LAUSR

Simple Summary Parrotfishes are among the most colorful and diverse inhabitants of the coral reefs and sea grass beds and are ecologically important in these habitats. Here, we presented the complete mitogenome sequences from twelve parrotfish species and conducted comparative analysis of mitogenome features among the seven published species for the first time. The comparative analysis revealed both the conserved and unique characteristics of parrotfish mitogenomes. The mitogenome structure, organization, gene overlaps, putative secondary structures of transfer RNAs, and codon usage were relatively conserved among all the analyzed species. However, the base composition and the intergenic spacers varied largely among species. All of the protein-coding genes were under purifying selection. Phylogenetic analysis revealed that the parrotfishes could be divided into two clades with distinct ecological adaptations. Early divergence of these two clades was probably related to the expansion of sea grass habitat, and later diversifications were likely associated with the geomorphology alternation since the closing of the Tethys Ocean. This work offered fundamental materials for further studies on the evolution and conservation of parrotfishes. Abstract In order to investigate the molecular evolution of mitogenomes among the family Scaridae, the complete mitogenome sequences of twelve parrotfish species were determined and compared with those of seven other parrotfish species. The comparative analysis revealed that the general features and organization of the mitogenome were similar among the 19 parrotfish species. The base composition was similar among the parrotfishes, with the exception of the genus Calotomus, which exhibited an unusual negative AT skew in the whole mitogenome. The PCGs showed similar codon usage, and all of them underwent a strong purifying selection. The gene rearrangement typical of the parrotfishes was detected, with the tRNAMet inserted between the tRNAIle and tRNAGln, and the tRNAGln was followed by a putative tRNAMet pseudogene. The parrotfish mitogenomes displayed conserved gene overlaps and secondary structure in most tRNA genes, while the non-coding intergenic spacers varied among species. Phylogenetic analysis based on the thirteen PCGs and two rRNAs strongly supported the hypothesis that the parrotfishes could be subdivided into two clades with distinct ecological adaptations. The early divergence of the sea grass and coral reef clades occurred in the late Oligocene, probably related to the expansion of sea grass habitat. Later diversification within the coral reef clade could be dated back to the Miocene, likely associated with the geomorphology alternation since the closing of the Tethys Ocean. This work provided fundamental molecular data that will be useful for species identification, conservation, and further studies on the evolution of parrotfishes.