The Palaeoptera problem asks which of the three possible branching orders relates the lineages Ephemeroptera (mayflies), Odonata (dragonflies and damselflies), and Neoptera (all other winged insects) at the base of the winged insects (Pterygota): Palaeoptera ((Ephemeroptera, Odonata) Neoptera), Metapterygota ((Odonata, Neoptera) Ephemeroptera), or Chiastomyaria ((Ephemeroptera, Neoptera) Odonata). The question, as framed by Thomas et al. (2013) and still open, has one coherent objective: a stable reconstruction of the earliest radiation of winged insects in which the species-tree topology at the pterygote root is established robustly against systematic error and the discordance among gene trees is partitioned between genuine biological processes (incomplete lineage sorting and introgression) and artifacts (outgroup choice, model misspecification, sparse sampling). The resolution carries direct implications for the morphological history of wings and for reconciling molecular divergence times with the first fossil appearances of winged insects. Despite taxon-rich and phylogenomic analyses (Thomas et al. 2013; Misof et al. 2014) and a dedicated reanalysis (Simon et al. 2018), published studies as recent as 2019–2021 continue to recover different topologies depending on data type, outgroups, and substitution models, so the problem remains open.

Background

Insects are the most species-rich animal group, and the winged insects (Pterygota) dominate it. Three lineages diverge at or near the base of Pterygota: Ephemeroptera (mayflies, aquatic nymphs that pass through a winged pre-adult stage, the subimago, unique among living insects to mayflies), Odonata (dragonflies and damselflies), and Neoptera (all remaining winged orders, unified by the ability to fold the wings flat over the abdomen). The order of these deepest divergences has been debated for over a century because each of the three possible rooted topologies has modern defenders: the Palaeoptera hypothesis groups Ephemeroptera with Odonata (citing shared wing characters such as the inability to fold the wings back over the abdomen, an anal brace, bristle-like antennae, and intercalary veins); the Metapterygota hypothesis groups Odonata with Neoptera (citing the mayfly-specific subimago and caudal filament (the long terminal tail filaments), and muscle and mandibular-artulation characters); and the Chiastomyaria hypothesis groups Ephemeroptera with Neoptera, making Odonata sister to the remaining pterygotes (citing characters of sperm transfer). The resolution matters because it determines the sequence in which flight-related structures arose and thus how the origin of insect wings and flight is reconstructed.

Molecular data have not settled the question: different markers, taxon samples, outgroups (the species used to root the ingroup tree), and substitution models have yielded strong apparent support for each topology. Two systematic-error sources were highlighted by Thomas, Trueman, Rambaut and Welch (2013): outgroup choice and limited ingroup sampling. Their study analyzed multigene datasets with up to 113 taxa and applied 'temporal rooting' — using fossil-calibrated relaxed molecular clocks (models in which substitution rates vary across branches, calibrated by dated fossils) so that the root is inferred from divergence-time information rather than from an outgroup — and found that both approaches favored Palaeoptera. The largest phylogenomic analysis to date (Misof et al. 2014, 1478 protein-coding genes) likewise recovered a monophyletic Palaeoptera and dated the origin of insect flight to the Early Devonian (about 406 million years ago) and the crown diversification of the extant winged lineages to the Mississippian (about 345 million years ago), implying an ancient, rapid radiation.

However, the deep divergence is exactly the regime in which inference is hardest. The internodes separating the three lineages are short relative to the evolutionary rates involved, so incomplete lineage sorting (ILS: ancestral polymorphisms that fail to sort before consecutive speciation events, making individual gene trees disagree with the species tree) and possibly introgression (gene flow between diverging lineages) are expected to be pervasive, while sparse independent markers make the ILS explanation hard to quantify or exclude. At the same time, systematic error is demonstrably present: inferred topologies flip with outgroup choice and with the substitution model, including site-heterogeneous models such as CAT-GTR (a Bayesian model giving each site its own amino-acid profile, designed to counter long-branch attraction, the spurious grouping of fast-evolving lineages). A dedicated reanalysis (Simon, Blanke and Meusemann 2018) showed that phylogenomic matrices hold 'overall' signal for Palaeoptera but substantial hidden signal for Chiastomyaria that standard inference does not detect, and that inferred topologies switch between strongly supported alternatives with small changes in accumulating signal. On the morphological side, quantitative support for Palaeoptera comes mainly from head characters (Blanke et al. 2012, 2013), leaving the homology of wing veins and of the wing-base (thoracic pleuron) structures, the placement of the extinct Palaeodictyopteroidea (a group of Paleozoic winged insects with beak-like mouthparts), and the origin of the neopteran wing-folding apparatus unsettled. Finally, the deep molecular dates sit tens of millions of years before the first unambiguous winged-insect fossils (latest Mississippian, about 328–324 million years ago), and whether this gap reflects a real ghost lineage, preservation and sampling bias, or calibration and rate-model artifacts is actively contested (Wang et al. 2016; Schachat et al. 2022).

Problem Statement

Which of the three possible branching orders at the base of the winged insects (Pterygota) is the true species tree — Palaeoptera ((Ephemeroptera, Odonata) Neoptera), Metapterygota ((Odonata, Neoptera) Ephemeroptera), or Chiastomyaria ((Ephemeroptera, Neoptera) Odonata) — and can that resolution be shown to reflect evolutionary history rather than systematic error? As framed by Thomas et al. (2013), resolving the problem has two clearly bounded deliverables. The first is the selection: name which of the three topologies is best supported and state the evidence that discriminates it from the other two — or, where no such evidence discriminates among them, name the leading candidate and state why the evidence is non-decisive. The second is the demonstrability assessment: determine whether that resolution can be shown to reflect evolutionary history rather than systematic error, where a positive assessment requires demonstrating stability of the chosen topology, at a minimum across datasets and outgroup choices, and additionally considering the further systematic-error sources — taxon sampling, substitution models (including site-heterogeneous versus site-homogeneous models), and relaxed-clock/temporal-rooting analyses with alternative fossil-calibration and rate-model assumptions — together with a correct partition of the discordance among basal-pterygote gene trees between genuine biological processes (incomplete lineage sorting and introgression) and artifacts. The partition requirement applies only where the independent markers and taxon sampling available make that attribution testable, and where they do not, the answer must say so explicitly rather than assert an untested partition or leave the question unaddressed. A negative assessment — that the available evidence does not discriminate among the three topologies, or cannot be shown to reflect evolutionary history rather than systematic error — likewise resolves the problem, but, like a positive assessment, it must be demonstrated rather than merely asserted: it must set out the datasets, outgroup choices, substitution models, and clock/calibration assumptions under which the inferred topology changes, or under which the three alternatives cannot be distinguished, together with the observations that would discriminate among them. The morphological consequences of a resolved topology (the homology of wing veins and wing-base structures, the placement of the extinct Palaeodictyopteroidea in the pterygote tree, and the origin of the wing-folding apparatus that distinguishes Neoptera from the non-folding wings of mayflies and dragonflies) and the relationship between molecular divergence times for the origin of the major winged lineages and their first fossil appearances are relevant implications and context of that resolution, and remain active research programs in their own right.

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