Pachyrhynchini (Curculionidae: Entiminae) UCE marker development

Phylogenomics via ultraconserved elements (UCEs) has led to improved phylogenetic reconstructions across the tree of life. However, inadvertently incorporating non-targeted DNA into the UCE marker design will lead to misinformation being incorporated into subsequent analyses. To date, the effectiveness of basic metagenomic filtering strategies has not been assessed in arthropods. Designing markers from museum specimens requires careful consideration of methods due to the high levels of microbial contamination typically found in such specimens. We investigate if contaminant sequences are carried forward into a UCE marker set we developed from insect museum specimens using a standard bioinformatics pipeline. We use four species of Pachyrhinchini (Curculionidae: Entiminae) and an outgroup to test if contamination makes its way into the UCE data set using standard practices at the time.