This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) Species Complex".

Valenzuela flavidus is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, Valenzuela aurantiacus was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain North American populations. Cytogenetic studies have demonstrated European all-female populations are triploid. However, males are often reported in North America suggesting diploidy for sexual populations. With the use of Illumina whole genome sequencing, genetic diversity among North American and European populations was explored with phylogenomic methods. Ploidy level was estimated by examining allele frequencies of read-mapped homologous gene regions. Results indicate divergent populations between Europe and North America. North American populations containing males are estimated to be diploid suggesting a different mechanism of genomic reproduction. These results suggest divergent population structure among European asexual and North American sexual members of V. flavidus providing insight for future studies to understand patterns of asexuality reported within the complex.

The following file contains all gene alignments, concatenated supermatrix, and mitochondrial alignment for this manuscript. In addition, the BAM files used to estimate allele frequencies. Also, gene trees for coalescent analysis, resultant treefiles from IQ-tree searches, and MCMCtree result.