Data from: Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae

The genetic architecture of adaptive traits can reflect the evolutionary history of populations and also shape divergence among populations. Despite this central role in evolution, relatively little is known regarding the genetic architecture of adaptive traits in nature, particularly for traits subject to known selection intensities. Here we quantitatively describe the genetic architecture of traits that are subject to known intensities of differential selection between host plant species in Timema cristinae stick insects. Specifically, we used phenotypic measurements of 10 traits and 211,004 single-nucleotide polymorphisms (SNPs) to conduct multilocus genome-wide association mapping. We identified a modest number of SNPs that were associated with traits and sometimes explained a large proportion of trait variation. These SNPs varied in their strength of association with traits, and both major and minor effect loci were discovered. However, we found no relationship between variation in levels of divergence among traits in nature and variation in parameters describing the genetic architecture of those same traits. Our results provide a first step toward identifying loci underlying adaptation in T. cristinae. Future studies will examine the genomic location, population differentiation, and response to selection of the trait-associated SNPs described here.Phenotypic measurements of Timema cristinaeFile contains all the raw phenotypic measurements for all individuals included in the genome-wide association mapping analyses ("individual" begins with "FHA") and the same measurements for individuals collected from two additional populations ("individual" begins with "VPC" or "HVA").Tcris_FHA_phenotypes.txtTcris_fin_mod_snpcntII.txtFile contains variant counts (snp calling) for each individual. This file was used to estimate genotype probabilities that were ultimately used to generate the composite genotypes (see "Tcris_pimass_composite_genotypes.txt" file for these) use in GWAS analyses carried out in piMASS.Tcris_pimass_composite_genotypes.txtInput genotype file for piMASS. Contains composite genotypic values for each individual.Tcris_pimass_FHA_hiPIP_snpFile contains all snps (snp_id) with Rao-Blackwell posterior inclusion probabilities (PIP_rb) greater than 0.01 and includes the trait a given snp was associated with (trait) and the estimate of beta given by piMASS (B_rb)