A comprehensive species-level phylogeny of the suboscine passerines using genome-scale data

The advent of high-throughput sequencing allows gathering genomic data at unprecedented scales, and it is bringing us closer to generating species-level phylogenies for large radiations in an efficient fashion. The suboscines (Suborder Tyranni) are a species-rich (~1300 spp) group of pantropical passerine birds that represent nearly 13% of all avian species. They reach their highest species richness in the Neotropics where they exhibit a wide range of morphologies, behaviors, and ecologies. Here, we present a species-level phylogeny of the suboscines based on 2389 loci comprising ultraconserved elements – UCEs (2305) and nuclear exons (84). We were able to include data for 1844 vouchered specimens and 16 outgroups representing 100% of genera and 99% of species. We recovered data for 158 toe-pad samples from museum study specimens that allowed having extinct or highly-endangered species in our matrix. On average, we recovered 2104 target loci per sample with an average length of 521 bp. We assessed phylogenetical signal across different types of markers and found that exons are less variable than UCEs and that their signal is highly congruent with previous phylogenetic hypothesis for the group obtained via Sanger sequencing. Finally, we describe general diversification patterns in the group and describe interesting findings from a taxonomic perspective.