Inconsistent performance of multi‐type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results

Abstract Reconstructing the tree of life is facing challenges in inferring accurate and robust phylogeny based on large data in the genomic era. Currently, universal single‐copy orthologs (USCOs), ultraconserved elements (UCEs) and mitochondrial genomes (mitogenomes) are widely used to reconstruct phylogeny. In this study, the higher‐level phylogeny of lacewings and allied orders (Neuropterida) is reconstructed based on USCOs, UCEs and mitogenomes assembled from 42 newly sequenced low‐coverage genomes (above 32.80X), representing all orders and all families except Rhachiberothidae, under various types of data filtering, model selection and strategies of tree reconstruction. Using relatively conservative criteria, we demonstrate that the topology based on amino acid matrices of the USCOs filtered by multifactorial strategies under the site heterogeneity model (LG + PMSF (C20)) is the most robust. The average bootstrap support (ABS) values, an important criterion in gene filtering, exhibit large variation among different repetitions. Applying fossil calibrations at deeper nodes close to the root of the phylogeny is demonstrated to facilitate more accurate estimation of evolutionary timescales by comparing three different calibration schemes (deeper nodes, shallower nodes and a combination of both). These results highlight the complexity of genomic data and offer an integrative solution to overcome systematic error in phylogenomic inference.