Multi-locus analysis reveals a different pattern of genetic diversity for mitochondrial and nuclear DNA between wild and domestic pigs in East Asia

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Ji, Yin Qiu ^a,b   Wu, Dong Dong ^a   Wu, Gui Sheng ^a,c   Wang, Guo Dong ^a   Zhang, Ya Ping ^a,c  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c YUNNAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS DNA; MITOCHONDRIAL DNA;

ARTICLE; ASIA; BOAR (MALE PIG); CELL NUCLEUS; CELLULAR DISTRIBUTION; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DOMESTIC PIG; DOMESTICATION; EAST ASIA; FEMALE; GENE LOCATION; GENE LOCUS; GENETIC MARKER; GENETIC VARIABILITY; GENOME ANALYSIS; GEOGRAPHIC ORIGIN; MALE; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; WILD ANIMAL; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; CLUSTER ANALYSIS; CROSS BREEDING; FAR EAST; FOUNDER EFFECT; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETICS; GEOGRAPHY; MITOCHONDRIAL GENE; MOLECULAR GENETICS; OPEN READING FRAME; POPULATION DYNAMICS; POPULATION GENETICS; SWINE;

SUIDAE; SUS SCROFA; SUS SCROFA DOMESTICA;

ANIMALS; BAYES THEOREM; CELL NUCLEUS; CLUSTER ANALYSIS; CROSSES, GENETIC; DNA, MITOCHONDRIAL; FAR EAST; FEMALE; FOUNDER EFFECT; GENES, MITOCHONDRIAL; GENETIC LOCI; GENETIC MARKERS; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; LINKAGE DISEQUILIBRIUM; MALE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; POPULATION DYNAMICS; RECOMBINATION, GENETIC; SUS SCROFA; SWINE;

EID: 80055105920     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026416     Document Type: Article

References (64)

1. Zeuner FE, (1963) A History of Domesticated Animals New York Harper & Row.
2. Darwin C, (1968) Variation of animals and plants under domestication London John Murray.
3. Clutton-Brock J, (1989) The Walking Larder: Patterns of Domestication, Pastoralism, and Predation London: Unwin Hyman.
4. Budiansky S, (1992) The Covenant of the Wild: Why Animals Chose Domestication New Haven Yale University Press.
5. Darwin C, (1868) Variation of animals and plants under domestication London John Murray.
6. Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS, (1998) Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci U S A 95: 4441-4446.
7. Tenaillon MI, U'Ren J, Tenaillon O, Gaut BS, (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol 21: 1214-1225.
8. Tanksley SD, McCouch SR, (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277: 1063-1066.
9. Scherf BD, (1995) World Watch List for Domestic Animal Diversity, 2nd Edition Rome FAO.
10. Larson G, Dobney K, Albarella U, Fang M, Matisoo-Smith E, et al. (2005) Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307: 1618-1621.
11. Giuffra E, Kijas JM, Amarger V, Carlborg O, Jeon JT, et al. (2000) The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154: 1785-1791.
12. Kijas JM, Andersson L, (2001) A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. J Mol Evol 52: 302-308.
13. Lum JK, McIntyre JK, Greger DL, Huffman KW, Vilar MG, (2006) Recent Southeast Asian domestication and Lapita dispersal of sacred male pseudohermaphroditic "tuskers" and hairless pigs of Vanuatu. Proc Natl Acad Sci U S A 103: 17190-17195.
14. Wu GS, Yao YG, Qu KX, Ding ZL, Li H, et al. (2007) Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biol 8: R245.
15. Larson G, Albarella U, Dobney K, Rowley-Conwy P, Schibler J, et al. (2007) Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proc Natl Acad Sci U S A 104: 15276-15281.
16. Ramirez O, Ojeda A, Tomas A, Gallardo D, Huang LS, et al. (2009) Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds. Mol Biol Evol 26: 2061-2072.
17. Larson G, Liu R, Zhao X, Yuan J, Fuller D, et al. (2010) Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc Natl Acad Sci U S A 107: 7686-7691.
18. Fang M, Larson G, Ribeiro HS, Li N, Andersson L, (2009) Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet 5: e1000341.
19. Li J, Yang H, Li JR, Li HP, Ning T, et al. (2010) Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication. Heredity.
20. Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, et al. (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316: 112-115.
21. Clark RM, Linton E, Messing J, Doebley JF, (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci U S A 101: 700-707.
22. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, et al. (2005) The effects of artificial selection on the maize genome. Science 308: 1310-1314.
23. Ojeda A, Rozas J, Folch JM, Perez-Enciso M, (2006) Unexpected high polymorphism at FABP4 gene unveils a complex history for pig populations. Genetics 174: 2119-2127.
24. Ojeda A, Wang L, Ren J, Angiolillo A, Cho IC, et al. (2008) Selection in the making: A Worldwide Survey of Haplotypic Diversity around a Causative Mutation in Porcine IGF2. Genetics 178: 1639-1652.
25. Ojeda A, Estelle J, Folch JM, Perez-Enciso M, (2008) Nucleotide variability and linkage disequilibrium patterns at the porcine FABP5 gene. Anim Genet 39: 468-473.
26. Scandura M, Iacolina L, Crestanello B, Pecchioli E, Di Benedetto MF, et al. (2008) Ancient vs. recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable? Mol Ecol 17: 1745-1762.
27. Amaral AJ, Megens HJ, Crooijmans RP, Heuven HC, Groenen MA, (2008) Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179: 569-579.
28. Fang M, Andersson L, (2006) Mitochondrial diversity in European and Chinese pigs is consistent with population expansions that occurred prior to domestication. Proc Biol Sci 273: 1803-1810.
29. Vize PD, Wells JR, (1987) Isolation and characterization of the porcine growth hormone gene. Gene 55: 339-344.
30. Maeda N, Ebert DL, Doers TM, Newman M, Hasler-Rapacz J, et al. (1988) Molecular genetics of the apolipoprotein B gene in pigs in relation to atherosclerosis. Gene 70: 213-229.
31. Yu TP, Schmitz CB, Rothschild MF, Tuggle CK, (1994) Expression pattern, genomic cloning and RFLP analyses of the swine PIT-1 gene. Anim Genet 25: 229-233.
32. Briley GP, Riggs PK, Womack JE, Hancock DL, Bidwell CA, (1996) Chromosomal localization of the porcine skeletal muscle calpain gene. Mamm Genome 7: 226-228.
33. Weaks RL, Ramsoondar JJ, Gallagher DS Jr, Nogues C, Piedrahita JA, (1997) Isolation, characterization and chromosomal localization of the porcine ciliary neurotrophic factor (CNTF) gene. Anim Genet 28: 354-357.
34. Skinner TM, Lopez-Corrales NL, Anderson SI, Loudon AL, Haley CS, et al. (2000) Genetic and physical mapping of the porcine melatonin receptor 1B gene (MTNR1B) to chromosome 9. Cytogenet Cell Genet 90: 53-55.
35. Knoll A, Stratil A, Reiner G, Peelman LJ, Van Poucke M, et al. (2002) Linkage and radiation hybrid mapping of the porcine calsequestrin 1 (CASQ1) gene to chromosome 4q. Anim Genet 33: 390-392.
36. te Pas MF, Leenhouwers JI, Knol EF, Booij M, Priem J, et al. (2003) Marker polymorphisms in the porcine genes for muscle glycogen synthase (GYS1) and muscle glycogen phosphorylase (PYGM). Anim Genet 34: 157-158.
37. Berg F, Gustafson U, Andersson L, (2006) The uncoupling protein 1 gene (UCP1) is disrupted in the pig lineage: a genetic explanation for poor thermoregulation in piglets. PLoS Genet 2: e129.
38. Blin N, Stafford DW, (1976) A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res 3: 2303-2308.
39. Li N, Stephens M, (2003) Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165: 2213-2233.
40. Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
41. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
42. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
43. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
44. Bandelt HJ, Forster P, Rohl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37-48.
45. Excoffier L, Smouse PE, Quattro JM, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
46. Excoffier L, Laval G, Schneider S, (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
47. Tajima F, (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
48. Tajima F, (1989) The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
49. Fu YX, Li WH, (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
50. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R, (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
51. Watterson GA, (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
52. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
53. Swofford DL, (2003) PAUP*: Phylogenetic Analysis Using Parsimony (* and other methods).Version 4.0b10 Sunderland, MA Sinauer Associates.
54. Kuhner MK, (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22: 768-770.
55. Bjornerfeldt S, Webster MT, Vila C, (2006) Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Res 16: 990-994.
56. Ingvarsson PK, (2004) Population subdivision and the Hudson-Kreitman-Aguade test: testing for deviations from the neutral model in organelle genomes. Genet Res 83: 31-39.
57. Pesole G, Gissi C, De Chirico A, Saccone C, (1999) Nucleotide substitution rate of mammalian mitochondrial genomes. J Mol Evol 48: 427-434.
58. Kumar S, Subramanian S, (2002) Mutation rates in mammalian genomes. Proc Natl Acad Sci U S A 99: 803-808.
59. Megens HJ, Crooijmans RP, San Cristobal M, Hui X, Li N, et al. (2008) Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication. Genet Sel Evol 40: 103-128.
60. Vila C, Seddon J, Ellegren H, (2005) Genes of domestic mammals augmented by backcrossing with wild ancestors. Trends Genet 21: 214-218.
61. Luo YB, Tao Y, Zhu JY, (2009) Preliminary Observation of Pig-bones Burials in the Qinglongquan Site. Jianghan archaeology 3: 58-65.
62. Yuan J, (2010) Zooarchaeological study on the domestic animals in ancient china. Quaternary sciences 30: 298-306.
63. Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898-902.
64. Beja-Pereira A, Caramelli D, Lalueza-Fox C, Vernesi C, Ferrand N, et al. (2006) The origin of European cattle: evidence from modern and ancient DNA. Proc Natl Acad Sci U S A 103: 8113-8118.