Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)

Genome-scale data have greatly facilitated the resolution of recalcitrant
nodes that Sanger-based datasets have been unable to resolve. However,
phylogenomic studies continue to utilize traditional methods such as
bootstrapping to estimate branch support; and high bootstrap values are
still interpreted as providing strong support for the correct topology.
Furthermore, relatively little attention is given to assessing
discordances between gene and species trees, and the underlying processes
that produce phylogenetic conflict. We generated novel genomic datasets to
characterize and determine the causes of discordance in Old World
Treefrogs (Family: Rhacophoridae)—a group that is fraught with conflicting
and poorly supported topologies among major clades. We showed that
incomplete lineage sorting was present at all nodes that exhibited high
levels of discordance, which was caused by extremely short internal
branches. We also clearly demonstrate that bootstrap values do not reflect
uncertainty or confidence for the correct topology, and hence, should not
be used as a measure of branch support in phylogenomic datasets. Overall,
we showed that species tree inference can be improved using a
total-evidence and multi-faceted approach that utilizes the most amount of
data and considers results from different analytical methods and datasets.