J Syst Evol

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Phylogenomics and the timetree of Hexapoda: Current advances and challenges

Shiyu Du1†, Yehao Wang2, 3†, Changfa Zhou1, Bingcai Liu2, Diying Huang2, Michael S. Engel4, 5, Chenyang Cai2, 3*   

  1. 1 College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
    2 State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China;
    3 Nanjing College, University of Chinese Academy of Sciences, Nanjing 211135, China;
    4 Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024-5192, USA;
    5 Dr Peretti Museum Foundation, Meggen, Switzerland
    †Equal contribution
    *Corresponding author.
    Chenyang Cai. E-mail: cycai@nigpas.ac.cn
  • Received:2026-05-25 Accepted:2026-10-10
  • Supported by:
    This work was supported by the National Key Research and Development Program of China (2024YFF0807601), and the National Natural Science Foundation of China (32600579).

Abstract: Hexapods are the most diverse terrestrial animals, yet their evolutionary history still contains major uncertainties, even after recent progress in phylogenomics and molecular dating. Large molecular datasets have clarified many deep relationships. Examples include support for hexapod monophyly, the early split of Protura, the monophyly of Palaeoptera, and the positions of important insect groups such as Hymenoptera and Zoraptera. By contrast, several ancient nodes remain problematic. Monophyly of Acercaria is still debated. Time estimates for the origin of major groups (e.g., crown Hexapoda and winged insects) also differ greatly among analyses. This spread reflects differences in methodology, limited and inconsistent use of fossil evidence, and unresolved phylogenetic relationships. In response, researchers increasingly pair traditional node dating with tip-dating strategies, typically implemented through total-evidence dating frameworks. Methods based on the fossilized birth-death (FBD) process and the Bayesian Brownian Bridge (BBB) model can use fossil information more directly and better reflect macroevolutionary dynamics. Even so, broad total-evidence studies that combine extensive gene sampling, dense taxon coverage, morphological data, and fossil information remain uncommon. Here, we review current results on hexapod phylogeny and divergence times, and we point out the main gaps that hinder a clear picture of early hexapod evolution. We argue that progress will require truly integrated analyses, uniting large-scale molecular datasets, comprehensive morphological matrices, and state-of-the-art phylogenetic and dating frameworks to build a more robust and reliable timescale for insect macroevolution.

Key words: Insects, Phylogeny, Divergence-time estimates, Fossils