Data from: Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies

Phylogenetic resolution of ancient rapid radiations has remained
problematic despite major advances in statistical approaches and DNA
sequencing technologies. Here we report on a combined phylogenetic
approach utilizing transcriptome data in conjunction with Sanger sequence
data to investigate a tandem of ancient divergences in the harvestmen
superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on
Sanger sequences to resolve nodes within and between closely related
genera, and use RNA-seq data from a subset of taxa to resolve a short and
ancient internal branch. We use several analytical approaches to explore
this succession of ancient diversification events, including concatenated
and coalescent-based analyses and maximum likelihood gene trees for each
locus. We evaluate the robustness of phylogenetic inferences using a
randomized locus sub-sampling approach, and find congruence across these
methods despite considerable incongruence across gene trees. Incongruent
gene trees are not recovered in frequencies expected from a simple
multispecies coalescent model, and we reject incomplete lineage sorting as
the sole contributor to gene tree conflict. Using these approaches we
attain robust support for higher-level phylogenetic relationships within
Ischyropsalidoidea.