final_filtered_vcf_file_ipyrad

This is the final cleaned and filtered VCF file output from the program ipyrad for our data (https://ipyrad.readthedocs.io/; Eaton, D. A. (2014). PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics, 30(13), 1844-1849.). There are 315 samples and 4,215 single nucleotide polymorphisms generated using genotyping by sequencing (GBS; Illumina). This file was generating by assembling GBS data using the ipyrad (0.7.13) pipeline on a high-throughput computing cluster (HTCondor). Samples: 295, 297, 298, 299, 300, 301, 303, 305, 306, 308, 309, 312, 313, 314 were removed prior to final analyses as they were technical replicates. Samples: 34, 36, 40, 43 were randomly selected from population 4033 and removed to balance sample sizes across populations. See published paper (Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests, Toczydlowski, Rachel, Waller, Donald) Methods section and Table S2 for more details about bioinformatic filtering and Stacks assembly parameters. We assembled the GBS data in two different programs and compared the outputs to test the robustness of our de novo assembly (see Supplemental materials for the published paper). We used Stacks output for all population genetic and landscape genetic analyses published in the paper.