Complete mitochondrial genomes of five Geophagus species: insights into phylogenetic relationships and taxonomic paraphyly.

In the study of Neotropical cichlid diversity, the complex evolutionary history of the Amazon basin makes the species radiation of the genus Geophagus a subject of profound research value. However, traditional morphological classification remains controversial due to convergent evolution, requiring more robust genomic evidence to define clear taxonomic boundaries. This study conducted a comprehensive analysis of the mitochondrial genomes of five Geophagus species, focusing on gene arrangement characteristics, selective pressure distribution, and molecular phylogenetic relationships. The results demonstrate that the mitogenomes of this group exhibit highly conserved gene orders and are under strong purifying selection, maintaining the functional stability of the oxidative phosphorylation system; phylogenetic analysis confirms that all newly sequenced species belong to the Surinamensis complex and reaffirms the significant paraphyly within Geophagus. Specifically, the close relationship between Geophagus brasiliensis and Mikrogeophagus provides strong support for the taxonomic proposal to segregate the Brasiliensis complex from Geophagus sensu stricto, while also highlighting the taxonomic misplacement of groups such as Astronotus and Heros. This research not only enriches the genetic resource database for Neotropical cichlids but also provides critical genomic evidence for understanding the species radiation and biogeographic evolution of this group within the complex Amazonian river system.