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De R, Nigam P, Williams AC, Goyal SP. Beyond consensus genotyping: a case study on the Asian elephant Elephas maximus. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01287-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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De R, Sharma R, Davidar P, Arumugam N, Sedhupathy A, Puyravaud JP, Selvan KM, Rahim PA, Udayraj S, Parida J, Digal DK, Kanagaraj R, Kakati K, Nigam P, Williams AC, Habib B, Goyal SP. Pan-India population genetics signifies the importance of habitat connectivity for wild Asian elephant conservation. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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3
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Athira TK, Vidya TNC. Elephant Social Systems: What Do We Know and How Have Molecular Tools Helped? J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00226-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Marasinghe MSLRP, Nilanthi RMR, Hathurusinghe HABM, Sooriyabandara MGC, Chandrasekara CHWMRB, Jayawardana KANC, Kodagoda MM, Rajapakse RC, Bandaranayake PCG. Revisiting traditional SSR based methodologies available for elephant genetic studies. Sci Rep 2021; 11:8718. [PMID: 33888797 PMCID: PMC8062488 DOI: 10.1038/s41598-021-88034-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants' dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.
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Affiliation(s)
- M S L R P Marasinghe
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - R M R Nilanthi
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - H A B M Hathurusinghe
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - M G C Sooriyabandara
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - C H W M R B Chandrasekara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - K A N C Jayawardana
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - M M Kodagoda
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - R C Rajapakse
- Department of National Zoological Gardens, Anagarika Dharmapala Mawatha, Dehiwala, 10350, Sri Lanka
| | - P C G Bandaranayake
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka.
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Aznar-Cormano L, Bonnald J, Krief S, Guma N, Debruyne R. Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics. Sci Rep 2021; 11:7227. [PMID: 33790303 PMCID: PMC8012363 DOI: 10.1038/s41598-021-86010-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/29/2021] [Indexed: 11/24/2022] Open
Abstract
It is important to determine the sex of elephants from their samples-faeces from the field or seized ivory-for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, particularly in terms of sensitivity and specificity, due to the degradation of DNA in these samples. These limitations have also prevented their use with ancient DNA samples of elephants or mammoths. Here we propose a novel TaqMan-MGB qPCR assay to address these difficulties. We designed it specifically to allow the characterization of the genetic sex for highly degraded samples of all elephantine taxa (elephants and mammoths). In vitro experiments demonstrated a high level of sensitivity and low contamination risks. We applied this assay in two actual case studies where it consistently recovered the right genotype for specimens of known sex a priori. In the context of a modern conservation survey of African elephants, it allowed determining the sex for over 99% of fecal samples. In a paleogenetic analysis of woolly mammoths, it produced a robust hypothesis of the sex for over 65% of the specimens out of three PCR replicates. This simple, rapid, and cost-effective procedure makes it readily applicable to large sample sizes.
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Affiliation(s)
- Laetitia Aznar-Cormano
- CNRS, Centre de Recherche en Paléontologie Paris (CR2P), Muséum national d'Histoire naturelle, Sorbonne Université, 57 rue Cuvier, CP 38, 75005, Paris, France
| | - Julie Bonnald
- CNRS, Eco-Anthropologie (EA), Muséum national d'Histoire naturelle, Université Paris Diderot, 17 place du Trocadéro, 75016, Paris, France
- Sebitoli Chimpanzee Project, Sebitoli Research Station, Kibale National Park, Fort Portal, Uganda
| | - Sabrina Krief
- CNRS, Eco-Anthropologie (EA), Muséum national d'Histoire naturelle, Université Paris Diderot, 17 place du Trocadéro, 75016, Paris, France
- Sebitoli Chimpanzee Project, Sebitoli Research Station, Kibale National Park, Fort Portal, Uganda
| | | | - Régis Debruyne
- Direction Générale Déléguée à la Recherche, à l'Expertise, la Valorisation et l'Enseignement (DGD-REVE), Muséum national d'Histoire naturelle, 57 rue Cuvier, CP 17, 75005, Paris, France.
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Bourgeois S, Ouitavon K, Kongmee P, Veeramaethaphan T, Kaden J, McEwing R. A simple sexing test for elephant species and its application to faecal DNA. J Appl Genet 2021; 62:507-509. [PMID: 33759056 DOI: 10.1007/s13353-021-00627-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/11/2020] [Accepted: 03/04/2021] [Indexed: 11/30/2022]
Abstract
We developed a novel real-time PCR assay for rapid sexing in all three elephant species, which amplifies small fragments of the orthologous sexual chromosome zinc finger protein genes ZFX/ZFY (65 bp). This assay is a simple, inexpensive and reliable tool that is suitable for non-invasive DNA samples and can be incorporated into larger SNP panels for individual identification and population genetic studies.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs Nationaux, B.P. 20379, Libreville, Gabon. .,WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, EH12 6TS, UK. .,Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - K Ouitavon
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, Thailand
| | - P Kongmee
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, Thailand
| | - T Veeramaethaphan
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, Thailand
| | - J Kaden
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, EH12 6TS, UK
| | - R McEwing
- TRACE Wildlife Forensics Network, PO Box 17477, Edinburgh, EH12 1NY, UK
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Chen Y, Sun Y, Atzeni L, Gibson L, Hua M, Li K, Shi K, Dudgeon D. Anthropogenic pressures increase extinction risk of an isolated Asian elephant (Elephas maximus) population in southwestern China, as revealed by a combination of molecular- and landscape-scale approaches. Integr Zool 2021; 17:1078-1094. [PMID: 33728791 DOI: 10.1111/1749-4877.12534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Identification of the effect of anthropogenic threats on ecosystem is crucial. We used molecular tools and remote sensing to evaluate the population status of an isolated Asian elephant population in southwestern China in response to changes in habitat suitability between 1989 and 2019. A total of 22 unique genotypes were identified from 117 dung samples collected between March and June 2018 using microsatellite DNA analysis, including 13 males and 9 females. Based on the size of fecal boli, 1 animal was a juvenile, 9 were subadults, and 12 were adults, indicating that recruitment was limited. The effective population size was small (15.3) but there was no signature of a recent population bottleneck. We observed a low genetic diversity (He = 0.46 ± 0.05) and a high level of inbreeding (Fis of 0.43 ± 0.11), suggesting low population viability and high risk of extinction. In total, these elephants lost nearly two thirds (62%) of their habitat in 3 decades. The expansion of agriculture and rubber plantations followed by an increase in human settlements after 1989 increased the isolation of this population. We recommend that resettlement of 800 inhabitants of 2 villages and the abandonment of associated farmland and rubber plantations would make an additional 20 km2 of suitable habitat available. This could allow a population increase of 14 elephants, possibly by translocating individuals from elsewhere in China. Our findings can be applied to the management and conservation of other fragmented populations in China or in other range countries of Asian elephants.
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Affiliation(s)
- Ying Chen
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.,School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Yakuan Sun
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.,Eco-Bridge Continental, Beijing, China
| | - Luciano Atzeni
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Luke Gibson
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Mei Hua
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, China
| | - Keyu Li
- School of Earth Sciences, Yunnan University, Kunming, China
| | - Kun Shi
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.,Eco-Bridge Continental, Beijing, China
| | - David Dudgeon
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
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Increasing conservation translocation success by building social functionality in released populations. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00604] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Roca AL, Ishida Y, Brandt AL, Benjamin NR, Zhao K, Georgiadis NJ. Elephant Natural History: A Genomic Perspective. Annu Rev Anim Biosci 2015; 3:139-67. [DOI: 10.1146/annurev-animal-022114-110838] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alfred L. Roca
- Department of Animal Sciences,
- Institute for Genomic Biology, and
| | | | | | - Neal R. Benjamin
- Department of Animal Sciences,
- College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; , , , , ,
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