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Polygenic selection within a single generation leads to subtle divergence among ecological niches

Citation

Ehrlich, Moritz; Wagner, Dominique N.; Oleksiak, Marjorie F.; Crawford, Douglas L. (2020), Polygenic selection within a single generation leads to subtle divergence among ecological niches, Dryad, Dataset, https://doi.org/10.5061/dryad.0gb5mkm0c

Abstract

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.

Methods

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.

Usage Notes

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.