Data from: Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis

Ploidy levels sometimes vary among individuals or populations, particularly in plants. When such variation exists, accurate determination of cytotype can inform studies of ecology or trait variation and is required for population genetic analyses. Here we propose and evaluate a statistical approach for distinguishing low-level ploidy variants (e.g., diploids, triploids and tetraploids) based on genotyping-by-sequencing data. The method infers cytotypes based on observed heterozygosity and the ratio of DNA sequences containing different alleles at thousands of heterozygous SNPs (i.e., allelic ratios). Whereas the method does not require prior information on ploidy, a reference set of samples with known ploidy can be included in the analysis if it is available. We explore the power and limitations of this method using simulated data sets and GBS data from natural populations of aspen (Populus tremuloides) known to include both diploid and triploid individuals. The proposed method was able to reliably discriminate among diploids, triploids and tetraploids in simulated data sets, and this was true for different levels of genetic diversity, inbreeding and population structure. Power and accuracy were minimally affected by low coverage (i.e., 2X), but did sometimes suffer when simulated mixtures of diploids, autotetraploids and allotetraploids were analyzed. Cytotype assignments based on the proposed method closely matched those from previous microsatellite and flow cytometry data when applied to GBS data from aspen. An R package (gbs2ploidy) implementing the proposed method is available from CRAN.R script to run gbs2ploidy on the aspen dataThis script formats and summarizes the aspen data and then runs gbs2ploidy on the data set. The files needed for analysis are included in this Dryad submission.aspenAnalysis.RAspen ID fileThis csv text file contains population and individual IDs for the aspen samples, as well as ploidy levels inferred from microsatellites or flow cytometry.DT_aspen_1Jul16.csvSimulation codeR script to generate the simulated data used to test gbs2ploidy.ploidySims.RSimulation dataThis is a R workspace object. It contains the simulation output from the allo- and autotetraploid simulations. It was generated with the ploidySims.R code also included with this Dryad submission.simsAlloTet.RdataAllele sepecific read countsThis file contains the allele specific read counts for the aspen data. Each row contains the data for one SNP and each pair of columns has the data for an individual. These two columns contain the number of reads of each allele (one allele per column) if the individual was heterozygous at that SNP. Otherwise there is a NA for each column.hetAlleleDepth.txtVariant file for the aspen dataThis vcf (variant call format) contains the filtered variant data for the aspen samples.filtered2x_aspenvariants.vcfFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 163876