The analysis of genetic variation in the mitochondrial genome and its application for the identification of Papilio species

Mitochondrial DNA (mtDNA) markers are ideal for evolutionary studies, including phylogeography, population genetics, phylogeny, etc. However, different mitochondrial genes always own different evolutionary rate. In this study, we analysed the genetic variation across the 16 complete mtDNA from 13 species in the genus Papilio and recognized the best DNA barcoding for Papilio species. The mitochondrial gene arrangement for each species shares a similar order, similar to the typical Papilionidae species, which indicated the relatively conservative state of gene arrangement in Papilio. The sliding window of genetic diversity showed that there was a significant difference in the genetic diversity of each gene in the mitochondrial genome of Papilio. The relatively mean clock rate of the ND1 was broadly lower than the other genes in mitochondrial genome of Papilio; while the ATP8 owns the largest values of mean clock rate. Those results suggested that the rate of evolution of each gene is not balanced and all mitochondrial genes except ND1 and ATP8 could act as barcoding for the identification of Papilio species. The phylogenetic analyses of complete mtDNA data for 13 Papilio species divided them into five major branches, which keep the same topological structure with previous studies.