproduce all genetic analyses
in the associated publication. Ehrlich2020_raw.vcf.gz can be used to
reproduce the filtering steps in the associated publication.
Ehrlich2020_taggingData.txt can be used to reproduce the morphological
analyses in the associated publication.