메뉴 건너뛰기




Volumn 52, Issue 5, 2003, Pages 705-716

Comparison of Likelihood and Bayesian Methods for Estimating Divergence Times Using Multiple Gene Loci and Calibration Points, with Application to a Radiation of Cute-Looking Mouse Lemur Species

Author keywords

Bayes method; Divergence times; Evolutionary rate; Local molecular clock; Maximum likelihood; Molecular clock

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; PROSIMIAN; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

EID: 0242571576     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150390235557     Document Type: Article
Times cited : (253)

References (42)
  • 1
    • 0036804729 scopus 로고    scopus 로고
    • Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny
    • ARIS-BROSOU, S., AND Z. YANG. 2002. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst. Biol. 51:703-714.
    • (2002) Syst. Biol. , vol.51 , pp. 703-714
    • Aris-Brosou, S.1    Yang, Z.2
  • 3
    • 0034944642 scopus 로고    scopus 로고
    • The inference of stepwise changes in substitution rates using serial sequence samples
    • DRUMMOND, A., R. FORSBERG, AND A. G. RODRIGO. 2001. The inference of stepwise changes in substitution rates using serial sequence samples. Mol. Biol. Evol. 18:1365-1371.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1365-1371
    • Drummond, A.1    Forsberg, R.2    Rodrigo, A.G.3
  • 4
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 6
    • 0000864568 scopus 로고    scopus 로고
    • Carnivoran phylogeny and rates of evolution: Morphological, taxic, and molecular
    • (J. Gittleman, ed.). Cornell Univ. Press, Ithaca, New York
    • FLYNN, J. J. 1996. Carnivoran phylogeny and rates of evolution: Morphological, taxic, and molecular. Pages 542-581 in Carnivore behavior, ecology, and evolution (J. Gittleman, ed.). Cornell Univ. Press, Ithaca, New York.
    • (1996) Carnivore Behavior, Ecology, and Evolution , pp. 542-581
    • Flynn, J.J.1
  • 8
    • 0000236012 scopus 로고
    • Time of origin of primates
    • GINGERICH, P. D., AND M. D. UHEN. 1994. Time of origin of primates. J. Hum. Evol. 27:443-445.
    • (1994) J. Hum. Evol. , vol.27 , pp. 443-445
    • Gingerich, P.D.1    Uhen, M.D.2
  • 9
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • GOLDMAN, N., AND Z. YANG . 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 10
    • 0034077901 scopus 로고    scopus 로고
    • A compound Poisson process for relaxing the molecular clock
    • HUELSENBECK, J. P., B. LARGET, AND D. SWOFFORD. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879-1892.
    • (2000) Genetics , vol.154 , pp. 1879-1892
    • Huelsenbeck, J.P.1    Larget, B.2    Swofford, D.3
  • 12
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • (H. N. Munro, ed.). Academic Press, New York
    • JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-123 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-123
    • Jukes, T.H.1    Cantor, C.R.2
  • 13
    • 0025307631 scopus 로고
    • Converting distance to time: Application to human evolution
    • KISHINO, H., AND M. Hasegawa. 1990. Converting distance to time: Application to human evolution. Methods Enzymol. 183:550-570.
    • (1990) Methods Enzymol. , vol.183 , pp. 550-570
    • Kishino, H.1    Hasegawa, M.2
  • 14
    • 0035103260 scopus 로고    scopus 로고
    • Performance of a divergence time estimation method under a probabilistic model of rate evolution
    • KISHINO, H., J. L. THORNE, AND W. J. BRUNO. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 352-361
    • Kishino, H.1    Thorne, J.L.2    Bruno, W.J.3
  • 15
    • 0029960344 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates
    • KUMAR, S. 1996. Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537-548.
    • (1996) Genetics , vol.143 , pp. 537-548
    • Kumar, S.1
  • 16
    • 0002740659 scopus 로고
    • A preliminary field-study of the lesser mouse lemur (Microcebus murinus)
    • MARTIN, R. D. 1972. A preliminary field-study of the lesser mouse lemur (Microcebus murinus). Z. Tierpsychol. Suppl. 9:43-89.
    • (1972) Z. Tierpsychol. Suppl. , vol.9 , pp. 43-89
    • Martin, R.D.1
  • 17
    • 0027340263 scopus 로고
    • Primate origins: Plugging the gaps
    • MARTIN, R. D. 1993. Primate origins: Plugging the gaps. Nature 363:223-234.
    • (1993) Nature , vol.363 , pp. 223-234
    • Martin, R.D.1
  • 18
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • MUSE, S. V., AND B. S. GAUT. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 20
    • 0034044313 scopus 로고    scopus 로고
    • Estimating the rate of molecular evolution: Incorporating non-comptemporaneous sequences into maximum likelihood phylogenetics
    • RAMBAUT, A. 2000. Estimating the rate of molecular evolution: Incorporating non-comptemporaneous sequences into maximum likelihood phylogenetics. Bioinformatics 16:395-399.
    • (2000) Bioinformatics , vol.16 , pp. 395-399
    • Rambaut, A.1
  • 21
    • 0031966291 scopus 로고    scopus 로고
    • Estimating divergence dates from molecular sequences
    • RAMBAUT, A., AND L. BROMHAM. 1998. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15:442-448.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 442-448
    • Rambaut, A.1    Bromham, L.2
  • 22
    • 0034530962 scopus 로고    scopus 로고
    • Taxonomic revision of mouse lemurs (Microcebus) in the western portions of Madagascar
    • RASOLOARISON, R. M., S. M. GOODMAN, AND J. U. GANZHORN. 2000. Taxonomic revision of mouse lemurs (Microcebus) in the western portions of Madagascar. Int. J. Primatol. 21:963-1019.
    • (2000) Int. J. Primatol. , vol.21 , pp. 963-1019
    • Rasoloarison, R.M.1    Goodman, S.M.2    Ganzhorn, J.U.3
  • 23
    • 0030773749 scopus 로고    scopus 로고
    • A nonparametric approach to estimating divergence times in the absence of rate constancy
    • SANDERSON, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1232.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 1218-1232
    • Sanderson, M.J.1
  • 24
    • 0036135468 scopus 로고    scopus 로고
    • Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach
    • SANDERSON, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 101-109
    • Sanderson, M.J.1
  • 28
    • 0035527373 scopus 로고    scopus 로고
    • Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?
    • SULLIVAN, J., AND D. L. SWOFFORD. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-729.
    • (2001) Syst. Biol. , vol.50 , pp. 723-729
    • Sullivan, J.1    Swofford, D.L.2
  • 29
    • 0029100727 scopus 로고
    • Phylogenetic test of the molecular clock and linearized trees
    • TAKEZAKI, N., A. RZHETSKY, AND M. NEI. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 823-833
    • Takezaki, N.1    Rzhetsky, A.2    Nei, M.3
  • 30
    • 0037129204 scopus 로고    scopus 로고
    • Using the fossil record to estimate the age of the last common ancestor of extant primates
    • TAVARÉ, S., C. R. MARSHALL, O. WILL, C. SOLIGOS, ET AL. 2002. Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature 416:726-729.
    • (2002) Nature , vol.416 , pp. 726-729
    • Tavaré, S.1    Marshall, C.R.2    Will, O.3    Soligos, C.4
  • 31
    • 0000731302 scopus 로고
    • Phylogenetic aspects of cetacean origins: A morphological perspective
    • THEWISSEN, J. G. M. 1994. Phylogenetic aspects of cetacean origins: A morphological perspective. J. Mammal. Evol. 2:157-184.
    • (1994) J. Mammal. Evol. , vol.2 , pp. 157-184
    • Thewissen, J.G.M.1
  • 32
    • 0036803223 scopus 로고    scopus 로고
    • Divergence time and evolutionary rate estimation with multilocus data
    • THORNE, J. L., AND H. KISHINO. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689-702.
    • (2002) Syst. Biol. , vol.51 , pp. 689-702
    • Thorne, J.L.1    Kishino, H.2
  • 33
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rate of evolution of the rate of molecular evolution
    • THORNE, J. L., H. KISHINO, AND I. S. PAINTER. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 34
    • 0035339920 scopus 로고    scopus 로고
    • Molecular phylogenetics: State of the art methods for looking into the past
    • WHELAN, S., P. LIÒ, AND N. GOLDMAN. 2001. Molecular phylogenetics: State of the art methods for looking into the past. Trends Genet. 17:262-272.
    • (2001) Trends Genet. , vol.17 , pp. 262-272
    • Whelan, S.1    Liò, P.2    Goldman, N.3
  • 35
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • YANG, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 36
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • YANG, Z. 1996a. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:367-372.
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
    • Yang, Z.1
  • 37
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • YANG, Z. 1996b. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
    • (1996) J. Mol. Evol. , vol.42 , pp. 587-596
    • Yang, Z.1
  • 38
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • YANG, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556 (http://abacus.gene.ucl.ac. uk/software/paml.html).
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 39
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
    • YANG, Z., N. GOLDMAN, AND A. FRIDAY. 1994. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11:316-324.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.3
  • 40
    • 0034633713 scopus 로고    scopus 로고
    • Remarkable species diversity in Malagasy mouse lemurs (Primates, Microcebus)
    • YODER, A. D., R. M. RASOLOARISON, S. M. GOODMAN, J. A. IRWIN, ET AL. 2000. Remarkable species diversity in Malagasy mouse lemurs (Primates, Microcebus). Proc. Natl. Acad. Sci. USA 97:11325-11330.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 11325-11330
    • Yoder, A.D.1    Rasoloarison, R.M.2    Goodman, S.M.3    Irwin, J.A.4
  • 41
    • 0033933640 scopus 로고    scopus 로고
    • Estimation of primate speciation dates using local molecular clocks
    • YODER, A. D., AND Z. YANG. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17:1081-1090.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1081-1090
    • Yoder, A.D.1    Yang, Z.2
  • 42
    • 0001895697 scopus 로고
    • Evolutionary divergence and convergence in proteins
    • (V. Bryson and H. J. Vogel, eds.). Academic Press, New York
    • ZUCKERKANDL, E., AND L. PAULING. 1965. Evolutionary divergence and convergence in proteins. Pages 97-166 in Evolving genes and proteins (V. Bryson and H. J. Vogel, eds.). Academic Press, New York.
    • (1965) Evolving Genes and Proteins , pp. 97-166
    • Zuckerkandl, E.1    Pauling, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.