Revisiting genetic structure of Wild Buffaloes Bubalus arnee Kerr, 1792 (Mammalia: Artiodactyla: Bovidae) in Koshi Tappu Wildlife Reserve, Nepal: an assessment for translocation programs
Main Article Content
Abstract
Koshi Tappu Wildlife Reserve (KTWR) has the last remaining Nepalese population of the Endangered Asiatic Wild Buffalo (Bubalus arnee Kerr, 1792). Individual animals protected inside KTWR may be of purely wild, domestic or hybrid origin, and the wild population is under potential threat due to habitat loss and genetic introgression from feral backcrosses. Identification of genetically pure wild individuals is important for identifying animals for translocation to other areas within their former range. In this study we have sequenced a highly variable 422bp region of the Cytochrome b gene of 36 animals, and added 61 published sequences of both River and Swamp Buffalo from Italy and some southern Asian countries including India. The haplotype diversities ranged from 0.286-0.589 with slightly higher diversities in domesticated individuals. The AMOVA analysis revealed that 97.217% of the genetic variation was contained within groups and 2.782% occurred among groups. An overall fixation index (FST) was found to be 0.02782 (p>0.05). Phylogenetic relationships derived through a reduced median network and maximum parsimony analyses reconfirmed the ancestral nature of the Wild Water Buffalo. Moreover, this study has reviewed recent achievements of molecular research in wild buffalo, assessed the technical capacities of research institutes in Nepal to conduct molecular research required for identifying pure wild individual in KTWR and more importantly initiated DNA bank and DNA sequence library of buffalos, which will enable an international collaboration for advanced molecular research in the future.
Article Details
Authors own the copyright to the articles published in JoTT. This is indicated explicitly in each publication. The authors grant permission to the publisher Wildlife Information Liaison Development (WILD) Society to publish the article in the Journal of Threatened Taxa. The authors recognize WILD as the original publisher, and to sell hard copies of the Journal and article to any buyer. JoTT is registered under the Creative Commons Attribution 4.0 International License (CC BY), which allows authors to retain copyright ownership. Under this license the authors allow anyone to download, cite, use the data, modify, reprint, copy and distribute provided the authors and source of publication are credited through appropriate citations (e.g., Son et al. (2016). Bats (Mammalia: Chiroptera) of the southeastern Truong Son Mountains, Quang Ngai Province, Vietnam. Journal of Threatened Taxa 8(7): 8953–8969. https://doi.org/10.11609/jott.2785.8.7.8953-8969). Users of the data do not require specific permission from the authors or the publisher.
References
ryal, A., T.K. Shrestha, A. Ram, W. Frey, C. Groves, H. Hemmer, M. Dhakal, R.K. Koirala, J.T. Heinen & D. Raubenheimer (2011). A call to save the wild water buffalo (Bubalus arnee) in Nepal. International Journal of Conservation Science 2(4): 261–268.
Bandelt, H.J., P. Forster & A. Röhl (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16(1): 37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036
Beyers, O., S. Hedges & U.S. Seal (1995). Asian wild cattle conservation assessment and management plan working document. IUCN/SSC Conservation Breeding Specialist Group: Apple Valley, MN. 121pp.
Choudhury, A. & J.S.F. Barker (2014). Wild Water Buffalo Bubalus arnee (Kerr, 1792), pp. 255–301 In: Melleti, M. & J. Burton (eds). Ecology, Evolution and Behaviour of Wild Cattle. Cambridge University Press, Cambridge, 512pp.
Ciani, E., P. Crepaldi, L. Nicoloso, E. Lasagna, F.M. Sarti, B. Moioli, F. Napolitano, A. Carta, G. Usai, M. D’Andrea, D. Marletta, R. Ciampolini, V. Riggio, M. Occidente, D. Matassino, D. Kompan, P. Modesto, N. Macciotta, P. Ajmoneâ€Marsan & F. Pilla (2014). Genome wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds. Animal Genetics 45(2): 256–266. https://doi.org/10.1111/age.12106
Colli, L., M. Milanesi, E. Vajana, D. Iamartino, L. Bomba, F. Puglisi, M.D. Corvo, E.L. Nicolazzi, S.S.E. Ahmed, J.R.V. Herrera, L. Cruz, S. Zhang, A. Liang, G. Hua, L. Yang, X. Hao, F. Zuo, S.J. Lai, S. Wang, R. Liu, Y. Gong, M. Mokhber, Y. Mao, F. Guan, A. Vlaic, B. Vlaic, L. Ramunno, G. Cosenza, A. Ahmad, I. Soysal, E.O. Ãœnal, M. Ketudat-Cairns, J.F. Garcia, Y.T. Utsunomiya, P.S. Baruselli, M.E.J. Amaral, R. Parnpai, M.G. Drummond, P. Galbusera, J. Burton, E. Hoal, Y. Yusnizar, C. Sumantri, B. Moioli, A. Valentini, A. Stella, J.L. Williams & P. Ajmone-Marsan (2018). New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data. Frontier in Genetics 9: 53. https://doi.org/10.3389/fgene.2018.00053
Conroy, C.J. & J.A. Cook (1999). MtDNA evidence for repeated pulses of speciation within arvicoline and murid rodents. Journal of Mammalian Evolution 6(3): 221–245. http://doi.org/10.1023/A:1020561623890
Corbet, G.B. & J.E. Hill (1992). Mammals of the Indomalayan Region. A Systematic Review. Oxford University Press, Oxford, UK, 488pp.
Dahmer, T. (1978). Status and Distribution of the Wild Buffalo (Bubalus bubalis) in Nepal. MS Thesis, University of Montana, Missoula, Montana, USA, 120pp.
Decker, J.E., S.D. McKay, M.M. Rolf, J.W. Kim, A.M. Alcalá, T. S. Sonstegard, O. Hanotte, A. Götherström, C.M. Seabury, L. Praharani, M.E. Babar, L.C.A. Regitano, M.A. Yildiz, M.P. Heaton, W.S. Liu, C.Z. Lei, J.M. Reecy, M. Saif-Ur-Rehman, R.D. Schnabel & J.F. Taylor (2014). Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genet. 10:e1004254. https://doi.org/10.1371/journal.pgen.1004254
Edea, Z., S.W. Kim, K.T. Lee, T.H. Kim & K.S. Kim (2014). Genetic Structure of and Evidence for Admixture between Western and Korean Native Pig Breeds Revealed by Single Nucleotide Polymorphisms. Asian-Australasian Journal of Animal Sciences 27(9): 1263–1269. https://doi.org/10.5713/ajas.2014.14096
Excoffier, L. & H.E.L. Lischer (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. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Flamand, J.R.B., D. Vankan, K.P. Gairhe, H. Duong & J.S.F. Barker (2003). Genetic identification of wild Asian water buffalo in Nepal. Animal Conservation 6(3): 265–270. https://doi.org/10.1017/S1367943003003329
Frankham, R., J.D. Ballou & D.A. Briscoe (2012). Introduction to conservation genetics. Cambridge University Press, UK, 618pp.
Groombridge, J.J., C. Raisin, R. Bristol & D.S. Richardson (2012). Genetic consequences of reintroductions and insights from population history, pp. 395–440. In: Ewen, J.G, D.P. Armstrong, K.A. Parker & P.J. Seddon (eds.). Reintroduction Biology: Integrating Science and Management. Wiley-Blackwell Publication.
Groves, C.P. (1996). The taxonomy of the Asian wild buffalo from the Asian mainland. International Journal of Mammalian Biology 61: 327–338.
Hedges, S. (1995). Asian Wild Cattle and Buffalo: Draft Status Report and Conservation Action Plan (Part I and II). Gland, Switzerland, 310pp.
Hedges, S. (2001). Asian Wild Cattle Specialist Group Quadrennial Report. Gland Switzerland, 122pp.
Heinen, J.T. (1993). Population viability and management recommendations for wild water buffalo (Bubalus bubalis) in Nepal. Biological Conservation 65(1): 29–34. https://doi.org/10.1016/0006-3207(93)90193-5
Heinen, J.T. (1995). Nature Preserves, pp. 551–561. In: Nierenberg, W.A. (ed.). Encyclopedia of Environmental Biology. Academic Press, San Diego, California, USA.
Heinen, J.T. (2001). A translocation proposal for Wild Buffalo (Bubalus bubalis) in Nepal: recommended management action in the face of uncertainty for a critically endangered species. Tiger Paper 28(3): 1–8.
Heinen, J.T. (2002). Phenotypic and behavioural characteristics used to identify Wild Buffalo (Bubalus bubalis) from feral backcrosses in Nepal. Journal of the Bombay Natural History Society 99: 173–183.
Heinen, J.T. & R.C. Kandel (2006). Threats to a small population: A census and conservation action plan for wild buffalo in Nepal. Oryx 40(3): 324–330. https://doi.org/10.1017/S0030605306000755
Heinen, J.T. & P. Paudel (2015). On the translocation of Asian buffalo Bubalus arnee in Nepal: are feral backcrosses worth conserving? Conservation Science 3: 11–19.
Heinen, J.T. & S. Shrikosamatara (1996). Status and protection of Asian wild cattle and buffalo. Conservation Biology 10(4): 931–934. https://doi.org/10.1046/j.1523-1739.1996.10040931.x
Iamartino, D., E.L. Nicolazzi, C.P. Van Tassell, J.M. Reecy, E.R. Fritz-Waters, J.E. Koltes, S. Biffani, T.S. Sonstegard, S.G. Schroeder, P. Ajmone-Marsan, R. Negrini, R. Pasquariello, P. Ramelli, A. Coletta, J.F. Garcia, A. Ali, L. Ramunno, G. Cosenza & D.A.A. de Oliveira (2017). Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis). Plos ONE 12(10): e0185220. https://doi.org/10.1371/journal.pone.0185220
IUCN (2013). IUCN Red List of Threatened Species. Version 2013.2. www.iucnredlist.org, downloaded on 24 May, 2014
Kandel, R.C., G.S. Solanki, M.K. Chalise & B.K. Sharma (2018). Population and Demography of Asian Wild Buffalo (Bubalus arnee Kerr, 1792) at Koshi Tappu Wildlife Reserve, Nepal. Journal of Emerging Trends in Economics and Management Sciences 9(4): 212–218.
Kandel, R.C., M. Shrestha, A. Saduala, K.C. Medha, J. Maharjan, G.S. Solanki, M.K. Chalise, M. Asada, O. Kaneko, R.C. Poudel & K. Pandey (2019). First report of malaria parasites in water buffalo in Nepal. Veterinary Parasitology: Regional Studies and Reports 18: 100348. https://doi.org/10.1016/j.vprsr.2019.100348
Kaul, R., A.C. Williams, K. Rithe, R. Steinmetz, & R. Mishra (2019). Bubalus arnee. The IUCN Red List of Threatened Species 2019: e.T3129A46364616. https://doi.org/10.2305/IUCN.UK.2019-1.RLTS.T3129A46364616.en. Downloaded on 10 November 2019.
Khatri, T.B., D.N. Shah & N. Mishra (2012). Wild Water Buffalo Bubalus arnee in Koshi Tappu Wildlife Reserve, Nepal: status, population and conservation importance. Journal of Threatened Taxa 4(14): 3294–3301. https://doi.org/10.11609/JoTT.o2990.3294-301
Kikkawa, Y., H. Yonekawa, H. Suzuki & T. Amano (1997). Analysis of genetic diversity of domestic water buffalo and anoas based on variations in the mitochondrial gene for cytochrome b. Animal Genetics 28(3): 195–201. https://doi.org/10.1111/j.1365-2052.1997.00101.x
Kocher, T.D., W.K. Thomas, A. Meyer, S.V. Edwards, S. Paabo, F.X. Villablanca & A.C. Wilson (1989). Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceeding of the National Academy of Science USA 86(16): 6196–6200. https://doi.org/10.1073/pnas.86.16.6196
KTWR (2016). Census of Asiatic Water Buffalo (Bubalus arnee) at Koshi Tappu Wildlife Reserve: 2016. Department of National Parks and Wildlife Reserve and Koshi Tappu Wildlife Reserve (KTWR), 78pp.
Kumar, S., M. Nagarajan, J.S. Sandhu, N. Kumar, V. Behl & G. Nishanth (2007). Mitochondrial DNA analyses of Indian water buffalo support a distinct genetic origin of river and swamp buffalo. Animal Genetics 38(3): 227–232. https://doi.org/10.1111/j.1365-2052.2007.01602.x
Kumar, S., G. Stecher & K. Tamura (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7): 1870–1874. https://doi.org/10.1093/molbev/msw054
Kuwayama, R. & T. Ozawa (2000). Phylogenetic relationships among European Red Deer, Wapiti, and Sika Deer inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 15: 115–123. https://doi.org/10.1006/mpev.1999.0731
Lau, C.H., R.D. Drinkwater, K. Yusoff, S.G. Tan, D.J.S. Hetzel & J.S.F. Barker (1998). Genetic diversity of Asian Water Buffalo (Bubalus bubalis): Mitochondrial DNA D-loop and cytochrome b sequence variation. Animal Genetics 29(4): 253–264. https://doi.org/10.1046/j.1365-2052.1998.00309.x
Lei, C.Z., W. Zhang, H. Chen, F. Lu, R.Y. Liu, X.Y. Yang, H.C. Zhang, Z.G. Liu, L.B. Yao, Z.F. Lu & Z.L. Zhao (2007). Independent maternal origin of Chinese Swamp Buffalo (Bubalus bubalis). Animal Genetics 38(2): 97–102. https://doi.org/10.1111/j.1365-2052.2007.01567.x
Librado, P. & J. Rozas (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451–1452. https://doi.org/10.1093/bioinformatics/btp187
Mishra, B.P., P.K. Dubey, B. Prakash, P. Kathiravan, S. Goyal, D.K. Sadana, G.C. Das, R.N. Goswami, V. Bhasin, B.K. Joshi & R.S. Kataria (2015). Genetic analysis of river, swamp and hybrid buffalo of north-east India throw new light on phylogeography of Water Buffalo (Bubalus bubalis). Journal of Animal Breeding and Genetics 132(6): 454–456. https://doi.org/10.1111/jbg.12141
Saitou, N. & M. Nei (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 24(4): 406–425. http://doi.org/10.1093/oxfordjournals.molbev.a040454
Shah, R., S. Tripathi & B. Bhatta (2017). Translocation of Wild Asian Buffalo (Bubalus arnee): a way forward to conservation in Nepal, pp. 175–178. In: Proceedings of the International Buffalo Symposium, 242pp.
Spillet, J.J. & K.M. Tamang (1966). Wildlife Conservation in Nepal. Journal of the Bombay Natural History Society 63: 557–572
Swofford, D.L. (2002). PAUP* Version 4.0 b10. Phylogenetic Analysis Using Parsimony (* and Other Methods)
Tanaka, K., C.D. Solis, J.S. Masangkay, K. Maeda, Y. Kawamoto & T. Namikawa (1996). Phylogenetic relationship among all living species of the genus Bubalis based on DNS sequences of the cytochrome b gene. Biochemical Genetics 34(11): 443–452. https://doi.org/10.1007/BF00570125
Tarszisz, E., C.R. Dickman & A.J. Munn (2014). Physiology in conservation translocations. Conservation Physiology 2(1): 1–19. https://doi.org/10.1093/conphys/cou054
Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin & D.G. Higgins (1997). The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24): 4876–4882. https://doi.org/10.1093/nar/25.24.4876
Zhang, Y., Y. Lu, M. Yindee, K.Y. Li, H.Y. Kuo, Y.T. Ju, S. Ye, M.O. Faruque, Q. Li, Y. Wang, V.C. Cuong, L.D. Pham, B. Bouahom, B. Yang, X. Liang, Z. Cai, D. Vankan, W. Manatchaiworakul, N. Kowlim, S. Duangchantrasiri, W. Wajjwalku, B. Colenbrander, Y. Zhang, P. Beerli, J.A. Lenstra & J.S. Barker (2016). Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Molecular Ecology 25(7): 1530–1550. https://doi.org/10.1111/mec.13518
Zhang, Y., D. Sun, Y. Yu and Y. Zhang (2007). Genetic diversity and differentiation of Chinese domestic buffalo based on 30 microsatellite markers. Animal Genetics 38: 569–575. https://doi.org/10.1111/j.1365-2052.2007.01648.x
Zhang, Y., D. Vankan, Y. Zhang & J.S. Barker (2011). Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and South East Asia: inferences on the region of domestication of the swamp buffalo. Animal Genetics 42(4): 366–377. https://doi.org/10.1111/j.1365-2052.2010.02166.x