Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

Version 1 : Received: 30 May 2019 / Approved: 31 May 2019 / Online: 31 May 2019 (10:27:44 CEST)
Version 2 : Received: 2 August 2019 / Approved: 4 August 2019 / Online: 4 August 2019 (16:54:42 CEST)

A peer-reviewed article of this Preprint also exists.


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.


Arachnida, Insect, Phylogenomics Methods, Target Enrichment, Ultraconserved Elements


Biology and Life Sciences, Insect Science

Comments (0)

We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.

Leave a public comment
Send a private comment to the author(s)
* All users must log in before leaving a comment
Views 0
Downloads 0
Comments 0
Metrics 0

Notify me about updates to this article or when a peer-reviewed version is published.
We use cookies on our website to ensure you get the best experience.
Read more about our cookies here.