The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny—a case study on dwarf chameleons

Abstract

Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (<i>Bradypodion</i>), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (<i>ND2</i>, <i>ND4</i>, <i>ND5</i>, <i>COI</i>, and <i>COIII</i>) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of <i>16S</i> commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with <i>ND2</i> weakened the resolution of <i>ND2</i>. We therefore recommend the avoidance of this <i>16S</i> fragment in future phylogenetic work.