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 phylogeographic questions at deep time scales to population level studies at shallow time scales. However, UCEs are underutilized in arthropod phylogenomics, and the methodology can be daunting for beginners. Our goal is to introduce UCEs phylogenomics to a wider audience by summarizing recent advances in UCE phylogenomics in arthropod research to familiarize readers with background theory and steps involved in UCEs phylogenomics. 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 UCEs pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. The UCEs pipeline can be divided into the following steps: 1) probe selection and design 2) wet lab work and sequencing, 3) bioinformatics, and 4) phylogenomic analyses. we provide quality-control tips to ensure that best results in data collection and downstream analyses. Our hope is to encourage increased adoption of UCEs in phylogenomics studies, deepen our understanding of the function of UCEs themselves across widely divergent taxa, and toward increased understanding of the tree of life.

Phylogenomics of the geometrid tribe Palyadini (Lepidoptera: Geometridae) reveals contrasting patterns of phylogenetic signal in wing colour characters

“…Choosing UCEs as a source of characters facilitated the phylogenomic inference in two ways. First, UCE protocols allowed the inclusion of old museum specimens (Zhang et al, 2019), which largely fail under traditional sequencing techniques, such as Sanger. In this study 75% of the specimens came from museum collections, one-third of which were older than 30 years (some of them being more than 100 years old), whereas only 25% were fresh material.…”

“…Unlike in the past when evolutionary inferences were based on phylogenetic trees generated with a handful of DNA fragments (e.g., Brower, 1996), next generation sequencing today provides access to millions of base pairs, and thus the opportunity to make inferences based on robust phylogenetic hypothesis. Among these new sequencing strategies, target enrichment of ultraconserved elements (UCEs) is a suitable option for several reasons: it is possible to work at shallow and deep evolutionary scales it has a high success rate with degraded or with small amounts of initial DNA, the wet lab protocol is fast and the bioinformatic tools are transparent in comparison with other next generation sequencing protocols (Zhang et al, 2019).…”