Resequencing and comparison of whole mitochondrial genome to gain insight into the evolutionary status of the Shennongjia golden snub-nosed monkey (SNJ ).

Shennongjia (SNJ ) is the smallest geographical population of . . The phylogenetic relationships among its genera and species and the biogeographic processes leading to their current distribution are largely unclear. To address these issues, we resequenced and obtained a new, complete mitochondrial genome of SNJ by next-generation sequencing and standard Sanger sequencing. We analyzed the gene composition, constructed a phylogenetic tree, inferred the divergence ages based on complete mitochondrial genome sequences, and analyzed the genetic divergence of 13 functional mtDNA genes. The phylogenetic tree and divergence ages showed that (the Tonkin snub-nosed monkey) was the first to diverge from the genus ca. 2.47 million years ago (Ma) and formed sister groups, and the second divergence from the genus occurred ca. 1.90 Ma. and diverged from the genus third, ca. 1.57 Ma. SNJ was the last to diverge within species in 0.08 Ma, and the most recent common ancestor of is 0.10 Ma. The analyses on gene composition showed SNJ was the newest geographic population of . The work will help to develop a more accurate protection policy for SNJ and facilitate further research on selection and adaptation of .