A new story of four Hexapoda classes: Protura as the sister to all other hexapods

Insects represent the most diverse animal group, yet previous phylogenetic analyses based on the morphological and molecular data have failed to agree on the evolutionary relationships of early insects and their six-legged relatives (together constituting the clade Hexapoda). In particular, the phylogenetic positions of the three early-diverging hexapod groups, the coneheads (Protura), springtails (Collembola), and two-pronged bristletails (Diplura), have been debated for over a century, with alternative topologies implying drastically different scenarios of the evolution of the insect body plan and hexapod terrestrialisation. We addressed this issue by sampling of all hexapod orders, and experimented with a broad range of across-site compositional heterogeneous models designed to tackle ancient divergences. Our analyses support Protura as the earliest-diverging hexapod lineage (Protura-sister) and Collembola as a sister group to the Diplura, a clade we refer to as Antennomusculata characterised by the shared possession of internal muscles in the antennal flagellum. The universally recognized Ellipura hypothesis is recovered under the site-homogenous LG model. Our cross-validation analysis shows that the CAT-GTR model that recovers Protura-sister fits significantly better than homogenous model. Furthermore, as a very unusual group, Protura as the first diverging lineage of hexapods is also supported by other lines of evidence, such as mitogenomics, comparative embryology, and sperm morphology. The backbone phylogeny of hexapods recovered in this study will facilitate the exploration of the underpinnings of hexapod terrestrialisation and mega-diversity.