Data from: Using ultraconserved elements to reconstruct the termite tree of life

The phylogenetic history of termites has been investigated using
mitochondrial genomes and transcriptomes. However, both sets of markers
have specific limitations. Mitochondrial genomes represent a single
genetic marker likely to yield phylogenetic trees presenting incongruences
with species trees, and transcriptomes can only be obtained from
well-preserved samples. In contrast, ultraconserved elements (UCEs)
include a great many independent markers that can be retrieved from poorly
preserved samples. Here, we designed termite-specific baits
targeting 50,616 UCE loci. We tested our UCE bait set on
42 samples of termites and three samples of Cryptocercus, for
which we generated low-coverage highly-fragmented genome assemblies and
successfully extracted in silico between 3,426 to 42,860
non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree,
reconstructed using the 5,934 UCE loci retrieved from upward of 75% of
samples, was congruent with transcriptome-based phylogenies, demonstrating
that our UCE bait set is reliable and phylogenetically informative.
Combined with non-destructive DNA extraction protocols, our UCE bait set
provides the tool needed to carry out a global taxonomic revision of
termites based on poorly preserved specimens such as old museum samples.
The Termite UCE database is maintained
at: https://github.com/oist/TER-UCE-DB/.