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Volumn 106, Issue 40, 2009, Pages 17077-17082

Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions

Author keywords

Alignment free genome comparison; Feature frequency profile (FFP); Mammalian phylogeny; Noncoding DNA; Nongenic regions of the genome

Indexed keywords

ALGORITHM; ANIMAL EXPERIMENT; ARTICLE; CHIMPANZEE; CONTROLLED STUDY; COW; EVOLUTIONARY ADAPTATION; EXON; GENE CONSTRUCT; GENOME; GENOME ANALYSIS; HOMOPLASY; HORSE; HUMAN; INTRON; MAMMAL; MONKEY; MOUSE; MUTATION RATE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RAT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EID: 70350131711     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0909377106     Document Type: Article
Times cited : (61)

References (48)
  • 3
    • 62449130191 scopus 로고    scopus 로고
    • Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
    • Sims GE, Jun SR, Wu GA, Kim SH (2009) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci USA 106:2677-2682.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 2677-2682
    • Sims, G.E.1    Jun, S.R.2    Wu, G.A.3    Kim, S.H.4
  • 4
    • 0242662461 scopus 로고    scopus 로고
    • Evolutionary discrimination of mammalian conserved nongenic sequences (CNGs)
    • Dermitzakis ET, et al. (2003) Evolutionary discrimination of mammalian conserved nongenic sequences (CNGs). Science 302:1033-1035.
    • (2003) Science , vol.302 , pp. 1033-1035
    • Dermitzakis, E.T.1
  • 5
    • 33646255212 scopus 로고    scopus 로고
    • Retroposed elements as archives for the evolutionary history of placental mammals
    • Kriegs JO, et al. (2006) Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol 4:e91.
    • (2006) PLoS Biol , vol.4
    • Kriegs, J.O.1
  • 7
    • 0034826388 scopus 로고    scopus 로고
    • Maximum likelihood analysis of the complete mitochondrial genomes eutherians and a reevaluation of the phylogeny of bats and insectivores
    • DOI 10.1007/s002390010241
    • Nikaido M, et al. (2001) Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevalution of the phylogeny of bats and insectivores. J Mol Evol 53:508-516. (Pubitemid 32889559)
    • (2001) Journal of Molecular Evolution , vol.53 , Issue.4-5 , pp. 508-516
    • Nikaido, M.1    Kawai, K.2    Cao, Y.3    Harada, M.4    Tomita, S.5    Okada, N.6    Hasegawa, M.7
  • 10
    • 38549137819 scopus 로고    scopus 로고
    • PhylomeDB: A database for genome-wide collections of gene phylogenies
    • DOI 10.1093/nar/gkm899
    • Huerta-Cepas J, Bueno A, Dopazo J, Gabaldon T (2008) PhylomeDB: A database for genome-wide collections of gene phylogenies. Nucleic Acids Res 36:D491-D496. (Pubitemid 351149772)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Huerta-Cepas, J.1    Bueno, A.2    Dopazo, J.3    Gabaldon, T.4
  • 11
    • 49749129961 scopus 로고    scopus 로고
    • Confirming the phylogeny ofmammalsby the use of large comparative sequence data sets
    • Prasad AB, AllardMW(2008) Confirming the phylogeny ofmammalsby the use of large comparative sequence data sets. Mol Biol Evol 25:1795-1808.
    • (2008) Mol Biol Evol , vol.25 , pp. 1795-1808
    • Prasad, A.B.1    Allard, M.W.2
  • 12
    • 58149178565 scopus 로고    scopus 로고
    • The UCSC genome browser database: 2008 update
    • Kuhn RM, et al. (2008) The UCSC genome browser database: 2008 update. Nucleic Acids Res 37:D755-D761.
    • (2008) Nucleic Acids Res , vol.37
    • Kuhn, R.M.1
  • 13
    • 0026458222 scopus 로고
    • Freeing phylogenies from artifacts of alignment
    • Thorne JL, Kishino H (1992) Freeing phylogenies from artifacts of alignment. Mol Biol Evol 9:1148-1162.
    • (1992) Mol Biol Evol , vol.9 , pp. 1148-1162
    • Thorne, J.L.1    Kishino, H.2
  • 16
    • 33847644967 scopus 로고    scopus 로고
    • Indel evolution of mammalian introns and the utility of noncoding nuclear markers in eutherian phylogenetics
    • Matthee CA, et al. (2007) Indel evolution of mammalian introns and the utility of noncoding nuclear markers in eutherian phylogenetics. Mol Phylogenet Evol 42:827-837.
    • (2007) Mol Phylogenet Evol , vol.42 , pp. 827-837
    • Matthee, C.A.1
  • 17
    • 0036853613 scopus 로고    scopus 로고
    • Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins
    • Poux C, van Rheede T,MadsenO, de JongWW(2002) Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins. Mol Biol Evol 19:2035-2037.
    • (2002) Mol Biol Evol , vol.19 , pp. 2035-2037
    • Poux, C.1    Van Rheede, T.2    Madsen, O.3    De Jong, W.W.4
  • 20
    • 23944505784 scopus 로고    scopus 로고
    • Aretroposon analysis of Afrotherian phylogeny
    • Nishihara H, et al. (2005)Aretroposon analysis of Afrotherian phylogeny. Mol Biol Evol 22:1823-1833.
    • (2005) Mol Biol Evol , vol.22 , pp. 1823-1833
    • Nishihara, H.1
  • 21
    • 0033964296 scopus 로고    scopus 로고
    • SINE insertions: Powerful tools for molecular systematics
    • DOI 10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z
    • ShedlockAM,OkadaN(2000) SINE insertions: Powerful tools for molecular systematics. Bioessays 22:148-160. (Pubitemid 30092081)
    • (2000) BioEssays , vol.22 , Issue.2 , pp. 148-160
    • Shedlock, A.M.1    Okada, N.2
  • 22
    • 0033793019 scopus 로고    scopus 로고
    • Rare genomic changes as a tool for phylogenetics
    • Rokas A, HollandPWH(2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 11:454-459.
    • (2000) Trends Ecol Evol , vol.11 , pp. 454-459
    • Rokas, A.1    Holland, P.W.H.2
  • 25
    • 0019951634 scopus 로고
    • Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences
    • DOI 10.1038/297197a0
    • Penny D, Foulds LR, Hendy MD (1982) Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297:197-200. (Pubitemid 12066444)
    • (1982) Nature , vol.297 , Issue.5863 , pp. 197-200
    • Penny, D.1    Foulds, L.R.2    Hendy, M.D.3
  • 28
    • 13144295005 scopus 로고    scopus 로고
    • Conserved non-genic sequences - An unexpected feature of mammalian genomes
    • DOI 10.1038/nrg1527
    • Dermitzakis ET, Reymond A, Antonarakis SE (2005) Conserved nongenic sequences: An unexpected feature of mammalian genomes. Nat Rev Genet 6:151-157. (Pubitemid 40179538)
    • (2005) Nature Reviews Genetics , vol.6 , Issue.2 , pp. 151-157
    • Dermitzakis, E.T.1    Reymond, A.2    Antonarakis, S.E.3
  • 30
    • 0141832717 scopus 로고    scopus 로고
    • Revisiting the Glires concept - Phylogenetic analysis of nuclear sequences
    • DOI 10.1016/S1055-7903(03)00079-4
    • Misawa K, Janke A (2003) Revisting the Glires concept - phylogenetic analysis of nuclear sequences. Mol Phylogenet Evol 28:320-327. (Pubitemid 37435997)
    • (2003) Molecular Phylogenetics and Evolution , vol.28 , Issue.2 , pp. 320-327
    • Misawa, K.1    Janke, A.2
  • 31
    • 66049158304 scopus 로고    scopus 로고
    • Breakpoint graphs and ancestral genome reconstructions
    • Max A. Alekseyev and Pavel A. Pevzner (2009) Breakpoint graphs and ancestral genome reconstructions. Genome Res 19: 943-957.
    • (2009) Genome Res , vol.19 , pp. 943-957
    • Alekseyev, M.A.1    Pevzner, P.A.2
  • 32
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410.
    • (1978) Syst Zool , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 33
    • 0033921902 scopus 로고    scopus 로고
    • Rates of conservation and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes
    • Zhang J (2000) Rates of conservation and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J Mol Evol 50:56-68.
    • (2000) J Mol Evol , vol.50 , pp. 56-68
    • Zhang, J.1
  • 36
    • 0004327233 scopus 로고
    • Johns Hopkins Univ Press, Baltimore, 5th Ed
    • Nowak, RM (1990) Walker's Mammals of the World (Johns Hopkins Univ Press, Baltimore), 5th Ed, Vol 1.
    • (1990) Walker's Mammals of the World , vol.1
    • Nowak, R.M.1
  • 37
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • DOI 10.1093/molbev/msh137
    • Phillips MJ, Delsuc F, Penny D (2004) Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 21:1455-1458. (Pubitemid 38823748)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.7 , pp. 1455-1458
    • Phillips, M.J.1    Delsuc, F.2    Penny, D.3
  • 38
    • 0025952777 scopus 로고
    • Archael phylogeny: Reexamination of the phylogenetic position of archaeoglobus fulgidus in light of certain composition-induced artifacts
    • Woese CR Achenbach L, Rouviere P, Madelco L (1991) Archael phylogeny: Reexamination of the phylogenetic position of archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst Appl Microbiol 14:364-371.
    • (1991) Syst Appl Microbiol , vol.14 , pp. 364-371
    • Woese, C.R.1    Achenbach, L.2    Rouviere, P.3    Madelco, L.4
  • 39
    • 0030829126 scopus 로고    scopus 로고
    • Effect of nucleotides excision repair on hprt gene mutations in rodent cells exposed to DNA ethylating agents
    • Op het Veld CW, Van Hees-Stuivenberg S, van Zeeland AA, Jansen JG (1997) Effect of nucleotides excision repair on hprt gene mutations in rodent cells exposed to DNA ethylating agents. Mutagenesis 12:417-424.
    • (1997) Mutagenesis , vol.12 , pp. 417-424
    • Op Het Veld, C.W.1    Van Hees-Stuivenberg, S.2    Van Zeeland, A.A.3    Jansen, J.G.4
  • 40
    • 0028343610 scopus 로고
    • Rate of transition and transversion in coding sequences since the human-rodent divergence
    • Collins DW, Jukes TH (1994) Rate of transition and transversion in coding sequences since the human-rodent divergence. Genomics 20:386-396.
    • (1994) Genomics , vol.20 , pp. 386-396
    • Collins, D.W.1    Jukes, T.H.2
  • 41
    • 0027500136 scopus 로고
    • Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis
    • Dixon MT, Hillis DM (1993) Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10:256-267. (Pubitemid 23040235)
    • (1993) Molecular Biology and Evolution , vol.10 , Issue.1 , pp. 256-267
    • Dixon, M.T.1    Hillis, D.M.2
  • 42
    • 33751039720 scopus 로고    scopus 로고
    • Bushes in the tree of life
    • Rokas A, Carroll SB (2006) Bushes in the tree of life. PLoS Biol 4: e352.
    • (2006) PLoS Biol , vol.4
    • Rokas, A.1    Carroll, S.B.2
  • 43
    • 54149110091 scopus 로고    scopus 로고
    • Distance conservation of transcription regulatory motifs in human promoters
    • Lu J, Luo L, Zhang Y (2008) Distance conservation of transcription regulatory motifs in human promoters. Comp Biol Chem 23:433-437.
    • (2008) Comp Biol Chem , vol.23 , pp. 433-437
    • Lu, J.1    Luo, L.2    Zhang, Y.3
  • 45
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny inference package
    • Version 3.2
    • Felsenstein J (1989) PHYLIP - Phylogeny inference package (Version 3.2). Cladistics 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 46
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 47
    • 0023375195 scopus 로고
    • The neighbor-joining method:Anewmethod for reconstructing phylogenetic trees
    • Saitou N, NeiM(1987) The neighbor-joining method:Anewmethod for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 48
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson DR, Foulds LR (1981) Comparison of phylogenetic trees. Math Biosci 53:131-147.
    • (1981) Math Biosci , vol.53 , pp. 131-147
    • Robinson, D.R.1    Foulds, L.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.