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 sever... Mehr ...

Verfasser: Richart, Casey
Hayashi, Cheryl
Marshal, Hedin
Dokumenttyp: other
Erscheinungsdatum: 2016
Verlag/Hrsg.: Zenodo
Schlagwörter: Taracus / unequal minority / Acuclavella / Hesperonemastoma / Ortholasma / Sabacon / Concatenation / resolution frequencies / Ischyropsalidoidea / multispecies coalescence / Ceratolasma / Ischyropsalis / gene trees / Trogulus / concordance factors
Sprache: unknown
Permalink: https://search.fid-benelux.de/Record/base-29261909
Datenquelle: BASE; Originalkatalog
Powered By: BASE
Link(s) : 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. ; all5_672loci_nex Nexus alignments of 672 loci containing transcriptomic sequence data from Trogulus, Ortholasma, Hesperonemastoma, Acuclavella, and Sabacon. 672lociCharacterizations_all5Dyspnoi 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. all5_672loci_concatRAxML Alignment and partitions file for the concatenated RAxML analysis of 672 loci all5_672loci_PhyML-trees 672 gene trees generated via PhyML all5_672loci_PhyML-BootstrapTrees 100 bootstrap trees for each of 672 loci analyses in Newick format all5_672loci_MrBayes_treFiles A MrBayes ...