Abstract
Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open‐source UCE probe set for beetles of the suborder Adephaga.
Highlights
The phylogenomics revolution is underway with targeted capture and enrichment approaches (Mamanova et al, 2010; McCormack, Hird, Zellmer, Carstens, & Brumfield, 2013) proving an effective and improved method for phylogenetic studies relative to multilo‐ cus Sanger techniques (Blaimer et al, 2015)
A second investigation by Van Dam et al, 2017 utilized this same probe set for a phylogenomic analysis of weevils, members of the same suborder of beetles used during the probe design (Faircloth, 2017)
We provide recommendations and discuss consider‐ ations for base genome choice and parameter selections to optimize the design of Ultraconserved elements (UCEs) probe sets using phyluce
Summary
UCEs allow for the inclusion of museum specimens (Blaimer, Lloyd, Guillory, & Brady, 2016; McCormack, Tsai, & Faircloth, 2016; Van Dam et al, 2017), even those preserved in formalin (Ruane & Austin, 2017), affording improved taxon sampling by removing limitations associated with specimen preservation style Another advantage to the use of UCEs is the ability to develop probe sets that target thousands of orthologous loci across members of a select organismal group, based on low coverage genomic reads from relatively few exemplar taxa (Faircloth, 2017). Branstetter, Longino, Ward, and Faircloth (2017) subsequently developed an expanded Hymenoptera UCE probe set tailored for use in ants, which success‐ fully increased locus capture for target ant taxa, but showed decreased capture rates for more distantly related ants, bees, and wasps In another example, Faircloth (2017) designed a Coleoptera UCE probe set, primarily using genomes from the beetle suborder Polyphaga. Our findings are applied to develop a new UCE probe set, optimized for beetles of the suborder Adephaga, using newly available genomic resources and incorporating previously published Coleoptera UCE loci
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