Data from: Extracting phylogenetic signal from phylogenomic data: higher-level relationships of the nightbirds (Strisores)

A well-resolved phylogeny would facilitate study of adaptation to
nocturnality in the avian superorder Strisores, a group that includes both
nocturnal and diurnal lineages. Based on previous estimates, it could be
hypothesized that there were multiple independent origins of nocturnality
in this group. In order to refine the Strisores phylogeny, we generated
genome-scale datasets of 2,289 – 4,243 ultra-conserved elements for 23
taxa representing all major living lineages in the group. Among the
considerations for using genome-scale, molecular sequence data in
phylogenomic analysis are issues related to GC content, GC variance and
their effects on model selection. In this study, we employed a variety of
analytical techniques to empirically investigate those issues in our data,
as well as biases and errors resulting from alignment trimming, taxon
selection and matrix completeness. Extensive analyses revealed conflict
within the data, especially in regard to variation in GC content, that
would not have been detected with more cursory study. Our results indicate
that readily available models of molecular evolution are insufficient to
encapsulate all phenomena present in genome-scale matrices, and that this
problem may be at the root of many current issues in phylogenomic
analysis. The analytical methods employed in this study are relevant to
phylogenomic analysis of any large, heterogeneous matrix. In conclusion,
we present a strongly supported estimate of the Strisores tree and discuss
potential evolutionary pathways of nocturnality in this clade.