While 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 49358 species, 13865 genera, 760 families, 31 orders. 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 mined test datasets of known species membership, 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 is fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, amongst other presumed applications.
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