The phylogenetic status of typical Chinese native pigs: Analyzed by Asian and European pig mitochondrial genome sequences

Journal of Animal Science and Biotechnology

Volumn 4, Issue 1, 2013, Pages

  Yu, Guanghui ^a   Xiang, Hai ^a   Wang, Jikun ^a   Zhao, Xingbo ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Mitochondrial DNA; Origin and evolution; Phylogenetic analysis; Pig

Indexed keywords

EID: 84894591596     PISSN: 16749782     EISSN: 20491891     Source Type: Journal    
DOI: 10.1186/2049-1891-4-9     Document Type: Article

References (42)

1. Larson G, Liu R, Zhao X, Yuan J, Fuller D, Barton L, Dobney K, Fan Q, Gu Z, Liu X-H. Patterns of east asian pig domestication, migration, and turnover revealed by modern and ancient DNA. PNAS 2010, 107:7686-7691. 10.1073/pnas.0912264107, 2867865, 20404179.
2. Lu H, Zhang J, Liu K-B, Wu N, Li Y, Zhou K, Ye M, Zhang T, Zhang H, Yang X. Earliest domestication of common millet (panicum miliaceum) in east asia extended to 10,000 years ago. PNAS 2009, 106:7367-7372. 10.1073/pnas.0900158106, 2678631, 19383791.
3. Wu G-S, Yao Y-G, Qu K-X, Ding Z-L, Li H, Palanichamy MG, Duan Z-Y, Li N, Chen Y-S, Zhang Y-P. Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in east asia. Genome Biol 2007, 8:R245. 10.1186/gb-2007-8-11-r245, 2258183, 18021448.
4. Brown WM, George M, Wilson AC. Rapid evolution of animal mitochondrial-DNA. PNAS 1979, 76:1967-1971. 10.1073/pnas.76.4.1967, 383514, 109836.
5. Brown WM, Prager EM, Wang A, Wilson AC. Mitochondrial-DNA sequences of primates - tempo and mode of evolution. J Mol Evol 1982, 18:225-239. 10.1007/BF01734101, 6284948.
6. Brown DR, Koehler CM, Lindberg GL, Freeman AE, Mayfield JE, Myers AM, Schutz MM, Beitz DC. Molecular analysis of cytoplasmic genetic-variation in holstein cows. J Anim Sci 1989, 67:1926-1932.
7. Luikart G, Gielly L, Excoffier L, Vigne JD, Bouvet J, Taberlet P. Multiple maternal origins and weak phylogeographic structure in domestic goats. PNAS 2001, 98:5927-5932. 10.1073/pnas.091591198, 33315, 11344314.
8. Wolstenholme DR. Animal mitochondrial-DNA - structure and evolution. Inter Rev Cyto-a Survey of Cell Biol 1992, 141:173-216.
9. Giles RE, Blanc H, Cann HM, Wallace DC. Maternal inheritance of human mitochondrial-DNA. PNAS 1980, 77:6715-6719. 10.1073/pnas.77.11.6715, 350359, 6256757.
10. Avise JC, Lansman RA, Shade RO. Use of restriction endonucleases to measure mitochondrial-DNA sequence relatedness in natural-populations .1. Population-structure and evolution in the genus peromyscus. Genetics 1979, 92:279-295. 1213949, 499767.
11. Cann RL, Brown WM, Wilson AC. Polymorphic sites and the mechanism of evolution in human mitochondrial-DNA. Genetics 1984, 106:479-499. 1224251, 6323246.
12. Watanabe T, Hayashi Y, Ogasawara N, Tomoita T. Polymorphism of mitochondrial-DNA in pigs based on restriction endonuclease cleavage patterns. Biochem Genet 1985, 23:105-113. 10.1007/BF00499116, 2986593.
13. Lan H, Shi LM. The origin and genetic differentiation of native breeds of pigs in southwest china - an approach from mitochondrial-DNA polymorphism. Biochem Genet 1993, 31:51-60. 10.1007/BF02399819, 8097084.
14. Huang YF, Shi XW, Zhang YP. Mitochondrial genetic variation in chinese pigs and wild boars. Biochem Genet 1999, 37:335-343. 10.1023/A:1018763311574, 10690429.
15. Gongora J, Fleming P, Spencer PBS, Mason R, Garkavenko O, Meyer JN, Droegemueller C, Lee JH, Moran C. Phylogenetic relationships of australian and new zealand feral pigs assessed by mitochondrial control region sequence and nuclear gpip genotype. Mol Phylogenet Evol 2004, 33:339-348. 10.1016/j.ympev.2004.06.004, 15336669.
16. Seabury CM, Bhattarai EK, Taylor JF, Viswanathan GG, Cooper SM, Davis DS, Dowd SE, Lockwood ML, Seabury PM. Genome-wide polymorphism and comparative analyses in the white-tailed deer (odocoileus virginianus): A model for conservation genomics. PLoS One 2011, 6:e15811. 10.1371/journal.pone.0015811, 3023705, 21283515.
17. Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P, Chamberlain AT, Sykes BC, Bradley DG. Genetic evidence for near-eastern origins of european cattle. Nature 2001, 410:1088-1091. 10.1038/35074088, 11323670.
18. Liu YP, Wu GS, Yao YG, Miao YW, Luikart G, Baig M, Beja-Pereira A, Ding ZL, Palanichamy MG, Zhang YP. Multiple maternal origins of chickens: Out of the asian jungles. Mol Phylogenet Evol 2006, 38:12-19. 10.1016/j.ympev.2005.09.014, 16275023.
19. Vila C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H. Widespread origins of domestic horse lineages. Science 2001, 291:474-477. 10.1126/science.291.5503.474, 11161199.
20. Giuffra E, Kijas JMH, Amarger V, Carlborg O, Jeon JT, Andersson L. The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics 2000, 154:1785-1791. 1461048, 10747069.
21. Larson G, Dobney K, Albarella U, Fang MY, Matisoo-Smith E, Robins J, Lowden S, Finlayson H, Brand T, Willerslev E. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 2005, 307:1618-1621. 10.1126/science.1106927, 15761152.
22. Fang M, Andersson L. Mitochondrial diversity in european and chinese pigs is consistent with population expansions that occurred prior to domestication. Proc Biol Sci 2006, 273:1803-1810. 10.1098/rspb.2006.3514, 1634785, 16790414.
23. Kijas JMH, Andersson L. A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtdna genome. J Mol Evol 2001, 52:302-308.
24. Hutchiso C, Newbold JE, Potter SS, Edgell MH. Maternal inheritance of mammalian mitochondrial-DNA. Nature 1974, 251:536-538. 10.1038/251536a0, 4423884.
25. Larson G, Dobney K, Albarella U, Matisoo-Smith E, Robins J, Lowden S, Rowley-Conwy P, Andersson L, Cooper A. Domesticated pigs in eastern indonesia - response. Science 2005, 309:381-381.
26. Larson G, Cucchi T, Fujita M, Matisoo-Smith E, Robins J, Anderson A, Rolett B, Spriggs M, Dolman G, Kim T-H. Phylogeny and ancient DNA of sus provides insights into neolithic expansion in island southeast asia and oceania. PNAS 2007, 104:4834-4839. 10.1073/pnas.0607753104, 1829225, 17360400.
27. Kim KI, Lee JH, Li K, Zhang YP, Lee SS, Gongora J, Moran C. Phylogenetic relationships of asian and european pig breeds determined by mitochondrial DNA d-loop sequence polymorphism. Anim Genet 2002, 33:19-25. 10.1046/j.1365-2052.2002.00784.x, 11849133.
28. Yang J, Wang J, Kijas J, Liu B, Han H, Yu M, Yang H, Zhao S, Li K. Genetic diversity present within the near-complete mtdna genome of 17 breeds of indigenous chinese pigs. J Hered 2003, 94:381-385. 10.1093/jhered/esg077, 14557390.
29. Ghivizzani SC, Mackay SLD, Madsen CS, Laipis PJ, Hauswirth WW. Transcribed heteroplasmic repeated sequences in the porcine mitochondrial-DNA d-loop region. J Mol Evol 1993, 37:36-47.
30. Lucchini V, Meijaard E, Diong CH, Groves CP, Randi E. New phylogenetic perspectives among species of south-east asian wild pig (sus sp.) based on mtdna sequences and morphometric data. J Zool 2005, 266:25-35.
31. Edgar RC. Muscle: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
32. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. Mega5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
33. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with beauti and the beast 1.7. Mol Biol Evol 2012, 29:1969-1973. 10.1093/molbev/mss075, 3408070, 22367748.
34. Librado P, Rozas J. Dnasp v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452. 10.1093/bioinformatics/btp187, 19346325.
35. Excoffier L, Lischer HEL. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under linux and windows. Mol Ecol Resour 2010, 10:564-567. 10.1111/j.1755-0998.2010.02847.x, 21565059.
36. Chen C-H, Huang H-L, Yang H-Y, Lai S-H, Yen N-T, Wu M-C, Huang M-C. Mitochondrial genome of taiwan pig (sus scrofa). Afr J Biotechnol 2011, 10:2556-2561.
37. Watanabe T, Hayashi Y, Kimura J, Yasuda Y, Saitou N, Tomita T, Ogasawara N. Pig mitochondrial-DNA - polymorphism, restriction map orientation, and sequence data. Biochem Genet 1986, 24:385-396. 10.1007/BF00499094, 3017295.
38. Okumura N, Ishiguro N, Nakano M, Hirai K, Matsui A, Sahara M. Geographic population structure and sequence divergence in the mitochondrial DNA control region of the japanese wild boar (sus scrofa leucomystax), with reference to those of domestic pigs. Biochem Genet 1996, 34:179-189. 10.1007/BF02407018, 8813051.
39. Jones GF. Genetic aspects of domestication, common breeds and their origin. The genetics of the pig 1998, 17-50. Wellingford, Oxon, UK: CAB International, Rothschild MF, Ruvinsky A.
40. Okumura N, Kurosawa Y, Kobayashi E, Watanobe T, Ishiguro N, Yasue H, Mitsuhashi T. Genetic relationship amongst the major non-coding regions of mitochondrial dnas in wild boars and several breeds of domesticated pigs. Anim Genet 2001, 32:139-147. 10.1046/j.1365-2052.2001.00757.x, 11493262.
41. Paszek A, Flickinger GH, Fontanesi L, Beattie CW, Rohrer GA, Alexander L, Schook LB. Evaluating evolutionary divergence with microsatellites. J Mol Evol 1998, 46:121-126. 10.1007/PL00006279, 9419232.
42. Luetkemeier ES, Sodhi M, Schook LB, Malhi RS. Multiple asian pig origins revealed through genomic analyses. Mol Phylogenet Evol 2010, 54:680-686. 10.1016/j.ympev.2009.11.004, 19900568.