Detection of cross-contamination and strong mitonuclear discordance in two species groups of sawfly genus Empria (Hymenoptera, Tenthredinidae): ipyrad dataset and an R script

The ipyrad dataset contains alignment of 19 413 ddRAD loci of 35 Empria specimens. The script takes as an input the ipyrad dataset and a table is produced for every locus (rows) and specimen (columns) where cells contain list of specimens that are identical to a specimen indicated in the column (the cell is empty if there are no identical specimens for a particular specimen and locus). Additional columns are added to get information per locus about identical specimens between two groups, the number of specimens, maximum, median and mean divergence. The two groups examined are longicornis (including E. tridentis, which taxonomically is not a member of the group, but closely related) and immersa groups. For both groups and for every locus, specimens are recorded that are identical to any member in the other group while different from specimens in its own group. The second table produced by the script lists the specimens in the dataset, the number of loci, and the normalised number of loci per specimen. Normalised numbers of loci were calculated as half of the maximum number of loci divided by the number of loci of a particular specimen in the dataset. Then the script proceeds to produce bar plots (output as pdf) for every specimen showing percent of loci and normalised percent of loci that are identical to a particular specimen while different from all others. Two additional bar plots are produced for longicornis and immersa groups to show percent of loci of a particular specimen that are identical to any specimen in the wrong group while different from specimens in its own group.<br>