1
|
Kuang W, Zinner D, Li Y, Yao X, Roos C, Yu L. Recent Advances in Genetics and Genomics of Snub-Nosed Monkeys ( Rhinopithecus) and Their Implications for Phylogeny, Conservation, and Adaptation. Genes (Basel) 2023; 14:genes14050985. [PMID: 37239345 DOI: 10.3390/genes14050985] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The snub-nosed monkey genus Rhinopithecus (Colobinae) comprises five species (Rhinopithecus roxellana, Rhinopithecus brelichi, Rhinopithecus bieti, Rhinopithecus strykeri, and Rhinopithecus avunculus). They are range-restricted species occurring only in small areas in China, Vietnam, and Myanmar. All extant species are listed as endangered or critically endangered by the International Union for Conservation of Nature (IUCN) Red List, all with decreasing populations. With the development of molecular genetics and the improvement and cost reduction in whole-genome sequencing, knowledge about evolutionary processes has improved largely in recent years. Here, we review recent major advances in snub-nosed monkey genetics and genomics and their impact on our understanding of the phylogeny, phylogeography, population genetic structure, landscape genetics, demographic history, and molecular mechanisms of adaptation to folivory and high altitudes in this primate genus. We further discuss future directions in this research field, in particular how genomic information can contribute to the conservation of snub-nosed monkeys.
Collapse
Affiliation(s)
- Weimin Kuang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-University of Göttingen, 37077 Göttingen, Germany
- Leibniz-Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Yuan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Xueqin Yao
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Christian Roos
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650500, China
| |
Collapse
|
2
|
Fu C, Ai Q, Cai L, Qiu F, Yao L, Wu H. Genetic Diversity and Population Dynamics of Leptobrachium leishanense (Anura: Megophryidae) as Determined by Tetranucleotide Microsatellite Markers Developed from Its Genome. Animals (Basel) 2021; 11:3560. [PMID: 34944336 PMCID: PMC8698065 DOI: 10.3390/ani11123560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Persisting declination of amphibians around the world has resulted in the public attaching importance to the conservation of their biodiversity. Genetic data can be greatly helpful in conservation planning and management, especially in species that are small in size and hard to observe. It is essential to perform genetic assessments for the conservation of Leptobrachium leishanense, an endangered toad and receiving secondary protection on the list of state-protected wildlife in China. However, current molecular markers with low reliability and efficiency hinder studies. Here, we sampled 120 adult toes from the population in the Leishan Mountain, 23 of which were used to develop tetranucleotide microsatellite markers based on one reference L. leishanense genome. After primer optimization, stability detection, and polymorphism detection, we obtained 12 satisfactory microsatellite loci. Then, we used these loci to evaluate the genetic diversity and population dynamics of the 120 individuals. Our results show that there is a low degree of inbreeding in the population, and it has a high genetic diversity. Recently, the population has not experienced population bottlenecks, and the estimated effective population size was 424.3. Accordingly, stabilizing genetic diversity will be key to population sustainability. Recovering its habitat and avoiding intentional human use will be useful for conservation of this species.
Collapse
Affiliation(s)
| | | | | | | | | | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan 430079, China; (C.F.); (Q.A.); (L.C.); (F.Q.); (L.Y.)
| |
Collapse
|
3
|
Spatial Genetic Structure and Demographic History of the Wild Boar in the Qinling Mountains, China. Animals (Basel) 2021; 11:ani11020346. [PMID: 33572967 PMCID: PMC7912324 DOI: 10.3390/ani11020346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The wild boar is native to the temperate region of Eurasia, which is now one of the most widely distributed mammals worldwide. The recent expansion in the wild boar population has attracted a lot of attention, which may cause great damage to ecosystems. Elucidating the patterns of the population structure, genetic diversity, population origin, and colonization route of wild boar is very helpful in the conservation and management of wild populations. Phylogeographic analysis has proven to be a powerful tool. Here, 82 samples of wild boars in 16 sampling locations were collected in Qinling Mountains (QM). Genetic analysis was conducted based on the mitochondrial control region and nuclear genes. The level of genetic diversity of wild boars in QM was lower than the total population in East Asia, but higher than European population. No obvious phylogeographic pattern were found. The effective population size was under demographic equilibrium in the past. Abstract Species dispersal patterns and population genetic structure can be influenced by geographical features. Qinling Mountains (QM) provide an excellent area for phylogeographic study. The phylogeography of Asian-wide wild boars revealed the colonization route. However, the impact of the QM on genetic diversity, genetic structure and population origin is still poorly understood. In this study, genetic analysis of wild boar in the QM was conducted based on the mitochondrial control region (943 bp) and twelve microsatellite loci of 82 individuals in 16 sampling locations. Overall genetic haplotype diversity was 0.86, and the nucleotide diversity was 0.0079. A total of 17 new haplotypes were detected. The level of genetic diversity of wild boars in QM was lower than in East Asia, but higher than in Europe. Phylogenetic analysis showed the weak genetic divergence in QM. Mismatch analysis, neutrality tests, and Bayesian Skyline Plot (BSP) results revealed that the estimates of effective population size were under demographic equilibrium in the past. Spatial analysis of molecular variance indicated no obvious phylogeographic structure.
Collapse
|
4
|
Li Y, Huang K, Tang S, Feng L, Yang J, Li Z, Li B. Genetic Structure and Evolutionary History of Rhinopithecus roxellana in Qinling Mountains, Central China. Front Genet 2021; 11:611914. [PMID: 33552131 PMCID: PMC7855588 DOI: 10.3389/fgene.2020.611914] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
The Qinling mountainous region is one of the world's biodiversity hotspots and provides refuges for many endangered endemic animals. The golden snub-nosed monkeys (Rhinopithecus roxellana) are considered as a flagship species in this area. Here, we depicted the genetic structure and evolutionary history via microsatellite markers and combination with the ecological niche models (ENMs) to elucidate the intraspecific divergent and the impacts of the population demography on our focal species. Our results revealed three distinct subpopulations of R. roxellana and also uncovered asymmetric historical and symmetric contemporary gene flow that existed. Our evolutionary dynamics analyses based on diyabc suggested that the intraspecific divergence accompanied with effective population sizes changes. The ENM result implied that the distribution range of this species experienced expansion during the last glacial maximum (LGM). Our results highlighted that geological factors could contribute to the high genetic differentiation within the R. roxellana in the Qinling Mountains. We also provided a new insight into conservation management plans with endangered species in this region.
Collapse
Affiliation(s)
- Yuli Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Shiyi Tang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhonghu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
5
|
Zhang BY, Hu HY, Song CM, Huang K, Dunn DW, Yang X, Wang XW, Zhao HT, Wang CL, Zhang P, Li BG. MHC-Based Mate Choice in Wild Golden Snub-Nosed Monkeys. Front Genet 2020; 11:609414. [PMID: 33408742 PMCID: PMC7779673 DOI: 10.3389/fgene.2020.609414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/23/2020] [Indexed: 11/15/2022] Open
Abstract
The genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and play a significant role in mate choice in many species. However, it remains unclear whether female mate choice in non-human primates is based on specific functional genes and/or genome-wide genes. The golden snub-nosed monkey (Rhinopithecus roxellana) lives in a multilevel society, which consists of several polygynous one-male-several-female units. Although adult females tend to mainly socialize with one adult male, females often initiate extra-pair copulations with other males resulting in a high proportion of offspring being fathered by extra-pair males. We investigated the effects of adaptive MHC genes and neutral microsatellites on female mate choice in a wild R. roxellana population. We sequenced 54 parent-offspring triads using two MHC class II loci (Rhro-DQA1 and Rhro-DQB1) and 20 microsatellites from 3 years of data. We found that the paternities of offspring were non-randomly associated with male MHC compositions not microsatellite genotypes. Our study showed that the fathers of all infants had significantly less variance for several estimates of genetic similarity to the mothers compared with random males at both MHC loci. Additionally, the MHC diversity of these fathers was significantly higher than random males. We also found support for choice based on specific alleles; compared with random males, Rhro-DQA1∗ 05 and Rhro-DQB1∗ 08 were more common in both the OMU (one-male unit) males and the genetic fathers of offspring. This study provides new evidence for female mate choice for MHC-intermediate dissimilarity (rather than maximal MHC dissimilarity) and highlights the importance of incorporating multiple MHC loci and social structure into studies of MHC-based mate choice in non-human primates.
Collapse
Affiliation(s)
- Bing-Yi Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Han-Yu Hu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Chun-Mei Song
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Xi Yang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | | | - Hai-Tao Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Cheng-Liang Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Pei Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China.,Xi'an Branch of Chinese Academy of Sciences, Xi'an, China
| |
Collapse
|
6
|
Li YL, Wang L, Wu JW, Ye XP, Garber PA, Yan Y, Liu JH, Li BG, Qi XG. Bachelor groups in primate multilevel society facilitate gene flow across fragmented habitats. Curr Zool 2020; 66:113-122. [PMID: 32211037 PMCID: PMC7083096 DOI: 10.1093/cz/zoaa006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 11/25/2022] Open
Abstract
In the face of ongoing habitat fragmentation, many primate species have experienced reduced gene flow resulting in a reduction of genetic diversity, population bottlenecks, and inbreeding depression, including golden snub-nosed monkeys Rhinopithecus roxellana. Golden snub-nosed monkeys live in a multilevel society composed of several 1 male harem units that aggregate to form a cohesive breeding band, which is followed by one or more bachelor groups composed of juvenile, subadult, and adult male members. In this research, we examine the continuous landscape resistance surface, the genetic diversity and patterns of gene flow among 4 isolated breeding bands and 1 all-male band in the Qinling Mountains, China. Landscape surface modeling suggested that human activities and ecological factors severely limit the movement of individuals among breeding bands. Although these conditions are expected to result in reduced gene flow, reduced genetic diversity, and an increased opportunity for a genetic bottleneck, based on population genetic analyses of 13 microsatellite loci from 188 individuals inhabiting 4 isolated breeding bands and 1 all-male band, we found high levels of genetic diversity but low levels of genetic divergence, as well as high rates of gene flow between males residing in the all-male band and each of the 4 breeding bands. Our results indicate that the movement of bachelor males across the landscape, along with their association with several different breeding bands, appears to provide a mechanism for promoting gene flows and maintaining genetic diversity that may counteract the otherwise isolating effects of habitat fragmentation.
Collapse
Affiliation(s)
- Yu-Li Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Lu Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jin-Wei Wu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Xin-Ping Ye
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Paul A Garber
- Anthropology Department, University of Illinois, Urbana, IL, 61801, USA
| | - Ying Yan
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jia-Hui Liu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Science, Kumming, 650223, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| |
Collapse
|
7
|
Li J, Li D, Xue Y, Wu B, He X, Liu F. Identifying potential refugia and corridors under climate change: A case study of endangered Sichuan golden monkey (Rhinopithecus roxellana) in Qinling Mountains, China. Am J Primatol 2019; 80:e22929. [PMID: 30380174 PMCID: PMC6644296 DOI: 10.1002/ajp.22929] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/06/2018] [Accepted: 09/20/2018] [Indexed: 01/09/2023]
Abstract
Climate change threatens endangered species and challenges current conservation strategies. Effective conservation requires vulnerability assessments for species susceptible to climate change and adaptive strategies to mitigate threats associated with climate. In this paper, we used the Maxent to model the impacts of climate change on habitat suitability of Sichuan golden monkey Rhinopithecus roxellana. Our results showed that (i) suitable habitat for Sichuan golden monkey was predicted to decrease by 37% in 2050s under climate change; (ii) the mean elevations of suitable habitat in the 2050s was estimated to shift 160 m higher; (iii) nature reserves protect 62% of current suitable habitat and 56% of future suitable habitat; and (iv) 49% of current suitable habitat was predicted to be vulnerable to future climate change. Given these results, we proposed conservation implications to mitigate the impacts of climate change on Sichuan golden monkey, including adjusting range of national park, establishing habitat corridors, and conducting long‐term monitoring.
Collapse
Affiliation(s)
- Jia Li
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry/Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Haidian, Beijing, China.,Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Diqiang Li
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry/Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Haidian, Beijing, China
| | - Yadong Xue
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry/Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Haidian, Beijing, China
| | - Bo Wu
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Xiaojia He
- The Administrative Center for China's Agenda 21, Beijing, China
| | - Fang Liu
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry/Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Haidian, Beijing, China
| |
Collapse
|
8
|
Liu J, Coomes DA, Gibson L, Hu G, Liu J, Luo Y, Wu C, Yu M. Forest fragmentation in China and its effect on biodiversity. Biol Rev Camb Philos Soc 2019; 94:1636-1657. [DOI: 10.1111/brv.12519] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/13/2019] [Accepted: 04/18/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Jiajia Liu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life SciencesZhejiang University Hangzhou Zhejiang China
- Forest Ecology and Conservation Group, Department of Plant SciencesUniversity of Cambridge Cambridge CB2 3EA U.K
| | - David A. Coomes
- Forest Ecology and Conservation Group, Department of Plant SciencesUniversity of Cambridge Cambridge CB2 3EA U.K
| | - Luke Gibson
- School of Environmental Science and EngineeringSouthern University of Science and Technology Shenzhen Guangdong China
| | - Guang Hu
- School of Civil Engineering and ArchitectureZhejiang Sci‐Tech University Hangzhou Zhejiang China
| | - Jinliang Liu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life SciencesZhejiang University Hangzhou Zhejiang China
| | - Yangqing Luo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life SciencesZhejiang University Hangzhou Zhejiang China
| | - Chuping Wu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life SciencesZhejiang University Hangzhou Zhejiang China
- Zhejiang Academy of Forestry Hangzhou Zhejiang China
| | - Mingjian Yu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life SciencesZhejiang University Hangzhou Zhejiang China
| |
Collapse
|
9
|
Abstract
Conservation genetics is a branch of conservation biology that uses molecular data to assist in the conservation and management of imperiled populations, subspecies, and species. In this review, I examine conservation action plans (CAPs)—instrumental documents designed to influence conservation policy—for selected primate species. I use the information contained in CAPs as a means to guide this review. The primary genetics-based topics that are mentioned in CAPs are genetic connectivity, inbreeding, and subspecies/species delimitation. I discuss these topics as well as historical demographic inference and hybridization using examples from wild primate species to illustrate the myriad ways in which genetics can assist in conservation efforts. I also discuss some recent technological advances such as genomic capture techniques and the potential to do molecular work in remote locations.
Collapse
Affiliation(s)
- Richard R. Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, USA
| |
Collapse
|
10
|
Ren Y, Huang K, Guo S, Pan R, Derek DW, Qi X, Wang X, Wang C, Zhao H, Yang B, Li F, Li B. Kinship promotes affiliative behaviors in a monkey. Curr Zool 2018; 64:441-447. [PMID: 30108624 PMCID: PMC6084570 DOI: 10.1093/cz/zox046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/10/2017] [Indexed: 11/14/2022] Open
Abstract
In social mammals, kinship is an important factor that often affects the interactions among individuals within groups. In primates that live in a multilevel society, kinship may affect affiliative patterns between individuals at different scales within the larger group. For this study, we use field observations and molecular methods to reveal the profiles of how kinship affects affiliative behaviors between individuals in a breeding band of wild golden snub-nosed monkeys (Rhinopithecus roxellana). We use a novel nonparametric test, the partition Mantel test, to measure independently the correlation between kinship and each of three affiliative behaviors. Our results show that more closely related females are more likely to groom each other. Average relatedness between adult females within the same one-male unit (OMU) is higher than that between adult females from different OMUs. We suggest that closely related females may reside in the same OMU in order to attain inclusive fitness benefits, and that kinship plays an important role in maintaining the social structure of this species.
Collapse
Affiliation(s)
- Yi Ren
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
- Institute of Zoology, Shaanxi Academy of Sciences, Xi’an, China
| | - Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
| | - Ruliang Pan
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
- The School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, Australia
| | - Dunn W Derek
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
| | - Xiaoguang Qi
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
| | - Xiaowei Wang
- Institute of Zoology, Shaanxi Academy of Sciences, Xi’an, China
| | - Chengliang Wang
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
- Institute of Zoology, Shaanxi Academy of Sciences, Xi’an, China
| | - Haitao Zhao
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
- Institute of Zoology, Shaanxi Academy of Sciences, Xi’an, China
| | - Bin Yang
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
- Institute of Zoology, Shaanxi Academy of Sciences, Xi’an, China
| | - Fangfang Li
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
- Institute of Zoology, Shaanxi Academy of Sciences, Xi’an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi’an, China
| |
Collapse
|
11
|
Zhang P, Huang K, Zhang B, Dunn DW, Chen D, Li F, Qi X, Guo S, Li B. High polymorphism in MHC-DRB genes in golden snub-nosed monkeys reveals balancing selection in small, isolated populations. BMC Evol Biol 2018. [PMID: 29534675 PMCID: PMC5851093 DOI: 10.1186/s12862-018-1148-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background Maintaining variation in immune genes, such as those of the major histocompatibility complex (MHC), is important for individuals in small, isolated populations to resist pathogens and parasites. The golden snub-nosed monkey (Rhinopithecus roxellana), an endangered primate endemic to China, has experienced a rapid reduction in numbers and severe population fragmentation over recent years. For this study, we measured the DRB diversity among 122 monkeys from three populations in the Qinling Mountains, and estimated the relative importance of different agents of selection in maintaining variation of DRB genes. Results We identified a total of 19 DRB sequences, in which five alleles were novel. We found high DRB variation in R. roxellana and three branches of evidence suggesting that balancing selection has contributed to maintaining MHC polymorphism over the long term in this species: i) different patterns of both genetic diversity and population differentiation were detected at MHC and neutral markers; ii) an excess of non-synonymous substitutions compared to synonymous substitutions at antigen binding sites, and maximum-likelihood-based random-site models, showed significant positive selection; and iii) phylogenetic analyses revealed a pattern of trans-species evolution for DRB genes. Conclusions High levels of DRB diversity in these R. roxellana populations may reflect strong selection pressure in this species. Patterns of genetic diversity and population differentiation, positive selection, as well as trans-species evolution, suggest that pathogen-mediated balancing selection has contributed to maintaining MHC polymorphism in R. roxellana over the long term. This study furthers our understanding of the role pathogen-mediated balancing selection has in maintaining variation in MHC genes in small and fragmented populations of free-ranging vertebrates. Electronic supplementary material The online version of this article (10.1186/s12862-018-1148-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Pei Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Bingyi Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Dan Chen
- Middle School Affiliated to Northwest University, Xi'an, China
| | - Fan Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiaoguang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China. .,Xi'an Branch of Chinese Academy of Science, Xi'an, China.
| |
Collapse
|
12
|
Duan YM, Huang K, QI XG, LI BG. Characterization of 29 highly polymorphic microsatellite markers for golden snub-nosed monkey (Rhinopithecus roxellana). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0658-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Diversity at two genetic loci associated with the major histocompatibility complex in the golden snub-nosed monkey (Rhinopithecus roxellana). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|