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Jiménez T, Peña-Villalobos I, Arcila J, Del Basto F, Palma V, Sabat P. The effects of urban thermal heterogeneity and feather coloration on oxidative stress and metabolism of pigeons (Columba livia). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169564. [PMID: 38142996 DOI: 10.1016/j.scitotenv.2023.169564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/23/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Urbanization stands out as a significant anthropogenic factor, exerting selective pressures on ecosystems and biotic components. A notable outcome of urbanization is thermal heterogeneity where the emergence of Urban Heat Islands is characterized by elevated air and surface temperatures compared to adjacent rural areas. Investigating the influence of thermal heterogeneity on urban animals could offer insights into how temperature variations can lead to phenotypic shifts. Urban pigeons (Columba livia) serve as an excellent model for studying urban thermal effects, given the melanism variations, which are associated with the pleiotropy of the melanocortin system. To examine the development of physiological plasticity in response to urban thermal variations, we conducted a study on pigeons in Santiago, Chile, during the rainy season. We assessed the influence of habitat on physiological traits related to metabolism and antioxidant capacities, which are theoretically affected by feather coloration. Our findings reveal that variations in melanism significantly impact pigeon physiology, affecting both antioxidant capacities and the mitochondrial activity of red blood cells. It was found that higher urban temperatures, from both the current sampling month and the prior sampling month (from CRU TS dataset), were negatively and strongly associated with lower antioxidant and metabolic activities. This suggests that elevated urban temperatures likely benefit the energetic budgets of pigeon populations and mitigate the negative effects of oxidative metabolism, with differential effects depending on feather colorations.
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Affiliation(s)
- Tomás Jiménez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Isaac Peña-Villalobos
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Laboratorio de Células troncales y Biología del Desarrollo, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Javiera Arcila
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco Del Basto
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Verónica Palma
- Laboratorio de Células troncales y Biología del Desarrollo, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Sabat
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile; Millennium Nucleus of Patagonian Limit of Life (LiLi)
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2
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Cetkovská E, Brandlová K, Ogden R, Černá Bolfíková B. Evaluation of the Impact of Population Management on the Genetic Parameters of Selected Spiral-Horned Antelopes. BIOLOGY 2024; 13:104. [PMID: 38392322 PMCID: PMC10886411 DOI: 10.3390/biology13020104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.
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Affiliation(s)
- Ema Cetkovská
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Karolína Brandlová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
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3
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Shaw RE, Spencer PB, Gibson LA, Dunlop JA, Kinloch JE, Mokany K, Byrne M, Moritz C, Davie H, Travouillon KJ, Ottewell KM. Linking life history to landscape for threatened species conservation in a multiuse region. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e13989. [PMID: 35979681 PMCID: PMC10100189 DOI: 10.1111/cobi.13989] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/24/2022] [Accepted: 08/01/2022] [Indexed: 05/24/2023]
Abstract
Landscape-scale conservation that considers metapopulation dynamics will be essential for preventing declines of species facing multiple threats to their survival. Toward this end, we developed a novel approach that combines occurrence records, spatial-environmental data, and genetic information to model habitat, connectivity, and patterns of genetic structure and link spatial attributes to underlying ecological mechanisms. Using the threatened northern quoll (Dasyurus hallucatus) as a case study, we applied this approach to address the need for conservation decision-making tools that promote resilient metapopulations of this threatened species in the Pilbara, Western Australia, a multiuse landscape that is a hotspot for biodiversity and mining. Habitat and connectivity were predicted by different landscape characteristics. Whereas habitat suitability was overwhelmingly driven by terrain ruggedness, dispersal was facilitated by proximity to watercourses. Although there is limited evidence for major physical barriers in the Pilbara, areas with high silt and clay content (i.e., alluvial and hardpan plains) showed high resistance to dispersal. Climate subtlety shaped distributions and patterns of genetic turnover, suggesting the potential for local adaptation. By understanding these spatial-environmental associations and linking them to life-history and metapopulation dynamics, we highlight opportunities to provide targeted species management. To support this, we have created habitat, connectivity, and genetic uniqueness maps for conservation decision-making in the region. These tools have the potential to provide a more holistic approach to conservation in multiuse landscapes globally.
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Affiliation(s)
- Robyn E. Shaw
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University, Australian Capital TerritoryCanberraAustralia
| | - Peter B. Spencer
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
| | - Lesley A. Gibson
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Judy A. Dunlop
- WA Feral Cat Working GroupPerthWestern AustraliaAustralia
| | - Janine E. Kinloch
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Karel Mokany
- CSIROCanberraAustralian Capital TerritoryAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University, Australian Capital TerritoryCanberraAustralia
| | - Harriet Davie
- Roy Hill Iron Ore Pty LtdPerthWestern AustraliaAustralia
| | | | - Kym M. Ottewell
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
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4
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McDonald MM, Cunneyworth PMK, Anderson AG, Wroblewski E. Mitochondrial genetic diversity and divergence dating of Angolan colobus monkeys (Colobus angolensis) in the eastern forests of Kenya and Tanzania: Implications for subspeciation and reconstructing historical biogeography. Am J Primatol 2022; 84:e23384. [PMID: 35389522 DOI: 10.1002/ajp.23384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 02/10/2022] [Accepted: 03/12/2022] [Indexed: 11/11/2022]
Abstract
Whether the Colobus angolensis that reside in the fragmented forests in eastern Kenya and Tanzania represent one subspecies or two has been debated for 50 years. Morphological and more recent genetic and ecological studies suggest that these populations represent two subspecies, C. a. palliatus and C. a. sharpei. However, their distribution of mitochondrial variation remains unresolved since the genetic study only characterized four populations at the range ends. Therefore, we characterized five populations in the area of the hypothesized subspecies divide. We identified eight new haplotypes which, combined with those previously identified, provided 26 haplotypes from nine populations for analysis. Haplotypes found south of the Rufiji River cluster together but separately from northern haplotypes. The largest sequence differences within cytochrome b occur between population pairs representing opposite sides of the river; their mean difference (1.5%) is more than that of other primate subspecies. Analysis of molecular variance attributes most of the variation to that north versus south of the river. These results support the previous subspecies distinction between C. a. palliatus (northern) and C. a. sharpei (southern), divided by the Rufiji River. The estimated time of the most recent common ancestor of all haplotypes indicates that the subspecies have been isolated from each other for approximately 550,000 years. The common ancestor of northern and southern haplogroups was 370,000 and 290,000 years ago, respectively. Nevertheless, the correlation between genetic and geographic distances suggests that isolation-by-distance contributed to population structuring. Significant variation among populations, with only three haplotypes shared between populations, also indicates that an extended period of isolation drove population distinctiveness. Considering these results, we evaluate hypotheses about the founding and differentiation of these subspecies during Pleistocene climatic fluctuations and propose a novel, more direct migration route from Central Africa to their current range navigating Lake Tanganyika, the central Tanzanian corridor, and the Rufiji River.
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Affiliation(s)
- Monica M McDonald
- AZA Reproductive Management Center, Saint Louis Zoo, Saint Louis, Missouri, USA.,Department of Anthropology, Washington University, St. Louis, Missouri, USA
| | | | - Aaron G Anderson
- Department of Anthropology, Washington University, St. Louis, Missouri, USA
| | - Emily Wroblewski
- Department of Anthropology, Washington University, St. Louis, Missouri, USA
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Cortes‐Miranda J, Véliz D, Flores‐Prado L, Sallaberry M, Vega‐Retter C. Genetic diversity and origin of a fish population recently colonizing a reservoir: The case of
Basilichthys microlepidotus
, central Chile. POPUL ECOL 2022. [DOI: 10.1002/1438-390x.12118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jorge Cortes‐Miranda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias Universidad de Chile Santiago Chile
| | - David Véliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias Universidad de Chile Santiago Chile
| | - Luis Flores‐Prado
- Instituto de Entomología Universidad Metropolitana de Ciencias de la Educación Santiago Chile
| | - Michel Sallaberry
- Departamento de Ciencias Ecológicas, Facultad de Ciencias Universidad de Chile Santiago Chile
| | - Caren Vega‐Retter
- Departamento de Ciencias Ecológicas, Facultad de Ciencias Universidad de Chile Santiago Chile
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6
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Chew PC, Christianus A, Zudaidy JM, Ina-Salwany MY, Chong CM, Tan SG. Microsatellite Characterization of Malaysian Mahseer ( Tor spp.) for Improvement of Broodstock Management and Utilization. Animals (Basel) 2021; 11:ani11092633. [PMID: 34573599 PMCID: PMC8471032 DOI: 10.3390/ani11092633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei's genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.
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Affiliation(s)
- Poh Chiang Chew
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Freshwater Fisheries Research Division, Fisheries Research Institute Glami Lemi, Jelebu 71650, Malaysia;
| | - Annie Christianus
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: ; Tel.: +60-3-8947-4884
| | - Jaapar M. Zudaidy
- Freshwater Fisheries Research Division, Fisheries Research Institute Glami Lemi, Jelebu 71650, Malaysia;
| | - Md Yasin Ina-Salwany
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Chou Min Chong
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Soon Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
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7
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Zheng Y, Zhang S, Lu Q, Zhang S, Wang L, Hong M, Nguyen T, Zhao J, Yao M. Population genetic patterns of a mangrove‐associated frog reveal its colonization history and habitat connectivity. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Yitao Zheng
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Shan Zhang
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Qi Lu
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Siyu Zhang
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Lijun Wang
- College of Life Sciences Hainan Normal University Haikou China
| | - Meiling Hong
- College of Life Sciences Hainan Normal University Haikou China
| | - Truong Nguyen
- Institute of Ecology and Biological Resources Academy of Science and Technology Hanoi Vietnam
- Vietnam Academy of Science and Technology Graduate University of Science and Technology Hanoi Vietnam
| | - Jindong Zhao
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Meng Yao
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
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8
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Vaissi S, Sharifi M. The least‐cost path analysis of landscape genetics identifies two dispersal routes for the threatened Kaiser's mountain newt (Caudata: Salamandridae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Somaye Vaissi
- Department of Biology, Faculty of Science Razi University Kermanshah Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science Razi University Kermanshah Iran
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9
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Que T, Wang H, Yang W, Wu J, Hou C, Pei S, Wu Q, Li LM, Wei S, Xie X, Huang H, Chen P, Huang Y, Wu A, He M, Nong D, Wei X, Wu J, Nong R, Huang N, Zhou Q, Lin Y, Lu T, Wei Y, Li S, Yao J, Zhong Y, Qin H, Tan L, Li Y, Li W, Liu T, Liu S, Yu Y, Qiu H, Jiang Y, Li Y, Liu Z, Huang CM, Hu Y. The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance. BMC Biol 2021; 19:67. [PMID: 33832502 PMCID: PMC8034193 DOI: 10.1186/s12915-021-00998-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/05/2021] [Indexed: 01/13/2023] Open
Abstract
Background Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche. Results In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies. Conclusions These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.
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Affiliation(s)
- Tengcheng Que
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Huifeng Wang
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Weifei Yang
- Annoroad Gene Technology, Beijing, 100176, China
| | - Jianbao Wu
- Guangxi Chongzuo white headed langur national nature reserve, Chongzuo, Guangxi, 532200, China
| | - Chenyang Hou
- School of Information and Management, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Surui Pei
- Annoroad Gene Technology, Beijing, 100176, China
| | - Qunying Wu
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Liu Ming Li
- Guangxi Reproductive Medical Research Center, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Shilu Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xing Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Hongli Huang
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Panyu Chen
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Yiming Huang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Aiqiong Wu
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Meihong He
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Dengpan Nong
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Xiao Wei
- Guangxi Chongzuo white headed langur national nature reserve, Chongzuo, Guangxi, 532200, China
| | - Junyi Wu
- Nanning Animal Zoo, Nanning, Guangxi, 530021, China
| | - Ru Nong
- Nanning Animal Zoo, Nanning, Guangxi, 530021, China
| | - Ning Huang
- Nanning Animal Zoo, Nanning, Guangxi, 530021, China
| | - Qingniao Zhou
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yaowang Lin
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Tingxi Lu
- School of Information and Management, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yongjie Wei
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Shousheng Li
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Jianglong Yao
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Yanli Zhong
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Huayong Qin
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Luohao Tan
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Yingjiao Li
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Weidong Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Tao Liu
- Annoroad Gene Technology, Beijing, 100176, China
| | - Sanyang Liu
- Annoroad Gene Technology, Beijing, 100176, China
| | - Yongyi Yu
- Annoroad Gene Technology, Beijing, 100176, China
| | - Hong Qiu
- Annoroad Gene Technology, Beijing, 100176, China
| | - Yonghua Jiang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Youcheng Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Cheng Ming Huang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Yanling Hu
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China. .,Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China. .,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China.
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10
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Westphal D, Mancini AN, Baden AL. Primate landscape genetics: A review and practical guide. Evol Anthropol 2021; 30:171-184. [PMID: 33720482 DOI: 10.1002/evan.21891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/12/2020] [Accepted: 02/17/2021] [Indexed: 11/06/2022]
Abstract
Landscape genetics is an emerging field that integrates population genetics, landscape ecology, and spatial statistics to investigate how geographical and environmental features and evolutionary processes such as gene flow, genetic drift, and selection structure genetic variation at both the population and individual levels, with implications for ecology, evolution, and conservation biology. Despite being particularly well suited for primatologists, this method is currently underutilized. Here, we synthesize the current state of research on landscape genetics in primates. We begin by outlining how landscape genetics has been used to disentangle the drivers of diversity, followed by a review of how landscape genetic methods have been applied to primates. This is followed by a section highlighting special considerations when applying the methods to primates, and a practical guide to facilitate further landscape genetics studies using both existing and de novo datasets. We conclude by exploring future avenues of inquiry that could be facilitated by recent developments as well as underdeveloped applications of landscape genetics to primates.
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Affiliation(s)
- Darice Westphal
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Amanda N Mancini
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Andrea L Baden
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA.,Department of Anthropology, Hunter College, New York, New York, USA
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11
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Valladares-Gómez A, Celis-Diez JL, Sepúlveda-Rodríguez C, Inostroza-Michael O, Hernández CE, Palma RE. Genetic Diversity, Population Structure, and Migration Scenarios of the Marsupial "Monito del Monte" in South-Central Chile. J Hered 2020; 110:651-661. [PMID: 31420661 DOI: 10.1093/jhered/esz049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 01/11/2023] Open
Abstract
In this study, we quantified the 3 pivotal genetic processes (i.e., genetic diversity, spatial genetic structuring, and migration) necessary for a better biological understanding and management of the singular "living-fossil" and near-threatened mouse opossum marsupial Dromiciops gliroides, the "Monito del Monte," in south-central Chile. We used 11 microsatellite loci to genotype 47 individuals distributed on the mainland and northern Chiloé Island. Allelic richness, observed and expected heterozygosity, inbreeding coefficient, and levels of genetic differentiation were estimated. The genetic structure was assessed based on Bayesian clustering methods. In addition, potential migration scenarios were evaluated based on a coalescent theory framework and Bayesian approach to parameter estimations. Microsatellites revealed moderate to high levels of genetic diversity across sampled localities. Moreover, such molecular markers suggested that at least 2 consistent genetic clusters could be identified along the D. gliroides distribution ("Northern" and "Southern" cluster). However, general levels of genetic differentiation observed among localities and between the 2 genetic clusters were relatively low. Migration analyses showed that the most likely routes of migration of D. gliroides occurred 1) from the Southern cluster to the Northern cluster and 2) from the Mainland to Chiloé Island. Our results could represent critical information for future conservation programs and for a recent proposal about the taxonomic status of this unique mouse opossum marsupial.
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Affiliation(s)
- Alejandro Valladares-Gómez
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Juan L Celis-Diez
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Casilla 4-D, Quillota, Chile
| | - Constanza Sepúlveda-Rodríguez
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Oscar Inostroza-Michael
- Laboratorio de Ecología Evolutiva y Filoinformática, Facultad de Ciencias Naturales y Ocenográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Cristián E Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática, Facultad de Ciencias Naturales y Ocenográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - R Eduardo Palma
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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12
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Kamalakkannan R, Bhavana K, Prabhu VR, Sureshgopi D, Singha HS, Nagarajan M. The complete mitochondrial genome of Indian gaur, Bos gaurus and its phylogenetic implications. Sci Rep 2020; 10:11936. [PMID: 32686769 PMCID: PMC7371690 DOI: 10.1038/s41598-020-68724-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/22/2020] [Indexed: 12/24/2022] Open
Abstract
The gaur is the largest extant cattle species and distributed across South and Southeast Asia. Around 85% of its current global population resides in India, however there has been a gradual decrease in the gaur population over the last two decades due to various anthropogenic activities. Mitochondrial genome is considered as an important tool for species identification and monitoring the populations of conservation concern and therefore it becomes an obligation to sequence the mitochondrial genome of Indian gaur. We report here for the first time 16,345 bp mitochondrial genome of four Indian gaur sequenced using two different approaches. Mitochondrial genome consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. Among the 37 genes, 28 were positioned on the H-strand and 9 were positioned on the L-strand. The overall base composition appeared to be 33.5% A, 27.2% T, 25.9% C and 13.4% G, which yielded a higher AT content. The phylogenetic analysis using complete mitochondrial genome sequences unambiguously suggested that gaur is the maternal ancestor of domestic mithun. Moreover, it also clearly distinguished the three sub species of B. gaurus i.e. B. gaurus gaurus, B. gaurus readei and B. gaurus hubbacki. Among the three sub species, B. gaurus gaurus was genetically closer to B. gaurus readei as compared to B. gaurus hubbacki. The findings of our study provide an insight into the genetic structure and evolutionary history of Indian gaur.
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Affiliation(s)
- Ranganathan Kamalakkannan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Karippadakam Bhavana
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Vandana R Prabhu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Dhandapani Sureshgopi
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Hijam Surachandra Singha
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Muniyandi Nagarajan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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13
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Melo-Carrillo A, Dunn JC, Cortés-Ortiz L. Low genetic diversity and limited genetic structure across the range of the critically endangered Mexican howler monkey (Alouatta palliata mexicana). Am J Primatol 2020; 82:e23160. [PMID: 32557717 DOI: 10.1002/ajp.23160] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 11/08/2022]
Abstract
Genetic diversity provides populations with the possibility to persist in ever-changing environments, where selective regimes change over time. Therefore, the long-term survival of a population may be affected by its level of genetic diversity. The Mexican howler monkey (Alouatta palliata mexicana) is a critically endangered primate restricted to southeast Mexico. Here, we evaluate the genetic diversity and population structure of this subspecies based on 83 individuals from 31 groups sampled across the distribution range of the subspecies, using 29 microsatellite loci. Our results revealed extremely low genetic diversity (HO = 0.21, HE = 0.29) compared to studies of other A. palliata populations and to other Alouatta species. Principal component analysis, a Bayesian clustering method, and analyses of molecular variance did not detect strong signatures of genetic differentiation among geographic populations of this subspecies. Although we detect small but significant FST values between populations, they can be explained by a pattern of isolation by distance. These results and the presence of unique alleles in different populations highlight the importance of implementing conservation efforts in multiple populations across the distribution range of A. p. mexicana to preserve its already low genetic diversity. This is especially important given current levels of population isolation due to the extreme habitat fragmentation across the distribution range of this primate.
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Affiliation(s)
- Adrián Melo-Carrillo
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Jacob C Dunn
- Behavioural Ecology Research Group, School of Life Sciences, Anglia Ruskin University, Cambridge, UK.,Biological Anthropology, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Cognitive Biology, University of Vienna, Vienna, Austria
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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14
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Wang W, Zheng Y, Zhao J, Yao M. Low genetic diversity in a critically endangered primate: shallow evolutionary history or recent population bottleneck? BMC Evol Biol 2019; 19:134. [PMID: 31242851 PMCID: PMC6595580 DOI: 10.1186/s12862-019-1451-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current patterns of population genetic variation may have been shaped by long-term evolutionary history and contemporary demographic processes. Understanding the underlying mechanisms that yield those patterns is crucial for informed conservation of endangered species. The critically endangered white-headed langur, Trachypithecus leucocephalus, is endemic to a narrow range in southwest China. This species shows very low genetic diversity in its 2 main relict populations, Fusui and Chongzuo. Whether this has been caused by a short evolutionary history or recent population declines is unknown. Therefore, we investigated the contributions of historical and recent population demographic changes to population genetic diversity by using 15 nuclear microsatellite markers and mitochondrial DNA (mtDNA) control region sequences. RESULTS Using genetic data from 214 individuals we found a total of 9 mtDNA haplotypes in the Fusui population but only 1 haplotype in the Chongzuo population, and we found an overall low genetic diversity (haplotype and nucleotide diversities: h = 0.486 ± 0.036; π = 0.0028 ± 0.0003). The demographic history inferred from mtDNA and microsatellite markers revealed no evidence for historical population size fluctuations or recent population bottlenecks. Simulations of possible population divergence histories inferred by DIYABC analysis supported a recent divergence of the Chongzuo population from the Fusui population and no population bottlenecks. CONCLUSIONS Despite severe population declines caused by anthropogenic activities in the last century, the low genetic diversity of the extant white-headed langur populations is most likely primarily due to the species' shallow evolutionary history and to a recent, local population founder event.
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Affiliation(s)
- Weiran Wang
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China.,Beijing National Day School, Beijing, 100871, China
| | - Yitao Zheng
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing, 100871, China. .,Institute of Ecology, Peking University, Beijing, 100871, China.
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15
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Firman RC, Ottewell KM, Fisher DO, Tedeschi JN. Range-wide genetic structure of a cooperative mouse in a semi-arid zone: Evidence for panmixia. J Evol Biol 2019; 32:1014-1026. [PMID: 31211909 DOI: 10.1111/jeb.13498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 12/20/2022]
Abstract
Landscape topography and the mobility of individuals will have fundamental impacts on a species' population structure, for example by enhancing or reducing gene flow and therefore influencing the effective size and genetic diversity of the population. However, social organization will also influence population genetic structure. For example, species that live and breed in cooperative groups may experience high levels of inbreeding and strong genetic drift. The western pebble-mound mouse (Pseudomys chapmani), which occupies a highly heterogeneous, semi-arid landscape in Australia, is an enigmatic social mammal that has the intriguing behaviour of working cooperatively in groups to build permanent pebble mounds above a subterranean burrow system. Here, we used both nuclear (microsatellite) and mitochondrial (mtDNA) markers to analyse the range-wide population structure of western pebble-mound mice sourced from multiple social groups. We observed high levels of genetic diversity at the broad scale, very weak genetic differentiation at a finer scale and low levels of inbreeding. Our genetic analyses suggest that the western pebble-mound mouse population is both panmictic and highly viable. We conclude that high genetic connectivity across the complex landscape is a consequence of the species' ability to permeate their environment, which may be enhanced by "boom-bust" population dynamics driven by the semi-arid climate. More broadly, our results highlight the importance of sampling strategies to infer social structure and demonstrate that sociality is an important component of population genetic structure.
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Affiliation(s)
- Renée C Firman
- Centre for Evolutionary Biology, University of Western Australia, Crawley, Western Australia, Australia
| | - Kym M Ottewell
- Science and Conservation, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, Kensington, Western Australia, Australia
| | - Diana O Fisher
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Jamie N Tedeschi
- Centre for Evolutionary Biology, University of Western Australia, Crawley, Western Australia, Australia
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16
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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.
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Affiliation(s)
- Richard R. Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, USA
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17
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Abstract
China is one of the most dynamic countries of the world and it shelters some amazing levels of biodiversity, including some very special primate species. However, primarily as a result of forest loss, most of which occurred in historical times, approximately 70% of China’s primate species have less than 3 000 individuals. Here I evaluate one road for future conservation/development that could produce very positive gains for China’s primates; namely forest restoration. I argue that for a large scale restoration project to be possible two conditions must be met; the right societal conditions must exist and the right knowledge must be in hand. This evaluation suggests that the restoration of native forest to support many of China’s primates holds great potential to advance conservation goals and to promote primate population recovery.
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Affiliation(s)
- Colin A Chapman
- Department of Anthropology, McGill University, Montréal Québec H3A 2T7, Canada; E-mail: .,Wildlife Conservation Society, Bronx New York 10460, USA.,Section of Social Systems Evolution, Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
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18
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Baas P, van der Valk T, Vigilant L, Ngobobo U, Binyinyi E, Nishuli R, Caillaud D, Guschanski K. Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:565-575. [PMID: 29313894 DOI: 10.1002/ajpa.23393] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/27/2017] [Accepted: 12/13/2017] [Indexed: 11/06/2022]
Abstract
OBJECTIVES The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range. MATERIALS AND METHODS We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population. RESULTS In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments. DISCUSSION Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.
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Affiliation(s)
- Pauline Baas
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tom van der Valk
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Linda Vigilant
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
| | - Urbain Ngobobo
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia
| | - Escobar Binyinyi
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia
| | - Radar Nishuli
- Institut Congolais pour la Conservation de la Nature, N4, Réserve de Faune à Okapis, Democratic Republic of Congo
| | - Damien Caillaud
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia.,Department of Anthropology, University of California, Davis, One Shields Ave, Davis, California
| | - Katerina Guschanski
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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