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Volumn 34, Issue 3-4, 2007, Pages 144-151

Understanding neutral genomic molecular clocks

Author keywords

Generation time effect; Molecular clock; Regional heterogeneity

Indexed keywords


EID: 67649428396     PISSN: 00713260     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11692-007-9010-7     Document Type: Article
Times cited : (7)

References (71)
  • 1
    • 0028220048 scopus 로고
    • Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
    • Akashi, H. (1994). Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy. Genetics, 136(3), 927-935.
    • (1994) Genetics , vol.136 , Issue.3 , pp. 927-935
    • Akashi, H.1
  • 3
    • 0035986891 scopus 로고    scopus 로고
    • Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution
    • Birdsell, J. A. (2002). Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Molecular Biology and Evolution, 19, 1181-1197.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 1181-1197
    • Birdsell, J.A.1
  • 4
    • 0034632812 scopus 로고    scopus 로고
    • Unexpectedly similar rates of nucleotide substitution found in male and female hominids
    • Bohossian, H. B., Skaletsky, H., & Page, D. C. (2000). Unexpectedly similar rates of nucleotide substitution found in male and female hominids. Nature, 406, 622-625.
    • (2000) Nature , vol.406 , pp. 622-625
    • Bohossian, H.B.1    Skaletsky, H.2    Page, D.C.3
  • 5
    • 0022534918 scopus 로고
    • Rates of DNA sequence evolution differ between taxonomic groups
    • Britten, R. J. (1986). Rates of DNA sequence evolution differ between taxonomic groups. Science, 231, 1393-1398.
    • (1986) Science , vol.231 , pp. 1393-1398
    • Britten, R.J.1
  • 8
    • 0036051359 scopus 로고    scopus 로고
    • Estimation of genetic distances from human and mouse introns
    • research
    • Castresana, J. (2002). Estimation of genetic distances from human and mouse introns. Genome Biology, 3(6), research0028.1-0028.7.
    • (2002) Genome Biology , vol.3 , Issue.6
    • Castresana, J.1
  • 9
    • 31144465926 scopus 로고    scopus 로고
    • Hearing silence: Non-neutral evolution at synonymous sites in mammals
    • Chamary, J. V., Parmley, J. L., & Hurst, L. D. (2006). Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nature Reviews Genetics, 7, 98-108.
    • (2006) Nature Reviews Genetics , vol.7 , pp. 98-108
    • Chamary, J.V.1    Parmley, J.L.2    Hurst, L.D.3
  • 11
    • 0035130163 scopus 로고    scopus 로고
    • Genomic divergence between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees
    • Chen, F. C., & Li, W.-H. (2001). Genomic divergence between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics, 68, 444-456.
    • (2001) American Journal of Human Genetics , vol.68 , pp. 444-456
    • Chen, F.C.1    Li, W.-H.2
  • 12
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    • Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., et al. (2005). Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308(5725), 1149-1154.
    • (2005) Science , vol.308 , Issue.5725 , pp. 1149-1154
    • Cheng, J.1    Kapranov, P.2    Drenkow, J.3    Dike, S.4    Brubaker, S.5    Patel, S.6
  • 13
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • Chimpanzee Sequencing and Analysis Consortium
    • Chimpanzee Sequencing and Analysis Consortium. (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437, 69-87.
    • (2005) Nature , vol.437 , pp. 69-87
  • 14
    • 18744395183 scopus 로고    scopus 로고
    • Numerous potentially functional but non-genic conserved sequences on human chromosome 21
    • Dermitzakis, E. T., Reymond, A., Lyle, R., Scamuffa, N., Ucla, C., Deutsch, S., et al. (2002). Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature, 420, 578-582.
    • (2002) Nature , vol.420 , pp. 578-582
    • Dermitzakis, E.T.1    Reymond, A.2    Lyle, R.3    Scamuffa, N.4    Ucla, C.5    Deutsch, S.6
  • 16
    • 0026086150 scopus 로고
    • The relative ratae of DNA evolution in primates
    • Easteal, S. (1991). The relative ratae of DNA evolution in primates. Molecular Biology and Evolution, 8(1), 115-127.
    • (1991) Molecular Biology and Evolution , vol.8 , Issue.1 , pp. 115-127
    • Easteal, S.1
  • 17
    • 0031252815 scopus 로고    scopus 로고
    • Male-driven evolution of DNA sequences in birds
    • Ellegren, H., & Fridolfsson, A. K. (1997). Male-driven evolution of DNA sequences in birds. Nature Genetics, 17, 182-184.
    • (1997) Nature Genetics , vol.17 , pp. 182-184
    • Ellegren, H.1    Fridolfsson, A.K.2
  • 18
    • 0024290622 scopus 로고
    • Why the rate of silent codon substitutions is variable within a vertebrate's genome
    • Filipski, J. (1988). Why the rate of silent codon substitutions is variable within a vertebrate's genome. Journal of Theoretical Biology, 134(2), 159-164.
    • (1988) Journal of Theoretical Biology , vol.134 , Issue.2 , pp. 159-164
    • Filipski, J.1
  • 19
    • 0034989085 scopus 로고    scopus 로고
    • Local rates of recombination are positively correlated with GC content in the human genome
    • Fullerton, S. M., Bernardo-Carvalho, A., & Clark, A. G. (2001). Local rates of recombination are positively correlated with GC content in the human genome. Molecular Biology and Evolution, 18(6), 1139-1142.
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.6 , pp. 1139-1142
    • Fullerton, S.M.1    Bernardo-Carvalho, A.2    Clark, A.G.3
  • 20
    • 0034766004 scopus 로고    scopus 로고
    • GC-content evolution in mammalian genomes: The biased gene conversion hypothesis
    • Galtier, N., Piganeau, G., Mouchiroud, D., & Duret, L. (2001). GC-content evolution in mammalian genomes: The biased gene conversion hypothesis. Genetics, 159, 907-911.
    • (2001) Genetics , vol.159 , pp. 907-911
    • Galtier, N.1    Piganeau, G.2    Mouchiroud, D.3    Duret, L.4
  • 21
    • 0001379254 scopus 로고
    • The role of immunologic differences in the phyletic development of human behavior
    • Goodman, M. (1961). The role of immunologic differences in the phyletic development of human behavior. Human Biology, 33, 131-162.
    • (1961) Human Biology , vol.33 , pp. 131-162
    • Goodman, M.1
  • 22
    • 0001244028 scopus 로고
    • Evolution of the immunologic species specificity of human serum proteins
    • Goodman, M. (1962). Evolution of the immunologic species specificity of human serum proteins. Human Biology, 34, 104-150.
    • (1962) Human Biology , vol.34 , pp. 104-150
    • Goodman, M.1
  • 23
    • 0026911443 scopus 로고
    • Higher rates of amino acid substitution in rodents than in humans
    • Gu, X., & Li, W.-H. (1992). Higher rates of amino acid substitution in rodents than in humans. Molecular Phylogenetics and Evolution, 1(3), 211-214.
    • (1992) Molecular Phylogenetics and Evolution , vol.1 , Issue.3 , pp. 211-214
    • Gu, X.1    Li, W.-H.2
  • 26
    • 34547753508 scopus 로고    scopus 로고
    • Rates of genome evolution and branching order from whole genome analysis
    • Huttley, G. A., Wakefield, M. J., & Easteal, S. (2007). Rates of genome evolution and branching order from whole genome analysis. Molecular Biology and Evolution, 24, 1772-1730.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1772-1730
    • Huttley, G.A.1    Wakefield, M.J.2    Easteal, S.3
  • 28
    • 0034795550 scopus 로고    scopus 로고
    • Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex
    • Jeffreys, A. J., Kauppi, L., & Neumann, R. (2001). Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genetics, 29, 217-222.
    • (2001) Nature Genetics , vol.29 , pp. 217-222
    • Jeffreys, A.J.1    Kauppi, L.2    Neumann, R.3
  • 30
    • 0035839057 scopus 로고    scopus 로고
    • The role of DNA methylation in mammalian epigenetics
    • Jones, P. A., & Takai, D. (2001). The role of DNA methylation in mammalian epigenetics. Science, 293, 1068-1070.
    • (2001) Science , vol.293 , pp. 1068-1070
    • Jones, P.A.1    Takai, D.2
  • 31
    • 15744388330 scopus 로고    scopus 로고
    • Evidence for widespread degradation of gene control regions in hominoid genomes
    • Keightley, P. D., Lercher, M. J., & Eyre-Walker, A. (2005). Evidence for widespread degradation of gene control regions in hominoid genomes. PLoS Biology, 3, e42.
    • (2005) PLoS Biology , vol.3
    • Keightley, P.D.1    Lercher, M.J.2    Eyre-Walker, A.3
  • 34
    • 0014831951 scopus 로고
    • Evolution of higher-organism DNA
    • Kohne, C. (1970). Evolution of higher-organism DNA. Quarterly Reviews of Biophysics, 3, 327-375.
    • (1970) Quarterly Reviews of Biophysics , vol.3 , pp. 327-375
    • Kohne, C.1
  • 35
    • 33644636376 scopus 로고    scopus 로고
    • Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites
    • Kondrashov, F. A., Ogurtsov, A. Y., & Kondrashov, A. S. (2006). Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology, 240, 616-626.
    • (2006) Journal of Theoretical Biology , vol.240 , pp. 616-626
    • Kondrashov, F.A.1    Ogurtsov, A.Y.2    Kondrashov, A.S.3
  • 37
    • 22944437097 scopus 로고    scopus 로고
    • Molecular clocks: Four decades of evolution
    • Kumar, S. (2005). Molecular clocks: Four decades of evolution. Nature Reviews Genetics, 6, 654-662.
    • (2005) Nature Reviews Genetics , vol.6 , pp. 654-662
    • Kumar, S.1
  • 39
    • 0014671880 scopus 로고
    • Rate of fixation of nucleotide substitutions in evolution
    • Laird, C. D., McConaughy, B. L., & McCarthy, B. J. (1969). Rate of fixation of nucleotide substitutions in evolution. Nature, 224, 149-154.
    • (1969) Nature , vol.224 , pp. 149-154
    • Laird, C.D.1    McConaughy, B.L.2    McCarthy, B.J.3
  • 40
    • 0036640951 scopus 로고    scopus 로고
    • Human SNP variability and mutation rate are higher in regions of high recombination
    • Lercher, M. J., & Hurst, L. D. (2002). Human SNP variability and mutation rate are higher in regions of high recombination. Trends in Genetics, 18(7), 337-340.
    • (2002) Trends in Genetics , vol.18 , Issue.7 , pp. 337-340
    • Lercher, M.J.1    Hurst, L.D.2
  • 42
    • 0036733675 scopus 로고    scopus 로고
    • Chromatin modification and epigenetic reprogramming in mammalian development
    • Li, E. (2002). Chromatin modification and epigenetic reprogramming in mammalian development. Nature Reviews Genetics, 3, 662-673.
    • (2002) Nature Reviews Genetics , vol.3 , pp. 662-673
    • Li, E.1
  • 44
    • 0023074036 scopus 로고
    • An evaluation of the molecular clock hypothesis using mammalian DNA sequences
    • Li, W.-H., Tanimura, M., & Sharp, P. M. (1987). An evaluation of the molecular clock hypothesis using mammalian DNA sequences. Journal of Molecular Evolution, 25, 330-342.
    • (1987) Journal of Molecular Evolution , vol.25 , pp. 330-342
    • Li, W.-H.1    Tanimura, M.2    Sharp, P.M.3
  • 46
    • 0037061501 scopus 로고    scopus 로고
    • Strong male-driven evolution of DNA sequences in humans and apes
    • Makova, K. D., & Li, W.-H. (2002). Strong male-driven evolution of DNA sequences in humans and apes. Nature, 416, 624-626.
    • (2002) Nature , vol.416 , pp. 624-626
    • Makova, K.D.1    Li, W.-H.2
  • 48
    • 2142773942 scopus 로고    scopus 로고
    • The fine-scale structure of recombination rate variation in the human genome
    • McVean, G. A. T., Myers, S. R., Hunt, S., Deloukas, P., Bentley, D. R., & Donnelly, P. (2004). The fine-scale structure of recombination rate variation in the human genome. Science, 304, 581-584.
    • (2004) Science , vol.304 , pp. 581-584
    • McVean, G.A.T.1    Myers, S.R.2    Hunt, S.3    Deloukas, P.4    Bentley, D.R.5    Donnelly, P.6
  • 49
    • 2442651458 scopus 로고    scopus 로고
    • Recombination drives the evolution of GC-content in the human genome
    • Meunier, J., & Duret, L. (2004). Recombination drives the evolution of GC-content in the human genome. Molecular Biology and Evolution, 21(6), 984-990.
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.6 , pp. 984-990
    • Meunier, J.1    Duret, L.2
  • 50
    • 0037372234 scopus 로고    scopus 로고
    • Recombination explains isochores in mammalian genomes
    • Montoya-Burgos, J. I., Boursot, P., & Galtier, N. (2003). Recombination explains isochores in mammalian genomes. Trends in Genetics, 19, 128-130.
    • (2003) Trends in Genetics , vol.19 , pp. 128-130
    • Montoya-Burgos, J.I.1    Boursot, P.2    Galtier, N.3
  • 51
    • 0035861441 scopus 로고    scopus 로고
    • Resoluion of the early placental mammal radiation using Bayesian phylogenetics
    • Murphy, W. J., Eizirik, E., O'Brien, S. J., Madsen, O., Scally, M., Douady, C. J., et al. (2001). Resoluion of the early placental mammal radiation using Bayesian phylogenetics. Science, 294, 2348-2351.
    • (2001) Science , vol.294 , pp. 2348-2351
    • Murphy, W.J.1    Eizirik, E.2    O'Brien, S.J.3    Madsen, O.4    Scally, M.5    Douady, C.J.6
  • 52
    • 26844482093 scopus 로고    scopus 로고
    • A fine-scale map of recombination rates and hotspots across the human genome
    • Oct. 14
    • Myers, S., Bottolo, L., Frreeman, C., McVean, G., & Donnelly, P. (2005). A fine-scale map of recombination rates and hotspots across the human genome. Science, 310(Oct. 14), 321-324.
    • (2005) Science , vol.310 , pp. 321-324
    • Myers, S.1    Bottolo, L.2    Frreeman, C.3    McVean, G.4    Donnelly, P.5
  • 53
    • 0033828761 scopus 로고    scopus 로고
    • Estimate of the mutation rate per nucleotide in humans
    • Nachman, M. W., & Crowell, S. L. (2000). Estimate of the mutation rate per nucleotide in humans. Genetics, 156(1), 297-304.
    • (2000) Genetics , vol.156 , Issue.1 , pp. 297-304
    • Nachman, M.W.1    Crowell, S.L.2
  • 54
    • 33745591114 scopus 로고    scopus 로고
    • Genetic evidence for complex speciation of humans and chimpanzees
    • Patterson, N., Richter, D. J., Gnerre, S., Lander, E. S., & Reich, D. (2006). Genetic evidence for complex speciation of humans and chimpanzees. Nature, 441, 1103-1108.
    • (2006) Nature , vol.441 , pp. 1103-1108
    • Patterson, N.1    Richter, D.J.2    Gnerre, S.3    Lander, E.S.4    Reich, D.5
  • 55
    • 0033539159 scopus 로고    scopus 로고
    • Evolutionary rate of a gene affected by chromosomal position
    • Perry, J., & Ashworth, A. (1999). Evolutionary rate of a gene affected by chromosomal position. Current Biology, 9, 987-989.
    • (1999) Current Biology , vol.9 , pp. 987-989
    • Perry, J.1    Ashworth, A.2
  • 56
    • 33748675254 scopus 로고    scopus 로고
    • An RNA gene expressed during cortical development evolved rapidly in humans
    • Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., et al. (2006). An RNA gene expressed during cortical development evolved rapidly in humans. Nature, 443, 167-172.
    • (2006) Nature , vol.443 , pp. 167-172
    • Pollard, K.S.1    Salama, S.R.2    Lambert, N.3    Lambot, M.-A.4    Coppens, S.5    Pedersen, J.S.6
  • 57
    • 16844377748 scopus 로고    scopus 로고
    • Fine-scale recombination patterns differ between chimpanzees and humans
    • Ptak, S. E., Hinds, D. A., Koehler, K., Nickel, B., Patil, N., Ballinger, D. G., et al. (2005). Fine-scale recombination patterns differ between chimpanzees and humans. Nature Genetics, 37(4), 429-434.
    • (2005) Nature Genetics , vol.37 , Issue.4 , pp. 429-434
    • Ptak, S.E.1    Hinds, D.A.2    Koehler, K.3    Nickel, B.4    Patil, N.5    Ballinger, D.G.6
  • 58
    • 0034253791 scopus 로고    scopus 로고
    • A genetic linkage map of the baboon (Papio hamadryas) genome based on human microsatellite polymorphisms
    • Rogers, J., Mahaney, M. C., et al. (2000). A genetic linkage map of the baboon (Papio hamadryas) genome based on human microsatellite polymorphisms. Genomics, 67, 237-247.
    • (2000) Genomics , vol.67 , pp. 237-247
    • Rogers, J.1    Mahaney, M.C.2
  • 59
    • 0014186296 scopus 로고
    • Immunological tie scale for hominid evolution
    • Sarich, V. M., & Wilson, A. C. (1967). Immunological tie scale for hominid evolution. Science, 158, 1200-1203.
    • (1967) Science , vol.158 , pp. 1200-1203
    • Sarich, V.M.1    Wilson, A.C.2
  • 60
    • 1942454210 scopus 로고    scopus 로고
    • Evidence that functional transcription units cover at least half of the human genome
    • Semon, M., & Duret, L. (2004). Evidence that functional transcription units cover at least half of the human genome. Trends in Genetics, 20, 229-232.
    • (2004) Trends in Genetics , vol.20 , pp. 229-232
    • Semon, M.1    Duret, L.2
  • 61
    • 0027286244 scopus 로고
    • Male-driven evolution of DNA sequences
    • Shimmin, L. C., Chang, B. H., & Li, W.-H. (1993). Male-driven evolution of DNA sequences. Nature, 362, 745-747.
    • (1993) Nature , vol.362 , pp. 745-747
    • Shimmin, L.C.1    Chang, B.H.2    Li, W.-H.3
  • 64
    • 0038781903 scopus 로고    scopus 로고
    • Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes
    • Subramanian, S., & Kumar, S. (2003). Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Research, 13, 838-844.
    • (2003) Genome Research , vol.13 , pp. 838-844
    • Subramanian, S.1    Kumar, S.2
  • 65
    • 20144387806 scopus 로고    scopus 로고
    • Comparison of fine-scale recombination rates in humans and chimpanzees
    • Winckler, W., Myers, S. R., Richter, D. J., Onofrio, R. C., McDonald, G. J., Bontrop, R. E., et al. (2005). Comparison of fine-scale recombination rates in humans and chimpanzees. Science, 308(5718), 107-111.
    • (2005) Science , vol.308 , Issue.5718 , pp. 107-111
    • Winckler, W.1    Myers, S.R.2    Richter, D.J.3    Onofrio, R.C.4    McDonald, G.J.5    Bontrop, R.E.6
  • 66
    • 0024497416 scopus 로고
    • Mutation rates differ among regions of the mammalian genome
    • Wolfe, K. H., Sharp, P. M., & Li, W.-H. (1989). Mutation rates differ among regions of the mammalian genome. Nature, 337, 283-285.
    • (1989) Nature , vol.337 , pp. 283-285
    • Wolfe, K.H.1    Sharp, P.M.2    Li, W.-H.3
  • 68
    • 0036897666 scopus 로고    scopus 로고
    • Slow molecular clocks in Old World monkeys, apes, and humans
    • Yi, S., Ellsworth, D. L., & Li, W.-H. (2002). Slow molecular clocks in Old World monkeys, apes, and humans. Molecular Biology and Evolution, 19(12), 2191-2198.
    • (2002) Molecular Biology and Evolution , vol.19 , Issue.12 , pp. 2191-2198
    • Yi, S.1    Ellsworth, D.L.2    Li, W.-H.3
  • 69
    • 17744373084 scopus 로고    scopus 로고
    • Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids
    • Yi, S., & Li, W.-H. (2005). Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids. Molecular Biology and Evolution, 22, 1223-1230.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 1223-1230
    • Yi, S.1    Li, W.-H.2
  • 70
    • 0346505475 scopus 로고    scopus 로고
    • Recombination has little effect on the rate of sequence divergence in pseudoausotomal boundary 1 among humans and great apes
    • Yi, S., Summers, T. J., Pearson, N. M., & Li, W.-H. (2004). Recombination has little effect on the rate of sequence divergence in pseudoausotomal boundary 1 among humans and great apes. Genome Research, 14, 37-43.
    • (2004) Genome Research , vol.14 , pp. 37-43
    • Yi, S.1    Summers, T.J.2    Pearson, N.M.3    Li, W.-H.4
  • 71
    • 0002331493 scopus 로고
    • Molecular disease, evolution, and genetic heterogeneity
    • In M. Kasha & B. Pullman (Eds.), New York: Academic Press
    • Zuckerkandl, E., & Pauling, L. B. (1962). Molecular disease, evolution, and genetic heterogeneity. In M. Kasha & B. Pullman (Eds.), Horizons in biochemistry (pp. 189-225). New York: Academic Press.
    • (1962) Horizons in Biochemistry , pp. 189-225
    • Zuckerkandl, E.1    Pauling, L.B.2


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