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Volumn 49, Issue 4, 2000, Pages 617-627

Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis

Author keywords

Character evolution; Consistency; Homoplasy; Transitions; Transversions; Weighted parsimony

Indexed keywords

ARTICLE; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY;

EID: 0034351389     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351500750049734     Document Type: Article
Times cited : (62)

References (40)
  • 1
    • 0020670470 scopus 로고
    • Human mitochondrial DNA variation and evolution: Analysis of nucleotide sequences from seven individuals
    • AQUADRO, C. F., AND B. D. GREENBERG. 1983. Human mitochondrial DNA variation and evolution: Analysis of nucleotide sequences from seven individuals. Genetics 103:287-312.
    • (1983) Genetics , vol.103 , pp. 287-312
    • Aquadro, C.F.1    Greenberg, B.D.2
  • 2
    • 0000142029 scopus 로고    scopus 로고
    • Measures of homoplasy
    • (M. J. Sanderson and L. Hufford, eds.). Academic Press, New York
    • ARCHIE, J. W. 1996. Measures of homoplasy. Pages 153-188 in Homoplasy, the recurrence of similarity in evolution (M. J. Sanderson and L. Hufford, eds.). Academic Press, New York.
    • (1996) Homoplasy, the Recurrence of Similarity in Evolution , pp. 153-188
    • Archie, J.W.1
  • 3
    • 0020328686 scopus 로고
    • Mitochondrial DNA sequences of primates: Tempo and mode of evolution
    • BROWN, W. M., E. M. PRAGER, A. WANG, AND A. C. WILSON. 1982. Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J. Mol. Evol. 18:225-239.
    • (1982) J. Mol. Evol. , vol.18 , pp. 225-239
    • Brown, W.M.1    Prager, E.M.2    Wang, A.3    Wilson, A.C.4
  • 4
    • 0029096506 scopus 로고
    • Sampling properties of DNA sequence data in phylogenetic analysis
    • CUMMINGS, M. P., S. P. OTTO, AND J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-22.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 814-822
    • Cummings, M.P.1    Otto, S.P.2    Wakeley, J.3
  • 5
    • 0023478742 scopus 로고
    • Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila
    • DESALLE, R., T. FREEDMAN, E. M. PRAGER, AND A. C. WILSON. 1987. Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila. J. Mol. Evol. 26:157-164.
    • (1987) J. Mol. Evol. , vol.26 , pp. 157-164
    • Desalle, R.1    Freedman, T.2    Prager, E.M.3    Wilson, A.C.4
  • 6
    • 84963028421 scopus 로고
    • A successive approximations approach to character weighting
    • FARRIS, J. S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18:374-385.
    • (1969) Syst. Zool. , vol.18 , pp. 374-385
    • Farris, J.S.1
  • 7
    • 0001306645 scopus 로고
    • A likelihood approach to character weighting and what it tells us about parsimony and compatibility
    • FELSENSTEIN, J. 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol. J. Linn. Soc. 16:183-196.
    • (1981) Biol. J. Linn. Soc. , vol.16 , pp. 183-196
    • Felsenstein, J.1
  • 8
    • 0014219557 scopus 로고
    • Evidence suggesting a non-random character to nucleotide replacements in naturally occurring mutations
    • FITCH, W. M. 1967. Evidence suggesting a non-random character to nucleotide replacements in naturally occurring mutations. J. Mol. Biol. 26:499-507.
    • (1967) J. Mol. Biol. , vol.26 , pp. 499-507
    • Fitch, W.M.1
  • 9
    • 0002212559 scopus 로고
    • Weighted parsimony: Does it work?
    • (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York
    • FITCH, W. M., AND J. YE. 1991. Weighted parsimony: Does it work? Pages 147-154 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
    • (1991) Phylogenetic Analysis of DNA Sequences , pp. 147-154
    • Fitch, W.M.1    Ye, J.2
  • 10
    • 0005705790 scopus 로고
    • Estimating character weights during tree search
    • GOLOBOFF, P. A. 1993. Estimating character weights during tree search. Cladistics 9:83-91.
    • (1993) Cladistics , vol.9 , pp. 83-91
    • Goloboff, P.A.1
  • 11
    • 0032127857 scopus 로고    scopus 로고
    • The 'evolutionary signal' of homoplasy in protein-coding gene sequences and its consequences for a priori weighting in phylogeny
    • HASSANIN, A., G. LECOINTRE, AND S. TILLIER. 1998. The 'evolutionary signal' of homoplasy in protein-coding gene sequences and its consequences for a priori weighting in phylogeny. C. R. Acad. Sci. Paris, Sciences de la vie 321:611-620.
    • (1998) C. R. Acad. Sci. Paris, Sciences de la Vie , vol.321 , pp. 611-620
    • Hassanin, A.1    Lecointre, G.2    Tillier, S.3
  • 12
    • 0031729578 scopus 로고    scopus 로고
    • Nucleotide substitution models and estimation of phylogeny
    • HÅSTAD, O., AND M. BJÖRKLUND. 1998. Nucleotide substitution models and estimation of phylogeny. Mol. Biol. Evol. 15:1381-1389.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1381-1389
    • Håstad, O.1    Björklund, M.2
  • 13
    • 0028362880 scopus 로고
    • Application and accuracy of molecular phylogenies
    • HILLIS, D. M., J. P. HUELSENBECK, AND C. W. CUNNINGHAM. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
    • (1994) Science , vol.264 , pp. 671-677
    • Hillis, D.M.1    Huelsenbeck, J.P.2    Cunningham, C.W.3
  • 14
    • 0020960762 scopus 로고
    • Transitions and transversions in evolutionary descent: An approach to understanding
    • HOLMQUIST, R. 1983. Transitions and transversions in evolutionary descent: An approach to understanding. J. Mol. Evol. 19:134-144.
    • (1983) J. Mol. Evol. , vol.19 , pp. 134-144
    • Holmquist, R.1
  • 15
    • 0025764044 scopus 로고
    • Evolution of the cytochrome b gene of mammals
    • IRWIN, D. M., T. D. KOCHER, AND A. C. WILSON. 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32:128-144.
    • (1991) J. Mol. Evol. , vol.32 , pp. 128-144
    • Irwin, D.M.1    Kocher, T.D.2    Wilson, A.C.3
  • 16
    • 0029000323 scopus 로고
    • Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA
    • JERMIIN, L. S., D. GRAUR, AND R. H. CROZIER. 1995. Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA. Mol. Biol. Evol. 12:558-563.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 558-563
    • Jermiin, L.S.1    Graur, D.2    Crozier, R.H.3
  • 17
    • 0032773940 scopus 로고    scopus 로고
    • Homoplasy increases phylogenetic structure
    • KÄLLERSJÖ, M., V. A. ALBERT, AND J. S. FARRIS. 1999. Homoplasy increases phylogenetic structure. Cladistics 15:91-93.
    • (1999) Cladistics , vol.15 , pp. 91-93
    • Källersjö, M.1    Albert, V.A.2    Farris, J.S.3
  • 19
    • 0001516337 scopus 로고
    • Rapid cladogenesis among the percoran ruminants: Evidence from mitochondrial DNA sequences
    • KRAUS, F., AND M. M. MIYAMOTO. 1991. Rapid cladogenesis among the percoran ruminants: Evidence from mitochondrial DNA sequences. Syst. Zool. 40:117-130.
    • (1991) Syst. Zool. , vol.40 , pp. 117-130
    • Kraus, F.1    Miyamoto, M.M.2
  • 20
    • 0021710490 scopus 로고
    • Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications
    • LI, W.-H., C.-I. WU, AND C.-C. LUO. 1984. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21:58-71.
    • (1984) J. Mol. Evol. , vol.21 , pp. 58-71
    • Li, W.-H.1    Wu, C.-I.2    Luo, C.-C.3
  • 21
    • 0032043787 scopus 로고    scopus 로고
    • Systematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequences
    • MARTIN, A. P., AND E. BERMINGHAM. 1998. Systematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequences. Mol. Phylogenet. Evol. 9:192-203.
    • (1998) Mol. Phylogenet. Evol. , vol.9 , pp. 192-203
    • Martin, A.P.1    Bermingham, E.2
  • 22
    • 0028156627 scopus 로고
    • Shortcomings of the cytochrome b gene as a molecular marker
    • MEYER, A. 1994. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 9:278-280.
    • (1994) Trends Ecol. Evol. , vol.9 , pp. 278-280
    • Meyer, A.1
  • 23
    • 0030484239 scopus 로고    scopus 로고
    • Rates of molecular evolution: Phylogenetic issues and applications
    • MINDELL, D. P., AND C. E. THACKER. 1996. Rates of molecular evolution: Phylogenetic issues and applications. Ann. Rev. Ecol. Syst. 27:279-303.
    • (1996) Ann. Rev. Ecol. Syst. , vol.27 , pp. 279-303
    • Mindell, D.P.1    Thacker, C.E.2
  • 24
    • 0032028997 scopus 로고    scopus 로고
    • Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences
    • NAYLOR, G. J. P., AND W. M. BROWN. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst. Biol. 47:61-76.
    • (1998) Syst. Biol. , vol.47 , pp. 61-76
    • Naylor, G.J.P.1    Brown, W.M.2
  • 25
  • 27
    • 0001329538 scopus 로고    scopus 로고
    • Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA
    • (D. E. Soltis, P. S. Soltis, and J. J. Doyle, eds.). Kluwer, Boston
    • OLMSTEAD, R. G., P. A. REEVES, AND A. C. YEN. 1998. Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA. Pages 164-187 in Molecular systematics of plants II, DNA sequencing (D. E. Soltis, P. S. Soltis, and J. J. Doyle, eds.). Kluwer, Boston.
    • (1998) Molecular Systematics of Plants II, DNA Sequencing , pp. 164-187
    • Olmstead, R.G.1    Reeves, P.A.2    Yen, A.C.3
  • 28
    • 84989419202 scopus 로고
    • Testing methods of evolutionary tree construction
    • PENNY, D., AND M. D. HENDY. 1985a. Testing methods of evolutionary tree construction. Cladistics 1:266-278.
    • (1985) Cladistics , vol.1 , pp. 266-278
    • Penny, D.1    Hendy, M.D.2
  • 29
    • 0002393841 scopus 로고
    • The use of tree comparison metrics
    • PENNY, D., AND M. D. HENDY. 1985b. The use of tree comparison metrics. Syst. Zool. 34:75-82.
    • (1985) Syst. Zool. , vol.34 , pp. 75-82
    • Penny, D.1    Hendy, M.D.2
  • 30
    • 0029907143 scopus 로고    scopus 로고
    • A critical study of homoplasy in molecular data with the use of a mophologically based cladogram, and its consequences for character weighting
    • PHILIPPE, H., G. LECOINTRE, H. L. VAN LE, AND H. LE GUYADER. 1996. A critical study of homoplasy in molecular data with the use of a mophologically based cladogram, and its consequences for character weighting. Mol. Biol. Evol. 13:1174-1186.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 1174-1186
    • Philippe, H.1    Lecointre, G.2    Van Le, H.L.3    Le Guyader, H.4
  • 31
    • 0029314481 scopus 로고
    • Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: Substitutional bias and information content of transitions relative to transversions
    • REEDER, T. W. 1995. Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: Substitutional bias and information content of transitions relative to transversions. Mol. Phylogenet. Evol. 4:203-222.
    • (1995) Mol. Phylogenet. Evol. , vol.4 , pp. 203-222
    • Reeder, T.W.1
  • 32
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • ROBINSON, D. F., AND L. R. FOULDS. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 33
    • 0028251187 scopus 로고
    • Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers
    • SIMON, C., F. FRATI, A. BECKENBACH, B. CRESPI, H. LIU, AND P. FLOOK. 1994. Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87:651-701.
    • (1994) Ann. Entomol. Soc. Am. , vol.87 , pp. 651-701
    • Simon, C.1    Frati, F.2    Beckenbach, A.3    Crespi, B.4    Liu, H.5    Flook, P.6
  • 35
    • 0001056906 scopus 로고
    • Parsimony, character-state reconstruction, and evolutionary inferences
    • (R. L. Mayden, ed.). Stanford University Press, Palo Alto, California
    • SWOFFORD, D. L., AND W. P. MADDISON. 1992. Parsimony, character-state reconstruction, and evolutionary inferences. Pages 186-223 in Systematics, historical ecology, and North American freshwater fishes (R. L. Mayden, ed.). Stanford University Press, Palo Alto, California.
    • (1992) Systematics, Historical Ecology, and North American Freshwater Fishes , pp. 186-223
    • Swofford, D.L.1    Maddison, W.P.2
  • 36
    • 84989483171 scopus 로고
    • Combinatorial weights in phylogenetic analysis: A statistical parsimony procedure
    • WHEELER, W. C. 1990. Combinatorial weights in phylogenetic analysis: A statistical parsimony procedure. Cladistics 6:269-275.
    • (1990) Cladistics , vol.6 , pp. 269-275
    • Wheeler, W.C.1
  • 37
    • 0025274493 scopus 로고
    • Phylogeny determination using dynamically weighted parsimony method
    • WILLIAMS, P. L., AND W. M. FITCH. 1990. Phylogeny determination using dynamically weighted parsimony method. Methods in Enz. 183:615-626.
    • (1990) Methods in Enz. , vol.183 , pp. 615-626
    • Williams, P.L.1    Fitch, W.M.2
  • 38
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • YANG, Z. 1996. 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
  • 39
    • 0032028624 scopus 로고    scopus 로고
    • On the best evolutionary rate for phylogenetic analysis
    • YANG, Z. 1998. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 47:125-133.
    • (1998) Syst. Biol. , vol.47 , pp. 125-133
    • Yang, Z.1
  • 40
    • 0029834015 scopus 로고    scopus 로고
    • Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates
    • ZARDOYA, R., AND A. MEYER. 1996. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13:933-942.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 933-942
    • Zardoya, R.1    Meyer, A.2


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