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Genetic diversity of the Sichuan snub-nosed monkey (Rhinopithecus roxellana) in Shennongjia National Park, China using RAD-seq analyses

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Abstract

The Sichuan snub-nosed monkey (Rhinopithecus roxellana) is an endangered species endemic to China, where the smallest population resides in Shennongjia National Park, Hubei Province. In this study, the genetic diversity of the Sichuan snub-nosed monkeys from two areas, Qianjiaping (QJP) and Dalongtan (DLT) in Shennongjia National Park was evaluated using single nucleotide polymorphisms (SNPs) data derived from restriction site-associated DNA sequencing (RAD-seq). A total of 41,260 SNP loci were found in 29 Sichuan snub-nosed monkey individuals. The genome-wide nucleotide diversity (π) of the Shennongjia population was 0.001842. The genetic differentiation (FST) between the QJP and DLT subpopulations was 0.034. The heterozygosity of individuals from QJP was 0.3475 ± 0.03696 and 0.3148 ± 0.03501 for individuals from DLT. Although the DLT and QJP subpopulations did not show significant genetic differences, genetic differentiation between the two subpopulations was confirmed using Bayesian cluster analysis, neighbor-joining trees and principal component analysis. These results suggest that the Shennongjia population of Sichuan snub-nosed monkey has relatively low genetic diversity at the genomic level. The little genetic differentiation noted between the DLT and QJP subpopulations likely due to natural and anthropogenic barriers which may exacerbate loss of genetic diversity of this endangered subpopulation.

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Data accessibility

Raw sequence data for this study will be available at the NCBI Sequence Read Archive after paper publishing, accession PRJNA471594.

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Acknowledgements

This study was funded by the Key Technology Program of Hubei Province (2019AC161) and Shennongjia National Park (2019SNJ003), and National Key Technology R&D Program of China (2013BAD03B02). The authors would like to thank Jingyuan Yang, Wanji Yang and Hui Yao for the fieldwork assistance and Dr. Fei Gao, Mr. Dongming Fang, Dr. Yue Hu, Dr. Qi Hu and Ph.D. student Du Zhang at Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences for their support of this project. The authors would like to thank Charlotte Hacker for assistance in editing this paper.

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Authors and Affiliations

  1. Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, 100091, China

    Yu Zhang, Diqiang Li & Yuguang Zhang

  2. Hunan University of Humanities, Science and Technology, Loudi, 417000, China

    Yunyun Zhou

  3. Beijing Key Laboratory of Captive Wildlife Technologies, Beijing, 100044, China

    Xuefeng Liu

  4. Shennongjia National Park, and Hubei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Monkey, Shennongjia, 442411, China

    Huiliang Yu

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  1. Yu Zhang
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Zhang, Y., Zhou, Y., Liu, X. et al. Genetic diversity of the Sichuan snub-nosed monkey (Rhinopithecus roxellana) in Shennongjia National Park, China using RAD-seq analyses. Genetica 147, 327–335 (2019). https://doi.org/10.1007/s10709-019-00073-3

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