Coevolution of Gene Families: Models, Algorithms, and Systems Biology

  • Tamir Tuller


A pair of gene families coevolves if the two gene families have correlative patterns of evolution. Recent studies in the field of evolutionary systems biology have demonstrated the advantages of exploiting co-evolutionary information. Specifically, it was shown that coevolution can be used for inferring physical and functional interactions, and ancestral genomic sequences; in addition, it was shown that co-evolution information can be utilized for understanding cellular systems and their evolution. To this end, corresponding models, algorithms, and statistical approaches have been developed. In this chapter, I review the recent advances in the field concentrating on algorithms for analyzing co-evolutionary information and their applications.


Evolutionary Tree Protein Interaction Network Reconstructed Ancestral State Ancestral Reconstruction Green Edge 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Barker D, Meade A, Pagel M (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics 23(1):14–20PubMedCrossRefGoogle Scholar
  2. Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A 102(40):14332–14337PubMedCrossRefGoogle Scholar
  3. Birin H, Tuller T (2011) Efficient algorithms for reconstructing gene content by co-evolution. BMC Bioinform 12:S12CrossRefGoogle Scholar
  4. Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG (2004) Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci U S A 101(26):9722–9727PubMedCrossRefGoogle Scholar
  5. Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO et al (2004) Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 5(5):R35PubMedCrossRefGoogle Scholar
  6. Bridgham JT, Carroll SM, Thornton JW (2006) Evolution of hormone-receptor complexity by molecular exploitation. Science 312(5770):97–101PubMedCrossRefGoogle Scholar
  7. Chang JT (1996) Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Math Biosci 137(1):51–73PubMedCrossRefGoogle Scholar
  8. Chen Y, Dokholyan NV (2006) The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet 22(8):416–419PubMedCrossRefGoogle Scholar
  9. Dagan T (2011) Phylogenomic networks. Trends Microbiol 19(10):483–491PubMedCrossRefGoogle Scholar
  10. Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6(5):361–375PubMedCrossRefGoogle Scholar
  11. Dieterich C, Clifton SW, Schuster LN, Chinwalla A, Delehaunty K et al (2008) The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet 40(10):1193–1198PubMedCrossRefGoogle Scholar
  12. Elias I, Tuller T (2007) Reconstruction of ancestral genomic sequences using likelihood. J Comput Biol 14(2):216–237PubMedCrossRefGoogle Scholar
  13. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376PubMedCrossRefGoogle Scholar
  14. Felsenstein J (1993) PHYLIP (phylogeny inference package) version 3.5c: Technical report, Department of genetics, University of Washington, SeattleGoogle Scholar
  15. Fitch W (1971) Toward defining the course of evolution: minimum change for a specified tree topology. Syst Z 20:406–416CrossRefGoogle Scholar
  16. Hershberg R, Yeger-Lotem E, Margalit H (2005) Chromosomal organization is shaped by the transcription regulatory network. Trends Genet 21(3):138–142PubMedCrossRefGoogle Scholar
  17. Hirsh AE, Fraser HB, Wall DP (2005) Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol 22(1):174–177PubMedCrossRefGoogle Scholar
  18. Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276(5310):227–232PubMedCrossRefGoogle Scholar
  19. Jermiin LS, Poladian L, Charleston MA (2005) Evolution. Is the “Big Bang” in animal evolution real? Science 310(5756):1910–1911PubMedCrossRefGoogle Scholar
  20. Juan D, Pazos F, Valencia A (2008) High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci U S A 105(3):934–939PubMedCrossRefGoogle Scholar
  21. Kelley BP, Sharan R, Karp RM, Sittler T, Root DE et al (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A 100(20):11394–11399PubMedCrossRefGoogle Scholar
  22. Kelley R, Ideker T (2005) Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23(5):561–566PubMedCrossRefGoogle Scholar
  23. Li G, Steel M, Zhang L (2008) More taxa are not necessarily better for the reconstruction of ancestral character states. Syst Biol 57(4):647–653PubMedCrossRefGoogle Scholar
  24. Lovell SC, Robertson DL (2010) An integrated view of molecular coevolution in protein–protein interactions. Mol Biol Evol 27(11):2567–2575PubMedCrossRefGoogle Scholar
  25. Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC et al (2006) Reconstructing contiguous regions of an ancestral genome. Genome Res 16(12):1557–1565PubMedCrossRefGoogle Scholar
  26. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S et al (2004) Superfamilies of evolved and designed networks. Science 303(5663):1538–1542PubMedCrossRefGoogle Scholar
  27. Ouzounis CA, Kunin V, Darzentas N, Goldovsky L (2006) A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective. Res Microbiol 157(1):57–68PubMedCrossRefGoogle Scholar
  28. Pagel M (1999a) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst Biol 48(3):612–622CrossRefGoogle Scholar
  29. Pagel M (1999b) Inferring the historical patterns of biological evolution. Nature 401(6756):877–884PubMedCrossRefGoogle Scholar
  30. Pazos F, Valencia A (2008) Protein co-evolution, co-adaptation and interactions. Embo J 27(20):2648–2655PubMedCrossRefGoogle Scholar
  31. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J et al (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317(5834):86–94PubMedCrossRefGoogle Scholar
  32. Sankoff D (1975) Minimal mutation trees of sequences. SIAM J Appl Math 28:35–42CrossRefGoogle Scholar
  33. Segre D, Deluna A, Church GM, Kishony R (2005) Modular epistasis in yeast metabolism. Nat Genet 37(1):77–83PubMedGoogle Scholar
  34. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S et al (2005) Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A 102(6):1974–1979PubMedCrossRefGoogle Scholar
  35. Snel B, Huynen MA (2004) Quantifying modularity in the evolution of biomolecular systems. Genome Res 14(3):391–397PubMedCrossRefGoogle Scholar
  36. Teeling EC, Springer MS, Madsen O, Bates P, O’Brien SJ et al (2005) A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307(5709):580–584PubMedCrossRefGoogle Scholar
  37. Thornton JW (2004) Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet 5(5):366–375PubMedCrossRefGoogle Scholar
  38. Tuller T, Mossel E (2010) Co-Evolution is incompatible with the markov assumption in phylogenetics. IEEE/ACM Trans Comput Biol Bioinform 2010:24Google Scholar
  39. Tuller T, Kupiec M, Ruppin E (2009a) Co-evolutionary networks of genes and cellular processes across fungal species. Genome Biol 10(5):R48PubMedCrossRefGoogle Scholar
  40. Tuller T, Felder Y, Kupiec M (2010a) Discovering local patterns of co-evolution: computational aspects and biological examples. BMC Bioinformatics 11(43):43PubMedCrossRefGoogle Scholar
  41. Tuller T, Birin H, Kupiec M, Ruppin E (2010b) Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples. J Comput Biol 17(9):1327–1344PubMedCrossRefGoogle Scholar
  42. Tuller T, Birin H, Gophna U, Kupiec M, Ruppin E (2009b) Reconstructing ancestral gene content by coevolution. Genome Res 20(1):122–132PubMedCrossRefGoogle Scholar
  43. Ulitsky I, Shamir R (2007) Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol 3(104):104PubMedGoogle Scholar
  44. Wu J, Kasif S, DeLisi C (2003) Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19(12):1524–1530PubMedCrossRefGoogle Scholar
  45. Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17(1):32–43PubMedCrossRefGoogle Scholar
  46. Zhang X, Kupiec M, Gophna U, Tuller T (2011) Analysis of coevolving gene families using mutually exclusive orthologous modules. Genome Biol Evol 3:413–423PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Department of Biomedical EngineeringTel Aviv UniversityRamat AvivIsrael

Personalised recommendations