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Volumn 31, Issue 6, 2014, Pages 1475-1489

Whole-genome sequencing of Tibetan Macaque (Macaca thibetana) provides new insight into the Macaque evolutionary history

Author keywords

demographic trajectories; genetic divergence; introgression; SNVs; Tibetan macaque; whole genome sequencing

Indexed keywords

INSULIN RECEPTOR;

EID: 84901413625     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu104     Document Type: Article
Times cited : (43)

References (61)
  • 2
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 57:289-300.
    • (1995) J R Stat Soc B. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 0033009077 scopus 로고    scopus 로고
    • A four-year study of the association between male dominance rank, residency status, and reproductive activity in rhesus macaques (Macaca mulatta)
    • Berard J. 1999. A four-year study of the association between male dominance rank, residency status, and reproductive activity in rhesus macaques (Macaca mulatta). Primates 40:159-175.
    • (1999) Primates , vol.40 , pp. 159-175
    • Berard, J.1
  • 4
    • 43549114766 scopus 로고    scopus 로고
    • Mitochondrial DNA sequence phylogeny of 4 populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis)
    • Blancher A, Bonhomme M, Crouau-Roy B, Terao K, Kitano T, Saitou N. 2008. Mitochondrial DNA sequence phylogeny of 4 populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis). J Hered. 99:254-264.
    • (2008) J Hered. , vol.99 , pp. 254-264
    • Blancher, A.1    Bonhomme, M.2    Crouau-Roy, B.3    Terao, K.4    Kitano, T.5    Saitou, N.6
  • 5
    • 60249086593 scopus 로고    scopus 로고
    • Assessing natural introgression in 2 biomedical model species, the rhesus macaque (Macaca mulatta) and the long-tailed macaque (Macaca fascicularis)
    • Bonhomme M, Cuartero S, Blancher A, Crouau-Roy B. 2009. Assessing natural introgression in 2 biomedical model species, the rhesus macaque (Macaca mulatta) and the long-tailed macaque (Macaca fascicularis). J Hered. 100:158-169.
    • (2009) J Hered. , vol.100 , pp. 158-169
    • Bonhomme, M.1    Cuartero, S.2    Blancher, A.3    Crouau-Roy, B.4
  • 6
    • 34447318657 scopus 로고    scopus 로고
    • Phylogenetic relationships and morphometric affinities of the Arunachal macaque Macaca munzala, a newly described primate from Arunachal Pradesh, northeastern India
    • Chakraborty D, Ramakrishnan U, Panor J, Mishra C, Sinha A. 2007. Phylogenetic relationships and morphometric affinities of the Arunachal macaque Macaca munzala, a newly described primate from Arunachal Pradesh, northeastern India. Mol Phylogenet Evol. 44: 838-849.
    • (2007) Mol Phylogenet Evol. , vol.44 , pp. 838-849
    • Chakraborty, D.1    Ramakrishnan, U.2    Panor, J.3    Mishra, C.4    Sinha, A.5
  • 7
    • 0002621876 scopus 로고
    • Fossil macaques, phyletic relationships and a scenario of deployment
    • In: Lindburg DG, editor New York: Van Nostrand Reinhold Co
    • Delson E. 1980. Fossil macaques, phyletic relationships and a scenario of deployment. In: Lindburg DG, editor. The macaques: studies in ecology, behavior, and evolution. New York: Van Nostrand Reinhold Co. p. 10-30.
    • (1980) The Macaques: Studies in Ecology, Behavior, and Evolution , pp. 10-30
    • Delson, E.1
  • 12
    • 0024940281 scopus 로고
    • The genus Macaca: A review of taxonomy and evolution
    • Fa JE. 1989. The genus Macaca: a review of taxonomy and evolution. Mammal Rev. 19:45-81.
    • (1989) Mammal Rev. , vol.19 , pp. 45-81
    • Fa, J.E.1
  • 13
    • 79959912920 scopus 로고    scopus 로고
    • Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque
    • Fang X, Zhang Y, Zhang R, Yang L, Li M, Ye K, Guo X,Wang J, Su B. 2011. Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. Genome Biol. 12:R63.
    • (2011) Genome Biol. , vol.12
    • Fang, X.1    Zhang, Y.2    Zhang, R.3    Yang, L.4    Li, M.5    Ye, K.6    Guo Xwang, J.7    Su, B.8
  • 15
    • 0346599403 scopus 로고    scopus 로고
    • An autoimmune disease, APECED, caused by mutations in a novel gene featuring two PHDtype zinc-finger domains
    • Finnish-German APECED Consortium
    • Finnish-German APECED Consortium. 1997. An autoimmune disease, APECED, caused by mutations in a novel gene featuring two PHDtype zinc-finger domains. Nat Genet. 17:399-403.
    • (1997) Nat Genet. , vol.17 , pp. 399-403
  • 16
    • 0016908692 scopus 로고
    • Provisional classifications and key to living species of macaques (primates: Macaca)
    • Fooden J. 1976. Provisional classifications and key to living species of macaques (primates: Macaca). Folia Primatol. 25:225-236.
    • (1976) Folia Primatol. , vol.25 , pp. 225-236
    • Fooden, J.1
  • 18
    • 80053386624 scopus 로고    scopus 로고
    • Bayesian inference of ancient human demography from individual genome sequences
    • Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. 2011. Bayesian inference of ancient human demography from individual genome sequences. Nat Genet. 43:1031-1034.
    • (2011) Nat Genet. , vol.43 , pp. 1031-1034
    • Gronau, I.1    Hubisz, M.J.2    Gulko, B.3    Danko, C.G.4    Siepel, A.5
  • 20
    • 73449149044 scopus 로고    scopus 로고
    • Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
    • Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5:e1000695.
    • (2009) PLoS Genet. , vol.5
    • Gutenkunst, R.N.1    Hernandez, R.D.2    Williamson, S.H.3    Bustamante, C.D.4
  • 21
    • 0029816997 scopus 로고    scopus 로고
    • Molecular phylogeny of macaques: Implications of nucleotide sequences from an 896-base pair region of mitochondrial DNA
    • Hayasaka K, Fujii K, Horai S. 1996. Molecular phylogeny of macaques: implications of nucleotide sequences from an 896-base pair region of mitochondrial DNA. Mol Biol Evol. 13:1044-1053.
    • (1996) Mol Biol Evol. , vol.13 , pp. 1044-1053
    • Hayasaka, K.1    Fujii, K.2    Horai, S.3
  • 23
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 24
    • 54449097114 scopus 로고    scopus 로고
    • Interspecies hybridization and the stratification of nuclear genetic variation of rhesus (Macaca mulatta) and long-tailed macaques (Macaca fascicularis)
    • Kanthaswamy S, Satkoski J, George D, Kou A, Erickson BJ, Smith DG. 2008. Interspecies hybridization and the stratification of nuclear genetic variation of rhesus (Macaca mulatta) and long-tailed macaques (Macaca fascicularis). Int J Primatol. 29:1295-1311.
    • (2008) Int J Primatol. , vol.29 , pp. 1295-1311
    • Kanthaswamy, S.1    Satkoski, J.2    George, D.3    Kou, A.4    Erickson, B.J.5    Smith, D.G.6
  • 25
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding nonsynonymous variants on protein function using the SIFT algorithm
    • Kumar P, Henikoff S, Ng PC. 2009. Predicting the effects of coding nonsynonymous variants on protein function using the SIFT algorithm. Nat Protoc. 4:1073-1082.
    • (2009) Nat Protoc. , vol.4 , pp. 1073-1082
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 26
    • 0032580152 scopus 로고    scopus 로고
    • A molecular timescale for vertebrate evolution
    • Kumar S, Hedges SB. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
    • (1998) Nature , vol.392 , pp. 917-920
    • Kumar, S.1    Hedges, S.B.2
  • 28
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9:357-359.
    • (2012) Nat Methods. , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 29
    • 54949097762 scopus 로고    scopus 로고
    • Genetic diversity analysis of Macaca thibetana based on mitochondrial DNA control region sequences
    • Li DM, Fan LQ, Ran JH, Yin HL,Wang HX, Wu SB, Yue BS. 2008. Genetic diversity analysis of Macaca thibetana based on mitochondrial DNA control region sequences. Mitochondr DNA. 19:446-452.
    • (2008) Mitochondr DNA. , vol.19 , pp. 446-452
    • Li, D.M.1    Fan, L.Q.2    Ran, J.H.3    Yin, H.L.4    Wang, H.X.5    Wu, S.B.6    Yue, B.S.7
  • 30
    • 79960914105 scopus 로고    scopus 로고
    • Inference of human population history from individual whole-genome sequences
    • Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493-496.
    • (2011) Nature , vol.475 , pp. 493-496
    • Li, H.1    Durbin, R.2
  • 32
    • 0037178321 scopus 로고    scopus 로고
    • SIV(mac) pathogenesis in rhesus macaques of Chinese and Indian origin compared with primary HIV infections in humans
    • Ling B, Veazey RS, Luckay A, Penedo C, Xu K, Lifson JD, Marx PA. 2002. SIV(mac) pathogenesis in rhesus macaques of Chinese and Indian origin compared with primary HIV infections in humans. AIDS 16: 1489-1496.
    • (2002) AIDS , vol.16 , pp. 1489-1496
    • Ling, B.1    Veazey, R.S.2    Luckay, A.3    Penedo, C.4    Xu, K.5    Lifson, J.D.6    Marx, P.A.7
  • 33
    • 79959241879 scopus 로고    scopus 로고
    • Characterization of intraocular pressure responses of the Tibetan monkey (Macaca thibetana)
    • Liu G, Zeng T, YuWH, Yan NH, Wang HX, Cai SP, Pang IH, Liu XY. 2011. Characterization of intraocular pressure responses of the Tibetan monkey (Macaca thibetana). Mol Vis. 17:1405-1413.
    • (2011) Mol Vis. , vol.17 , pp. 1405-1413
    • Liu, G.1    Zeng, T.2    Yu, W.H.3    Yan, N.H.4    Wang, H.X.5    Cai, S.P.6    Pang, I.H.7    Liu, X.Y.8
  • 34
    • 58049198421 scopus 로고    scopus 로고
    • IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral bloodmononuclear cells
    • LiuS,WangH, Jin Y,PodolskyR,ReddyMV,PedersenJ,BodeB,ReedJ, Steed D, Anderson S, et al. 2009. IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral bloodmononuclear cells. HumMol Genet. 18:358-365.
    • (2009) Hum Mol Genet. , vol.18 , pp. 358-365
    • Liu, S.1    Wang, H.2    Jin, Y.3    Podolsky, R.4    Reddy, M.V.5    Pedersen, J.6    Bode, B.7    Reed, J.8    Steed, D.9    Anderson, S.10
  • 35
    • 54949152199 scopus 로고    scopus 로고
    • Sequence variation of mitochondrial DNA control region and population genetic diversity of Tibetan macaques Macaca thibetana in the Huangshan Mountain
    • Liu Y, Li JH, Zhao JY. 2006. Sequence variation of mitochondrial DNA control region and population genetic diversity of Tibetan macaques Macaca thibetana in the Huangshan Mountain. Acta Zool Sin. 52:724-730.
    • (2006) Acta Zool Sin. , vol.52 , pp. 724-730
    • Liu, Y.1    Li, J.H.2    Zhao, J.Y.3
  • 36
    • 65249131713 scopus 로고    scopus 로고
    • Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes
    • Nejentsev S, Walker N, Riches D, EgholmM, Todd JA. 2009. Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 324:387-389.
    • (2009) Science , vol.324 , pp. 387-389
    • Nejentsev, S.1    Walker, N.2    Riches, D.3    Egholm, M.4    Todd, J.A.5
  • 37
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen R, Paul JS, Albrechtsen A, Song YS. 2011. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 12: 443-451.
    • (2011) Nat Rev Genet. , vol.12 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 38
  • 39
    • 84887099761 scopus 로고    scopus 로고
    • Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: Male-driven evolution, demography, and natural selection
    • Osada N, Nakagome S, Mano S, Kameoka Y, Takahashi I, Terao K. 2013. Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection. Genetics 195:1027-1035.
    • (2013) Genetics , vol.195 , pp. 1027-1035
    • Osada, N.1    Nakagome, S.2    Mano, S.3    Kameoka, Y.4    Takahashi, I.5    Terao, K.6
  • 40
    • 77954560960 scopus 로고    scopus 로고
    • Ancient genome wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M mulatta
    • Osada N, Uno Y, Mineta K, Kameoka Y, Takahashi I, Terao K. 2010. Ancient genome wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta. Mol Ecol. 19:2884-2895.
    • (2010) Mol Ecol. , vol.19 , pp. 2884-2895
    • Osada, N.1    Uno, Y.2    Mineta, K.3    Kameoka, Y.4    Takahashi, I.5    Terao, K.6
  • 42
    • 62449182499 scopus 로고    scopus 로고
    • Inference of historical changes in migration rate from the lengths of migrant tracts
    • Pool JE, Nielsen R. 2009. Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181:711-719.
    • (2009) Genetics , vol.181 , pp. 711-719
    • Pool, J.E.1    Nielsen, R.2
  • 44
    • 79959923522 scopus 로고    scopus 로고
    • G:Profiler - A web server for functional interpretation of gene lists (2011 update)
    • Reimand J, Arak T, Vilo J. 2011. g:Profiler-a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res. 39: W307-W315.
    • (2011) Nucleic Acids Res. , vol.39
    • Reimand, J.1    Arak, T.2    Vilo, J.3
  • 45
    • 34247352040 scopus 로고    scopus 로고
    • Evolutionary and biomedical insights from the rhesus macaque genome
    • Rhesus Macaque Genome Sequencing and Analysis Consortium
    • Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234.
    • (2007) Science , vol.316 , pp. 222-234
  • 47
    • 0017622897 scopus 로고
    • Differences in the virulence of Plasmodium knowlesi for Macaca irus (fascicularis) of Philippine and Malayan origins
    • Schmidt LH, Fradkin R, Harrison J, Rossan RN. 1977. Differences in the virulence of Plasmodium knowlesi for Macaca irus (fascicularis) of Philippine and Malayan origins. Am J Trop Med Hyg. 26:612-622.
    • (1977) Am J Trop Med Hyg. , vol.26 , pp. 612-622
    • Schmidt, L.H.1    Fradkin, R.2    Harrison, J.3    Rossan, R.N.4
  • 49
    • 55449124031 scopus 로고    scopus 로고
    • Determining genetic background in captive stocks of cynomolgus macaques (Macaca fascicularis)
    • Stevison LS, Kohn MH. 2008. Determining genetic background in captive stocks of cynomolgus macaques (Macaca fascicularis). J Med Primatol. 37:311-317.
    • (2008) J Med Primatol. , vol.37 , pp. 311-317
    • Stevison, L.S.1    Kohn, M.H.2
  • 53
    • 0038641049 scopus 로고    scopus 로고
    • Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys
    • Tosi AJ, Morales JC, Melnick DJ. 2003. Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys. Evolution 57: 1419-1435.
    • (2003) Evolution , vol.57 , pp. 1419-1435
    • Tosi, A.J.1    Morales, J.C.2    Melnick, D.J.3
  • 55
    • 80755189340 scopus 로고    scopus 로고
    • Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques
    • YanG, ZhangG, Fang X, Zhang Y, Li C, Ling F, Cooper DN, LiQ, Li Y, van Gool AJ, et al. 2011. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol. 29:1019-1023.
    • (2011) Nat Biotechnol. , vol.29 , pp. 1019-1023
    • Yan, G.1    Zhang, G.2    Fang, X.3    Zhang, Y.4    Li, C.5    Ling, F.6    Cooper, D.N.7    Li, Q.8    Li, Y.9    Van Gool, A.J.10
  • 56
    • 84901394859 scopus 로고    scopus 로고
    • A primary analyze and measurement on partial biochemistry index of peripheral blood cells of Macaca thibetana
    • Yang F, Wang HX, Zhou L, Ai YX, Zeng T. 2010. A primary analyze and measurement on partial biochemistry index of peripheral blood cells of Macaca thibetana. Sichuan J Zool. 29:256-258.
    • (2010) Sichuan J Zool. , vol.29 , pp. 256-258
    • Yang, F.1    Wang, H.X.2    Zhou, L.3    Ai, Y.X.4    Zeng, T.5
  • 57
    • 84878031224 scopus 로고    scopus 로고
    • Genetic variation between two Tibetan macaque (Macaca thibetana) populations in the eastern China based on mitochondrial DNA control region sequences
    • Yao YF, Zhong LJ, Liu BF, Li JY, Ni QY, Xu HL. 2013. Genetic variation between two Tibetan macaque (Macaca thibetana) populations in the eastern China based on mitochondrial DNA control region sequences. Mitochondr DNA. 24:267-275.
    • (2013) Mitochondr DNA. , vol.24 , pp. 267-275
    • Yao, Y.F.1    Zhong, L.J.2    Liu, B.F.3    Li, J.Y.4    Ni, Q.Y.5    Xu, H.L.6
  • 58
    • 0002495165 scopus 로고
    • Mating competition and intergroup transfer of males in Tibetan macaques (Macaca thibetana) at Mt Emei, China
    • Zhao QK. 1994. Mating competition and intergroup transfer of males in Tibetan macaques (Macaca thibetana) at Mt Emei, China. Primates 35:57-68.
    • (1994) Primates , vol.35 , pp. 57-68
    • Zhao, Q.K.1
  • 59
    • 0036629768 scopus 로고    scopus 로고
    • The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan Plateau: Review and speculation
    • Zheng BX, Xu QQ, Shen YP. 2002. The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan Plateau: review and speculation. Quaternary Int. 97-98: 93-101.
    • (2002) Quaternary Int. , vol.97-98 , pp. 93-101
    • Zheng, B.X.1    Xu, Q.Q.2    Shen, Y.P.3
  • 60
    • 84892832355 scopus 로고    scopus 로고
    • Genetic diversity of two Tibetan macaque (Macaca thibetana) populations from Guizhou and Yunnan in China based on mitochondrial DNA D-loop sequences
    • Zhong LJ, Zhang MW, Yao YF, Ni QY, Mu J, Li CQ, Xu HL. 2013. Genetic diversity of two Tibetan macaque (Macaca thibetana) populations from Guizhou and Yunnan in China based on mitochondrial DNA D-loop sequences. Genes Genomics. 35:205-214.
    • (2013) Genes Genomics. , vol.35 , pp. 205-214
    • Zhong, L.J.1    Zhang, M.W.2    Yao, Y.F.3    Ni, Q.Y.4    Mu, J.5    Li, C.Q.6    Xu, H.L.7


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