Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens. Issue 3 (18th March 2022)

• Record Type: Journal Article
• Authors: Van Dam, Alex R.; Covas Orizondo, Javier O.; Lam, Athena W.; McKenna, Duane D.; Van Dam, Matthew H.
• Is Part Of: Ecology and evolution. Volume 12:Issue 3(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-03-18
• Subjects: contamination -- insects -- museum specimens -- ultraconserved elements; Ecology -- Periodicals; Evolution -- Periodicals; 577.05
• DOI: 10.1002/ece3.8625
• Languages: English
• ISSNs: 2045-7758

Abstract

Abstract: 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 find that the methods currently employed by most researchers do not exclude contamination from the final set of targets. Lastly, we highlight several paths forward for reducing contamination in UCE marker design. Abstract : We investigate if genomic bacterial and laboratory contamination is introduced into ultraconserved element (UCE) probe design from five novel Coleoptera museum specimens. Our findings indicate that even very clean samples have contamination that is carried into the UCE probe design. These results indicate that metagenomic filtering should be a consideration in UCE probe design.