Data for A phylogenomic tree of wood-warblers (Aves: Parulidae): dealing with good, bad, and ugly samples

The New World warblers (Parulidae) are a model group for ecological and evolutionary analyses. However, current phylogenetic relationships across this family are based upon few loci. Here we use ultraconserved elements (UCEs) to estimate a rigorous species-level phylogeny for the family. As is true for many groups, high-quality tissues were unavailable for some taxa. Thus, we explored methods for incorporating sequences derived from historical (toe pad) samples to expand the phylogenetic datasets. We recovered an average of 4186 UCE loci and mitochondrial bycatch data (supplemented with published mitochondrial data) from 96% of all currently recognized species. We found that the UCE phylogeny built with alignments with less than 70% of gaps and ambiguities recovered the most robust phylogenetic relationships for this family, representing 102 taxa (101 species). Using this phylogeny as a topological backbone and adding ten low quality samples effectively generated an overall well supported phylogeny, representing 112 taxa (108 species, ~90% of all species). Based on this tree, we then added in seven poor quality samples and six of those were placed within their expected genera. We also explored the phylogenetic positions of the likely extinct <i>Leucopeza semperi</i> and the endangered <i>Catharopeza bishopi</i> where very limited data was obtained.Here, we have included original alignments (zip files), concatenated datasets (in NEXUS format), the best-fit partitioning models estimated by IQ-TREE, individual gene trees, ASTRAL tree, concatenation trees and mitogenome tree.