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 ====Introduction à la Phylogénie==== ====Introduction à la Phylogénie====
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 Copyright © 1999-2012 Copyright © 1999-2012
  
-La page originale disponible à l’adresse http://www.talkorigins.org/faqs/comdesc/phylo.html+Page originale disponible à l’adresse http://www.talkorigins.org/faqs/comdesc/phylo.html 
 +\\ 
 +\\ Navigation : 
 +  * [[comdesc|Introduction]] 
 +  * [[Comdesc-evidences|Preuve scientifique et méthode scientifique]] 
 +  * [[Comdesc-phylo|Introduction à la phylogénétique]] 
 +  * [[Comdesc-1|Partie 1: L'arbre phylogénétique universel unique]] 
 +  * [[Comdesc-2|Partie 2. Histoire passée]] 
 +  * [[Comdesc-3|Partie 3. Opportunisme évolutionniste]] 
 +  * [[Comdesc-4|Partie 4. Preuve moléculaire]] 
 +  * [[Comdesc-5|Partie 5. Changement]] 
 +  * [[Comdesc-closing|Remarques finales]] 
 +  * [[Comdesc-glossaire|Glossaire]]
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   * Attraction de longues branches: les lignages qui ont divergé il y a relativement longtemps auront tendance à se "regrouper" dans une reconstruction phylogénétique dans certaines conditions. Les raisons mathématiques sont quelque peu compliquées, mais l'utilisation de gènes (ou de régions de gènes) évoluant plus lentement permet de résoudre le problème.   * Attraction de longues branches: les lignages qui ont divergé il y a relativement longtemps auront tendance à se "regrouper" dans une reconstruction phylogénétique dans certaines conditions. Les raisons mathématiques sont quelque peu compliquées, mais l'utilisation de gènes (ou de régions de gènes) évoluant plus lentement permet de résoudre le problème.
  
- * Variation du taux entre les lignages: les taux de substitution de nucléotides peuvent différer d’un lignage à l’autre; cela peut contribuer à attirer de longues branches et à créer des topologies d'arbre incorrectes. Cependant, les méthodes du maximum de vraisemblance et des moindres carrés sont particulièrement utiles ici.+  * Variation du taux entre les lignages: les taux de substitution de nucléotides peuvent différer d’un lignage à l’autre; cela peut contribuer à attirer de longues branches et à créer des topologies d'arbre incorrectes. Cependant, les méthodes du maximum de vraisemblance et des moindres carrés sont particulièrement utiles ici.
  
   * Variation du taux au sein d'un seul gène: les taux de substitution de nucléotides peuvent varier sur la longueur d'un seul gène, ce qui exacerbe également l'attraction de longues branches.   * Variation du taux au sein d'un seul gène: les taux de substitution de nucléotides peuvent varier sur la longueur d'un seul gène, ce qui exacerbe également l'attraction de longues branches.
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 ====Références==== ====Références====
  
-Albert, J., Wahlberg, J., Leitner, T., Escanilla, D. and Uhlen, M. (1994) "Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes." J Virol 68: 5918-24. [[[http://www.ncbi.nlm.nih.gov/pubmed/7520096|PubMed]]] +Albert, J., Wahlberg, J., Leitner, T., Escanilla, D. and Uhlen, M. (1994) "Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes." J Virol 68: 5918-24. [[http://www.ncbi.nlm.nih.gov/pubmed/7520096|PubMed]]
  
-Arnold, C., Balfe, P. and Clewley, J. P. (1995) "Sequence distances between env genes of HIV-1 from individuals infected from the same source: implications for the investigation of possible transmission events." Virology 211: 198-203. [[[http://www.ncbi.nlm.nih.gov/pubmed/7645211|PubMed]]] +Arnold, C., Balfe, P. and Clewley, J. P. (1995) "Sequence distances between env genes of HIV-1 from individuals infected from the same source: implications for the investigation of possible transmission events." Virology 211: 198-203. [[http://www.ncbi.nlm.nih.gov/pubmed/7645211|PubMed]] 
  
-Atchely, W. R., and Fitch, W. M. (1991) "Gene trees and the origins of inbred strains of mice." Science 254: 554-558. [[[http://www.ncbi.nlm.nih.gov/pubmed/1948030|PubMed]]] +Atchely, W. R., and Fitch, W. M. (1991) "Gene trees and the origins of inbred strains of mice." Science 254: 554-558. [[http://www.ncbi.nlm.nih.gov/pubmed/1948030|PubMed]]
  
 Avise, J. C., and Wollenberg, K. (1997) "Phylogenetics and the origin of species." PNAS 94: 7748-7755. http://www.pnas.org/cgi/ content/full/94/15/7748  Avise, J. C., and Wollenberg, K. (1997) "Phylogenetics and the origin of species." PNAS 94: 7748-7755. http://www.pnas.org/cgi/ content/full/94/15/7748 
Ligne 213: Ligne 224:
 Brooks, D. R., and McLennan, D. A. (1991) Phylogeny, ecology, and behavior. Chicago: University of Chicago Press.  Brooks, D. R., and McLennan, D. A. (1991) Phylogeny, ecology, and behavior. Chicago: University of Chicago Press. 
  
-Bush, R. M., C. A. Bender, et al. (1999) "Predicting the evolution of human influenza A." Science 286: 1921-1925. [[[http://www.ncbi.nlm.nih.gov/pubmed/10583948|PubMed]]] +Bush, R. M., C. A. Bender, et al. (1999) "Predicting the evolution of human influenza A." Science 286: 1921-1925. [[http://www.ncbi.nlm.nih.gov/pubmed/10583948|PubMed]]
  
-Doolittle, W. F. (1999) "Phylogenetic Classification and the Universal Tree." Science 284: 2124. [[[http://www.ncbi.nlm.nih.gov/pubmed/10381871|PubMed]]] +Doolittle, W. F. (1999) "Phylogenetic Classification and the Universal Tree." Science 284: 2124. [[http://www.ncbi.nlm.nih.gov/pubmed/10381871|PubMed]]
  
-Doolittle, W. F. (2000) "The nature of the universal ancestor and the evolution of the proteome." Current Opinion in Structural Biology 10: 355-358. [[[http://www.ncbi.nlm.nih.gov/pubmed/10851188|PubMed]]] +Doolittle, W. F. (2000) "The nature of the universal ancestor and the evolution of the proteome." Current Opinion in Structural Biology 10: 355-358. [[http://www.ncbi.nlm.nih.gov/pubmed/10851188|PubMed]]
  
 Edwards, A. W. F. and Cavalli-Sforza, L. L. (1963) "The reconstruction of evolution." Annals of Human Genetics 27: 105-106.  Edwards, A. W. F. and Cavalli-Sforza, L. L. (1963) "The reconstruction of evolution." Annals of Human Genetics 27: 105-106. 
Ligne 229: Ligne 240:
 Felsenstein, J. (1981) "A likelihood approach to character weighting and what it tells us about parsimony and compatibility." Biol J Linn Soc Lond 16: 183-196.  Felsenstein, J. (1981) "A likelihood approach to character weighting and what it tells us about parsimony and compatibility." Biol J Linn Soc Lond 16: 183-196. 
  
-Felsenstein, J. (1981) "Evolutionary trees from DNA sequences: A maximum likelihood approach." J Mol Evol 17: 368-376. [[[http://www.ncbi.nlm.nih.gov/pubmed/7288891|PubMed]]] +Felsenstein, J. (1981) "Evolutionary trees from DNA sequences: A maximum likelihood approach." J Mol Evol 17: 368-376. [[http://www.ncbi.nlm.nih.gov/pubmed/7288891|PubMed]] 
  
 Felsenstein, J. (1985) "Confidence limits on phylogenies: an approach using the bootstrap." Evolution 39: 783-791.  Felsenstein, J. (1985) "Confidence limits on phylogenies: an approach using the bootstrap." Evolution 39: 783-791. 
Ligne 247: Ligne 258:
 Hillis, D. M., and Bull, J. J. (1993) "An empirical test of bootstrapping as a method for assessing confidence on phylogenetic analysis." Syst. Biol. 42: 182-192.  Hillis, D. M., and Bull, J. J. (1993) "An empirical test of bootstrapping as a method for assessing confidence on phylogenetic analysis." Syst. Biol. 42: 182-192. 
  
-Hillis, D. M., J. J. Bull, et al. (1992) "Experimental phylogenetics: Generation of a known phylogeny." Science 255: 589-592. [[[http://www.ncbi.nlm.nih.gov/pubmed/1736360|PubMed]]] +Hillis, D. M., J. J. Bull, et al. (1992) "Experimental phylogenetics: Generation of a known phylogeny." Science 255: 589-592. [[http://www.ncbi.nlm.nih.gov/pubmed/1736360|PubMed]] 
  
-Holmes, E. C., Zhang, L. Q., Simmonds, P., Rogers, A. S. and Brown, A. J. (1993) "Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon." J Infect Dis 167: 1411-4. [[[http://www.ncbi.nlm.nih.gov/pubmed/8501332|PubMed]]] +Holmes, E. C., Zhang, L. Q., Simmonds, P., Rogers, A. S. and Brown, A. J. (1993) "Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon." J Infect Dis 167: 1411-4. [[http://www.ncbi.nlm.nih.gov/pubmed/8501332|PubMed]] 
  
-Hudson, R. R. (1992) "Gene trees, species trees and the segregation of ancestral alleles." Genetics 131: 509-513. [[[http://www.ncbi.nlm.nih.gov/pubmed/1644284|PubMed]]] +Hudson, R. R. (1992) "Gene trees, species trees and the segregation of ancestral alleles." Genetics 131: 509-513. [[http://www.ncbi.nlm.nih.gov/pubmed/1644284|PubMed]]
  
-Huelsenbeck, J. P., Ronquist, F., Nielsen, R., and Bollback, J. P. (2001) "Bayesian inference of phylogeny and its impact on evolutionary biology." Science 294: 2310-2314. [PubMed] +Huelsenbeck, J. P., Ronquist, F., Nielsen, R., and Bollback, J. P. (2001) "Bayesian inference of phylogeny and its impact on evolutionary biology." Science 294: 2310-2314. [[http://www.ncbi.nlm.nih.gov/pubmed/11743192|PubMed]]
  
 Kitching, I. J., Forey, P. L., Humphries, C. J., and Williams, D. M. (1998) Cladistics: The Theory and Practice of Parsimony Analysis. Second Edition. The Systematics Association Publication No. 11. Oxford: Oxford University Press.  Kitching, I. J., Forey, P. L., Humphries, C. J., and Williams, D. M. (1998) Cladistics: The Theory and Practice of Parsimony Analysis. Second Edition. The Systematics Association Publication No. 11. Oxford: Oxford University Press. 
Ligne 259: Ligne 270:
 Li, W.-H. (1997) Molecular Evolution. Sunderland, MA: Sinauer Associates.  Li, W.-H. (1997) Molecular Evolution. Sunderland, MA: Sinauer Associates. 
  
-Machuca, R., Jorgensen, L. B., Theilade, P. and Nielsen, C. (2001) "Molecular investigation of transmission of human immunodeficiency virus type 1 in a criminal case." Clin Diagn Lab Immunol 8: 884-90. [[[http://www.ncbi.nlm.nih.gov/pubmed/11527797|PubMed]]] +Machuca, R., Jorgensen, L. B., Theilade, P. and Nielsen, C. (2001) "Molecular investigation of transmission of human immunodeficiency virus type 1 in a criminal case." Clin Diagn Lab Immunol 8: 884-90. [[http://www.ncbi.nlm.nih.gov/pubmed/11527797|PubMed]]
  
 Maddison, W. P., and Maddison, D. R. (1992) MacClade. Sunderland, MA: Sinauer Associates.  Maddison, W. P., and Maddison, D. R. (1992) MacClade. Sunderland, MA: Sinauer Associates. 
Ligne 265: Ligne 276:
 Nei, M. and Kumar, S. (2000) Molecular Evolution and Phylogenetics. New York, NY: Oxford University Press.  Nei, M. and Kumar, S. (2000) Molecular Evolution and Phylogenetics. New York, NY: Oxford University Press. 
  
-Nichols, R. (2001) "Gene trees and species trees are not the same." Trends Ecol Evol. 16: 358-364. [[[http://www.ncbi.nlm.nih.gov/pubmed/11403868|PubMed]]] +Nichols, R. (2001) "Gene trees and species trees are not the same." Trends Ecol Evol. 16: 358-364. [[http://www.ncbi.nlm.nih.gov/pubmed/11403868|PubMed]]
  
-Ou, C. Y., Ciesielski, C. A., Myers, G., Bandea, C. I., Luo, C. C., Korber, B. T., Mullins, J. I., Schochetman, G., Berkelman, R. L., Economou, A. N. and et al. (1992) "Molecular epidemiology of HIV transmission in a dental practice." Science 256: 1165-71. [[[http://www.ncbi.nlm.nih.gov/pubmed/1589796|PubMed]]] +Ou, C. Y., Ciesielski, C. A., Myers, G., Bandea, C. I., Luo, C. C., Korber, B. T., Mullins, J. I., Schochetman, G., Berkelman, R. L., Economou, A. N. and et al. (1992) "Molecular epidemiology of HIV transmission in a dental practice." Science 256: 1165-71. [[http://www.ncbi.nlm.nih.gov/pubmed/1589796|PubMed]]
  
 Swofford, D. L., Olsen, G. J., Waddell, P. J., and Hillis, D. M. (1996) "Phylogenetic inference." In Molecular Systematics, pp 407-514. Hillis, D. M., Moritiz, C. and Mable, B. K. eds., Sunderland, Massachusetts: Sinauer.  Swofford, D. L., Olsen, G. J., Waddell, P. J., and Hillis, D. M. (1996) "Phylogenetic inference." In Molecular Systematics, pp 407-514. Hillis, D. M., Moritiz, C. and Mable, B. K. eds., Sunderland, Massachusetts: Sinauer. 
  
-Veenstra, J., Schuurman, R., Cornelissen, M., van't Wout, A. B., Boucher, C. A., Schuitemaker, H., Goudsmit, J. and Coutinho, R. A. (1995) "Transmission of zidovudine-resistant human immunodeficiency virus type 1 variants following deliberate injection of blood from a patient with AIDS: characteristics and natural history of the virus." Clin Infect Dis 21: 556-60. [[[http://www.ncbi.nlm.nih.gov/pubmed/8527543|PubMed]]] +Veenstra, J., Schuurman, R., Cornelissen, M., van't Wout, A. B., Boucher, C. A., Schuitemaker, H., Goudsmit, J. and Coutinho, R. A. (1995) "Transmission of zidovudine-resistant human immunodeficiency virus type 1 variants following deliberate injection of blood from a patient with AIDS: characteristics and natural history of the virus." Clin Infect Dis 21: 556-60. [[http://www.ncbi.nlm.nih.gov/pubmed/8527543|PubMed]] 
  
-Vogel, G. (1997) "Phylogenetic analysis: getting its day in court." Science 275: 1559-60. [[[http://www.ncbi.nlm.nih.gov/pubmed/9072818|PubMed]]] +Vogel, G. (1997) "Phylogenetic analysis: getting its day in court." Science 275: 1559-60. [[http://www.ncbi.nlm.nih.gov/pubmed/9072818|PubMed]]
  
 Woese, C. (1998) "The universal ancestor." PNAS 95: 6854-6859. http://www.pnas.org/cgi/ content/full/95/12/6854  Woese, C. (1998) "The universal ancestor." PNAS 95: 6854-6859. http://www.pnas.org/cgi/ content/full/95/12/6854 
  
-Wu, C. I. (1991) "Inferences of species phylogeny in relation to segregation of ancient polymorphisms." Genetics 127: 429-435. [[[http://www.ncbi.nlm.nih.gov/pubmed/2004713|PubMed]]] +Wu, C. I. (1991) "Inferences of species phylogeny in relation to segregation of ancient polymorphisms." Genetics 127: 429-435. [[http://www.ncbi.nlm.nih.gov/pubmed/2004713|PubMed]]
  
 Yirrell, D. L., Robertson, P., Goldberg, D. J., McMenamin, J., Cameron, S. and Leigh Brown, A. J. (1997) "Molecular investigation into outbreak of HIV in a Scottish prison." Bmj 314: 1446-50. http://bmj.com/cgi/content/full/314/7092/1446?view=full&pmid=9167560  Yirrell, D. L., Robertson, P., Goldberg, D. J., McMenamin, J., Cameron, S. and Leigh Brown, A. J. (1997) "Molecular investigation into outbreak of HIV in a Scottish prison." Bmj 314: 1446-50. http://bmj.com/cgi/content/full/314/7092/1446?view=full&pmid=9167560 
  
-Zhu, T., B. Korber, et al. (1998) "An African HIV-1 sequence from 1959 and implications for the origin of the epidemic." Nature 391: 594-597. [[[http://www.ncbi.nlm.nih.gov/pubmed/9468138|PubMed]]] +Zhu, T., B. Korber, et al. (1998) "An African HIV-1 sequence from 1959 and implications for the origin of the epidemic." Nature 391: 594-597. [[http://www.ncbi.nlm.nih.gov/pubmed/9468138|PubMed]
 + 
 +==== Navigation ==== 
 +  * [[comdesc|Plus de 29 preuves de la Macroevolution - Introduction]] 
 +  * [[Comdesc-evidences|Preuve scientifique et méthode scientifique]] 
 +  * [[Comdesc-1|Partie I. Un arbre phylogénétique unique et historique]] 
 +  * [[Comdesc-2|Partie 2. Histoire passée]] 
 +  * [[Comdesc-3|Partie 3. Opportunisme évolutionniste]] 
 +  * [[Comdesc-4|Partie 4. Preuve moléculaire]] 
 +  * [[Comdesc-5|Partie 5. Changement]] 
 +  * [[Comdesc-closing|Remarques finales]] 
 +  * [[comdesc-glossaire|Glossaire]] 
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