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.
Highlights
The Rhinopithecus genus has five species, including three species that only live in China, the Sichuan golden monkey (Rhinopithecus roxellana), the Guizhou golden monkey (Rhinopithecus brelichi), and the Yunnan golden monkey (Rhinopithecus bieti)
Rhinopithecus roxellana was distributed widely in China during the Pleistocene; today, wild R. roxellana populations only exist in three isolated mountainous regions, including the Minshan and Qionglai mountains in Sichuan and Gansu provinces (SG), the Qinling mountains in Shaanxi province (QL), and the Shennongjia National Nature Reserve (SNJ) in Hubei province
We resequenced the Mitochondrial DNA (mtDNA) of SNJ R. roxellana and obtained 217.09 Mb of raw data and 226.95 Mb of raw data from Illumina- Pipeline
Summary
The Rhinopithecus genus (snub-nosed monkeys) has five species, including three species that only live in China, the Sichuan golden monkey (Rhinopithecus roxellana), the Guizhou golden monkey (Rhinopithecus brelichi), and the Yunnan golden monkey (Rhinopithecus bieti). Mitochondrial DNA (mtDNA) has been widely used as a molecular marker in phylogenetic and phylogeographic studies of the Rhinopithecus genus and other primates because it is high mutation and substitution rates, low effective population size, high copy number, rare gene recombination, maternal transmission, and easy accessibility (Finstermeier et al, 2013; Kolleck et al, 2013; Liedigk et al, 2012; Yang et al, 2012; Yu et al, 2011; Zhang, 1998). We analyzed the mitochondrial genomic divergence and phylogenetic relationships within the R. roxellana species and the Rhinopithecus genus to determine whether R. roxellana is a monotypic or polytypic species and assess the divergence ages and evolutionary status of the SNJ population within R. roxellana
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