title: Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys.
abstract: Snub-nosed monkeys (genus Rhinopithecus) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over the past 2 million years, associated with glacial advances and retreats and population isolation, have shaped snub-nosed monkey demography and evolution. We further identified several hypoxia-related genes under selection in R. bieti (black snub-nosed monkey), a species that exploits habitats higher than any other nonhuman primate. These results provide the first detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in this radiation of endangered primates.
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School lim@ioz.ac.cn lirq@novogene.cn xmzhou0103@163.com.
authors.forename: Xuming
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Xuehong
authors.initials: X
authors.lastname: Meng
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Zhijin
authors.initials: Z
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Chang
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Boshi
authors.initials: B
authors.lastname: Wang
authors.affiliation: College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China.
authors.forename: Mingzhou
authors.initials: M
authors.lastname: Li
authors.affiliation: Biodiversity and Sustainable Places Research Institute, Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom.
authors.forename: Pablo Orozco-Ter
authors.initials: PO
authors.lastname: Wengel
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Tian
authors.affiliation: Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, China.
authors.forename: Changlong
authors.initials: C
authors.lastname: Wen
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Ziming
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Anthropology, University of Illinois at Urbana-Champaign Program in Ecology and Evolutionary Biology, University of Illinois at Urbana-Champaign.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Garber
authors.affiliation: College of Nature Conservation, Beijing Forestry University, Beijing, China.
authors.forename: Huijuan
authors.initials: H
authors.lastname: Pan
authors.affiliation: School of Life Sciences, Shaanxi Normal University, XiXi'an, China.
authors.forename: Xinping
authors.initials: X
authors.lastname: Ye
authors.affiliation: College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China.
authors.forename: Zuofu
authors.initials: Z
authors.lastname: Xiang
authors.affiliation: Biodiversity and Sustainable Places Research Institute, Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Bruford
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University.
authors.forename: Scott V
authors.initials: SV
authors.lastname: Edwards
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Yinchuan
authors.initials: Y
authors.lastname: Cao
authors.affiliation: Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, China.
authors.forename: Shuancang
authors.initials: S
authors.lastname: Yu
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Lianju
authors.initials: L
authors.lastname: Gao
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Zhisheng
authors.initials: Z
authors.lastname: Cao
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Guangjian
authors.initials: G
authors.lastname: Liu
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Baoping
authors.initials: B
authors.lastname: Ren
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Fanglei
authors.initials: F
authors.lastname: Shi
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School.
authors.forename: Zalan
authors.initials: Z
authors.lastname: Peterfi
authors.affiliation: College of Life Sciences, China West Normal University, Nanchong, Sichuan, China.
authors.forename: Dayong
authors.initials: D
authors.lastname: Li
authors.affiliation: College of Life Sciences, Northwest University, Xi'an, China.
authors.forename: Baoguo
authors.initials: B
authors.lastname: Li
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China.
authors.forename: Junsheng
authors.initials: J
authors.lastname: Li
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School.
authors.forename: Vadim N
authors.initials: VN
authors.lastname: Gladyshev
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China lim@ioz.ac.cn lirq@novogene.cn xmzhou0103@163.com.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China lim@ioz.ac.cn lirq@novogene.cn xmzhou0103@163.com.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
mesh_terms: D000064:Acclimatization / Q000235:genetics; D000220:Adaptation, Biological / Q000235:genetics; D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D016673:Colobinae / Q000235:genetics*; D017753:Ecosystem; D014644:Genetic Variation; D000860:Hypoxia / Q000235:genetics / Q000378:metabolism / Q000662:veterinary*; D056186:Metagenomics / Q000379:methods; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000662:veterinary
keywords: demographics; genetic adaptation; genetic diversity; population genomics; snub-nosed monkeys