Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective

Genome-scale data have the potential to clarify phylogenetic relationships
across the tree of life, but have also revealed extensive gene tree
conflict. This seeming paradox, whereby larger datasets both increase
statistical confidence and uncover significant discordance, suggests that
understanding sources of conflict is important for accurate reconstruction
of evolutionary history. We explore this paradox in squamate reptiles, the
vertebrate clade comprising lizards, snakes, and amphisbaenians. We
collected an average of 5103 loci for 91 species of squamates that span
higher-level diversity within the clade, which we augmented with publicly
available sequences for an additional 17 taxa. Using a locus-by-locus
approach, we evaluated support for alternative topologies at 17
contentious nodes in the phylogeny. We identified shared properties of
conflicting loci, finding that rate and compositional heterogeneity drives
discordance between gene trees and species tree and that conflicting loci
rarely overlap across contentious nodes. Finally, by comparing our tests
of nodal conflict to previous phylogenomic studies, we confidently resolve
nine of the 17 problematic nodes. We suggest this locus-by-locus and
node-by-node approach can be used to build consensus on which topological
resolutions remain uncertain in phylogenomic studies of other contentious
groups.