Open AccessMetagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens
Author(s) -
Van Dam Alex R.,
Covas Orizondo Javier O.,
Lam Athena W.,
McKenna Duane D.,
Van Dam Matthew H.
Publication year - 2022
Publication title -
ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.17
H-Index - 63
ISSN - 2045-7758
DOI - 10.1002/ece3.8625
Subject(s) - phylogenomics , metagenomics , biology , contamination , cluster analysis , phylogenetic tree , pipeline (software) , set (abstract data type) , computational biology , computer science , artificial intelligence , ecology , gene , genetics , clade , programming language
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.