Genetic Diversity of Green Peafowl (Pavo muticus) in Northern Thailand Based on Mitochondrial DNA Control Region Sequences
Keywords:
D-loop, genetic variation, mitochondrial DNA, peafowl, phylogenyAbstract
The population size of green peafowl (Pavo muticus L.) has declined dramatically in Thailand. It is currently found in two geographically isolated regions in the northern and western areas. Here, we assessed the level of genetic variation of this endangered bird species to examine the influence of habitat fragmentation. We collected moulted feather and egg specimens of wild individuals from three populations in the North: Wiang Lor Wildlife Sanctuary (WLO-1 and WLO-2) and Tappaya Lor Non-Hunting Area (TPL). Mitochondrial control region sequences were obtained and analyzed. The results revealed that P. muticus in all populations showed a high level of haplotype diversity (0.784, n = 72), implying high genetic diversity. The haplotype diversity in WLO-1 population was higher than in other two populations. On phylogenetic trees and a haplotype network, the haplotypes of P. muticus individuals did not form a separate cluster, regardless of their distribution ranges, and three haplotypes were found in the three populations. By combining the present results with the previous data, our genetic investigations revealed that P. muticus populations in Thailand exhibited a low genetic difference (4.31%) between the two regional populations with no statistical significance. This suggests that there is no subdivision of wild populations.
References
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Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123: 585-595.
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30: 2725-2729.
Thompson, J.D., Higgins, D.G. and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680.
Weir, B.S. and Cockerham, C.C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38: 1358-1370.
Ashley, M.V. and Dow, B.D. 1994. The use of microsatellite analysis in population biology: background, methods and potential applications. In: Schierwater S, Streit B, Wagner GP, DeSalle R (eds). Molecular Ecology and Evolution: Approaches and Applications, Birkhāuser Verlag Basel, Switzerland, pp 185–201.
Bandelt, H-J., Forster, P. and Röhl, A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16: 37-48.
Bei, Y., Chen, W., Sun, B., Li, J., Lai, J. and Meng, S. 2014. Population structure of the endangered Hume's pheasant (Syrmaticus humiae) inferred from a partial sequence of the mitochondrial DNA control region. Biochemical Systematics and Ecology, 57: 69-77.
BirdLife International. 2015. Species factsheet: Pavo muticus. Available from: http://www.birdlife.org/
datazone/species/index.html.
Brickle, N.W. 2002. Habitat use, predicted distribution and conservation of green peafowl (Pavo muticus) in Dak Lak province, Vietnam. Biological Conservation, 105: 189-197.
Delacour, J. 1977. The Pheasant of the world. The World Association, England.
Desjardins, P. and Morais, R. 1990. Sequence and gene organization of the chicken mitochondrial genome. Journal of Molecular Biology, 212: 599-634.
Dong, L., Zhang, J., Sun, Y., Liu, Y., Zhang, Y. and Zheng, G. 2010. Phylogeographic patterns and conservation units of a vulnerable species, Cabot's tragopan (Tragopan caboti), endemic to southeast China. Conservation Genetics, 11: 2231-2242.
Excoffier, L. and Lischer, H.E.L. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10: 564-567.
Felsenstein, J. and Kishino, H. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology, 42: 193-200.
Frankham, R. 1995. Conservation genetics. Annual Review of Genetics, 29: 305-327.
Fu, Y.X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147: 915¬-925.
Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59: 307-321.
Grueber, C.E., King, T.M., Waters, J.M. and Jamieson, I.G. 2008. Isolation and characterization of microsatellite loci from the endangered New Zealand takahe (Gruiformes; Rallidae; Porphyrio hochstetteri). Molecular Ecology Resources, 8: 884-886.
IUCN. 2014. IUCN Red List of Threatened Species. Available from: http://www.iucnredlist.org.
Jiang, P.P., Ge, Y.F., Lang, Q.L. and Ding, P. 2007. Genetic structure among wild populations of Elliot's Pheasant Syrmaticus ellioti in China from mitochondrial DNA analyses. Bird Conservation International, 17: 177-185.
Johnsgard, P.A. 1999. Pheasants of the world: biology and natural history. 2nd ed, Swan Hill Press, London.
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16: 111-120.
Librado, P. and Rozas, J. 2009. DnaSP version 5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.
Liukkonen-Anttila, T., Ratti, O., Kvist, L., Helle, P. and Orell, M. 2004. Lack of genetic structuring and subspecies differentiation in the capercaillie (Tetrao urogallus) in Finland. Annales Zoologici Fennici, 41: 619-633.
Lobo, D., Godinho, R., Álvares1, F., López-Bao, J.V. and Rodríguez, A. 2015. A new method for noninvasive genetic sampling of saliva in ecological research. PLoS ONE, 10: e0139765. doi:10.1371/journal.pone.0139765.
McGowan, P.J.K., Duckworth, J.W., Wen, X., van Balen, B., Yang, X., Khan, M.K.M., Yatim, S.H., Thanga, L., Setiawan, I. and Kaul, R. 1999. A review of the status of the green peafowl Pavo muticus and recommendations for future action. Bird Conservation International, 9: 331-348.
Meckvichai, W. and Arsirapoj, S. 2009. Morphology and identification of feathers of gallopheasants in Thailand. Print at me Press, Bangkok.
Meckvichai, W., Arsirapoj, S., Wanghongsa, S. and Pitdakham, C. 2007. Status and distribution of green peafowl in Thailand. In “Proceedings of the 4th International Galliformes Symposium” Sichuan, China, 2007.
Pinthong, T. 2009. Effect of environmental and human use factors to abundance of green peafowl Pavo muticus at Huai Tab Saloa and Huai Songtang, Huai Kha Khaeng Wildlife Sanctuary, Uthai Thani Province. Master thesis, Chulalongkorn University.
Ponsena, P. 1988. Biological characteristics and breeding behaviours of green peafowl (Pavo muticus (Linnaeus)) in Huai Kha Khaeng Wildlife Sanctuary. Thai Journal of Forestry, 7: 303-131.
Randi, E. and Lucchini, V. 1998. Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. Journal of Molecular Evolution, 47: 449-462.
Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4: 406-425.
Saridnirun, G., Meckvichai, W. and Dumrongroj-watthana, P. 2016. Seasonal distribution and habitat use of the green peafowl Pavo muticus, Linnaeus 1766, in Wiang Lor Wildlife Sanctuary, Phayao Province, northern Thailand. Chiang Mai Journal of Science, 43: 1-16.
Sawangtham, T., Meckvichai, W. and Wiwegweaw, A. 2015. Genetic variation of green peafowl Pavo muticus in northern and western Thailand based on mitochondrial D-loop sequences. In “Proceedings of the 10th Conference on Science and Technology for Youth” Bangkok, Thailand, 2015, pp 23-31.
Sukumal, N., Dowell, S.D. and Savini, T. 2017. Micro-habitat selection and population recovery of the endangered green peafowl Pavo muticus in western Thailand: implications for conservation guidance. Bird Conservation International, 27: 414-430.
Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123: 585-595.
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30: 2725-2729.
Thompson, J.D., Higgins, D.G. and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680.
Weir, B.S. and Cockerham, C.C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38: 1358-1370.
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2018-04-01
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SAWANGTHAM, T. and WIWEGWEAW, A. 2018. Genetic Diversity of Green Peafowl (Pavo muticus) in Northern Thailand Based on Mitochondrial DNA Control Region Sequences. Tropical Natural History. 18, 1 (Apr. 2018), 11–23.
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