Genomes and Fossils Resolve a Century-Old Mystery of Insect Wing Evolution

For more than a hundred years, evolutionary biologists have argued about one of the most fundamental branching points in the tree of life: how the first winged insects split into the major lineages that dominate the skies today. That dispute, known to entomologists as the Palaeoptera Problem, has now been largely settled. A new study published in the Proceedings of the National Academy of Sciences on October 13 combines extensive new genome sequencing with fossil-calibrated molecular clocks to show that mayflies and dragonflies together form a single evolutionary group, and that the two great wing designs seen in modern insects were invented independently along separate paths. The work was led by Professor Cai Chenyang’s team at the Nanjing Institute of Geology and Palaeontology of the Chinese Academy of Sciences and Professor Zhou Changfa’s team at Nanjing Normal University.

The stakes of this question are enormous. Insects are the most species-rich group of animals on Earth, with more than one million formally described living species, and the origin of powered flight in insects stands among the most transformative events in the history of terrestrial life. Wings opened up the air as a habitat, transformed pollination and predation, and set the stage for the staggering diversity that followed. Yet the relationships among the three major pterygote lineages, Ephemeroptera (mayflies), Odonata (dragonflies and damselflies), and Neoptera (insects capable of folding their wings back over their bodies), remained stubbornly unresolved, with competing hypotheses each backed by different bodies of evidence.

Three rival scenarios defined the debate. The Palaeoptera hypothesis holds that mayflies and odonates share a common ancestor, forming a clade called Palaeoptera that is the sister group of all other winged insects. The Chiastomyaria hypothesis instead pairs dragonflies with a grouping of mayflies and neopterans. The Metapterygota hypothesis takes the opposite arrangement, pairing mayflies with neopterans and leaving dragonflies on the earliest branch. Because these topologies imply very different histories for how wings were structured, how they moved, and how insect flight first evolved, resolving them has been a central challenge in reconstructing the insect tree of life.

The new study attacked the problem with an unusually comprehensive dataset. The researchers sequenced 16 new genomes from Chinese mayflies, a lineage that had been chronically undersampled in previous phylogenomic work, and integrated genomic and transcriptomic data from more than 100 insect species overall. This effort substantially closed the gaps in both taxon sampling and gene sampling that had plagued earlier analyses. The team then constructed two large amino-acid supermatrices built from universal single-copy orthologous nuclear genes, ensuring that the comparisons were based on genes present in exactly one copy across the sampled species and therefore less likely to mislead through ancient duplications.

What distinguishes the study is the systematic rigor applied to the analysis. Rather than relying on a single method, the researchers examined phylogenetic signals using both concatenation approaches, which pool all genes into one matrix, and multispecies coalescent methods, which model how individual gene trees relate to the underlying species tree. They deployed multiple evolutionary models, performed formal topological tests, dissected signals at the level of individual sites in the alignments, and ran simulation analyses to check whether their methods could recover the true tree under known sources of error. Across all of these diverse frameworks, the results consistently supported the monophyly of Palaeoptera: mayflies and odonates are sister groups, together forming the sister clade of Neoptera.

That consistency matters because the study also explains why the problem had resisted resolution for so long. During the rapid early radiation of winged insects, the researchers found that a combination of incomplete lineage sorting, in which ancestral genetic polymorphisms are randomly partitioned among descendant lineages, and gene tree estimation error affected approximately 40 percent of the gene trees in their dataset. This produced widespread topological discordance between individual gene trees and the true species tree. Different analytical frameworks handled this noise differently, which is precisely why earlier phylogenomic studies reached competing conclusions. By quantifying the scale of the problem and applying methods robust to it, the team was able to cut through the conflicting signals.

The resolution of the tree carries a profound implication for how we understand the origin of insect flight. Because mayflies and dragonflies, which cannot fold their wings flat over their bodies, form a group that is sister to the foldable-winged Neoptera, the non-foldable wings of Palaeoptera and the foldable wings of Neoptera are both novel traits that were independently acquired from an ancestral winged insect. In other words, the wing-folding mechanism of neopterans was not the retention of a primitive condition lost by mayflies and dragonflies; it was a later innovation. The ancestral winged insect already had wings, but neither the rigid flight apparatus of modern palaeopterans nor the folding hinge of modern neopterans.

To place these branching events in time, the researchers used molecular-clock analyses calibrated with 13 carefully selected fossil reference points. The results indicate that crown-group Pterygota, the lineage containing all living winged insects and their most recent common ancestor, originated in the Early Devonian, while crown-group Palaeoptera arose later, in the Late Devonian. Crucially, the analysis supports the conclusion that insect wings evolved only once. The subsequent history of the group was one of divergence and independent refinement of two very different flight architectures rather than repeated origins of flight itself.

The functional consequences of those two architectures shaped everything that followed. In neopterans, the wing-folding mechanism is enabled by rotation of the independent third axillary sclerite, a small skeletal element at the wing base that allows the hindwings to be tucked back over the abdomen. This seemingly modest anatomical feature provided the morphological and ecological foundations for the explosive radiation of Neoptera after the Carboniferous, since insects that could fold their wings could crawl through vegetation, burrow, and exploit microhabitats closed to insects with permanently outstretched wings. Mayflies and dragonflies, by contrast, evolved highly specialized rigid wing-base complexes adapted for gliding or high-speed predatory flight, trading the flexibility of folding for performance in the air.

The reconstructed evolutionary scenario shows that after the initial divergence of winged insects, Palaeoptera and Neoptera rapidly split and evolved their distinct wing structures in parallel: Neoptera developing its unique wing-folding apparatus, and Palaeoptera developing rigid wing bases for high-performance direct flight. Together, these innovations shaped the flight biomechanics and the species diversity of winged insects observed in nature today. The study was funded by the National Key R&D Program of China, the National Natural Science Foundation of China, and the China Postdoctoral Science Foundation. By uniting dense genome sampling, rigorous phylogenetic testing, and fossil-calibrated dating, the work demonstrates how a question posed in the nineteenth century can finally be answered with the tools of the twenty-first, and it offers a template for resolving other deep branches in the tree of life where rapid ancient radiations have scattered contradictory signals across the genomes of living species.

Subject of Research: Phylogenomic resolution of early winged insect evolution and the Palaeoptera Problem

Article Title: Genomic and fossil evidence sheds new light on the early evolution of winged insects

Article References: Genomic and fossil evidence sheds new light on the early evolution of winged insects. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: phylogenomics, Palaeoptera, insect evolution, mayflies, dragonflies, Neoptera, insect wings, molecular clock, Devonian, incomplete lineage sorting, fossils, PNAS