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
Published Dec 04, 2016 on Dryad.
Cite this dataset
Richart, Casey; Hayashi, Cheryl; Marshal, Hedin (2016). 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 [Dataset]. Dryad. https://doi.org/10.5061/dryad.3mr26
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.
Nexus alignments of 672 loci containing transcriptomic sequence data from Trogulus, Ortholasma, Hesperonemastoma, Acuclavella, and Sabacon.
An .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.
Alignment and partitions file for the concatenated RAxML analysis of 672 loci
672 gene trees generated via PhyML
100 bootstrap trees for each of 672 loci analyses in Newick format
A MrBayes consensus tree and the tree files from each (2) runs for 672 loci
The 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 resulting tree files for MP-EST, STAR, and concatenated RAxML analyses.
Alignments for 14 loci and these loci concatenated for expanded panel analyses in Nexus format.
RAxML gene trees for 14 loci used in expanded panel analyses.
Results from models of evolution analyses used in expanded panel analyses, returned from jModelTest and PartitionFinder.