Muhammad Khairul Anwar ROSLI, Syed Mohamad Fahmi SHABTHAR SYED, Jeffrine Japning ROVIE RYAN, Ramlah ZAINUDDIN, Salmah YAAKOP, Badrul Munir MD-ZAIN, Md Nor SHUKOR

Phylogenetic relationships of the vulnerable wild cattle, Malayan gaur(Bos gaurus hubbacki), and its hybrid, the selembu, based on maternal markers

The gaur (Bos gaurus) is one of the two extant wild cattle species that can be found in several Asian countries. This species is threatened by extinction due to declining wild populations. Selembu is the name of the Malayan gaur × domestic cattle hybrid. We planned this study to determine the position of the Malayan gaur and its hybrid, the selembu, in the phylogenetics of the genus Bos (Bos gaurus, Bos javanicus, Bos indicus,and Bos taurus). The mitochondrial 12S rRNA gene and the control region (D-loop) were sequenced in 29 Bos samples. Sequences from one water buffalo (Bubalus) were used as an outgroup. Phylogenetic trees were reconstructed using neighbor-joining and maximum parsimony in PAUP 4.0b10 and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur belongs to its own monophyletic clade that is distinct from other species of the genus Bos. Selembu samples were grouped in zebu and/or taurine cattle clades. The results also indicated that there are significant embranchment differences in the tree topologies between wild (Malayan gaur and banteng/Bali cattle) and domestic (taurine cattle, zebu cattle, and selembu) cattle. The results showed the complete maternal inheritance situation among the studied samples of all cattle species.

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Ang A, Srivasthan A, Md-Zain BM, Ismail MRB, Meier R (2012). Low genetic variability in the recovering urban banded leaf monkey population of Singapore. Raffles B Zool 60: 589594.
Ang KC, Leow JWH, Yeap WK, Hood S, Mahani MC, Md-Zain BM (2011). Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers. Genet Mol Res 10: 640649.
Bradley DG, MacHugh DE, Cunningham P, Loftus RT (1996). Mitochondrial diversity and the origin of African and European cattle. P Natl Acad Sci USA 93: 51315135.
Buntjer JB, Otsen M, Nijman IJ, Kuiper MT, Lenstra JA (2002). Phylogeny of bovine species based on AFLP fingerprinting. Heredity 88: 4651.
Cai X, Chen H, Lei CZ, Wang S, Xue K, Zhang B (2007). MtDNA diversity and genetic lineages of eighteen cattle breeds from Bos taurus and Bos indicus in China. Genetica 131: 175183.
Cai X, Gou X, Jiang L (2011). Bioinformatic analysis of phylogenetic evolution of Chinese cattle. In:The 5th International Conference on Bioinformatics and Biomedical Engineering; Wuhan, China. New York, NY, USA: IEEE, pp. 13. Conry PJ (1989).
Gaur Bos gaurus and development in Malaysia. Biol Conser v 49: 4765.
Dadi H, Tibbo M, Takahashi Y, Nomura K, Hanada H, Amano A (2009). Variation in mitochondrial DNA and maternal genetic ancestry of Ethiopian cattle populations. Anim Genet40: 556559.
Duckworth JW, Steinmetz R, Timmins RJ, Pattanavibool A, Than Z, Do T, Hedges S (2008). Bos gaurus. IUCN Red List of Threatened Species. Gland, Switzerland: IUCN.
Epstein H (1971). The Origin of the Domestic Animals of Africa. 1st ed. New York, NY, USA: African Publishing Corporation.
Ginja C, Penedo MC, Melucci L, Quiroz J, Martinez Lopez OR, Revidatti MA, Martinez-Martinez A, Delgado JV, Gama LT (2010). Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms. Anim Genet 41: 128141.
Groves C (2003). Taxonomy of ungulates of the Indian Subcontinent. J Bombay Nat Hist Soc 100: 341362.
Groves CP (1981). Systematic relationships in the Bovini (Artiodactyla, Bovidae). J Zool Syst Evol 19: 264278.
Gu Z, Zhao X, Li N, Wu C (2007). Complete sequence of the yak (Bos grunniens) mitochondrial genome and its evolutionary relationship with other ruminants. Mol Phylogenet Evol 42: 248255.
Hassanin A, Ropiquet A (2004). Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937. Mol Phylogenet Evol 33: 896907.
Hassanin A, Ropiquet A, Cornette R, Tranier M, Pfeffer P, Candegabe P, Lemaire M (2006). Has the kourpey (Bos sauveli Ubain, 1937) been domesticated in Cambodia? C R Biol 329: 124135.
Hillis DM, Moritz C, Mable BK (1996). Molecular Systematics. 2nd ed. Sunderland, MA, USA: Sinauer Associates Inc.
Kikkawa Y, Takada T, Sutopo, Nomura K, Namikawa T, Yonekawa H, Amano T (2003). Phylogenies using mtDNA and SRY provide evidence for male-mediated introgression in Asian domestic cattle. Anim Genet 34: 96101.
Kim KI, Lee JH, Lee SS, Yang YH(2003). Phylogenetic relationships of Northeast Asian cattle to other cattle populations determined using mitochondrial DNA D-Loop sequence polymorphism. Biochem Genet 41: 9198.
Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablanca FX, Wilson AC (1989). Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. P Natl Acad Sci USA 86: 61966200.
Lai SJ, Liu YP, Liu Y X, Li XW, Yao YG (2006). Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation. Mol Phylogenet Evol 38: 146154.
Lenstra JA, Bradley DG (1999). Systematics and phylogeny of cattle. In: Fries R, Ruvinsky A, editors. The Genetics of Cattle. Oxford, UK: CABI Publishing, pp. 114.
Li SP, Chang H, Ma GL, Cheng HY (2008). Molecular phylogeny of the gayal in Yunnan China inferred from the analysis of cytochrome b gene entire sequences. Asian Austral J Anim 21: 789793.
Lim LS, Ang KC, Mahani MC, Shahrom AW, Md-Zain BM(2010). Mitochondrial DNA polymorphism and phylogenetic relationships of Proto Malays in Peninsular Malaysia. J Biol Sci10: 7183.
Ma G, Chang H, Li S, Chen H, Ji D, Geng R, Chang C, Li Y (2007). Phylogenetic relationships and status quo of colonies for gayal based on analysis of cytochrome b gene partial sequences. J Genet Genomics 34: 413419.
MacEachern S, McEwan J, Goddard M (2009). Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae). BMC Genomics 10: 177.
MacHugh DE, Shriver MD, Loftus RT, Cunningham P, Bradley DG(1997). Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics 146: 10711086.
Mamat-Hamidi, Idris I, Hilmi M (2009). Karyotype of Malayan Gaur (Bos gaurus hubbacki), Sahiwal-Friesian cattle and Gaur x cattle hybrid backcrosses. Pak J Biol Sci12: 896901.
Matthee CA, Davis SK (2001) Molecular insights into the evolution of the family Bovidae: a nuclear DNA perspective. Mol Biol Evol18: 12201230.
Md-Zain BM, Lee SJ, Lakim M, Ampeng A, Mahani MC (2010). Phylogenetic position of Tarsius bancanus based on partial cytochrome b DNA sequences. J Biol Sci 10: 348354.
Medway L (1983). Wild mammals of Malaya (Peninsular Malaysia) and Singapore. Kuala Lumpur, Malaysia: Oxford University Press.
Mohamad K, Olsson M, Andersson G, Purwantara B, Van Tol HTA, Rodriguez-Martinez H, Colenbrander B, Lenstra JA (2012). The origin of Indonesian cattle and conservation genetics of the Bali cattle breed. Reprod Dom Anim 47: 1820.
Mohamad K, Olsson M, Van-Tol HTA, Rodriguez-Martinez H, Colenbrander B, Lenstra JA (2009). On the origin of Indonesian cattle. PLoS One 4: e5490.
Pevsner J (2009). Bioinformatics and Functional Genomics. 2nd ed. Hoboken, NJ, USA: Wiley-Blackwell.
Posada D, Crandall KA (1998). MODELTEST: testing the models of DNA substitution. Bioinformatics 14: 817818.
Sahir O (2001). Breeding performance of the Malaysian captive gaur. J Wildl Parks 19: 2532.
Schreiber A, Seibold I, Notzold G, Wink M (1999). Cytochrome b gene haplotypes characterize chromosomal lineages of anoa, the Sulawesi dwarf buffalo (Bovidae: Bubalus sp.). J Hered 90: 165176.
Simon C, Nigro L, Sullivan J, Holsinger K, Martin, A, Grapputo A, Franke A, McIntosh C (1996). Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes. Mol Biol Evol 13: 923932.
Stock F, Edwards CJ, Bollongino R, Finlay EK, Burger J (2009). Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine population. Anim Genet 40: 694700.
Swofford DL (2002). Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4.0 Beta. Sunderland, MA, USA: Sinauer Associates.
Syed-Shabthar SMF, Rosli MKA, Mohd-Zin NAA, Romaino SMN, Fazly-Ann ZA, Mahani MC, Abas-Mazni O, Zainuddin R, Yaakop S, Md-Zain BM (2013). The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers. Mol Biol Rep40: 51655176.
Vasilev VA, Steklenev EP, Morozova EV, Semenova SK(2002). DNA fingerprinting of individual species and intergeneric and interspecific hybrids of genera Bos and Bison, subfamily Bovinae. Genetika38: 515520.
Verkaar ELC, Nijman IJ, Beeke M, Hanekamp E, Lenstra JA (2004). Maternal and paternal lineages in cross-breeding bovine species. Has wisent a hybrid origin? Mol Biol Evol 21: 11651170.
Vun VF, Mahani MC, Lakim M, Ampeng A, Md-Zain BM(2011). Phylogenetic relationships of leaf monkeys (Presbytis; Colobinae) based on cytochrome b and 12S rRNA genes. Genet Mol Res 10: 368381.
Wall DA, Davis SK, Read BM (1992). Phylogenetic relationships in the subfamily Bovinae (Mammalia: artiodactyla) based on ribosomal DNA. J Mammal 73: 262275.
Wilson DE, Reeder DAM (2005). Mammal Species of the World. A Taxonomic and Geographic Reference. 3rd ed. Baltimore, MD, USA: Johns Hopkins University Press.
Yusof E (1981). Seladang (Bos gaurus hubbacki) in Malaysia. Kuala Lumpur, Malaysia: Department of Wildlife and National Parks.