Phylogenomics of the ant subfamily Formicinae, based on UCE sequences

Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has not yet been extensively compared with traditional Sanger sequencing data sets. Moreover, UCE data on invertebrates, such as insects, is sparse. We compared the phylogenetic potency and informativeness of 959 UCE loci with a multi-locus data set of ten nuclear markers, by testing these two types of data and methods in their ability to resolve and date the evolutionary history of the ant subfamily Formicinae. Phylogenetic estimations show that UCEs are superior in resolving ancient and shallow relationships of formicine ants, demonstrated by increased node support and a more resolved phylogeny. Quantifications of phylogenetic informativeness further evidence a two-fold increase relative to the 10-gene data set. We were able to significantly improve formicine tribal classification based on our comprehensive UCE phylogeny for the group. Our divergence age estimations, using both UCE and Sanger data, indicate that crown-group formicine ants (104–117 Ma) are relatively older than previous studies have suggested. Biogeographic analyses infer the diversification of the subfamily as fairly spread out across all continents with no particular and apparent hub of cladogenesis. Much of the early history of the clade, however, remains uncertain due to ancient rapid divergence events unsolvable even with our genomic data. Our comparative study highlights the promise of UCEs for insect phylogenomics, as well as limitations, and will prove highly useful for the growing number of evolutionary biologists considering the transition from Sanger to next-generation sequencing approaches.