Mitogenomic Insights into Phylogeny, Biogeography and Adaptive Evolution of the Genus Typhlomys (Rodentia: Platacanthomyidae)

Soft-furred tree mice (genus <i>Typhlomys</i>), which are native to southern China and northern Vietnam, are unique rodents capable of echolocation. Little is known about their taxonomy, ecology, and natural history. In this study, we generated the complete mitochondrial genomes of seven species/putative species of <i>Typhlomys</i>. We conducted a comprehensive comparative analysis of these mitochondrial genomes focusing on sequence length, A+T content, A/T bias, A+T-rich regions, overlapping and intergenic spacer regions, nucleotide composition, relative synonymous codon usage, ancestral distributions, and the non-synonymous/synonymous substitution ratio (Ka/Ks). Additionally, we analyzed the phylogeny and adaptive evolution of these species/putative species. The mitogenomes of <i>Typhlomys</i> ranged from 16,487 to 17,380 bp in length, encoding the complete set of 37 genes typically found in mammalian mitogenomes. The base composition exhibited an A+T bias. The most frequently used codons were CUA (Leu), AGC (Ser), GGA (Gly) and UUA (Leu), UUG, CUG, CGU and GCG were the less frequently used codons. Ancestral distribution reconstruction suggests that <i>Typhlomys</i> originated in Central or Southwestern China. Notably, we found that the Ka/Ks ratio of the <i>ND5</i> gene in <i>T. huangshanensis</i> was greater than 1, indicating that this gene has undergone positive selection for efficient respiration in higher elevations and colder climates.