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

Snakeheads of the genus Channa display remarkable diversity in body size and ecology, yet evolutionary relationships within several species complexes remain unresolved. Channa pyrophthalmus, 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 C. pyrophthalmus and perform comparative mitogenomic analyses across 18 Channa species. Phylogenetic analyses based on mitochondrial protein-coding genes robustly place C. pyrophthalmus as the sister lineage to C. gachua 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 C. pyrophthalmus and C. gachua 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 ND5 marks the ancestral lineage of giant snakeheads, indicating adaptive shifts in mitochondrial bioenergetics. Additionally, accelerated evolution in ATP8 was detected in rheophilic lineages. Together, these findings link geological vicariance and mitochondrial metabolic evolution to body size diversification in Channa.