Natural selection drives the evolution of chiton mitochondrial genomes: evidence from a resolved phylogenomic framework

Complete mitochondrial genomes are invaluable resources for studying evolutionary processes and adaptation. Their small size and unique inheritance patterns make them powerful markers for reconstructing phylogenetic relationships and investigating the selective pressures that shape organismal biology. While their utility to resolve deep divergences has been questioned previously, it has been suggested that increased taxon sampling is required to improve mitogenomic phylogenies. To unravel the evolution of Polyplacophora, we sequenced the complete mitogenomes of two chiton species, from the Indian coast, Acanthochitona mahensis Winckworth, 1927 and Plaxiphora tricolor Thiele, 1910 and compiled a comprehensive data matrix of 44 chiton species. Contrary to the recent critiques about the utility of mitogenomic data, our mitogenomic analysis using 13 protein-coding genes (PCGs) recovered a robust phylogeny congruent with the most recent taxonomic classifications. Importantly, we recovered a monophyletic Plaxiphora within Acanthochitonina, breaking a long branch observed in previous phylogenies, and recovered Schizochiton as a sister group to the suborder. To understand the drivers of polyplacophoran radiation, we analysed the underlying evolutionary forces across the mitogenomes. Branch-site models detected episodes of positive selection in 11 PCGs, while the Mixed Effects Model of Evolution identified episodic diversifying selection in seven of the 13 PCGs. Furthermore, our findings indicate a pattern of non-neutral evolution at synonymous codon sites, suggesting that these sites are not evolving solely by random drift. These results provide compelling evidence that natural selection, rather than purely neutral processes, has been a key driver in the evolution and diversification of the chiton mitochondrial genomes.