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

Reconstructing the tree of life is facing challenges to infer 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 Neuropterida is reconstructed based on USCOs, UCEs, and mitogenomes assembled from 42 newly sequenced low-coverage genomes (above 32.80X), representing all orders and almost all families except Rhachiberothidae, under various settings in data filtering, model selection, and strategy of tree reconstruction. According to cautious evaluation, the topology based on amino acids matrices of the USCOs filtered by multifactorial strategies under the site heterogeneity model (LG + PMSF (C20)) is demonstrated to be the most robust. The average bootstrap support (ABS) values, an important criterion in gene filtering, show great variations between different repetitions. Applying fossils calibration at deeper nodes close to the root of the phylogeny is demonstrated to facilitate 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 the systematic error in phylogenomic inference.