Mitogenome Characteristics and Phylogenetic Analysis of Six Apistogramma Species

The Neotropical cichlid genus Apistogramma represents one of the most taxonomically diverse and ecologically significant groups of South American freshwater fishes, yet its evolutionary history and species boundaries remain poorly understood due to a lack of comprehensive genomic resources. To address this gap, this study investigated the complete mitogenomic characteristics of six representative Apistogramma species (A. agassizii, A. allpahuayo, A. baenschi, A. nijsseni, A. resticulosa, and A. cacatuoides) to establish a robust molecular framework for species identification and phylogenetic reconstruction. The results showed that Apistogramma mitogenomes are highly conserved. All six Apistogramma species exhibited significant AT bias. Selection pressure analysis revealed that the Ka/Ks ratios for all 13 protein-coding genes were between 0 and 1, indicating that these genes were under purifying selection. Differential site analysis identified nad5, cox1, and nad4 as ideal molecular markers for rapid Apistogramma species identification owing to higher proportions of variable sites. Phylogenetic analysis recovered Apistogramma as a strongly supported monophyletic clade (BP = 100, PP = 1.00), within which A. nijsseni clustered with A. baenschi and A. cacatuoides with A. agassizii. These internal phylogenetic relationships are consistent with the calculated genetic distances and previous morphological groupings. These findings provide an important theoretical basis and data support for rapid species identification, genetic evolutionary research, and divergence time estimation within Apistogramma.