DOI: 10.5061/dryad.9mf1pr7
title: Data from: Assessing support for Blaberoidea phylogeny suggests optimal locus

description: Phylogenomics seeks to use next-generation data to robustly infer an
 organism’s evolutionary history. Yet, the practical caveats of
 phylogenomics motivates investigation of improved efficiency, particularly
 when quality of phylogenies are questionable. To achieve improvements, one
 goal is to maintain or enhance the quality of phylogenetic inference while
 severely reducing dataset size. We approach this by assessing which kinds
 of loci in phylogenomic alignments provide the majority of support for a
 phylogenetic inference of cockroaches in Blaberoidea. We examine locus
 substitution rate, saturation, evolutionary divergence, rate
 heterogeneity, stabilizing selection, and a priori information content as
 traits that may determine optimality. Our controlled experimental design
 is based on 265 loci for 102 blaberoidean taxa and 22 outgroup species.
 Loci with high substitution rate, low saturation, low sequence distance,
 low rate heterogeneity, and strong stabilizing selection derive more
 support for phylogenetic relationships. We found that some phylogenetic
 information content estimators may not be meaningful for assessing
 information content a priori. We use these findings to design concatenated
 datasets with an optimized subsample of 100 loci. The tree inferred from
 the optimized subsample alignment was largely identical to that inferred
 from all 265 loci but with less evidence of long branch attraction,
 improved statistical support, and potential 4-6x improvements to
 computation time. Supported by phylogenetic and morphological evidence, we
 erect three newly named clades (Anallactinae Evangelista & Wipfler
 subfam. nov., Orkrasomeria tax. nov. Evangelista, Wipfler, &
 Béthoux, and Hemithyrsocerini Evangelista tribe nov.) and propose other
 taxonomic modifications. The diagnosis of Pseudophyllodromiidae
 Grandcolas, 1996 is modified to accommodate Anallactinae and
 Pseudophyllodromiinae Vickery & Kevan, 1983. The diagnosis of
 Ectobiidae Brunner von Wattenwyl, 1865 is modified to add novel
 morphological characters.
description:   <b>Datasets</b> This compressed archive contains all files relevant to our datasets. [Datasets.7z: 7.8 MB]   The archive contains the following subdirectories:   <b>Alignments</b> Nine compressed archives each containing Phyloinformatica output for alignment concatenation. The nine archives represent different combinations of loci as explained in the main text.   <b>PartitionFinder</b> Contains the alignment used for determining partitioning and model scheme in PartitionFinder 2. Configuration files and output best schemes are given for the same alignment with data blocks predefined in two ways (blocks as genes only or as genes and codon positions).   <b>265loci.7z</b> Compressed archive with alignments for 265 genetic loci for all taxa in this study.   <b>Blaberoidea preliminary taxonomy.xlsx</b> Workbook giving preliminary tribal and generic groupings of all hypothesized Blaberoidea, with notes and citations for groupings. Hypotheses utilized to design taxon sampling.   <b>Loci Features.xlsx</b> Spreadsheet of all loci and their features relevant to the tests done in this study. See methods in main text for details on how values were calculated.   <b>TaxonList.xlsx</b> A list of all taxa included in the analysis, their names, voucher number assignments, assembly names (NCBI SRA SRP155429), collection information, assembly information and alignment missing data counts.       <b>Results</b> This folder contains all files relevant to results of analyses. [results.7z: 221.1 MB]   The archive contains the following subdirectories:   <b>RADICAL output files</b> Output files corresponding to main RADICAL analyses and some other RADICAL tests discussed in the Supplementary material. See contained RADICAL-README.txt file for more details about files and folder structure.   <b>Trees</b> Nine trees, in Newick format, inferred from the nine concatenated alignments in our analysis. See methods in main paper for details about tree inference.