title: 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.
abstract: 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.
authors.affiliation: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA; Department of Biology, University of California, Riverside, CA 92521, USA. Electronic address: pileated@gmail.com.
authors.forename: Casey H
authors.initials: CH
authors.lastname: Richart
authors.affiliation: Department of Biology, University of California, Riverside, CA 92521, USA.
authors.forename: Cheryl Y
authors.initials: CY
authors.lastname: Hayashi
authors.affiliation: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.
authors.forename: Marshal
authors.initials: M
authors.lastname: Hedin
mesh_terms: D000818:Animals; D001097:Arachnida / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics; D056426:Genetic Loci; D049810:Genetic Speciation; D049750:Genome, Insect / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D059467:Transcriptome
keywords: Concatenation; Concordance factors; Gene trees; Incomplete lineage sorting; Multispecies coalescence; Unequal minority resolution frequencies