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Yan J, Song C, Liang J, La Y, Lai J, Pan R, Huang Z, Li B, Zhang P. Moderate Genetic Diversity of MHC Genes in an Isolated Small Population of Black-and-White Snub-Nosed Monkeys ( Rhinopithecus bieti). Animals (Basel) 2024; 14:2276. [PMID: 39123802 PMCID: PMC11310952 DOI: 10.3390/ani14152276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species.
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Affiliation(s)
- Jibing Yan
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Chunmei Song
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Jiaqi Liang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Yanni La
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Jiandong Lai
- Baima Snow Mountain National Nature Reserve Administrative Bureau, Diqing 674500, China;
| | - Ruliang Pan
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
- International Center of Biodiversity and Primat Conservation, Dali University, Dali 671003, China
- School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Zhipang Huang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China;
| | - Baoguo Li
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
- Shaanxi Institute of Zoology, Xi’an 710032, China
- College of Life Science, Yanan University, Yanan 710032, China
| | - Pei Zhang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
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Creating small food-habituated groups might alter genetic diversity in the endangered Yunnan snub-nosed monkey. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2020.e01422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Moraes BÁLCDE, Borges DB, Souza-Alves JP, Boubli JP, Bezerra B. Microsatellite Markers for Bearded Capuchins (Sapajus libidinosus): Transferability and Characterization. AN ACAD BRAS CIENC 2021; 93:e20190802. [PMID: 33470383 DOI: 10.1590/0001-3765202120190802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/07/2019] [Indexed: 11/22/2022] Open
Abstract
Natural Sapajus libidinosus populations are in continuous decline due to fragmentation, habitat loss, and the illegal pet trade. They live in Caatinga scrub forests, which already lost over 50% of their original cover. The lack of studies on S. libidinosus population genetics means that we do not know how they are being affected by this striking habitat loss and other anthropogenic disturbances. Polymorphic markers are not available for the study of S. libidinosus diversity and population genetics. Thus, here we aimed to test the transferability of 14 microsatellite markers to S. libidinosus. These microsatellites were previously isolated from Cebus capucinus (white-faced capuchin), species belonging to the same subfamily (Cebinae) as the study species. We found that six of the tested microsatellite markers (tetra-nucleotide) were cross-amplified in our target species. All loci were polymorphic. The number of alleles varied from 4 to 7, and the expected heterozygosity ranged from 0.588 to 0.869. The microsatellite markers transferred to S. libidinosus and characterised in our study will be valuable tools to evaluate the genetic variability of both wild and captive populations. They will considerably reduce the costs of microsatellite isolations, helping to prioritise currently limited research and conservation budgets in Brazil.
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Affiliation(s)
- BÁrbara L C DE Moraes
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Biologia Animal, Laboratório de Ecologia Comportamento e Conservação, Departamento de Zoologia, Centro de Biociências, Av. Prof. Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil.,University of Salford, School of Environment and Life Sciences, Peel Building, Salford Western Gateway, Salford M5 4WX, United Kingdom
| | - Daniela B Borges
- Universidade Estadual de Santa Cruz, Laboratório de Marcadores Moleculares, Departamento de Biologia, Campus Soane Nazaré de Andrade, Rodovia Ilhéus-Itabuna, s/n, Km 16, 45662-900 Ilhéus, BA, Brazil.,University of Salford, School of Environment and Life Sciences, Peel Building, Salford Western Gateway, Salford M5 4WX, United Kingdom
| | - JoÃo Pedro Souza-Alves
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Biologia Animal, Laboratório de Ecologia Comportamento e Conservação, Departamento de Zoologia, Centro de Biociências, Av. Prof. Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
| | - Jean Phillipe Boubli
- University of Salford, School of Environment and Life Sciences, Peel Building, Salford Western Gateway, Salford M5 4WX, United Kingdom
| | - Bruna Bezerra
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Biologia Animal, Laboratório de Ecologia Comportamento e Conservação, Departamento de Zoologia, Centro de Biociências, Av. Prof. Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
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Ishizuka S, Kawamoto Y, Sakamaki T, Tokuyama N, Toda K, Okamura H, Furuichi T. Paternity and kin structure among neighbouring groups in wild bonobos at Wamba. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171006. [PMID: 29410812 PMCID: PMC5792889 DOI: 10.1098/rsos.171006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/02/2018] [Indexed: 06/08/2023]
Abstract
Although both bonobos and chimpanzees are male-philopatric species, outcomes of male-male reproductive competition seem to be more closely associated with mating success in chimpanzees. This suggests that the extent of male reproductive skew is lower in bonobos. In addition, between-group male-male reproductive competition is more lethal in chimpanzees. This suggests that between-group differentiation in male kinship is lower in bonobos. We analysed the paternity of 17 offspring in two bonobo groups and estimated the relatedness of individuals among three neighbouring groups by using DNA extracted from non-invasive samples at Wamba, in the Democratic Republic of the Congo. The alpha males sired at least nine of 17 offspring. This supports a previous finding that the male reproductive skew is higher in bonobos than that in chimpanzees. Average relatedness among males within groups was significantly higher than that among males across groups, whereas there was no significant difference among females between within and across groups. These results are consistent with male philopatry, highly skewed reproductive success of males and female dispersal. Higher average relatedness among males within groups suggest that the differences in hostility towards males of different groups between bonobos and chimpanzees may be explained by factors other than kinship.
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Affiliation(s)
- Shintaro Ishizuka
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
- Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Tetsuya Sakamaki
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Nahoko Tokuyama
- Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Kazuya Toda
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
- Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Hiroki Okamura
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Takeshi Furuichi
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
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Establishment of a microsatellite set for noninvasive paternity testing in free-ranging Macaca mulatta tcheliensis in Mount Taihangshan area, Jiyuan, China. Zool Stud 2015; 54:e8. [PMID: 31966095 DOI: 10.1186/s40555-014-0100-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 12/25/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Within multi-male and multi-female mammalian societies, paternity assignment is crucial for evaluating male reproductive success, dominance hierarchy, and inbreeding avoidance. It is, however, difficult to determine paternity because of female promiscuity during reproduction. Noninvasive molecular techniques (e.g., fecal DNA) make it possible to match the genetic father to his offspring. In the current study, a troop of free-ranging Taihangshan macaques (Macaca mulatta tcheliensis) in Mt. Taihangshan area, Jiyuan, China, was selected for studying the paternity. We successfully screened a set of microsatellite loci from fecal DNA and evaluated the efficiency of these loci for paternity testing using clearly recorded data of maternity. RESULTS The results showed that: 1) ten loci out of 18 candidate microsatellite loci were amplified successfully in the fecal samples of Taihangshan macaques. The error probability in maternity assignments and paternity testing was very low as indicated by their power of discrimination (0.70 to 0.95), power of exclusion (0.43 to 0.84), and the values of polymorphic information content ranging from 0.52 to 0.82; 2) the combined probability of exclusion in paternity testing for ten qualified loci was as high as 99.999%, and the combined probability of exclusion reached 99.99% when the seven most polymorphic loci were adopted; 3) the offspring were assigned to their biological mother correctly and also matched with their genetic father. CONCLUSIONS We concluded that the ten polymorphic microsatellite loci, especially a core set of seven most polymorphic loci, provided an effective and reliable tool for noninvasive paternity testing in free-ranging rhesus macaques.
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Kolleck J, Yang M, Zinner D, Roos C. Genetic diversity in endangered Guizhou snub-nosed monkeys (Rhinopithecus brelichi): contrasting results from microsatellite and mitochondrial DNA data. PLoS One 2013; 8:e73647. [PMID: 24009761 PMCID: PMC3756984 DOI: 10.1371/journal.pone.0073647] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/24/2013] [Indexed: 12/30/2022] Open
Abstract
To evaluate the conservation status of a species or population it is necessary to gain insight into its ecological requirements, reproduction, genetic population structure, and overall genetic diversity. In our study we examined the genetic diversity of Rhinopithecus brelichi by analyzing microsatellite data and compared them with already existing data derived from mitochondrial DNA, which revealed that R. brelichi exhibits the lowest mitochondrial diversity of all so far studied Rhinopithecus species. In contrast, the genetic diversity of nuclear DNA is high and comparable to other Rhinopithecus species, i.e. the examined microsatellite loci are similarly highly polymorphic as in other species of the genus. An explanation for these differences in mitochondrial and nuclear genetic diversity could be a male biased dispersal. Females most likely stay within their natal band and males migrate between bands, thus mitochondrial DNA will not be exchanged between bands but nuclear DNA via males. A Bayesian Skyline Plot based on mitochondrial DNA sequences shows a strong decrease of the female effective population size (Nef) starting about 3,500 to 4,000 years ago, which concurs with the increasing human population in the area and respective expansion of agriculture. Given that we found no indication for a loss of nuclear DNA diversity in R. brelichi it seems that this factor does not represent the most prominent conservation threat for the long-term survival of the species. Conservation efforts should therefore focus more on immediate threats such as development of tourism and habitat destruction.
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Affiliation(s)
- Jakob Kolleck
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Mouyu Yang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Fanjingshan National Nature Reserve, Jiangkou, China
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- * E-mail:
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Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model. CHINESE SCIENCE BULLETIN-CHINESE 2011. [DOI: 10.1007/s11434-011-4634-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Liu Z, Ren B, Wu R, Zhao L, Hao Y, Wang B, Wei F, Long Y, Li M. The effect of landscape features on population genetic structure in Yunnan snub-nosed monkeys (Rhinopithecus bieti) implies an anthropogenic genetic discontinuity. Mol Ecol 2009; 18:3831-46. [PMID: 19732331 DOI: 10.1111/j.1365-294x.2009.04330.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Tibetan Plateau is one of the top 10 biodiversity hotspots in the world and acts as a modern harbour for many rare species because of its relatively pristine state. In this article, we report a landscape genetic study on the Yunnan snub-nosed monkey (Rhinopithecus bieti), a primate endemic to the Tibetan Plateau. DNA was extracted from blood, tissue and fecal samples of 135 wild individuals representing 11 out of 15 extant monkey groups. Ten microsatellite loci were used to characterize patterns of genetic diversity. The most striking feature of the population structure is the presence of five subpopulations with distinct genetic backgrounds and unique spatial regions. The population structure of R. bieti appears to be shaped by anthropogenic landscape features as gene flow between subpopulations is strongly impeded by arable land, highways and human habitation. A partial Mantel test showed that 36.23% (r = 0.51, P = 0.01) of the genetic distance was explained by habitat gaps after controlling for the effect of geographical distance. Only 4.92% of the genetic distance was explained by geographical distance in the partial Mantel test, and no significant correlation was found. Estimation of population structure history indicates that environmental change during the last glacial maximum and human impacts since the Holocene, or a combination of both, have shaped the observed population structure of R. bieti. Increasing human activity on the Plateau, especially that resulting in habitat fragmentation, is becoming an important factor in shaping the genetic structure and evolutionary potential of species inhabiting this key ecosystem.
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Affiliation(s)
- Zhijin Liu
- Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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