DOI: 10.5061/dryad.cp91mj7
title: Data from: SNP-skimming: a fast approach to map loci generating quantitative variation in natural populations

description: Genome-wide association mapping (GWAS) is a method to estimate the
 contribution of segregating genetic loci to trait variation. A major
 challenge for applying GWAS to non-model species has been generating dense
 genome-wide markers that satisfy the key requirement that marker data is
 error-free. Here we present an approach to map loci within natural
 populations using inexpensive shallow genome sequencing. This 'SNP
 skimming' approach involves two steps: an initial genome-wide scan to
 identify putative targets followed by deep sequencing for confirmation of
 targeted loci. We apply our method to a test dataset of floral dimension
 variation in the plant Penstemon virgatus, a member of a genus that has
 experienced dynamic floral adaptation that reflects repeated transitions
 in primary pollinator. The ability to detect SNPs that generate phenotypic
 variation depends on population genetic factors such as population allele
 frequency, effect size, and epistasis as well as sampling effects
 contingent on missing data and genotype uncertainty. However, both
 simulations and the Penstemon data suggest that the most significant tests
 from the initial SNP skim are likely to be true positives – loci with
 subtle but significant quantitative effects on phenotype. We discuss the
 promise and limitations of this method and consider optimal experimental
 design for a given sequencing effort. Simulations demonstrate that
 sampling a larger number of individual at the expense of average read
 depth per individual maximizes the power to detect loci.
description: Floral phenotypic
 dataMean phenotypic
 measurements for the 291 sampled individuals. Here, Indiv is our
 identication number for the plant, "TubeL" is floral tube
 length, "Width" is floral tube width, and "StamenL" is
 stamen filament length. Units for the three measurements is
 millimeters.floral.phenos.txtslimsnps2.4.vcfVariant call file listing genotypes for the filtered set of SNPs in the initial scan used in downstream analyses. Individuals are present in numerical order in the file.slimsnps2.4.reest.AFsMaximum likelihood estimates for allele frequency of the reference allele (q) for the filtered set of SNPs (initial scan).slimsnps2.4.MLE.TubeLMaximum likelihood estimates for genetic effects on floral tube length (initial scan).slimsnps2.4.MLE.StamenLMaximum likelihood estimates for genetic effects on stamen filament length (initial scan).slimsnps2.4.MLE.WidthMaximum likelihood estimates for genetic effects on floral tube width (initial scan).amplicons.slim.RPI400Variant call file listing genotypes for filtered SNPs after amplicon sequencing used in downstream analyses.amplicons.slim.RPI400.MLE.StamenLMaximum likelihood estimates for genetic effects on stamen filament length (amplicon SNPs).amplicons.slim.RPI400.MLE.TubeLMaximum likelihood estimates for genetic effects on floral tube length (amplicon SNPs).amplicons.slim.RPI400.WidthMaximum likelihood estimates for genetic effects on floral tube width (amplicon SNPs).initial.data.near.focalsitesVariant call file listing genotypes for the all SNPs in the initial scan in the vicinity of SNPs targeted for amplicon sequencing (including sites that did not meet our strict filtering requirements in the initial scan).initial.data.near.focalsites.MLE.StamenLMaximum likelihood estimates for genetic effects on stamen filament length (initial scan, SNPs near targeted sites).initial.data.near.focalsites.MLE.TubeLMaximum likelihood estimates for genetic effects on floral tube length (initial scan, SNPs near targeted sites).