Skip to main content
SpringerLink
Log in

Molecular Phylogenetics: Mathematical Framework and Unsolved Problems

  • Chapter
Structural Approaches to Sequence Evolution

Part of the book series: Biological and Medical Physics, Biomedical Engineering ((BIOMEDICAL))

Phylogenetic relationship is essential in dating evolutionary events, reconstructing ancestral genes, predicting sites that are important to natural selection, and, ultimately, understanding genomic evolution. Three categories of phylogenetic methods are currently used: the distance-based, the maximum parsimony, and the maximum likelihood method. Here, I present the mathematical framework of these methods and their rationales, provide computational details for each of them, illustrate analytically and numerically the potential biases inherent in these methods, and outline computational challenges and unresolved problems. This is followed by a brief discussion of the Bayesian approach that has been recently used in molecular phylogenetics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. J. Felsenstein, Inferring Phylogenies (Sinauer, Sunderland, MA, 2004)

    Google Scholar 

  2. W.-H. Li, Molecular Evolution (Sinauer, Sunderland, MA, 1997)

    Google Scholar 

  3. M. Nei, S. Kumar, Molecular Evolution and Phylogenetics (Oxford University Press, New York, 2000)

    Google Scholar 

  4. S. Kumar, K. Tamura, I.B. Jakobsen, M. Nei, Bioinformatics 17, 1244 (2001)

    Article  Google Scholar 

  5. D.L. Swofford, Phylogenetic Analysis Using Parsimony (* and Other Methods), 4th edn. (Sinauer, Sunderland, MA, 2000)

    Google Scholar 

  6. X. Xia, Z. Xie, J. Hered. 92, 371 (2001)

    Article  Google Scholar 

  7. X. Xia, Data Analysis in Molecular Biology and Evolution (Kluwer, Boston, 2001)

    Google Scholar 

  8. Z. Yang, Phylogenetic Analysis by Maximum Likelihood (PAML) (University College, London, 2002) version 3.12

    Google Scholar 

  9. J.P. Huelsenbeck, F. Ronquist, R. Nielsen, J.P. Bollback, Science 294, 2310 (2001)

    Article  ADS  Google Scholar 

  10. T.H. Jukes, C.R. Cantor, in Evolution of Protein Molecules. ed. by H.N. Munro. Mammalian Protein Metabolism (Academic, New York, 1969) pp. 21-123

    Google Scholar 

  11. M. Kimura, J. Mol. Evol. 16, 111 (1980)

    Article  Google Scholar 

  12. K. Tamura, M. Nei, Mol. Biol. Evol. 10, 512 (1993)

    Google Scholar 

  13. M. Kimura, T. Ohta, J. Mol. Evol. 2, 87 (1972)

    Article  Google Scholar 

  14. K. Tamura, S. Kumar, Mol. Biol. Evol. 19, 1727 (2002)

    Google Scholar 

  15. J.P. Huelsenbeck, B. Larget, M.E. Alfaro, Mol. Biol. Evol. 21, 1123 (2004)

    Article  Google Scholar 

  16. J.A. Lake, Proc. Natl. Acad. Sci. USA 91, 1455 (1994)

    Article  ADS  Google Scholar 

  17. P.J. Lockhart, M.A. Steel, M.D. Hendy, D. Penny, Mol. Biol. Evol. 11, 605 (1994)

    Google Scholar 

  18. M.S. Rosenberg, S. Kumar, Mol. Biol. Evol. 20, 610 (2003)

    Article  Google Scholar 

  19. X. Xia, Syst. Biol. 49, 87 (2000)

    Article  Google Scholar 

  20. X. Xia, Z. Xie, K.M. Kjer, Syst. Biol. 52, 283 (2003)

    Article  Google Scholar 

  21. J. Adachi, M. Hasegawa, J. Mol. Evol. 42, 459 (1996)

    Article  Google Scholar 

  22. H. Kishino, T. Miyata, M. Hasegawa, J. Mol. Evol. 31, 151 (1990)

    Article  Google Scholar 

  23. M.O. Dayhoff, R.M. Schwartz, B.C. Orcutt, in A Model of Evolutionary Change in Proteins. ed. by M.O. Dayhoff. Atlas of Protein Sequence and Structure, vol. 5, suppl. 3, (National Biomedical Research Foundation, Washington DC, 1978) pp. 345-352

    Google Scholar 

  24. D.T. Jones, W.R. Taylor, J.M. Thornton, Comput. Appl. Biosci. 8, 275 (1992)

    Google Scholar 

  25. X. Xia, W.H. Li, J. Mol. Evol. 47, 557 (1998)

    Article  Google Scholar 

  26. X. Xia, Z. Xie, Mol. Biol. Evol. 19, 58 (2002)

    Google Scholar 

  27. N. Goldman, Z. Yang, Mol. Biol. Evol. 11, 725 (1994)

    Google Scholar 

  28. S.V. Muse, B.S. Gaut, Mol. Biol. Evol. 11, 715 (1994)

    Google Scholar 

  29. Z. Yang, R. Nielsen, Mol. Biol. Evol. 17, 32 (2000)

    Google Scholar 

  30. X. Xia, Genetics 44, 1309 (1996)

    Google Scholar 

  31. X. Xia, Genetics 149, 37 (1998)

    Google Scholar 

  32. X. Xia, Gene 345, 13 (2005)

    Article  Google Scholar 

  33. T. Ikemura, in Correlation Between Codon Usage and tRNA Content in Micro-organisms. ed. by D.L. Hatfield, B. Lee, J. Pirtle. Transfer RNA in Protein Synthesis (CRC, Boca Raton, FL, 1992) pp. 87-111

    Google Scholar 

  34. N. Saitou, M. Nei, Mol. Biol. Evol. 4, 406 (1987)

    Google Scholar 

  35. W.M. Fitch, E. Margoliash, Science 155, 279 (1967)

    Article  ADS  Google Scholar 

  36. R. Desper, O. Gascuel, J. Comput. Biol. 9, 687 (2002)

    Article  Google Scholar 

  37. X. Xia, Z. Xie, M. Salemi, L. Chen, Y. Wang, Mol. Phylogenet. Evol. 26, 1 (2003)

    Article  Google Scholar 

  38. G.B. Golding, Mol. Biol. Evol. 1, 125 (1983)

    Google Scholar 

  39. M. Nei, T. Gojobori, Mol. Biol. Evol. 3, 418 (1986)

    Google Scholar 

  40. L. Jin, M. Nei, Mol. Biol. Evol. 7, 82 (1990)

    Google Scholar 

  41. P.J. Waddell, Statistical Methods of Phylogenetic Analysis: Including Hadamard Conjugations, LogDet Transforms, and Maximum Likelihood. PhD Thesis, Massey University, New Zealand (1995)

    Google Scholar 

  42. J. Felsenstein, Syst. Zool. 27, 401 (1978)

    Article  Google Scholar 

  43. N. Takezaki, M. Nei, J. Mol. Evol. 39, 210 (1994)

    Google Scholar 

  44. M.D. Hendy, D. Penny, Syst. Zool. 38, 297 (1989)

    Article  Google Scholar 

  45. M. Nei, Annu. Rev. Genet. 30, 371 (1996)

    Article  Google Scholar 

  46. M. Nei, Molecular Evolutionary Genetics(Columbia University Press, New York, 1987)

    Google Scholar 

  47. J.T. Chang, Math. Biosci. 137, 51 (1996)

    Article  MATH  MathSciNet  Google Scholar 

  48. K. Tamura, M. Nei, S. Kumar, Proc. Natl. Acad. Sci. USA 101, 11030 (2004)

    Article  ADS  Google Scholar 

  49. C. Medigue, T. Rouxel, P. Vigier, A. Henaut, A. Danchin, J. Mol. Biol. 222, 851(1991)

    Article  Google Scholar 

  50. E.V. Koonin, Mol. Microbiol. 50, 725 (2003)

    Article  Google Scholar 

  51. H. Philippe, C.J. Douady, Curr. Opin. Microbiol. 6, 498 (2003)

    Article  Google Scholar 

  52. C.G. Kurland, B. Canback, O.G. Berg, Proc. Natl. Acad. Sci. USA 100, 9658 (2003)

    Article  ADS  Google Scholar 

  53. J.R. Brown, Nat. Rev. Genet. 4, 121 (2003)

    Article  Google Scholar 

  54. J.A. Eisen, Curr. Opin. Genet. Dev. 10, 606 (2000)

    Article  Google Scholar 

  55. X. Xia, J. Mol. Evol. 57, S21 (2003)

    Article  Google Scholar 

  56. X. Xia, Mol. Biol. Evol. 15, 336 (1998)

    Google Scholar 

  57. B. Kolaczkowski, J.W. Thornton, Nature 431, 980 (2004)

    Article  ADS  Google Scholar 

  58. J. Felsenstein, Annu. Rev. Genet. 22, 521 (1988)

    Article  Google Scholar 

  59. W.K. Hastings, Biometrika 57, 97 (1970)

    Article  MATH  Google Scholar 

  60. N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, E. Teller, J. Chem. Phys. 21, 1087 (1953)

    Article  ADS  Google Scholar 

  61. D. Baron, J. Cocquet, X. Xia, M. Fellous, Y. Guiguen, R.A. Veitia, J. Mol. Endocrinol. 33, 705 (2004)

    Article  Google Scholar 

  62. D. Zwickl, M. Holder, Syst. Biol. 53, 877 (2004)

    Article  Google Scholar 

  63. K.M. Pickett, C.P. Randle, Mol. Phylogenet. Evol. 34, 203 (2005)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CAREG and Biology Department, University of Ottawa, K1N 6N5, Ottawa, Ontario, Canada

    Xuhua Xia

Authors
  1. Xuhua Xia
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Fac. de Ciencias, Universidad Autonoma Madrid, Cantoblanco, 28049, Madrid, Spain

    Ugo Bastolla

  2. Institut für Festkörperphysik, TU Darmstadt, Hochschulstr. 8, 64289, Darmstadt, Germany

    Markus Porto

  3. Dipartimento di Fisica, Universita di Milano-Bicocca, Piazza della Scienza 3, 29126, Milano, Italy

    H. Eduardo Roman

  4. Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK

    Michele Vendruscolo

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Xia, X. (2007). Molecular Phylogenetics: Mathematical Framework and Unsolved Problems. In: Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M. (eds) Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-35306-5_8

Download citation

Publish with us

Policies and ethics

Search

Navigation