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 ... : all5_672loci_nexNexus alignments of 672 loci containing transcriptomic sequence data from Trogulus, Ortholasma, Hesperonemastoma, Acuclavella, and Sabacon.672lociCharacterizations_all5DyspnoiAn .xls file characterizing aspects of the 672 loci used in phylogenetic analyses, including: evolutionary rates and branch lengths, AT and AT3 content, bootstrap distributions, subsampled loci, hidden support analyses, and concordance factors.all5_672loci_concatRAxMLAlignment and partitions file for the concatenated RAxML analysis of 672 lociall5_672loci_PhyML-trees672 gene trees generated via PhyMLall5_672loci_PhyML-BootstrapTrees100 bootstrap trees for each of 672 loci analyses in Newick formatall5_672loci_MrBayes_treFilesA MrBayes consensus tree and the tree files from each (2) runs for 672 lociRandomGeneSetsThe loci used for subsampled data. This includes 80 total subsampes, 10 each for 25, 50, 100, 200, 300, 400, 500, and 600 subsampled loci. This includes partition files for concatenated analyses, and the ...