Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

Abstract

Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree

“…Finally, for this and any other study, we propose that following the exploration and detection of highly conflicting relationships, the use of whole-genome sequencing data should be focused on targeting markers with enough potential phylogenetic signal to resolve problematic regions. Future genomic work might identify new regions of the genome that have desirable properties related to phylogenetic signal and functionality that could be targeted as molecular markers in nonmodel organisms and improve species tree reconstruction ( Van Dam et al 2021 ). At the present, understanding the biological complexity of currently available molecular marker types and incorporating these features into realistic evolutionary models will be necessary to overcome differences in limitations of phylogenomic analyses ( Reddy et al 2017 ; Simion et al 2020 ).…”

Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens

“…Coverage-based approaches work well with clean starting material, but when samples are old, coverage tends to be lower or uneven (Blaimer et al, 2016;McCormack et al, 2016;Van Dam et al, 2017). Other authors have developed pipelines to harvest UCE's from exons (Van Dam et al, 2021), or simply blast scaffolds to exon accessions on NCBI. While both of these approaches are likely to reduce bacterial contamination, they will not reduce contamination from microbial eukaryotes in the tissue, and worse still, they rely on the assumption that loci containing exons retrieved by blast to the database of choice are not underlying mis-annotations contributed by algorithm-based gene annotation programs, as opposed to experimentally proven annotations.…”

Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus

“…Compared with traditional methods, the use of genomic data makes it more efficient to assemble organelle genomes and develop microsatellite markers [ 17 , 18 ]. The assembled genomic data can be used to identify single-copy homologous genes [ 19 , 20 , 21 ]; in addition, the whole genome of a single species can also be used to predict a population’s historical dynamics. In this study, the whole genome data for shimofuri goby were obtained using Illumina sequencing technology.…”