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An Approach for Determining Evolutionary Distance in Network-Based Phylogenetic Analysis

  • Tingting Zhou
  • Keith C. C. Chan
  • Yi Pan
  • Zhenghua Wang
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Abstract

Network-based phylogenetic analysis explores phylogenetic relationships among different organisms by comparing their biological networks, especially metabolic networks. The differences between networks, often expressed as evolutionary distances, are normally measured using the plain Jaccard distance. In this paper, we show enzymes are different in phylogenetic conservation and topological importance, which are correlated significantly. Inspired by this observation, we propose a new approach to determine evolutionary distances. Our approach considers not only the number of different enzymes in different organisms, but also the phylogenetic or topological difference of individual enzymes. The resulting evolutionary distance measures are compared with the plain Jaccard distance by use of 16s rRNA-based distance as reference. It shows that new distance measures make errors smaller in all test cases of comparison.

Keywords

network-based phylogenetic analysis metabolic network comparison evolutionary distance Jaccard distance phylogenetic conservation topological importance 

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References

  1. 1.
    Hong, S.H., Kim, T.Y., Lee, S.Y.: Phylogenetic analysis based on genome-scale metabolic pathway reaction content. Applied Microbiology and Biotechnology 65(2), 203–210 (2004)CrossRefGoogle Scholar
  2. 2.
    Wolfa, Y.I., Rogozina, I.B., Grishinb, N.V., Koonin, E.V.: Genome trees and the tree of life. Trends in Genetics 18(9), 472–479 (2002)CrossRefGoogle Scholar
  3. 3.
    Sauer, U.: Metabolic networks in motion: 13 C-based flux analysis. Molecular Systems Biology 2(62) (2006)Google Scholar
  4. 4.
    Forst, C.V., Flamm, C., Hofacker, I.L., Stadler, P.F.: Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics 7(1), 67–78 (2006)CrossRefGoogle Scholar
  5. 5.
    Liao, L., Kim, S., Tomb, J.F.: Genome comparisons based on profiles of metabolic pathways. In: Proc. of the 6th International Conference on Knowledge-Based Intelligent Information and Engineering Systems, pp. 469–476 (2002)Google Scholar
  6. 6.
    Ma, H.W., Zeng, A.P.: Phylogenetic comparison of metabolic capacities of organisms at genome level. Molecular Phylogenetics and Evolution 31(1), 204–213 (2004)CrossRefGoogle Scholar
  7. 7.
    Tohsato, Y.: A Method for Species Comparison of Metabolic Networks Using Reaction Profile. IPSJ Digital Courier 2(0), 685–690 (2006)CrossRefGoogle Scholar
  8. 8.
    Peregrin-Alvarez, J.M., Tsoka, S., Ouzounis, C.A.: The Phylogenetic Extent of Metabolic Enzymes and Pathways. Genome Research 13(3), 422–427 (2003)CrossRefGoogle Scholar
  9. 9.
    Liu, W., Lin, W., Davis, A., Jordan, F., Yang, H., Hwang, M.: A network perspective on the topological importance of enzymes and their phylogenetic conservation. BMC Bioinformatics 8(121) (2007)Google Scholar
  10. 10.
    Zhu, D., Qin, Z.S.: Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics 6(8) (2005)Google Scholar
  11. 11.
    Zhang, Y., Zhang, Z., Ling, L., Shi, B., Chen, R.: Conservation analysis of small RNA genes in Escherichia coli. Bioinformatics 20(5), 599–603 (2004)CrossRefGoogle Scholar
  12. 12.
    Yamada, T., Kanehisa, M., Goto, S.: Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics 7(1) (2006)Google Scholar
  13. 13.
    Lu, C., Zhang, Z., Leach, L., Kearsey, M.J., Luo, Z.W.: Impacts of yeast metabolic network structure on enzyme evolution. Genome Biology 8(407) (2007)Google Scholar
  14. 14.
    Vitkup, D., Kharchenko, P., Wagner, A.: Influence of metabolic network structure and function on enzyme evolution. Genome Biology 7(R39) (2006)Google Scholar
  15. 15.
    Aittokallio, T., Schwikowski, B.: Graph-based methods for analysing networks in cell biology. Briefings in Bioinformatics 7(3), 243 (2006)CrossRefGoogle Scholar
  16. 16.
    Mason, O., Verwoerd, M.: Graph Theory and Networks in Biology. IET Syst. Biol. 1(2), 89–119 (2007)CrossRefGoogle Scholar
  17. 17.
    Brandes, U.: A faster algorithm for betweenness centrality. Journal of Mathematical Sociology 25(2), 163–177 (2001)zbMATHGoogle Scholar
  18. 18.
    Ma, H.W., Zeng, A.P.: Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19(2), 270–277 (2003)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Tingting Zhou
    • 1
    • 2
  • Keith C. C. Chan
    • 2
  • Yi Pan
    • 3
  • Zhenghua Wang
    • 1
  1. 1.National Laboratory for Paralleling and Distributed Processing, School of ComputerNational University of Defense TechnologyChangsha, HunanP.R. of China
  2. 2.Department of computingThe Hong Kong Polytechnic UniversityHong KongChina
  3. 3.Department of Computer ScienceGeorgia State UniversityAtlantaUSA

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