Estimating population size and genetic diversity of Asian elephant in the Shangyong Nature Reserve

doi:10.17520/biods.2014247

Abstract

Abstract:

Asian elephant (Elephas maximus) is a first class protected species in China. Estimation of the population size and genetic variability is crucial to the management and conservation of this species. A genetic survey was conducted using multi locus genotyping of noninvasively collected fecal samples of the Asian elephant population in the Shangyong Nature Reserve, Yunnan Province of China. Amplification of 185 fecal DNA samples by 7 microsatellite primers resulted in a total of 59 unique genotypes. The average number of alleles was 3.86, the average observed and expected heterozygosity and polymorphism information content (PIC), was 0.52, 0.42 and 0.34, respectively. Accumulation curve method and capture mark re-capture were used to evaluate the population size. Results indicated that the population size in Shangyong Nature Reserve was 76 ± 8 (from 67 to 99 individuals, 95% confidence interval). Overall, a moderate level of genetic variability was observed in the Shangyong population, which was similar to a population in the Mengyang region.

Key words: Asian elephant, microsatellite, accumulation curve method, capture mark re-capture method, population size, genetic diversity

Changhuan He, Yu Zhou, Lifan Wang, Li Zhang. Estimating population size and genetic diversity of Asian elephant in the Shangyong Nature Reserve[J]. Biodiv Sci, 2015, 23(2): 202-209.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.biodiversity-science.net/EN/10.17520/biods.2014247

https://www.biodiversity-science.net/EN/Y2015/V23/I2/202

Figures/Tables 5

References 35

1	Bellemain E, Swenson JE, Tallmon O, Brunberg S, Taberlet P (2005) Estimating population size of elusive animals with DNA from hunter-collected feces: four methods for brown bears.Conservation Biology, 19, 150-161.
2	Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms.American Journal of Human Genetics, 32, 314-331.
3	Cai QX (蔡清秀), Lin L (林柳), Pan WJ (潘文婧), Luo SJ (罗述金), Zhang L (张立) (2008) Screening microsatellite DNA markers and genetic variation analysis of wild Asian elephant population in Mengyang Nature Reserve.Acta Theriologica Sinica(兽类学报), 28, 126-134. (in Chinese with English abstract)
4	Eggert LS, Eggert JA, Woodruff DS (2003) Estimating population sizes for elusive animals: the forest elephants of Kakum National Park, Ghana.Molecular Ecology, 12, 1389-1402.
5	Feng LM (冯利民), Zhang L (张立) (2005) Habitat selection by Asian elephant (Elephas maximus) in Xishuangbanna, Yunnan, China.Acta Theriologica Sinica(兽类学报), 25, 229-236. (in Chinese with English abstract)
6	Fernando P, Vidya TNC, Payne J, Stuewe M, Davison G, Alfred RJ, Andau P, Bosi E, Kilbourn A, Melnick DJ (2003) DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation.PLoS Biology, 1, e6.
7	Flagstad Ø, Pradhan NMB, 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, 181-190.
8	Frankham R, Ballou JD, Briscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press, London.
9	Frantz AC, Pope LC, Carpenter PJ, Roper TJ, Wilson GJ, Delahay RJ, Burke T (2003) Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Molecular Ecology, 12, 1649-1661.
10	Hong YY (洪艳云), Li DQ (李迪强), Yi TY (易图永), Zhang YG (张于光), Liu Y (刘毅) (2009) Screening microsatellite primers and their application for individual identification in faecal DNA from Procapra praprzewalskii.Chinese Agricultural Science Bulletin(中国农学通报), 24(9), 54-58. (in Chinese with English abstract)
11	Huang L (黄磊), Wang YQ (王义权) (2004) The application of microsatellite DNA markers in conservation genetics of endangered animals.Biodiversity Science(生物多样性), 12, 528-533. (in Chinese with English abstract)
12	Kohn MH, York EC, Kamradt DA, Haugt G, Sauvajot RM, Wayne RK (1999) Estimating population size by genotyping faeces.Proceedings of the Royal Society B: Biological Sciences, 266, 657-663.
13	Lin L (林柳), Jin YF (金延飞), Chen DK (陈德坤), Guo XM (郭贤明), Luo AD (罗爱东), Zhao JW (赵建伟), Wang QY (王巧燕), Zhang L (张立) (2014) Population and habitat status of Asian elephants (Elephas maximus) in Mengla Sub-reserve of Xishuangbanna National Nature Reserve, Yunnan of China.Acta Ecologica Sinica(生态学报), 34, 1725-1735. (in Chinese with English abstract)
14	Lin L (林柳), Zhang LT (张龙田), Luo AD (罗爱东), Wang LF (王利繁), Zhang L (张立) (2011) Population dynamics, structure and seasonal distribution pattern of Asian elephant (Elephas maximus) in Shangyong protected area, Yunnan, China.Acta Theriologica Sinica(兽类学报), 31, 226-234. (in Chinese with English abstract)
15	Miller CR, Joyce P, Waits LP (2005) A new method for estimating the size of small populations from genetic mark-recapture data.Molecular Ecology, 14, 1991-2005.
16	Otis DL, Burnham KP, White GC (1978) Statistical inference from capture data on closed animal populations.Wildlife Monographs, 62, 1-135.
17	Petit E, Valiere N (2006) Estimating population size with noninvasive capture-mark-recapture data.Conservation Biology, 20, 1062-1073.
18	Prugh LR, Ritland CE, Arthur SM, Krebs CJ (2005) Monitoring coyote population dynamics by genotyping faeces.Molecular Ecology, 14, 1585-1596.
19	Sheng Y (盛岩), Zheng WH (郑蔚虹), Pei KQ (裴克全), Ma KP (马克平) (2002) Applications of microsatellites in population biology.Acta Phytoecologica Sinica(植物生态学报), 26, 119-126. (in Chinese with English abstract)
20	Solberg KH, Bellemain E, Drageset OM, Taberlet P, Swenson JE (2006) An evaluation of field and non-invasive genetic methods to estimate brown bear (Ursus arctos) population size.Biological Conservation, 128, 158-168.
21	Sukumar R (2003) The Living Elephants: Evolutionary Ecology, Behavior, and Conservation. Oxford University Press, London.
22	Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, Escaravage N, Waits LP, Bouvet J (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research, 24, 3189-3194.
23	Tian XM (田新民), Zhang MH (张明海) (2010) Population size and sex ratio of wapiti (Cervus elephus xanthopygus) as revealed by fecal DNA.Acta Ecologica Sinica(生态学报), 30, 6249-6254. (in Chinese with English abstract)
24	Valière N (2002) GIMLET: a computer program for analysing genetic individual identification data.Molecular Ecology Notes, 2, 377-379.
25	Vidya TNC, Varma S, Dang NX, van Thanh T, Sukmar 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, 1471-1478.
26	Vidya TNC, Fernando P, Melnick DJ, Sukumar R (2005) Population differentiation within and among Asian elephant (Elephas maximus) populations in southern India.Heredity, 94, 71-80.
27	Vidya TNC, Sukumar R (2005a) Social organization of the Asian elephant (Elephas maximus) in southern India inferred from microsatellite DNA.Journal of Ethology, 23, 205-210.
28	Vidya TNC, Sukumar R (2005b) Amplification success and feasibility of using microsatellite loci amplified from dung to population genetic studies of the Asian elephant (Elephas maximus).Current Science, 88, 489-492.
29	Wasser SK, Houston CS, Koehler GM, Cadd GG, Fain SR (1997) Techniques for application of faecal DNA methods to field studies of Ursids.Molecular Ecology, 6, 1091-1097.
30	White GC, Burnham KP (1999) Program MARK: survival estimation from populations of marked animals.Bird Study, 46, s120-s138.
31	Yang F (杨帆), Zhang L (张立) (2012) Population genetic structure and population genetic diversity analysis based on mitochondrial DNA of Asian elephant (Elephas maximus) in China.Acta Theriologica Sinica(兽类学报), 32, 90-100. (in Chinese with English abstract)
32	Zhang L (张立), Wang N (王宁), Wang YN (王宇宁), Ma LC (马利超) (2003) A preliminary study on the habitat and behaviors of Asian elephant (Elephas maximus) in Simao, Yunnan, China.Acta Theriologica Sinica(兽类学报), 23, 185-192. (in Chinese with English abstract)
33	Zhang L, Ma LC, Feng LM (2006) New challenges facing traditional nature reserves: Asian elephant (Elephas maximus) conservation in China.Integrative Zoology, 1, 179-187.
34	Zhang XH (张秀华), Wu DJ (吴登俊) (2006) Study on sex-identification of ruminant using SRY gene and microsatellite markers.Hereditas (Beijing)(遗传), 28, 133-138. (in Chinese with English abstract)
35	Zhan XJ, Li M, Zhang ZJ, Goossens B, Chen YP, Wang HJ, Bruford MW, Wei FW (2006) Molecular censusing doubles giant panda population estimate in a key nature reserve.Current Biology, 16, R451-R452.

位点Locus	矫正随机识别概率P_id/biased	无偏随机识别概率P_id/unbiased	同胞识别概率P_id-sib
M2	6.656e-01	6.656e-01	8.221e-01
P14	3.762e-01	3.762e-01	5.952e-01
P15	7.712e-01	7.624e-01	8.796e-01
P19	2.529e-01	2.437e-01	5.214e-01
P21	3.294e-01	3.160e-01	5.932e-01
P23	1.532e-01	1.421e-01	4.509e-01
P24	4.810e-01	4.697e-01	6.938e-01
Total	1.185e-03	9.523e-04	4.164e-02

位点Locus	矫正随机识别概率P_id/biased	无偏随机识别概率P_id/unbiased	同胞识别概率P_id-sib
M2	6.656e-01	6.656e-01	8.221e-01
P14	3.762e-01	3.762e-01	5.952e-01
P15	7.712e-01	7.624e-01	8.796e-01
P19	2.529e-01	2.437e-01	5.214e-01
P21	3.294e-01	3.160e-01	5.932e-01
P23	1.532e-01	1.421e-01	4.509e-01
P24	4.810e-01	4.697e-01	6.938e-01
Total	1.185e-03	9.523e-04	4.164e-02

方法 Method	模型 Model	种群数量 Population size	95%置信区间 95% CI
聚集曲线法	Chessel 方程	67 ± 4	46-66
Accumulation curve	Eggert 方程	83 ± 15	53-103
	Kohn 方程	132 ± 30	73-175
分子标记重捕法	Mark M(t)	76 ± 8	67-99
Capture mark re-capture	Capwire TIRM	110	81-138

方法 Method	模型 Model	种群数量 Population size	95%置信区间 95% CI
聚集曲线法	Chessel 方程	67 ± 4	46-66
Accumulation curve	Eggert 方程	83 ± 15	53-103
	Kohn 方程	132 ± 30	73-175
分子标记重捕法	Mark M(t)	76 ± 8	67-99
Capture mark re-capture	Capwire TIRM	110	81-138

位点 Locus	基因型数量 Genotype number	等位基因数目 Allele number	片段长度 Size range (bp)	期望杂合度 Expected heterozygosity (H_e)	观察杂合度 Observed heterozygosity (H_o)	多态信息含量 Polymorphism information content (PIC)	有效等位基因数目 Effective number of alleles (N_e)
M2	59	4	131-147	0.19	0.20	0.18	1.23
P14	59	2	145-149	0.50	0.93	0.37	1.99
P15	59	2	123-125	0.13	0.07	0.12	1.15
P19	59	5	145-155	0.58	0.78	0.51	2.41
P21	59	7	210-226	0.48	0.64	0.30	1.72
P23	59	5	221-229	0.67	0.76	0.63	3.08
P24	59	2	162-164	0.35	0.22	0.29	1.55
平均 Mean	59	3.86	/	0.42	0.52	0.34	1.88