Genomic characterization and curation of UCEs improves species tree reconstruction: Supplementary Material S1

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 4 different sets of UCE markers by genomic category
from 5 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 2 or more UCEs, corresponding
to non-overlapping segments of a single gene. We considered these UCEs to
be non-independent, merged all UCEs that belonged to a particular gene,
constructed gene and species trees, and then evaluated the subsequent
effect of merging co-genic UCEs on gene and species tree reconstruction.
Average bootstrap support for merged UCE gene trees was significantly
improved across all datasets 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.