Evolutionary relationships among birds in Neoaves, the clade comprising the vast 
majority of avian diversity, have vexed systematists due to the ancient, rapid 
radiation of numerous lineages. We applied a new phylogenomic approach to 
resolve relationships in Neoaves using target enrichment (sequence capture) and 
high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. 
We collected sequence data from UCE loci for 32 members of Neoaves and one 
outgroup (chicken) and analyzed data sets that differed in their amount of 
missing data. An alignment of 1,541 loci that allowed missing data was 87% 
complete and resulted in a highly resolved phylogeny with broad agreement 
between the Bayesian and maximum-likelihood (ML) trees. Although results from 
the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees 
differed to a greater extent in this analysis, suggesting that increasing from 
416 to 1,541 loci led to increased stability and resolution of the tree. Novel 
results of our study include surprisingly close relationships between 
phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and 
the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos 
(Musophagidae). This phylogeny bolsters support for monophyletic waterbird and 
landbird clades and also strongly supports controversial results from previous 
studies, including the sister relationship between passerines and parrots and 
the non-monophyly of raptorial birds in the hawk and falcon families. Although 
significant challenges remain to fully resolving some of the deep relationships 
in Neoaves, especially among lineages outside the waterbirds and landbirds, this 
study suggests that increased data will yield an increasingly resolved avian 
phylogeny.