Using genetic tools to inform conservation of fragmented populations of Asian elephants (Elephas maximus) across their range in China.
demography
elephas maximus
genetic diversity
interpopulation variation
national park
Journal
Integrative zoology
ISSN: 1749-4877
Titre abrégé: Integr Zool
Pays: Australia
ID NLM: 101492420
Informations de publication
Date de publication:
May 2023
May 2023
Historique:
medline:
15
5
2023
pubmed:
3
9
2022
entrez:
2
9
2022
Statut:
ppublish
Résumé
A herd of 15 Chinese elephants attracted international attention during their 2021 northward trek, motivating the government to propose establishment of an Asian elephant national park. However, planning is hampered by a lack of genetic information on the remaining populations in China. We collected DNA from 497 dung samples from all 5 populations encompassing the entire range of elephants in China and used mitochondrial and microsatellite markers to investigate their genetic and demographic structure. We identified 237 unique genotypes (153 females, 84 males), representing 81% of the known population. However, the effective population size was small (28, range 25-32). Historic demographic contraction appeared to account for low haplotype diversity (H
Identifiants
pubmed: 36052971
doi: 10.1111/1749-4877.12680
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
453-468Subventions
Organisme : National Forestry and Grassland Administration of China
ID : 20080131
Informations de copyright
© 2022 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.
Références
Ahlering MA, Hailer F, Roberts MT, Foley C (2011). A simple and accurate method to sex savannah, forest and Asian elephants using noninvasive sampling techniques. Molecular Ecology Resources 11, 831-4.
Ahlering MA, Hedges S, Johnson A, Tyson M, Schuttler SG, Eggert LS (2011). Genetic diversity, social structure, and conservation value of the elephants of the Nakai Plateau, Lao PDR, based on non-invasive sampling. Conservation Genetics 12, 413-22.
Allendorf FW (1986). Genetic drift and the loss of alleles versus heterozygosity. Zoo Biology 5, 181-90.
Amos W, Harwood J (1998). Factors affecting levels of genetic diversity in natural populations. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 353, 177-86.
Bourgeois S, Kaden J, Senn H et al. (2019). Improving cost-efficiency of faecal genotyping: New tools for elephant species. PLoS ONE 14, e0210811.
Campos-Arceiz A, de la Torre JA, Wei K et al. (2021). The return of the elephants: How two groups of dispersing elephants attracted the attention of billions and what can we learn from their behavior. Conservation Letters 14, e12836.
Cao H, Liu J, Fu C et al. (2017). Urban expansion and its impact on the land use pattern in Xishuangbanna since the reform and opening up of China. Remote Sensing 9, 137-58.
Chen F, Tang F, Wang D et al. (2019). Research on Asian Elephant National Park. Forestry Construction 6, 23-9.
Chen Y, Sun Y, Atzeni L et al. (2021). 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. Integrative Zoology, pp. 1-17. https://doi.org/10.1111/1749-4877.12534
Do C, Waples RS, Peel D, Macbeth G, Tillett BJ, Ovenden JR (2014). NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources 14, 209-14.
Du YR, Guo SC, Wang ZF et al. (2010). Demographic history of the Tibetan antelope Pantholops hodgsoni (chiru). Journal of Systematics and Evolution 48, 490-6.
Earl DA (2012). STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359-61.
Eggert L, Eggert J, Woodruff D (2003). Estimating population sizes for elusive animals: The forest elephants of Kakum National Park, Ghana. Molecular Ecology 12, 1389-402.
Elvin M (2008). The Retreat of the Elephants: An Environmental History of China. Yale University Press, New Haven.
Excoffier L, Lischer HE (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564-7.
Feng L, Zhang L (2005). Habitat selection by Asian elephant (Elephas maximus) in Xishuangbanna, Yunnan, China. Acta Theriologica Sinica 25, 229-36.
Fernando P, Pfrender ME, Encalada SE, Lande R (2000). Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant. Heredity 84, 362-72.
Fernando P, Vidya T, Rajapakse C, Dangolla A, Melnick D (2003). Reliable noninvasive genotyping: Fantasy or reality? Journal of Heredity 94, 115-23.
Flagstad Ø, Pradhan NM, Kvernstuen LG, Wegge P (2012). Conserving small and fragmented populations of large mammals: Non-invasive genetic sampling in an isolated population of Asian elephants in Nepal. Journal for Nature Conservation 20, 181-90.
Fleischer RC, Perry EA, Muralidharan K, Stevens EE, Wemmer CM (2001). Phylogeography of the Asian elephant (Elephas maximus) based on mitochondrial DNA. Evolution 55, 1882-92.
Frankham R, Ballou SEJD, Briscoe DA, Ballou JD (2002). Introduction to Conservation Genetics. Cambridge University Press, Cambridge.
Galpern P, Manseau M, Hettinga P, Smith K, Wilson P (2012). Allelematch: An R package for identifying unique multilocus genotypes where genotyping error and missing data may be present. Molecular Ecology Resources 12, 771-8.
Garza J, Williamson E (2001). Detection of reduction in population size using data from microsatellite loci. Molecular Ecology 10, 305-18.
Goossens B, Sharma R, Othman N et al. (2016). Habitat fragmentation and genetic diversity in natural populations of the Bornean elephant: Implications for conservation. Biological Conservation 196, 80-92.
Gray TNE, Vidya TNC, Potdar S, Bharti DK, Sovanna P (2014). Population size estimation of an Asian elephant population in eastern Cambodia through non-invasive mark-recapture sampling. Conservation Genetics 15, 803-10.
Hedges S, Lawson D (2006). Dung Survey Standards for the MIKE Programme. CITES MIKE Programme, Central Coordinating Unit, Nairobi, Kenya.
Huang Y, Tan D, Bai L et al. (2019). Habitat suitability analysis of Asian elephants along the proposed expressway from Simao to Jiangcheng. Forestry Construction 6, 67-73.
Hurni K, Fox J (2018). The expansion of tree-based boom crops in mainland Southeast Asia: 2001 to 2014. Journal of Land Use Science 13, 198-219.
IUCN Asian Elephant Specialist Group (2021). Resources for Asian elephant conservation. Available from URL: https://www.asesg.org/
Jakobsson M, Rosenberg NA (2007). CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801-6.
Johnsingh A, Williams AC (1999). Elephant corridors in India: Lessons for other elephant range countries. Oryx 33, 210-4.
Kalinowski ST, Taper ML, Marshall TC (2007). Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16, 1099-106.
Khounboline K (2011). Current status of Asian elephants in Lao PDR. Gajah 35, 62-6.
Knowles LL, Richards CL (2005). Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation. Molecular Ecology 14, 4023-32.
Kongrit C, Siripunkaw C, Brockelman W, Akkarapatumwong V, Wright T, Eggert L (2008). Isolation and characterization of dinucleotide microsatellite loci in the Asian elephant (Elephas maximus). Molecular Ecology Resources 8, 175-7.
Kusza S, Suchentrunk F, Pucher H, Mar KU, Zachos FE (2018). High levels of mitochondrial genetic diversity in Asian elephants (Elephas maximus) from Myanmar. Hystrix 29, 152-4.
Leigh JW, Bryant D (2015). popart: Full-feature software for haplotype network construction. Methods in Ecology and Evolution 6, 1110-6.
Liang J, Liu Y, Ying L, Li P, Xu Y, Shen Z (2014). Road impacts on spatial patterns of land use and landscape fragmentation in three parallel rivers region, Yunnan Province, China. Chinese Geographical Science 24, 15-27.
Librado P, Rozas J (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-2.
Lin L, Zhang L, Luo A, Wang L, Zhang L (2011). Population dynamics, structure and seasonal distribution pattern of Asian elephant (Elephas maximus) in Shangyong Protected Area, Yunnan, China. Acta Theriologica Sinica 31, 226-34.
Lino A, Fonseca C, Rojas D, Fischer E, Pereira MJR (2019). A meta-analysis of the effects of habitat loss and fragmentation on genetic diversity in mammals. Mammalian Biology 94, 69-76.
Liow LH, Fortelius M, Bingham E et al. (2008). Higher origination and extinction rates in larger mammals. PNAS 105, 6097-102.
Liu P, Wen H, Lin L, Liu J, Zhang L (2016). Habitat evaluation for Asian elephants (Elephas maximus) in Lincang: Conservation planning for an extremely small population of elephants in China. Biological Conservation 198, 113-21.
Luikart G, Cornuet J-M (1998). Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology 12, 228-37.
Luikart G, Sherwin W, Steele B, Allendorf F (1998). Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Molecular Ecology 7, 963-74.
Mohanarangan A, Chinnaiyan S, Kaliyaperumal S, Shanmugavelu S, Desai AA (2022). Age-specific differences in Asian elephant defecation, dung decay, detection and their implication for dung count. Ecological Solutions and Evidence 3, e12145.
Paetkau D, Calvert W, Stirling I, Strobeck C (1995). Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4, 347-54.
Peakall R, Smouse PE (2006). GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Resources 6, 288-95.
Piry S, Luikart G, Cornuet J-M (1999). Computer note. BOTTLENECK: A computer program for detecting recent reductions in the effective size using allele frequency data. Journal of Heredity 90, 502-3.
Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945-59.
Puyravaud JP, Cushman S, Davidar P, Madappa D (2017). Predicting landscape connectivity for the Asian elephant in its largest remaining subpopulation. Animal Conservation 20, 225-34.
Qin T, Yuan X (2021). China's practice of promoting biodiversity conservation in transboundary areas. Biodiversity Science 29, 220-30.
R Core Team 2019. R: A Language and Environment for Statistical Computing. Available from URL: https://www.R-project.org/
Rice WR (1989). Analyzing tables of statistical tests. Evolution 43, 223-5.
Rosenberg NA (2004). DISTRUCT: A program for the graphical display of population structure. Molecular Ecology Resources 4, 137-8.
Rousset F (2008). genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources 8, 103-6.
Songer M, Aung M, Allendorf TD, Calabrese JM, Leimgruber P (2016). Drivers of change in Myanmar's wild elephant distribution. Tropical Conservation Science 9, 1-10.
Taberlet P, Griffin S, Goossens B et al. (1996). Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research 24, 3189-94.
Tyson M, Hedges S, Sitompul A (2002). WCS-Indonesia Sumatran Elephant Project: Six month report for January-June, 2002. Wildlife Conservation Society, Jakarta, Indonesia.
Väli Ü, Dombrovski V, Dzmitranok M, Maciorowski G, Meyburg B-U (2019). High genetic diversity and low differentiation retained in the European fragmented and declining Greater Spotted Eagle (Clanga clanga) population. Scientific Reports 9, 3064.
Van Oosterhout C, Hutchinson WF, Wills DP, Shipley P (2004). MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Resources 4, 535-8.
Varma S, Dang NX, Van Thanh T, Sukumar R (2008). The Asian elephants Elephas maximus of Cat Tien National Park, Vietnam: Status and conservation of a vanishing population. Oryx 42, 92-9.
Vidya T, Fernando P, Melnick D, Sukumar R (2005). Population differentiation within and among Asian elephant (Elephas maximus) populations in southern India. Heredity 94, 71-80.
Vidya T, Sukumar R, Melnick DJ (2009). Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants. Proceedings of the Royal Society B: Biological Sciences 276, 893-902.
Vidya T, Varma S, Dang NX, Van Thanh T, Sukumar R (2007). Minimum population size, genetic diversity, and social structure of the Asian elephant in Cat Tien National Park and its adjoining areas, Vietnam, based on molecular genetic analyses. Conservation Genetics 8, 1471-8.
Wang L, Li Z, Luo A, Zhang Z, Yang L (2015). Preliminary study on biodiversity conservation measures along China-Laos border. Forest Inventory and Planning 40, 149-52.
Williams C, Tiwari S, Goswami V et al. (2020). Elephas maximus. The IUCN Red List of Threatened Species 2020: e.T7140A45818198.
Yang F, Zhang L (2012). Population genetic structure and population genetic diversity analysis based on mitochondrial DNA of Asian elephant (Elephas maximus) in China. Acta Theriologica Sinica 32, 90-100.
Zhang B, Li M, Zhang Z et al. (2007). Genetic viability and population history of the giant panda, putting an end to the “evolutionary dead end”? Molecular Biology and Evolution 24, 1801-10.
Zhang H, Dou H, Chen L, Sha W, Zhao J (2015). Genetic diversity and phylogenetic analysis of wolves from different geographical regions of China. Acta Ecologica Sinica 35, 1869-81.
Zhang J (2014). Social factors influencing status and change in the distribution of Asian elephants in China. School of History and Civilization Doctoral, 284.
Zhang L, Dong L, Lin L et al. (2015). Asian elephants in China: Estimating population size and evaluating habitat suitability. PLoS ONE 10, e0124834.
Zhang L, Wang N, Wang Y, Ma L (2003). A preliminary study on the habitat and behaviors of Asian elephant (Elephas maximus) in Simao, Yunnan, China. Acta Theriologica Sinica 23, 185-92.