메뉴 건너뛰기




Volumn 138, Issue 13, 2011, Pages 1737-1749

Genome sequences reveal divergence times of malaria parasite lineages

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHIMPANZEE; CONTROLLED STUDY; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; HYPOTHESIS; LAST COMMON ANCESTOR; MALARIA; MALARIA FALCIPARUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM; PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; PLASMODIUM FALCIPARUM; PLASMODIUM GALLINACEUM; PLASMODIUM KNOWLESI; PLASMODIUM VIVAX; PRIORITY JOURNAL; ANIMAL; CLASSIFICATION; EVOLUTION; GENETICS; HAPLORHINI; HOMINID; HOST PARASITE INTERACTION; HUMAN; MOLECULAR EVOLUTION; PAN TROGLODYTES; PARASITOLOGY; PHYLOGENY; PHYSIOLOGY;

EID: 84856290479     PISSN: 00311820     EISSN: 14698161     Source Type: Journal    
DOI: 10.1017/S0031182010001575     Document Type: Article
Times cited : (44)

References (76)
  • 1
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-fit models of protein evolution
    • Abascal, F., Zardoya, R. and Posada, D. (2005). ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105.
    • (2005) Bioinformatics , vol.21 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 7
    • 42049083799 scopus 로고    scopus 로고
    • Saturation and base composition bias explain phylogenomic conflict in Plasmodium
    • Dávalos, L. M. and Perkins, S. L. (2008). Saturation and base composition bias explain phylogenomic conflict in Plasmodium. Genomics 91, 433-442.
    • (2008) Genomics , vol.91 , pp. 433-442
    • Dávalos, L.M.1    Perkins, S.L.2
  • 8
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond, A. J. and Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7, 214.
    • (2007) BMC Evolutionary Biology , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 13
    • 0032493346 scopus 로고    scopus 로고
    • The evolution of primate malaria parasites based on the gene encoding cytochrome b from the linear mitochondrial genome
    • Escalante, A. A., Freeland, D. E., Collins, W. E. and Lal, A. A. (1998). The evolution of primate malaria parasites based on the gene encoding cytochrome b from the linear mitochondrial genome. Proceedings of the National Academy of Sciences, USA 95, 8124-8129.
    • (1998) Proceedings of the National Academy of Sciences, USA , vol.95 , pp. 8124-8129
    • Escalante, A.A.1    Freeland, D.E.2    Collins, W.E.3    Lal, A.A.4
  • 14
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 15
    • 67651163808 scopus 로고    scopus 로고
    • Patterns of co-speciation and host switching in primate malaria parasites
    • Garamszegi, L. Z. (2009). Patterns of co-speciation and host switching in primate malaria parasites. Malaria Journal 8, 110.
    • (2009) Malaria Journal , vol.8 , pp. 110
    • Garamszegi, L.Z.1
  • 16
    • 0037357461 scopus 로고    scopus 로고
    • Estimation of divergence times for major lineages of primate species
    • Glazko, G. V. and Nei, M. (2003). Estimation of divergence times for major lineages of primate species. Molecular Biology and Evolution 20, 424-434.
    • (2003) Molecular Biology and Evolution , vol.20 , pp. 424-434
    • Glazko, G.V.1    Nei, M.2
  • 17
    • 0000958812 scopus 로고
    • Can Uganda's gorillas survive? - A survey of the Bwindi Forest Reserve
    • Harcourt, A. H. (1981). Can Uganda's gorillas survive? - A survey of the Bwindi Forest Reserve. Biological Conservation 19, 269-282.
    • (1981) Biological Conservation , vol.19 , pp. 269-282
    • Harcourt, A.H.1
  • 19
    • 70349657718 scopus 로고    scopus 로고
    • Rodents (Rodentia)
    • (ed. Hedges, S. B. and Kumar, S.), Oxford University Press, New York
    • Honeycutt, R. L. (2009). Rodents (Rodentia). In The Timetree of Life (ed. Hedges, S. B. and Kumar, S.), pp. 490-494. Oxford University Press, New York.
    • (2009) The Timetree of Life , pp. 490-494
    • Honeycutt, R.L.1
  • 20
    • 34548602874 scopus 로고    scopus 로고
    • Gorillas on the list
    • Hopkin, M. (2007). Gorillas on the list. Nature 449, 127.
    • (2007) Nature , vol.449 , pp. 127
    • Hopkin, M.1
  • 21
    • 33744486308 scopus 로고    scopus 로고
    • Incorporating a rapid-impact package for neglected tropical diseases with programs for HIV/AIDS, tuberculosis, and malaria
    • Hotez, P. J., Molyneux, D. H., Fenwick, A., Ottesen, E., Ehrlich Sachs, S. and Sachs, J. D. (2006). Incorporating a rapid-impact package for neglected tropical diseases with programs for HIV/AIDS, tuberculosis, and malaria. PLoS Medicine 3, e102.
    • (2006) PLoS Medicine , vol.3
    • Hotez, P.J.1    Molyneux, D.H.2    Fenwick, A.3    Ottesen, E.4    Ehrlich Sachs, S.5    Sachs, J.D.6
  • 22
    • 33845793082 scopus 로고    scopus 로고
    • Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium
    • Hughes, A. L., and French, J. O. (2007). Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium. Gene 387, 31-37.
    • (2007) Gene , vol.387 , pp. 31-37
    • Hughes, A.L.1    French, J.O.2
  • 23
    • 0025029143 scopus 로고
    • Evolutionary relationships of class II major-histocompatibilitycomplex genes in mammals
    • Hughes, A. L. and Nei, M. (1990). Evolutionary relationships of class II major-histocompatibilitycomplex genes in mammals. Molecular Biology and Evolution 7, 491-514.
    • (1990) Molecular Biology and Evolution , vol.7 , pp. 491-514
    • Hughes, A.L.1    Nei, M.2
  • 24
    • 0035823291 scopus 로고    scopus 로고
    • Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum
    • Hughes, A. L. and Verra, F. (2001). Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum. Proceedings of the Royal Society of London B 268, 1855-1860.
    • (2001) Proceedings of the Royal Society of London B , vol.268 , pp. 1855-1860
    • Hughes, A.L.1    Verra, F.2
  • 25
    • 0036698225 scopus 로고    scopus 로고
    • Extensive polymorphism and ancient origin of Plasmodium falciparum
    • Hughes, A. L. and Verra, F. (2002). Extensive polymorphism and ancient origin of Plasmodium falciparum. Trends in Parasitology 18, 348-351.
    • (2002) Trends in Parasitology , vol.18 , pp. 348-351
    • Hughes, A.L.1    Verra, F.2
  • 26
    • 77956231682 scopus 로고    scopus 로고
    • Malaria parasite sequences from chimpanzee support the co-speciation hypothesis for the origin of virulent human malaria (Plasmodium falciparum)
    • Hughes, A. L. and Verra, F. (2010). Malaria parasite sequences from chimpanzee support the co-speciation hypothesis for the origin of virulent human malaria (Plasmodium falciparum). Molecular Phylogenetics and Evolution 57, 135-143.
    • (2010) Molecular Phylogenetics and Evolution , vol.57 , pp. 135-143
    • Hughes, A.L.1    Verra, F.2
  • 30
    • 77952382039 scopus 로고    scopus 로고
    • That was then but this is now: Malaria research in the time of an eradication agenda
    • Kappe, S. H., Vaughn, A. M., Boddey, J. A. and Cowman, A. F. (2010). That was then but this is now: malaria research in the time of an eradication agenda. Science 328, 862-866.
    • (2010) Science , vol.328 , pp. 862-866
    • Kappe, S.H.1    Vaughn, A.M.2    Boddey, J.A.3    Cowman, A.F.4
  • 31
    • 0014372912 scopus 로고
    • Malaria parasites of Thamnomys rutilans (Rodentia, Muridae) in Nigeria
    • Killick-Kendrick, R. (1968). Malaria parasites of Thamnomys rutilans (Rodentia, Muridae) in Nigeria. Bulletin of the World Health Organization 38, 822-824.
    • (1968) Bulletin of the World Health Organization , vol.38 , pp. 822-824
    • Killick-Kendrick, R.1
  • 33
    • 34250753191 scopus 로고    scopus 로고
    • Virulence and resistance in malaria: Who drives the outcome of the infection?
    • Lefevre, T., Sanchez, M., Ponton, F., Hughes, D. and Thomas, F. (2007). Virulence and resistance in malaria: who drives the outcome of the infection? Trends in Parasitology 23, 299-302.
    • (2007) Trends in Parasitology , vol.23 , pp. 299-302
    • Lefevre, T.1    Sanchez, M.2    Ponton, F.3    Hughes, D.4    Thomas, F.5
  • 35
    • 0026053092 scopus 로고
    • Low nucleotide diversity in man
    • Li, W.-H. and Sadler, L. A. (1991). Low nucleotide diversity in man. Genetics 129, 513-523.
    • (1991) Genetics , vol.129 , pp. 513-523
    • Li, W.-H.1    Sadler, L.A.2
  • 37
    • 0001419091 scopus 로고
    • Anthropological implications of sickle cell gene distribution in West Africa
    • Livingstone, F. B. (1958). Anthropological implications of sickle cell gene distribution in West Africa. American Anthropologist 60, 531-561.
    • (1958) American Anthropologist , vol.60 , pp. 531-561
    • Livingstone, F.B.1
  • 38
    • 41049117759 scopus 로고    scopus 로고
    • A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): Evolution of life-history traits and host switches
    • Martinsen, E. S., Perkins, S. L. and Schall, J. J. (2008). A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): Evolution of life-history traits and host switches. Molecular Phylogenetics and Evolution 47, 261-273.
    • (2008) Molecular Phylogenetics and Evolution , vol.47 , pp. 261-273
    • Martinsen, E.S.1    Perkins, S.L.2    Schall, J.J.3
  • 40
    • 0032169951 scopus 로고    scopus 로고
    • Divergent evolutionary constraints on mitochondrial and nuclear genomes of malaria parasites
    • McIntosh, M. T., Srivasta, R. and Vaidya, A. B. (1998). Divergent evolutionary constraints on mitochondrial and nuclear genomes of malaria parasites. Molecular and Biochemical Parasitology 95, 69-80.
    • (1998) Molecular and Biochemical Parasitology , vol.95 , pp. 69-80
    • McIntosh, M.T.1    Srivasta, R.2    Vaidya, A.B.3
  • 42
    • 72449210137 scopus 로고    scopus 로고
    • Phylogeny of asian primate malarias inferred fromapicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile
    • Mitsui, H., Arisue, N., Sakihama, N., Inagaki, Y., Horii, T., Hasegawa, M., Tanabe, K. and Hashimoto, T. (2010). Phylogeny of Asian primate malarias inferred fromapicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile. Gene 450, 32-38.
    • (2010) Gene , vol.450 , pp. 32-38
    • Mitsui, H.1    Arisue, N.2    Sakihama, N.3    Inagaki, Y.4    Horii, T.5    Hasegawa, M.6    Tanabe, K.7    Hashimoto, T.8
  • 44
    • 0037130233 scopus 로고    scopus 로고
    • Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum
    • Mu, J., Duan, J., Markova, K., Joy, D., Huynh, C. Q., Branch, O. H., Li, W.-H. and Su, X. (2002). Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature 418, 323-326.
    • (2002) Nature , vol.418 , pp. 323-326
    • Mu, J.1    Duan, J.2    Markova, K.3    Joy, D.4    Huynh, C.Q.5    Branch, O.H.6    Li, W.-H.7    Su, X.8
  • 46
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei, M. and Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3, 418-426.
    • (1986) Molecular Biology and Evolution , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 49
    • 0036801380 scopus 로고    scopus 로고
    • A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences
    • Perkins, S. L. and Schall, J. J. (2002). A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. Journal of Parasitology 88, 972-978.
    • (2002) Journal of Parasitology , vol.88 , pp. 972-978
    • Perkins, S.L.1    Schall, J.J.2
  • 52
    • 0030208897 scopus 로고    scopus 로고
    • Phylogenetic relationship among the malaria parasites based on small subunit rRNA gene sequences: Monophyletic nature of the human malaria parasite, Plasmodium falciparum
    • Qari, S. H., Shi, Y. P., Pieniazek, N. J., Collins, W. E. and Lal, A. A. (1996). Phylogenetic relationship among the malaria parasites based on small subunit rRNA gene sequences: monophyletic nature of the human malaria parasite, Plasmodium falciparum. Molecular Phylogenetics and Evolution 6, 157-165.
    • (1996) Molecular Phylogenetics and Evolution , vol.6 , pp. 157-165
    • Qari, S.H.1    Shi, Y.P.2    Pieniazek, N.J.3    Collins, W.E.4    Lal, A.A.5
  • 54
    • 77954593415 scopus 로고    scopus 로고
    • A molecular clock for malaria parasites
    • Ricklefs, R. E. and Outlaw, D. C. (2010). A molecular clock for malaria parasites. Science 329, 226-229.
    • (2010) Science , vol.329 , pp. 226-229
    • Ricklefs, R.E.1    Outlaw, D.C.2
  • 55
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist, F. and Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 56
    • 44649136815 scopus 로고    scopus 로고
    • Origins of human malaria: Rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax
    • Roy, S.W. and Irimia, M. (2008). Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax. Molecular Biology and Evolution 25, 1192-1198.
    • (2008) Molecular Biology and Evolution , vol.25 , pp. 1192-1198
    • Roy, S.W.1    Irimia, M.2
  • 57
    • 0030773749 scopus 로고    scopus 로고
    • A nonparametric approach to estimating divergence timescales in the absence of rate constancy
    • Sanderson, M. J. (1997). A nonparametric approach to estimating divergence timescales in the absence of rate constancy. Molecular Biology and Evolution 15, 1218-1231.
    • (1997) Molecular Biology and Evolution , vol.15 , pp. 1218-1231
    • Sanderson, M.J.1
  • 58
    • 0026736562 scopus 로고
    • Phylogeny of Plasmodium species: Estimation and inference
    • Siddall, M. E. and Barta, J. R. (1992). Phylogeny of Plasmodium species: estimation and inference. Journal of Parasitology 78, 567-568.
    • (1992) Journal of Parasitology , vol.78 , pp. 567-568
    • Siddall, M.E.1    Barta, J.R.2
  • 59
    • 0032924868 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous substitution rates in diatoms: A comparison between chloroplast and nuclear genes
    • Sorhannus, U. and Fox, M. (1999). Synonymous and nonsynonymous substitution rates in diatoms: a comparison between chloroplast and nuclear genes. Journal of Molecular Evolution 48, 209-212.
    • (1999) Journal of Molecular Evolution , vol.48 , pp. 209-212
    • Sorhannus, U.1    Fox, M.2
  • 60
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. (2006). RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 61
    • 79951675256 scopus 로고    scopus 로고
    • Primates (Primates)
    • (ed. Hedges, S. B. and Kumar, S.), Oxford University Press, New York
    • Steiper, M. E. and Young, N. M. (2009). Primates (Primates) In The Timetree of Life (ed. Hedges, S. B. and Kumar, S.), pp. 482-486. Oxford University Press, New York.
    • (2009) The Timetree of Life , pp. 482-486
    • Steiper, M.E.1    Young, N.M.2
  • 62
    • 84990137020 scopus 로고
    • Forest and primate conservation in East Africa
    • Struhsaker, T. T. (1981). Forest and primate conservation in East Africa. African Journal of Ecology 19, 99-114.
    • (1981) African Journal of Ecology , vol.19 , pp. 99-114
    • Struhsaker, T.T.1
  • 63
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24, 1596-1599.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 64
    • 0027157960 scopus 로고
    • Estimation of the numberof nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura, K. and Nei, M. (1993). Estimation of the numberof nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10, 512-526.
    • (1993) Molecular Biology and Evolution , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 66
    • 0029100727 scopus 로고
    • Phylogenetic test of the molecular clock and linearized trees
    • Takezaki, N., Rzhetsky, A. and Nei, M. (1995). Phylogenetic test of the molecular clock and linearized trees. Molecular Biology and Evolution 12, 823-833.
    • (1995) Molecular Biology and Evolution , vol.12 , pp. 823-833
    • Takezaki, N.1    Rzhetsky, A.2    Nei, M.3
  • 67
    • 0035865322 scopus 로고    scopus 로고
    • A map of human genome sequence variation containing 1·42 million single nucleotide polymorphisms
    • The International SNP Map Working Group.
    • The International SNP Map Working Group. (2002). A map of human genome sequence variation containing 1·42 million single nucleotide polymorphisms. Nature 409, 928-933.
    • (2002) Nature , vol.409 , pp. 928-933
  • 68
    • 0027968068 scopus 로고
    • CLUSTAL W: Improvement of the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G. and Gibson, T. J. (1994). CLUSTAL W: improvement of the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 70
    • 0032822086 scopus 로고    scopus 로고
    • Drug resistance in Plasmodium falciparum malaria
    • Warhurst, D. C. (1999). Drug resistance in Plasmodium falciparum malaria. Infection 27, S55-S58.
    • (1999) Infection , vol.27
    • Warhurst, D.C.1
  • 71
    • 0026334859 scopus 로고
    • Plasmodium falciparum appears to have arisen as a result of lateral transfer between avian and human hosts
    • Waters, A. P., Higgins, D. G. and McCutchan, T. F. (1991). Plasmodium falciparum appears to have arisen as a result of lateral transfer between avian and human hosts. Proceedings of the National Academy of Sciences,USA88, 3140-3144.
    • (1991) Proceedings of the National Academy of Sciences,USA , vol.88 , pp. 3140-3144
    • Waters, A.P.1    Higgins, D.G.2    McCutchan, T.F.3
  • 73
    • 34249089649 scopus 로고    scopus 로고
    • Origins of major human infectious diseases
    • Wolfe, N. D., Dunavan, C. P. and Diamond, J. (2007). Origins of major human infectious diseases. Nature 447, 279-283.
    • (2007) Nature , vol.447 , pp. 279-283
    • Wolfe, N.D.1    Dunavan, C.P.2    Diamond, J.3
  • 74
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang, Z. (2007) PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24, 1586-1591.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 75
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang, Z. and Nielsen, R. (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution 17, 32-43.
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 76
    • 78651160766 scopus 로고
    • A study of Plasmodium berghei in Thamnomys surdaster, and in other experimental hosts
    • Yoeli, M. and Most, H. (1964). A study of Plasmodium berghei in Thamnomys surdaster, and in other experimental hosts. American Journal of Tropical Medicine and Hygiene 13, 659-663.
    • (1964) American Journal of Tropical Medicine and Hygiene , vol.13 , pp. 659-663
    • Yoeli, M.1    Most, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.