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. 2017 May 15;7(12):4456-4464.
doi: 10.1002/ece3.3011. eCollection 2017 Jun.

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

Yanyun Hong  1   2 , Hairui Duo  3 , Juyun Hong  4 , Jinyuan Yang  5 , Shiming Liu  1 , Lianghui Yu  5 , Tuyong Yi  1   2
Affiliations

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

Yanyun Hong et al. Ecol Evol. .

Abstract

Shennongjia Rhinopithecus roxellana (SNJ R. roxellana) is the smallest geographical population of R. roxellana. 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 R. roxellana 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 R. avunculus (the Tonkin snub-nosed monkey) was the first to diverge from the Rhinopithecus genus ca. 2.47 million years ago (Ma). Rhinopithecus bieti and Rhinopithecus strykeri formed sister groups, and the second divergence from the Rhinopithecus genus occurred ca. 1.90 Ma. R. roxellana and R. brelichi diverged from the Rhinopithecus genus third, ca. 1.57 Ma. SNJ R. roxellana was the last to diverge within R. roxellana species in 0.08 Ma, and the most recent common ancestor of R. roxellana is 0.10 Ma. The analyses on gene composition showed SNJ R. roxellana was the newest geographic population of R. roxellana. The work will help to develop a more accurate protection policy for SNJ R. roxellana and facilitate further research on selection and adaptation of R. roxellana.

Keywords: Rhinopithecus roxellana; Shennongjia Rhinopithecus roxellana; divergence ages; mitochondrial genome (mtDNA); next‐generation sequencing; phylogenetic analyses.

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Figures

Figure 1
Figure 1
The photograph of Rhinopithecu roxellana in Shennongjia National Nature Reserve. It would be used as the graphical table of contents
Figure 2
Figure 2
Evolutionary relationships of Rhinopithecus genus was inferred using the neighbor‐joining method. The evolutionary distances were computed using the maximum composite likelihood method and are shown as the number of base substitutions per site
Figure 3
Figure 3
Evolutionary relationships of timetree. The evolutionary history was inferred using the neighbor‐joining method. Divergence times were showed in the branch in the topology tree
Figure 4
Figure 4
Molecular phylogenetic analysis was conducted by maximum‐likelihood method (timetree). Divergence times were showed on the branch in the topology tree
See this image and copyright information in PMC

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