Data from: Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae)

The anomaly zone, defined by the presence of gene tree topologies that are
more probable than the true species tree, presents a major challenge to
the accurate resolution of many parts of the Tree of Life. This
discrepancy can result from consecutive rapid speciation events in the
species tree. Similar to the problem of long-branch attraction, including
more data via loci concatenation will only reinforce the support for the
incorrect species tree. Empirical phylogenetic studies often employ
coalescent-based species tree methods to avoid the anomaly zone, but to
this point these studies have not had a method for providing any direct
evidence that the species tree is actually in the anomaly zone. In this
study, we use 16 species of lizards in the family Scincidae to investigate
whether nodes that are difficult to resolve place the species tree within
the anomaly zone. We analyze new phylogenomic data (429 loci), using both
concatenation and coalescent-based species tree estimation, to locate
conflicting topological signal. We then use the unifying principle of the
anomaly zone, together with estimates of ancestral population sizes and
species persistence times, to determine whether the observed phylogenetic
conflict is a result of the anomaly zone. We identify at least three
regions of the Scindidae phylogeny that provide demographic signatures
consistent with the anomaly zone, and this new information helps reconcile
the phylogenetic conflict in previously published studies on these
lizards. The anomaly zone presents a real problem in phylogenetics, and
our new framework for identifying anomalous relationships will help
empiricists leverage their resources appropriately for investigating and
overcoming this challenge.