Data from: Adaptation via pleiotropy and linkage: association mapping reveals a complex genetic architecture within the stickleback Eda locus
Archambeault, Sophie; Bärtschi, Luis; Merminod, Aurélie; Peichel, Catherine (2020), Data from: Adaptation via pleiotropy and linkage: association mapping reveals a complex genetic architecture within the stickleback Eda locus, Dryad, Dataset, https://doi.org/10.5061/dryad.05qfttf0j
Description of datasets: This work includes association mapping of multiple phenotypes to genetic markers within the Eda locus for three different sets of stickleback collections: (1) lab crosses of Puget Sound marine stickleback heterozygous for the freshwater Eda haplotype; (2) lab crosses of Puget Sound marine stickleback heterozygous for the freshwater NAKA SNP; and (3) wild-caught stickleback from the polymorphic, freshwater Lake Washington population.
Please see the associated manuscript for sample processing, phenotypic trait measurements and genotyping details.
Genotypes: Genotypes for the Lake Washington wild-caught fish are presented in three versions: raw, trimmed, and filled. Raw genotypes are the collected genotypes and therefore contain missing information as not all fish were successfully genotyped at every marker. The trimmed and filled genotype files have been processed to remove missing data in two different ways as described in the manuscript. The results in the manuscript are based on the trimmed Lake Washington genotype file, but the filled genotype file gives qualitatively similar results. There were relatively few missing genotypes for the NAKA and Puget Sound datasets, so the raw genotypes are uploaded and used in the analysis.
Trait values & outliers: The trait values are uploaded in the unedited form as well as the trimmed form, where outliers have been removed. Outliers were considered values > 4 SD from the mean of the sample. Please see the manuscript for descriptions of additional removed outliers such as rare wild-caught fish that were outside the age class of the fish caught in the fall. The trimmed dataset is used in the uploaded analysis script.
Follow the instructions in the "calculating.LODs.and.p-vals.R" script to run the analyses of the three mapping datasets.