DOI: 10.5061/dryad.0gb5mkm0c
title: Polygenic selection within a single generation leads to subtle divergence among ecological niches

description: 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.
description: 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:
 <strong>Ehrlich2020_raw.vcf.gz</strong> contains the
 raw, unfiltered variant calls attained by genotyping-by-sequencing of
 240 <em>Fundulus heteroclitus</em> 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 <em>F.
 heteroclitus</em> 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
 <strong>Ehrlich2020_meta.txt</strong>).
 <strong>Ehrlich2020_filtered.vcf.gz</strong> contains
 the variant calls used in the analyses presented in the associated
 publication. See publication for the specific filtering steps.
 <strong>Ehrlich2020_meta.txt</strong> contains
 metadata pertaining to each genotyped sample e.g. sampling site, sampling
 season. It also shows which samples were misidentified as <em>F.
 heteroclitus </em>and therefore removed from further
 analysis.
 <strong>Ehrlich2020_taggingData.txt </strong>contains
 data associated with the tagging and recapturing of <em>F.
 heteroclitus</em> individuals in spring and fall 2016 respectively.
 It also contains weight and length data used in the morphological analysis
 presented in the associated publication.
description: <strong>Ehrlich2020_filtered.vcf.gz</strong> can be
 used to reproduce all genetic analyses in the associated
 publication.
 <strong>Ehrlich2020_raw.vcf.gz </strong>can be used
 to reproduce the filtering steps in the associated publication.
 <strong>Ehrlich2020_taggingData.txt </strong>can be
 used to reproduce the morphological analyses in the associated
 publication.