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Psocodea Phylogenomic dataset from: Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): combining sequence data and Exploring compositional bias solutions in Next Generation Datasets

Citation

de Moya, Robert (2020), Psocodea Phylogenomic dataset from: Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): combining sequence data and Exploring compositional bias solutions in Next Generation Datasets, Dryad, Dataset, https://doi.org/10.5061/dryad.c59zw3r50

Abstract

This dataset includes all alignments used for the phylogenomic analysis of Psocodea. In this dataset, includes all result files of phylogenomic analyses completed. This includes maximum likelihood, astral, MCMCtree, quartet sampling, and all gene trees. Any relevant input files are included, and any materials are available upon request.

The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

Methods

Please refer to the publication for details.

Funding

National Science Foundation, Award: DEB-0612938

National Science Foundation, Award: DEB-1342604

National Science Foundation, Award: XSEDE DEB-16002

National Science Foundation, Award: DEB-1855812

National Science Foundation, Award: DEB-1925487

National Science Foundation, Award: DEB-1239788

Japan Society for the Promotion of Science, Award: 15H04409

Japan Society for the Promotion of Science, Award: 19H03278