Insights into adaptive evolution in different locomotor modes and phylogeny of Sciuridae from mitogenomes of flying and tree squirrels

Mitogenomes offer valuable insights into evolutionary adaptation. Squirrels have evolved two distinct locomotor modes, gliding and scansorial climbing. To explore whether such locomotor disparities are reflected at the mitogenome level, we newly sequenced the Priapomys leonardi mitogenome and compared it with published mitogenomes of gliding (flying squirrels) and scansorial (tree squirrels). Our result revealed highly conserved mitogenomic organization across both tribes, with consistent gene arrangement, nucleotide composition, codon site base composition, and codon usage patterns. Evolutionary rates showed higher Ka/Ks ratios of ATP8, COX1, CYTB, and ND5 genes in the Pteromyini than in the Sciurini. Codon usage bias was more than in flying squirrels than in tree squirrels. These results suggested that divergent natural selection acted on these both lineages. We reconstructed the phylogenetic tree of the family Sciuridae. Phylogenetic analysis robustly revealed four monophyletic subfamilies: Ratufinae, Sciurinae, Xerinae, and Callosciurinae. The phylogenetic relationship among these subfamilies was ((Callosciurinae + Xerinae) + Sciurinae) + Ratufinae, with high nodal support. Phylogenetic reconstruction placed Priapomys leonardi within Sciuridae, and supported a sister relationship between Pteromyini (flying squirrels) and Sciurini (tree squirrels). This study provides insights into locomotor mode-linked adaptive evolution and offers a genetic foundation for future research on sciurid phylogeny and species evolution.