Comparative Mitogenomics of Channa pyrophthalmus Unveils Orogeny-Driven Speciation and Lineage-Specific Adaptive Evolution in Snakeheads

Snakeheads of the genus <i>Channa</i> display remarkable diversity in body size and ecology, yet evolutionary relationships within several species complexes remain unresolved. <i>Channa pyrophthalmus</i>, a recently described dwarf species endemic to Myanmar, represents a key lineage for investigating allopatric diversification in freshwater fishes. Here, we report the first complete mitochondrial genome of <i>C. pyrophthalmus</i> and perform comparative mitogenomic analyses across 18 <i>Channa</i> species. Phylogenetic analyses based on mitochondrial protein-coding genes robustly place <i>C. pyrophthalmus</i> as the sister lineage to <i>C. gachua</i> sensu stricto, supporting recent taxonomic revisions. While mitochondrial coding regions are highly conserved across the genus, the control region exhibits pronounced lineage-specific structural variation driven by tandem repeats. Divergence-time estimation dates the split between <i>C. pyrophthalmus</i> and <i>C. gachua</i> to ∼7.1 Ma (Late Miocene), a timeline congruent with the Late Miocene accelerated uplift of the Indo-Burman Ranges. Selection analyses reveal contrasting evolutionary regimes: pervasive purifying selection characterizes the dwarf lineage, whereas episodic positive selection on <i>ND5</i> marks the ancestral lineage of giant snakeheads, indicating adaptive shifts in mitochondrial bioenergetics. Additionally, accelerated evolution in <i>ATP8</i> was detected in rheophilic lineages. Together, these findings link geological vicariance and mitochondrial metabolic evolution to body size diversification in <i>Channa</i>.