Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

Abstract

Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and biogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCEs in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

“…For a comprehensive and informative overview of the theory and practice of UCEs for arthropod phylogenomics, see Zhang et al . ().…”

“…These techniques are reviewed briefly in Table 2 and have been covered in more detail elsewhere (e.g. Lemmon & Lemmon, 2013;McCormack, 2013;Wen et al, 2015;Zhang et al, 2019).…”

“…For a comprehensive and user-friendly guide to working on the command line see the Happy Belly Bioinformatics tutorials (https://astrobiomike.github.io/unix/). For a comprehensive and informative overview of the theory and practice of UCEs for arthropod phylogenomics, see Zhang et al (2019).…”

Global domination by crazy ants: phylogenomics reveals biogeographical history and invasive species relationships in the genus Nylanderia (Hymenoptera: Formicidae)

“…Over the past 5 years, ant systematics has been revolutionized by the development and increased availability of tools designed to capture genomic DNA from ants and other Hymenoptera through targeted enrichment of UCEs (Zhang et al ., ). The most recent Hymenoptera probe sets can capture up to as many as 2590 UCE loci from each specimen (Branstetter et al ., ).…”

Streamlining universal single‐copy orthologue and ultraconserved element design: A case study in Collembola

“…Yet reference single‐copy orthologues are absent in most low‐hierarchy groups, with focus placed instead on higher‐level, benchmarking universal single‐copy orthologue ( BUSCO ) sets (six major biological clades so far; Simão, Waterhouse, Ioannidis, Kriventseva, & Zdobnov, 2015; Waterhouse et al, 2018). Furthermore, probes designed for enriching insect UCEs are almost exclusively available for large insect orders (Zhang, Williams, & Lucky, 2019c), such as Coleoptera (Faircloth, 2017), Diptera (Faircloth, 2017), Hemiptera (Faircloth, 2017), Lepidoptera (Faircloth, 2017) and Hymenoptera (Branstetter, Longino, Ward, & Faircloth, 2017; Faircloth, Branstetter, White, & Brady, 2015). We cannot accurately build a complete tree of life relying only on higher‐level marker sets, so we must build generalizable pipelines to accelerate genomic resource development across understudied groups.…”