Covering All Bases: A Universal Metazoan UCE Probe Set to Democratize Phylogenomics

Biology is in a genomics era, but many researchers may still be alienated from these techniques as a lack of genomic resources remains for many animal groups, necessitating further democratization. Hybrid capture is a popular phylogenomic approach in molecular systematics, with ultraconserved elements being the most popular. However, access to ultraconserved element data is more expensive per sample relative to other commonly used genetic/genomic approaches. Using published genomes, we developed a metazoan ultraconserved element probe set, the universality of which allows multiple research groups working on vastly different animal lineages to share costs and resources across labs. We demonstrated the utility of this probe set both in silico against 58 published metazoan genomes and in vitro with 130 samples representing 33 metazoan phyla, showing that these probes target loci useful for both deep and shallow level relationships. The proportion of target ultraconserved elements sequenced by the Metazoa probe is equivalent to that of taxon-specific probe sets, but from across all animal phyla. We explored general patterns of ultraconserved element recovery across Metazoa using published genomes and the majority of publicly available ultraconserved element probe sets. The Metazoa probe set is available in three forms: the full set, containing 19,986 probes targeting 2,146 loci, a set containing 10,749 probes targeting 1,022 loci, and the reduced cost set, containing 5,098 probes targeting 466 loci. The development of a universal ultraconserved element probe set should expand the use of genomic data to a much larger segment of the zoological community, with strong potential for broad applications in phylogenomics across all animal phyla.