Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
Data files
Feb 12, 2024 version files 7.44 GB
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mykiss_gsi_cat_norm_alleles_REFERENCE_nomissing.fz.txt
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README.md
Abstract
Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.
README: Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
https://doi.org/10.5061/dryad.qfttdz0qg
Description of the data and file structure
Sequence data were collected from modified Nextera library preparation, dual-index sequencing on NextSeq 500. Sequence data were then processed with PoolParty, and filtered to SNPs observed in at least one individual in each of 74 geographic samples. This file represents allele frequencies for those SNPs, mapped to the genome assembly of the Swanson line of rainbow trout (Oncorhynchus mykiss): GCF_002163495.1. Meta-data lines are preceded with '#', and spacing cells in meta-data lines contain 'NA' (not applicable).
The file is TEXT (txt) formatted and tab-delimited.
Sharing/Access information
NCBI BioProject containing the sequence data
Code/Software
These data were processed with PoolParty2 (https://github.com/stuartwillis/poolparty). See also Willis et al. 2022 Molecular Ecology Resources: https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13888
Methods
modified Nextera library preparation, dual-index sequencing on NextSeq 500, processed with PoolParty2