Plant Soil Environ., 2007, 53(10):442-446 | DOI: 10.17221/2194-PSE

A short guide to phylogeny reconstruction

E. Michu
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic

This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

Keywords: sequence alignment; phylogenetic analysis; neighbor-joining; maximum parsimony; maximum likelihood; Bayesian inference

Published: October 31, 2007  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
Michu E. A short guide to phylogeny reconstruction. Plant Soil Environ. 2007;53(10):442-446. doi: 10.17221/2194-PSE.
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    References

    1. Baldauf S.L. (2003): Phylogeny for the faint of heart: a tutorial. Trends Genet., 19: 345-351. Go to original source... Go to PubMed...
    2. Bergsten J. (2005): A review of long-branch attraction. Cladistics, 21: 163-193. Go to original source... Go to PubMed...
    3. Desfeux C., Lejeune B. (1996): Systematics of Euromediterranean silene (Caryophyllaceae): Evidence from a phylogenetic analysis using ITS sequences. Life Sci., 319: 351-358.
    4. Do C.B., Mahabhashyam M.S.P., Brudno M., Batzoglou S. (2005): PROBCONS: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15: 330-340. Go to original source... Go to PubMed...
    5. Doyle J.J., Gaut B.S. (2000): Evolution of genes and taxa: a primer. Plant Mol. Biol., 42: 1-23. Go to original source...
    6. Edgar R.C. (2004): MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32: 1792-1797. Go to original source... Go to PubMed...
    7. Felsenstein J. (1985): Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783-791. Go to original source... Go to PubMed...
    8. Felsenstein J. (2004): Inferring Phylogenies. Sinauer Associates, Sanderland, Massachusets.
    9. Galtier N., Gouy M., Gautier C. (1996): SeaView and PhyloWin, two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci., 12: 543-548. Go to original source... Go to PubMed...
    10. Hall T.A. (1999): Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98NT. Nucleic Acids Symp. Ser. 41: 95-98.
    11. Harrison C.J., Langdale J.A. (2006): A step by step guide to phylogeny reconstruction. Plant J., 45: 561-572. Go to original source... Go to PubMed...
    12. Hillis D.M., Bull J.J. (1993): An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analyses. Syst. Biol., 42: 182-192. Go to original source...
    13. Holder M., Lewis P.O. (2003): Phylogeny estimation: traditional and Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754-755. Go to original source... Go to PubMed...
    14. Huelsenbeck J.P.H., Larget B., Miller R.E., Ronquist F. (2002): Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol., 51: 673-688. Go to original source... Go to PubMed...
    15. Huelsenbeck J.P., Rannala B., Masly J.P. (2000): Accomodating phylogenetic uncertainty in evolutionary studies. Science, 288: 2349-2350. Go to original source... Go to PubMed...
    16. Huelsenbeck J.P., Ronquist F. (2001): MRBAYES: Bayesian inference of phylogeny. Bioinformatics, 17: 754-755. Go to original source... Go to PubMed...
    17. Katoh K., Misawa K., Kuma K., Miyata T. (2002): MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30: 3059-3066. Go to original source... Go to PubMed...
    18. Kumar S., Tamura K., Nei M. (2004): MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment briefings. Bioinformatics, 5: 150-163. Go to original source... Go to PubMed...
    19. Notredame C., Higgins D., Heringa J. (2000): T-Coffee: A novel method for multiple sequence alignments. J. Mol. Biol., 302: 205-217. Go to original source... Go to PubMed...
    20. Parida L., Floratos A., Rigoutsos I. (1998): Musca: An algorithm for constrained alignment of multiple data sequences. In: Proc. 9 th Workshop on Genome Informatics, Tokyo, Japan.
    21. Perrière G., Gouy M. (1996): WWW-Query: An online retrieval system for biological sequence banks. Biochimie, 78: 364-369. Go to original source... Go to PubMed...
    22. Saitou N., Nei M. (1987): The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4: 406-25. Go to PubMed...
    23. Sanderson M.J., Driskell A.C. (2003): The challenge of constructing large phylogenetic trees. Trends Plant Sci., 8: 374-379. Go to original source... Go to PubMed...
    24. Simmons M.P. (2000): A fundamental problem with amino-acid-sequence characters for phylogenetic analyses. Cladistics, 16: 274-282. Go to original source... Go to PubMed...
    25. Simmons M.P., Freudenstein J.V. (2002): Artifacts of coding amino acids and other composite characters for phylogenetic analysis. Cladistics, 18: 354-365. Go to original source... Go to PubMed...
    26. Soltis D.E., Albert V.A., Savolainen V., Hilu K., Qiu Y.L., Chase M.W., Farris J.S., Stefanović S., Rice D.W., Palmer J.D., Soltis P.S. (2004): Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics. Trends Plant Sci., 9: 477-483. Go to original source... Go to PubMed...
    27. Thompson J.D., Higgins D.G., Gibson T.J. (1994): CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22: 4673-4680. Go to original source... Go to PubMed...

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content