DOI: 10.5061/dryad.27114
title: Data from: Construction of a species-level tree of life for the insects and utility in taxonomic profiling

description: Although comprehensive phylogenies have proven an invaluable tool in
 ecology and evolution, their construction is made increasingly challenging
 both by the scale and structure of publically available sequences. The
 distinct partition between gene-rich (genomic) and species-rich (DNA
 barcode) data is a feature of data that has been largely overlooked, yet
 presents a key obstacle to scaling supermatrix analysis. I present a
 phyloinformatics framework for draft construction of a species-level
 phylogeny of insects (Class Insecta). Matrix-building requires separately
 optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and
 species-rich markers, whereas tree-building requires hierarchical
 inference in order to capture species-breadth while retaining deep-level
 resolution. The phylogeny of insects contains 49,358 species, 13,865
 genera, 760 families. Deep-level splits largely reflected previous
 findings for sections of the tree that are data rich or unambiguous, such
 as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and
 relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and
 Cucujiformia (Coleoptera). However, analysis of bias, matrix construction
 and gene-tree variation suggests confidence in some relationships (such as
 in Polyneoptera) is less than has been indicated by the matrix bootstrap
 method. To assess the utility of the insect tree as a tool in query
 profiling several tree-based taxonomic assignment methods are compared.
 Using test data sets with existing taxonomic annotations, a tendency is
 observed for greater accuracy of species-level assignments where using a
 fixed comprehensive tree of life in contrast to methods generating smaller
 de novo reference trees. Described herein is a solution to the discrepancy
 in the way data are fit into supermatrices. The resulting tree facilitates
 wider studies of insect diversification and application of advanced
 descriptions of diversity in community studies, among other presumed
 applications.
description: pipeline_files.tarSet of files required by the pipeline. Includes: InsectaCoreOrthologs (insect core orthologs processed and in single file); InsMito_sumtrees.procd (example summary tree from the mitogenome analysis, which can be used to constrain a species level tree); H03InsProf.muscle.fas (insect COI barcode profile based on Hebert et al. 2003); 12S_profile (set of 12S sequences); treePL_config_file (configuration file for treePL)transcriptomes_supermatrix.nexsupermatrix in nexus format, built from nuclear orthologs taken from 33 transcriptomes, including all insect ordersmitogenome_supermatrix.nexSupermatrix of protein coding genes of 806 mitogenomesspecieslevel_supermatrix.nexSpecies-level insect supermatrix. In nexus format. 8 genes and 49338 species.species_level_treeSpecies level tree of life for insects, in Newick format. Can be input into high capacity tree viewers and also used in further downstream analysisspecies_level_tree.processedSpecies level tree in Newick format. Processed: has been rerooted and made ultrametric. Can be read with high capacity tree viewing software.ConstraintsSet of relational constraints used in species level inference. Human readable in tab delimited text format, with Linux newlines.relational_constraints_tabdelimDevelopment Commands and NotesText file containing all commands used during development of this project. For user friendly implementation of the central protocol, see SOPHI documents instead.ITOL1_Development_Commands_and_Notes.txtOnline_Supplemental_Document_PDFOnline Supplement. PDF format. Contains supplementary methods, results, discussion, references, figures and tables.species_level_tree_HRas per figure 4 of the paper, except high resolution with more complete labeling. png image format.