In this study, we apply a genome-scale set of molecular markers, ultraconserved elements, to fully resolve the phylogeny of a family of secretive, nocturnal birds, the potoos (Nyctibiidae). This dataset provides an opportunity to explore some challenges of phylogenetic analyses of genome-scale datasets, which we address in several ways. We generate data matrices ranging between 2,610-4,175 loci (1,477,319-3,848,295 aligned base pairs) that represent versions of the data differing in whether or not alignments were trimmed prior to concatenation, and whether 100% or 75% of all taxa were required to be represented by data for inclusion of a given locus. These matrices are analyzed with both maximum likelihood and coalescent algorithms, to check for artifacts of concatenation. Then, we subsample our data matrix by locus into randomly-selected replicates of 125-1,000 loci, and compare the topologies and statistical support of the resulting trees to look for evidence of systematic error. In analyses of complete matrices, we find strong statistical support for all ingroup nodes of the tree with no evidence for systematic error introduced by alignment trimming, missing data, or concatenation. We find further support for that topology in our subsampling analyses and statistical topology tests. The earliest branch of the tree separates Nyctibius bracteatus from the rest of the potoos, followed successively by N. grandis and N. aethereus. Two pairs of species, N. jamaicensis plus N. griseus, and N. leucopterus plus N. aethereus comprise the distal tips of the tree. Finally, we compare our strongly supported topology to those of previous studies, and use the phylogeny to examine the evolutionary history of potoos. This article is protected by copyright. All rights reserved.
