Comparative Mitogenomics of Pedetontus and Pedetontinus (Insecta: Archaeognatha) Unveils Phylogeny, Divergence History, and Adaptive Evolution

Archaeognatha is phylogenetically positioned as the basal lineage relative to all extant insect orders and comprises approximately 600 described species. The internal phylogenetic relationships and divergence times within this ancient order have long been a subject of scientific debate. In this study, we assembled 14 mitochondrial genomes from species within the genera <i>Pedetontus</i> and <i>Pedetontinus</i> to clarify the phylogenetic relationship and estimate divergence times within Archaeognatha. Phylogenetic analyses revealed that both Machilidae and Machilinae are paraphyletic; <i>Pedetontinus</i> included in this analysis formed a well-supported monophyletic clade, whereas the sampled <i>Pedetontus</i> species were not recovered as a monophyletic clade. Divergence time estimates indicate that Archaeognatha originated during the Late Carboniferous (301.15 Mya, 95% HPD: 298.88-303.67 Mya), with subsequent diversification spanning from the Mesozoic era to the present. The adaptive radiation of epiphytic bryophytes and potential coevolutionary interactions between plants and insects are proposed to have significantly contributed to the diversification of Archaeognatha. Based on multiple lines of evidence, we propose that the current morphological criteria for species delineation within <i>Pedetontus</i> (<i>Pd.</i>) require revision to better reflect its evolutionary history. In the branch-site model analysis, when <i>Pd. silvestrii</i>-collected from temperate regions-was designated as the foreground branch, two positively selected sites were detected at the 66th position of the <i>Cytb</i> and the 34th position of <i>ATP6</i>. When <i>Pd. hainanensis</i> and <i>Pd. bawanglingensis</i>-collected from tropical regions-were used as the foreground branches, six positively selected sites were identified at the 622nd position of <i>Cytb</i>, the 499th position of <i>ATP6</i>, and the 623rd, 873rd, 1106th, and 1141st positions of <i>COI</i>.