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Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies

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Advances in Computational Biology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 680))

Abstract

Thirty-six single genes of 6 plants inferred 18 unique trees using maximum parsimony. Such incongruence is an important challenge. How to reconstruct the congruent tree is still one of the most challenges in molecular phylogenetics. For resolving this problem, a genome-wide EST data mining approach was systematically investigated by retrieving a large size of EST data of 144 shared genes of 6 green plants from GenBank. The results show that the concatenated alignments approach overcame incongruence among single-gene phylogenies and successfully reconstructed the congruent tree of 6 species with 100% jackknife support across each branch when 144 genes was used. Jackknife supports of correct branches increased with number of genes linearly, but the number of wrong branches also increased linearly. For inferring the congruent tree, a minimum of 30 genes were required. This approach may provide potential power in resolving conflictions of phylogenies.

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References

  1. Goodman M, Romero-Herrera AE, Dene H, Czelusniak J, Tashian RE (1982) Amino acid sequence evidence on the phylogeny of primates, other eutherians. In: Goodman M (Ed) Macromolecular Sequences in Systematic and Evolutionary Biology. Plenum, New York, pp. 115–191.

    Chapter  Google Scholar 

  2. Hedges SB (1994) Molecular evidence for the origin of birds. Proc Natl Acad Sci USA 91:2621–2624.

    Article  PubMed  CAS  Google Scholar 

  3. Russo CAM, Takezaki N, Nei M (1996) Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phytogeny. Mol Biol Evol 13:525–536.

    Article  PubMed  CAS  Google Scholar 

  4. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124–2128.

    Article  PubMed  CAS  Google Scholar 

  5. Wolf YI, Rogozin IB, Grishin NV, Koonin EV (2002) Genome trees, the tree of life. Trends Genet 18:472–479.

    Article  PubMed  CAS  Google Scholar 

  6. Yang Z (1996) Maximum-likelihood models for combined analysis of multiple sequence data. J Mol Evol 42:587–596.

    Article  PubMed  CAS  Google Scholar 

  7. Huelsenbeck JP, Bull JJ, Cunningham CW (1996) Combining data in phylogenetic analysis. TREE 11:152–158.

    PubMed  CAS  Google Scholar 

  8. Kluge AG (1989) A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst Zool 38:7–25.

    Article  Google Scholar 

  9. Miyamoto MM, Fitch WM (1995) Testing species phylogenies and phylogenetic methods with congruence. Syst Biol 44:64–76.

    Google Scholar 

  10. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972–977

    Article  PubMed  CAS  Google Scholar 

  11. Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798–804.

    Article  PubMed  CAS  Google Scholar 

  12. Gee H (2003) Evolution, ending incongruence. Nature 425:782.

    Article  PubMed  CAS  Google Scholar 

  13. Soltis DE et al (2004) Genome-scale data, angiosperm relationships, and ending incongruence: A cautionary tale in phylogenetics. Trends Plant Sci 9:477–483.

    Article  PubMed  CAS  Google Scholar 

  14. Fitz-Gibbon ST, House CH (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucl Acids Res 27:4218–4222.

    Article  PubMed  CAS  Google Scholar 

  15. Phillips MJ, Delsuc F, Penny D (2004) Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 21:1455–1458.

    Article  PubMed  CAS  Google Scholar 

  16. Panchen AL (1992) Classification, Evolution and the Nature of Biology. Cambridge University Press, Cambridge.

    Book  Google Scholar 

  17. Cronquist A (1981) An Integrated System of Classification of Flowering Plants. Columbia University Press, New York.

    Google Scholar 

  18. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882.

    Article  PubMed  CAS  Google Scholar 

  19. Swofford D (2002) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) (Version 4). Sinauer Associates, Sunderland, MA.

    Google Scholar 

  20. Kurzman CP, Robnett CJ (2003) Phylogenetic relationships among yeasts of the ‘Saccharomyces complex’ determined from multigene sequence analysis. FEM Yeast Res 3:417–432.

    Article  Google Scholar 

  21. Barkman TJ et al (2000) Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. Proc Natl Acad Sci USA 97:13166–13177.

    Article  PubMed  CAS  Google Scholar 

  22. Brown JR, Douady JD, Italia MJ, Marchall WE, Stanhope MJ (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28:281–285.

    Article  PubMed  CAS  Google Scholar 

  23. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Part of this research was conducted by YS at Atlantic Bioinformatics Centre. This work was partially supported by the NSERC grant ORGPIN 341854, the CRC grant 950-2-3617, and the CFI grant 203617.

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Correspondence to Yunfeng Shan .

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Shan, Y., Gras, R. (2010). Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies. In: Arabnia, H. (eds) Advances in Computational Biology. Advances in Experimental Medicine and Biology, vol 680. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5913-3_27

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