Genotype likelihoods for low-coverage whole-genome sequencing data of yellow warblers

The following datasets include the required input files used to empirically test population assignment in WGSassign on Yellow Warbler data. The file \"yewa.known.ind105.ds_2x.beagle.gz\" includes the filtered variants of 105 Yellow Warbler individuals output as genotype likelihoods and stored in a Beagle-formatted file. The ID file, \"yewa.known.ind105.reference.IDs.txt\", is a tab-delimited file with 2 columns, the first being the sample ID, and the second being the known reference population. The sample order in the ID file should match that of the input beagle file. To measure the assignment accuracy of WGSassign, we used leave-one-out cross validation using the input beagle file and our ID file., We used WGSassign on data from yellow warblers to test its accuracy when applied to individuals from a species exhibiting isolation by distance (Bay et al. 2021; Gibbs et al. 2000). Previous work on yellow warblers has found weak differentiation between populations, with pairwise FST values on the order of 0.01 or less (Gibbs et al. 2000). Blood samples from 105 individuals was collected via brachial venipuncture in the years 2020 and 2021. These served as reference samples from 3 populations—North, Central, and South—previously described in Bay et al. (2021) and Gibbs et al. (2000). We extracted DNA from blood using the manufacturer’s protocol for Qiagen DNEasy Blood and Tissue Kits. Whole genome sequencing libraries were prepared following modifications of Illumina’s Nextera Library Preparation protocol (Schweizer & DeSaix 2023) and sequenced on a HiSeq 4000 at Novogene Corporation Inc., with a target sequencing depth of 2X per individual.
Sequences were trimmed with TrimGalore ve..., , # WGSassign Yellow Warbler Dataset

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The following datasets include the required input files used to empirically test population assignment in WGSassign on Yellow Warbler data. This includes a beagle file, entitled yewa.known.ind105.ds_2x.beagle.gz, and a text file entitled, yewa.known.ind105.reference.IDs.txt.

## Description of the data and file structure

To measure the assignment accuracy of WGSassign, we used leave-one-out cross validation (the --loo specification in WGSassign) using the input beagle file (yewa.known.ind105.ds_2x.beagle.gz) and our ID file (yewa.known.ind105.reference.IDs.txt).

The file \"yewa.known.ind105.ds_2x.beagle.gz\" includes the filtered variants of 105 Yellow Warbler individuals output as genotype likelihoods and stored in a Beagle-formatted file. In a Beagle-formatted file, the first column is the marker chromosome and position, the second column is the major allele, and the third column is the minor allele. The following columns include three columns ...