The landmark phylogenomic analysis of Misof et al. (2014) resolved much of the order-level backbone of insect phylogeny and dated the origin of insects to the Early Ordovician (~479 Ma), but left three linked questions explicitly unresolved: the branching order of the early winged-insect lineages (mayflies, dragonflies and damselflies, and all other winged insects - the long-standing 'Palaeoptera problem'); the position of Psocodea (bark lice and parasitic lice), which molecular trees place as sister to the holometabolous insects against morphological evidence for a monophyletic Paraneoptera; and the reconciliation of Ordovician-Silurian molecular dates with a fossil record devoid of undisputed insects before the Devonian. A decade of follow-up work - reanalyses of the original dataset, expanded mitochondrial genomes, morphology-based character systems, independent molecular clocks, and a 2026 genome-scale framework - has deepened rather than settled the conflict: each node still receives contradictory support across data types and analytical methods. The problem is to resolve these deep relationships and the insect timescale with evidence robust to the identified sources of systematic error.

Background

Insects (class Insecta) account for the majority of described animal species, and their early evolutionary history frames how biologists interpret the origin of flight, of complete metamorphosis, and of the major terrestrial radiations. Winged insects (Pterygota) comprise three primary lineages: Ephemeroptera (mayflies, aquatic nymphs with a winged adult stage that is unique in moulting), Odonata (dragonflies and damselflies), and Neoptera (all remaining winged insects, which can fold their wings flat over the abdomen). The branching order of these three lineages has been contested for decades under three competing hypotheses: Palaeoptera (mayflies plus dragonflies as a clade, sister to Neoptera), Metapterygota (dragonflies plus Neoptera, with mayflies sister to the rest), and Chiastomyaria (mayflies plus Neoptera, with dragonflies sister to the rest). This 'Palaeoptera problem' long predates the genomic era; it was treated with relaxed-clock phylogenetics by Thomas et al. (2013) and remains a canonical example of a short, deep internode that resists resolution.

A second deep question concerns Paraneoptera (also called Acercaria or the hemipteroid orders): Psocodea (bark lice/book lice and their descendants, the parasitic lice), Thysanoptera (thrips), and Hemiptera (true bugs, aphids, cicadas and relatives). Morphology has traditionally supported the monophyly of this assemblage, but large molecular analyses instead recover Psocodea as the sister group of Holometabola - insects with complete metamorphosis (beetles, moths, flies, bees, wasps and allies) - which would make Paraneoptera paraphyletic.

Third, there is the timescale. Phylogenomics - phylogenetic inference from genome-scale sequence data such as the transcriptomes (sequenced expressed genes) assembled by the 1KITE consortium - allows divergence times to be estimated from sequences calibrated against dated fossils. The fossil record of undisputed winged insects begins only in the mid-Carboniferous, about 328-324 million years ago (Ma), while fossil-calibrated molecular studies place the origin of winged insects substantially earlier (molecular estimates spanning roughly 440-370 Ma, and of insects as a whole near 479 Ma), implying long 'ghost' lineages - intervals that must have existed but left no recognized fossils.

The largest such study, by Misof and colleagues (2014), analyzed protein-coding genes from transcriptomes sampling all major insect orders and their close relatives, resolved much of the ordinal backbone, and dated the origin of insects to approximately 479 Ma (Early Ordovician). The authors themselves flagged the residuals that define this problem: the nodes establishing the monophyly of Palaeoptera and its sister relationship to Neoptera received low support and would need corroboration; the proposed Psocodea-Holometabola sister-group relationship did not receive support in all statistical tests; and the inferred Early Ordovician-Silurian origins of insects stand against an insect fossil record that is essentially empty through the Cambrian-Silurian interval. The dating methodology was contested in print almost immediately (a Science exchange between Tong et al. 2015 and the original authors' response, Kjer et al. 2015), and subsequent reanalyses have pushed both the relationships and the dates in different directions.

Problem Statement

Complete the resolution of early insect phylogeny and its timescale that Misof et al. (2014) left unfinished, at three linked nodes of the insect tree:

  1. Determine the branching order of Ephemeroptera, Odonata, and Neoptera at the base of the winged insects - that is, decide among the Palaeoptera, Metapterygota, and Chiastomyaria hypotheses - with evidence robust to the systematic errors (compositional heterogeneity, outgroup choice, conflicting signal across gene partitions) that currently make analyses of the same or larger datasets flip between strongly supported but mutually incompatible topologies.

  2. Determine the position of Psocodea: is it the sister group of Holometabola (making Paraneoptera paraphyletic), or is Paraneoptera (Psocodea + Thysanoptera + Hemiptera) monophyletic, as morphology suggests.

  3. Reconcile the molecular timescale of early insect evolution with the fossil record: establish whether insects and winged insects originated in the Ordovician-Silurian as the original chronogram and some later analyses imply (in which case the multi-ten-million-year absence of fossils before the Devonian must be explained), or whether the early dates are artifacts of calibration and taxon sampling (as reanalyses argue), thereby resolving the conflict between the inferred early origins and the essentially empty Cambrian-Silurian insect fossil record.

The three parts share one objective: a stable, congruence-tested framework for the deep insect tree and its calendar, replacing the current situation in which different well-sampled data types and methods return contradictory answers. The deliverable is the three determinations themselves, each resolved by evidence that is stable across independent data types and model classes and each reported together with the congruence tests that establish it; because analyses of the same or larger data can each be strongly supported yet mutually incompatible, the support of any single analysis does not by itself constitute resolution.

References

  1. Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., Frandsen, P. B., Ware, J., Flouri, T., Beutel, R. G., Niehuis, O., Petersen, M., et al. (101 authors; last author Zhou, X.; 1KITE consortium). Phylogenomics resolves the timing and pattern of insect evolution. Science 346(6210): 763-767 (2014). DOI: 10.1126/science.1257570. https://doi.org/10.1126/science.1257570
  2. Tong, K. J., Duchene, S., Ho, S. Y. W., Lo, N. Comment on 'Phylogenomics resolves the timing and pattern of insect evolution'. Science 349(6247): 487 (2015). DOI: 10.1126/science.aaa5460. https://doi.org/10.1126/science.aaa5460
  3. Kjer, K. M., Ware, J. L., Rust, J., Wappler, T., Lanfear, R., Jermiin, L. S., et al. (27 authors, incl. Misof, B.). Response to Comment on 'Phylogenomics resolves the timing and pattern of insect evolution'. Science 349(6247): 487 (2015). DOI: 10.1126/science.aaa7136. https://doi.org/10.1126/science.aaa7136
  4. Thomas, J. A., Trueman, J. W. H., Rambaut, A., Welch, J. J. Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny. Systematic Biology 62(2): 285-297 (2013). DOI: 10.1093/sysbio/sys093. https://doi.org/10.1093/sysbio/sys093
  5. Simon, S., Blanke, A., Meusemann, K. Reanalyzing the Palaeoptera problem - The origin of insect flight remains obscure. Arthropod Structure & Development 47(4): 328-338 (2018). DOI: 10.1016/j.asd.2018.05.002. https://doi.org/10.1016/j.asd.2018.05.002
  6. Johnson, K. P., Dietrich, C. H., Friedrich, F., Beutel, R. G., Wipfler, B., Peters, R. S., Allen, J. M., Petersen, M., Donath, A., Walden, K. K. O., et al. Phylogenomics and the evolution of hemipteroid insects. Proceedings of the National Academy of Sciences USA 115(50): 12775-12780 (2018). DOI: 10.1073/pnas.1815820115. https://doi.org/10.1073/pnas.1815820115
  7. Li, H., Shao, R., Song, N., Song, F., Jiang, P., Li, Z., Cai, W. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Scientific Reports 5: 8527 (2015). DOI: 10.1038/srep08527. https://doi.org/10.1038/srep08527
  8. Song, N., Li, X., Yin, X., Li, X., Yin, J., Pan, P. The mitochondrial genomes of palaeopteran insects and insights into the early insect relationships. Scientific Reports 9: 17765 (2019). DOI: 10.1038/s41598-019-54391-9. https://doi.org/10.1038/s41598-019-54391-9
  9. Yu, D.-N., Yu, P., Zhang, L., Storey, K. B., Gao, X., Zhang, J.-Y. Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations. PeerJ 9: e11402 (2021). DOI: 10.7717/peerj.11402. https://doi.org/10.7717/peerj.11402
  10. Chesters, D. The phylogeny of insects in the data-driven era. Systematic Entomology 45(3): 540-551 (2020). DOI: 10.1111/syen.12414. https://doi.org/10.1111/syen.12414
  11. Kawata, A., Ogawa, N., Yoshizawa, K. Morphology of the pterothoracic musculature in Paraneoptera and its phylogenetic implication (Insecta: Neoptera). Journal of Morphology 285(6): e21712 (2024). DOI: 10.1002/jmor.21712. https://doi.org/10.1002/jmor.21712
  12. Wipfler, B., Letsch, H., Frandsen, P. B., Kapli, P., Mayer, C., Bartel, D., Buckley, T. R., Donath, A., et al. Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects. Proceedings of the National Academy of Sciences USA 116(8): 3024-3029 (2019). DOI: 10.1073/pnas.1817794116. https://doi.org/10.1073/pnas.1817794116
  13. Wang, Y.-H., Engel, M. S., Rafael, J. A., Wu, H.-Y., Redei, D., Xie, Q., Wang, G., Liu, X.-G., Bu, W. Fossil record of stem groups employed in evaluating the chronogram of insects (Arthropoda: Hexapoda). Scientific Reports 6: 38939 (2016). DOI: 10.1038/srep38939. https://doi.org/10.1038/srep38939
  14. Schachat, S. R., Goldstein, P., DeSalle, R., Bobo, D., Boyce, C. K., Payne, J. L., Labandeira, C. C. Illusion of flight? Absence, evidence and the age of winged insects. Biological Journal of the Linnean Society 138(2): 143-168 (2023; online 2022-12-19). DOI: 10.1093/biolinnean/blac137. https://doi.org/10.1093/biolinnean/blac137
  15. Prokop, J., Nel, A., Engel, M. S. Diversity, Form, and Postembryonic Development of Paleozoic Insects. Annual Review of Entomology 68: 401-429 (2023). DOI: 10.1146/annurev-ento-120220-022637. https://doi.org/10.1146/annurev-ento-120220-022637
  16. Cameron, S. L. Insect Mitochondrial Genomics: A Decade of Progress. Annual Review of Entomology 70: 83-101 (2025). DOI: 10.1146/annurev-ento-013024-015553. https://doi.org/10.1146/annurev-ento-013024-015553
  17. Mei, Y. A genome-based framework for the insect tree of life reveals the distinct biological drivers of phylogenomic conflict. Mendeley Data, V3, 20 April 2026 (dataset). DOI: 10.17632/gdjymdxm4r.3. https://doi.org/10.17632/gdjymdxm4r.3