Phylogenetic analysis and comparison between cow and buffalo (including Egyptian buffaloes) mitochondrial displacement-loop regions

References

• Abdel-Rahman SM, Ahmed MM. Rapid and sensitive identification of Buffalo's, cattle's, and sheep's milk using species-specific PCR and PCR-RFLP techniques. Food Control 2007; 18: 1246–1249
   Web of Science ®Google Scholar
• Allard MW, Miyamoto MM, Jarecki L, Kraus F, Tennant MR. DNA systematics and evolution of the artiodactyl family Bovidae. Proc Natl Acad Sci USA 1992; 89: 3972–3976
   PubMed Web of Science ®Google Scholar
• Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI–BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389–3402
   PubMed Web of Science ®Google Scholar
• Anderson S, de Bruijn MH, Coulson AR, Eperon IC, Sanger F, Young IG. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol 1982; 156: 683–717
   PubMed Web of Science ®Google Scholar
• Boettcher PJ, Freeman AE, Johnston SD, Smith RK, Beitz DC, McDaniel BT. Relationships between polymorphism for mitochondrial deoxyribonucleic acid and yield traits of Holstein cows. J Dairy Sci 1996; 79: 647–654
   PubMed Web of Science ®Google Scholar
• Bottero MT, Civera T, Anastasio A, Turi RM, Rosati S. Identification of cow's milk in “buffalo” cheese by duplex polymerase chain reaction. J Food Protect 2002; 65(2)362–366
   PubMed Web of Science ®Google Scholar
• Bradley DG, Cunningham EP. Genetic aspects of domestication, common breeds and their origins. The genetics of cattle, R Fries, A Ruvinsky. CABI Publishing, Oxon 1999; 15–31
   Google Scholar
• Cymbron T, Loftus RT, Malheiro MI, Bradley DG. Mitochondrial sequence variation suggests an African influence in Portuguese cattle. Proc R Soc B 1999; 266: 597–603
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 2004; 32: 1792–1797
   PubMed Web of Science ®Google Scholar
• Gatesy J, Amato G, Vrba E, Schaller G, Desalle R. A cladistic analysis of mitochondrial ribosomal DNA from Bovidae. Mol Phylogenet Evol 1997; 7: 303–319
   PubMed Web of Science ®Google Scholar
• Groves P, Shields GF. Phylogenetics of the Caprinae based on cytochrome b sequence. Mol Phylogenet Evol 1996; 5: 467–476
   PubMed Web of Science ®Google Scholar
• Hall TA. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41: 95–98
   Google Scholar
• Hassanin A, Douzery EJ. Evolutionary affinities of the enigmatic saola (Pseudoryx nghetinhensis) in the context of the molecular phylogeny of Bovidae. Proc R Soc London Ser B Biol Sci 1999; 266: 893–900
   PubMed Web of Science ®Google Scholar
• Hassanin A, Pasquet E, Vigne J-D. Molecular systematics of the subfamily Caprinae (Artiodactyla, Bovidae) as determined from cytochrome b sequences. J Mammal Evol 1998; 5: 217–236
   Google Scholar
• Kierstein G, Vallinoto M, Silva A, Schneider MP, Iannuzzi L, Brenig B. Analysis of mitochondrial D-loop region casts new light on domestic water buffalo (Bubalus bubalis) phylogeny. Mol Phylogenet Evol 2004; 30(2)308–324
   PubMed Web of Science ®Google Scholar
• Kumar S, Tamura K, Nei M. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinformatics 2004; 5: 150–163
   PubMed Web of Science ®Google Scholar
• Kumar S, Nagarajan M, Sandhu JS, Kumar N, Behl V, Nishanth G. Mitochondrial DNA analyses of Indian water buffalo support a distinct genetic origin of river and swamp buffalo. Anim Genet 2007; 38: 227–232
   PubMed Web of Science ®Google Scholar
• Loftus RT, MacHugh DE, Bradley DG, Sharp PM, Cunningham P. Evidence for two independent domestications of cattle. Proc Natl Acad Sci USA 1994; 91(7)2757–2761
   PubMed Web of Science ®Google Scholar
• Magee DA, Meghen C, Harrison S, Troy CS, Cymbron T, Gaillard C, et al. A partial African ancestry for the Creole cattle populations of the Caribbean. J Hered 2002; 93: 429–432
   PubMed Web of Science ®Google Scholar
• Mannen H, Kojima T, Oyama K, Mukai F, Ishida T, Tsuji S. Effect of mitochondrial DNA variation on carcass traits of Japanese black cattle. J Anim Sci 1998; 76: 36–41
   PubMed Web of Science ®Google Scholar
• Mannen H, Morimoto ML, Oyamat K, Mukai F, Tsuji S. Identification of mitochondrial DNA substitutions related to meat quality in Japanese black cattle. J Anim Sci 2003; 81: 68–73
   PubMed Web of Science ®Google Scholar
• Matthee CA, Robinson TJ. Cytochrome B phylogeny of the family Bovidae: Resolution within the alcelaphini, antilopini, neotragini and tragelaphini. Mol Phylogenet Evol 1999; 12: 31–46
   PubMed Web of Science ®Google Scholar
• Parma P, Erra-pujadab M, Feliginic M, Greppid G, Ennee G. Water buffalo (Bubalus bubalis): Complete nucleotide mitochondrial genome sequence. DNA Seq 2004; 15(5/6)369–373
   PubMedGoogle Scholar
• Ramadan HAI. 2007. Direct submission of Egyptian buffalo D-loop sequence data to National Center for Biotechnology Information (NCBI) GenBank Database. Accession Numbers: EF396995–EF396999 and EF536326–EF536329.
   Google Scholar
• Ronquist F, Huelsenbeck JP. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003; 19: 1572–1574
   PubMed Web of Science ®Google Scholar
• Salerno A. The buffaloes of Italy. The husbandry and health of the domestic buffalo, WR Cockrill. FAO, Rome 1974; 737–747
   Google Scholar
• Schutz MM, Freeman AE, Lindberg GL, Koehler CM, Beitz DC. The effect of mitochondrial DNA on milk production and health of dairy cattle. Livestock Prod Sci 1994; 37: 283–295
   Google Scholar
• Sudo A, Honzawa S, Nonaka I, Goto Y. Leigh syndrome caused by mitochondrial DNA G13513A mutation: Frequency and clinical features in Japan. J Hum Genet 2004; 49(2)92–96
   PubMed Web of Science ®Google Scholar
• Suzuki R, Kemp SJ, Teale AJ. Polymerase chain reaction analysis of mitochondrial DNA polymorphism in N'dama and zebu cattle. Anim Genet 1993; 24: 339–343
   PubMed Web of Science ®Google Scholar
• Taanman JW. The mitochondrial genome: Structure, transcription, translation and replication. Biochim Biophys Acta 1999; 1410: 103–123
   PubMed Web of Science ®Google Scholar
• Tanaka K, Solis CD, Masangkay JS, Maeda KI, Kawamoto Y, Namikawa T. Phylogenetic relationship among all living species of the genus Bubalus based on DNA sequences of the cytochrome b gene. Biochem Genet 1996; 34: 443–452
   PubMed Web of Science ®Google Scholar
• Tartaglia M, Saulle E, Pestalozza S, Morelli L, Antonucci G, Battaglia PA. Detection of bovine mitochondrial DNA in ruminant feeds: A molecular approach to test for the presence of bovine-derived materials. J Food Protect 1998; 61: 513–518
   PubMed Web of Science ®Google Scholar
• Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl Acids Res 1994; 22: 4673–4680
   PubMed Web of Science ®Google Scholar
• Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P, et al. Genetic evidence for Near-Eastern origins of European cattle. Nature 2001; 410: 1088–1091
   PubMed Web of Science ®Google Scholar