Characterization and phylogenetic implications of the mitochondrial genomes of the Phyllidiidae (Gastropoda, Nudibranchia) from the South China Sea

The Phyllidiidae (Gastropoda, Nudibranchia) is a family widely found on coral reefs of tropical waters. To date, their phylogenetic relationships remain controversial at various taxonomic levels. Here we sequenced the complete mitochondrial genomes (mitogenome) of 12 specimens representing nine species from the South China Sea, compared their mitogenomic features and reconstructed the phylogeny of Phyllidiidae. The assembled mitogenomes were 14,543-15,075 bp long containing the typical elements of the 37 genes in the same order. Phylogenetic analysis based on the 13 protein-coding genes revealed that the genera Phyllidia and Phyllidiopsis were closely related, and Phyllidiella was sister to them. Within each genus, inconsistent topology was frequently found between the mitogenomic and morphological trees, cautioning the need for a further integrative taxonomy. The species Phyllidiella pustulosa was proven to be a species complex as three distinctly separated clades appeared. Divergence time estimation dated the origin of the Phyllidiidae at c. 40.33 million years ago (MYA), while the crown ages of the three genera dated back from c. 31.98 to 15.80 MYA, all falling in the period from the Neogene to Paleogene, a time characterized by dramatic climate shifts that might have facilitated species diversification.