Despite a decade of phylogenomic studies, the branching order at the short, ancient internodes of the winged-insect (Pterygota) tree remains unresolved. Three interlocking questions are open: (1) the basal pterygote split — whether mayflies and dragonflies form a clade (Palaeoptera), whether dragonflies group with the wing-folding insects (Metapterygota), or whether mayflies do (Chiastomyaria); (2) the ordinal backbone of Polyneoptera, in particular the position of the enigmatic order Zoraptera and the placements of Dermaptera and Plecoptera; and (3) whether Paraneoptera and Holometabola together form a clade (Eumetabola). The source study (Simon et al. 2012) further showed that the underlying gene-wise signals conflict and asked which taxa, genes, or character systems reflect the true species history. Later genome-scale analyses (Misof et al. 2014; Johnson et al. 2018; Wipfler et al. 2019; Yu et al. 2021; Su et al. 2024; Wang et al. 2026) have supported mutually contradictory resolutions that flip with taxon sampling, data type, and model of sequence evolution, so a robust resolution with identified sources of systematic error remains an open problem.

Background

Insects are the most species-rich animal class, and the winged insects (Pterygota) dominate terrestrial animal diversity. The deepest branches of the pterygote tree are notoriously hard to resolve because the early radiation was ancient and apparently rapid, leaving very short internal branches (internodes) that carry little phylogenetic signal relative to the changes accumulating along the long terminal branches. Three groupings anchor the relevant terminology. Ephemeroptera (mayflies) and Odonata (dragonflies and damselflies) are the two orders whose adults cannot fold their wings back over the abdomen; Neoptera comprises all remaining winged orders, which can. Depending on the true tree, one of three hypotheses holds at the basal pterygote split: Palaeoptera (mayflies plus dragonflies as sister to Neoptera), Metapterygota (dragonflies plus Neoptera, making mayflies the earliest-diverging winged insects), or Chiastomyaria (mayflies plus Neoptera). Within Neoptera, Polyneoptera is an infraclass of about eleven orders (including cockroaches and termites (Blattodea), mantids, crickets and grasshoppers (Orthoptera), stoneflies (Plecoptera), earwigs (Dermaptera), stick insects, webspinners, ice-crawlers, heelwalkers, and the small cryptic order Zoraptera, the 'ground lice'); Paraneoptera comprises the true bugs, cicadas, lice, and thrips lineages; Holometabola comprises the holometabolous orders (beetles, wasps, flies, butterflies, and others) that undergo complete metamorphosis. Eumetabola is the hypothesized clade Paraneoptera + Holometabola. A phylogenomic study infers relationships from hundreds or thousands of orthologous genes assembled into a supermatrix; individual gene trees often disagree with each other (gene-wise incongruence), and analytical artifacts (systematic error) — for example unequal amino-acid composition across lineages, long-branch attraction, outgroup choice, and sparse taxon sampling — can mimic or override the true historical signal. Site-heterogeneous models (which let amino-acid preferences vary across sequence sites) and the multispecies coalescent (a model reconciling gene trees with a species tree) are two later tools for diagnosing such conflicts. The source study (Simon et al. 2012) contributed the first transcriptomic data for Dermaptera, Plecoptera, and Zoraptera, assembled matrices of up to 78 species and 1,579 putatively orthologous genes, and analyzed how node support grows with gene number (their RADICAL approach: randomized progressive concatenation of gene subsets) across functional gene classes (eukaryotic orthologous-group, or KOG, categories). It recovered Metapterygota with 99–100% bootstrap support but showed that different functional gene classes favor Palaeoptera instead, found the (Dermaptera, Plecoptera) grouping only weakly supported (43–53%), could not resolve Eumetabola (39–54% bootstrap), and concluded that contemporary molecular data were insufficient for these ancient splits, calling for independent genomic characters such as gene order, genome rearrangements, and intron or transposon positions.

Problem Statement

Determine the true branching order at the deep, short internodes of the winged-insect (Pterygota) tree, with evidence robust to systematic error, by resolving jointly: (1) the basal pterygote split — establishing which of the three hypotheses Palaeoptera (Ephemeroptera+Odonata sister to Neoptera), Metapterygota (Odonata sister to Neoptera), or Chiastomyaria (Ephemeroptera sister to Neoptera) is correct; (2) the ordinal backbone of Polyneoptera, in particular the phylogenetic position of Zoraptera and the placements of Dermaptera and Plecoptera relative to the remaining polyneopteran orders; and (3) the relationships among the neopteran infraclasses — in particular whether Eumetabola (Paraneoptera+Holometabola) is monophyletic. In addition, identify which data partitions (taxon sets, gene functional classes, genome-level character systems such as gene order, rearrangements, or intron positions) carry the species-tree signal at these internodes, i.e. resolve whether the observed conflicting signals reflect systematic error or genuine biological incongruence. A complete answer must satisfy all four deliverables above: it must state, for each named node, the best-supported topology and its node support under each model class; identify which data partitions carry the species-tree signal; and demonstrate that the resolution is concordant across at least one site-homogeneous and at least one site-heterogeneous substitution model and is corroborated by at least one character system independent of the nucleotide or amino-acid alignment (such as gene order, genome rearrangements, or intron or transposon positions), with the sources of the earlier conflicting signals diagnosed. Where the evidence instead shows a given internode to be not robustly resolvable, that conclusion counts as a complete answer for that node when it states the best-supported topology and its node support under each model class and diagnoses whether the discordance reflects systematic error or genuine biological incongruence.

References

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