Molecular Phylogenetic Trees: Topology of Multiparametric Poly-Genic/Phenic Tree Exhibits Higher Taxonomic Fidelity than Uniparametric Trees for Mono-Genic/Phenic Traits

  • Sohan Prabhakar Modak
  • M. Milner Kumar
  • Rhishikesh Bargaje


Darwin (On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life, John Murray, London 1859) used polygenic traits or characters to describe the relationships among a set of organisms in the form of phylogenetic trees that generally overlap the taxonomic hierarchy. Recently, phylogenetic trees are being constructed for single genes or proteins from a set of species for which sequences are available. Such trees for a given set of species exhibit different topologies for different genes or proteins causing considerable controversy due to the lack of an appropriate benchmark for taxonomic relationships. One of the solutions offered is to end-to-end ligate (concatenate) multiple sequences and generate a polygene or polyprotein string and align these among a set of species to construct phylogenetic trees that exhibit topologies comparable to taxonomic hierarchy. Nevertheless, the problem remains as trees using rRNA sequences do not offer a satisfactory benchmark to taxonomic hierarchy. We have developed an algorithm that compares the topology of a given phylogenetic tree to the taxonomic tree for the same set of species and estimates the clade-by-clade correspondence or Taxonomic fidelity between them. We further describe a novel method, “Darwin’s Dream,” based on Euclidean geometry to estimate all-pairs distances among species for at least three traits/characters/sequences. The topology of phylogenetic trees for polygenic traits built using this method offer superior Taxonomic fidelity to that for either uniparametric trees, for rRNA or even concatenated sequences. A consensus phylogeny for three mitochondrial polypeptides shows that using both Euclidean geometry and concatenation method, hemichordates and cephalochordates cluster with echinoderms at the root of chordates, while Urochordates group with protostomes. The method was further extended to generate a consensus polygenic tree for 15 tRNA synthetases from prokaryotes which exhibited superior taxonomic fidelity than trees for single proteins or 16 s rDNA or even that for 15 concatenated sequences. The method is also applicable for immunocrossreactivity or a combination of beta globin gene- and coding nucleotide sequences and amino acid sequences of beta globin polypeptide.


Phylogenetic Tree Tree Topology Neighbor Join Taxonomic Tree Sister Clade 
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.



A part of the work in this review contributed to the Ph.D. thesis of Milner Kumar at Karnatak University, Dharwad, India. We thank Prof. S. A. Nevagi for encouragement and Prof. N. K. Ganguly, New Delhi, India and Dr. Georges Spohr, Geneva, Switzerland, for critical comments.


  1. Archie JW (1989) Homoplasy excess ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. Syst Biol 38:253–269Google Scholar
  2. Bansode AJ (1985) Evolutionary relationship in Chiroptera: biochemical analysis, pp 1–163. PhD thesis, University of Poona, Pune, IndiaGoogle Scholar
  3. Bargaje, R, Milner Kumar M, Modak SP (2012) Multiparametric phylogeny of 15 amino acyl tRNA synthetases and taxonomic fidelity (submitted for publication)Google Scholar
  4. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW (2012) GenBank. Nucleic Acids Res 40:D48–D53PubMedCrossRefGoogle Scholar
  5. Blair JE, Hedges SB (2005) Molecular phylogeny and divergence times of deuterostome animals. Mol Biol Evol 22:2275–2284PubMedCrossRefGoogle Scholar
  6. Boake CR, Arnold SJ, Breden F, Meffert LM, Ritchie MG, Taylor BJ, Wolf JB, Moore AJ (2002) Genetic tools for studying adaptation and the evolution of behavior. Am Nat 160(suppl 6):S143–S159PubMedCrossRefGoogle Scholar
  7. Brocchieri L (2001) Phylogenetic inferences from molecular sequences: review and critique. Theor Popul Biol 59(1):27–40Google Scholar
  8. Brown WM, George M, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci U S A 76:1967–1971PubMedCrossRefGoogle Scholar
  9. Brusca RC, Brusca GJ (2003) Invertebrates. Sinauer Associates, SunderlandGoogle Scholar
  10. Cao Y, Waddell PJ, Okada N, Hasegawa M (1998) The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates. Mol Biol Evol 15:1637–1646PubMedCrossRefGoogle Scholar
  11. Chapus C, Dufraigne C, Edwards S, Giron A, Fertil B, Deschavanne P (2005) Exploration of phylogenetic data using a global sequence analysis method. BMC Evol Biol 5:63PubMedCrossRefGoogle Scholar
  12. Darwin C (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, LondonGoogle Scholar
  13. Delsuc F, Brinkmann H, Chourrout D, Philippe H (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439:965–968PubMedCrossRefGoogle Scholar
  14. Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B (1999) Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol 16:1391–1399 PubMedCrossRefGoogle Scholar
  15. Edwards SV, Fertil B, Giron A, Deschavanne PJ (2002) A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Syst Biol 51:599–613PubMedCrossRefGoogle Scholar
  16. Farris JS (1989) The retention index and the rescaled consistency index. Cladistics 5:417–419CrossRefGoogle Scholar
  17. Federhen S (2012) The NCBI taxonomy database. Nucleic Acids Res 40:D136–D143PubMedCrossRefGoogle Scholar
  18. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution (N Y) 39:783–791Google Scholar
  19. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, SeattleGoogle Scholar
  20. Fertil B, Massin M, Lespinats S, Devic C, Dumee P, Giron A (2005) GENSTYLE: exploration and analysis of DNA sequences with genomic signature. Nucleic Acids Res 33(Web Server issue):W512–W515Google Scholar
  21. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279–284PubMedCrossRefGoogle Scholar
  22. Fitch WM, Markowitz E (1970) An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet 4:579–593PubMedCrossRefGoogle Scholar
  23. Gadagkar SR, Rosenberg MS, Kumar S (2005) Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J Exp Zool B Mol Dev Evol B 304:64–74CrossRefGoogle Scholar
  24. Goodman M, Moore GW (1975) Darwinian evolution in the genealogy of haemoglobin. Nature 253:603–608PubMedCrossRefGoogle Scholar
  25. Hennig W (1965) Phylogenetic systematics. Annu Rev Entomol 10:97–116CrossRefGoogle Scholar
  26. Hennig W (1975) Cladistic analysis or cladistic classification? A reply to Ernst Mayr. Syst Zool 24:244–256CrossRefGoogle Scholar
  27. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  28. Kamakaka RT (1984) Homology of lens crystallins in Reptilia, pp 1–24. M Phil Dissertation, University of Poona, Pune, IndiaGoogle Scholar
  29. King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188:107–116PubMedCrossRefGoogle Scholar
  30. Kulkarni SN (1985) Homology of Amphibian lens crystallins, pp 1–36. M Phil Dissertation, University of Poona, Pune, IndiaGoogle Scholar
  31. Lewin B, Krebs JE, Goldstein ES, Kilpatrick ST (2009) Lewin’s genes 10. Jones and Bartlett, MassachusettsGoogle Scholar
  32. Mayr E (1970) Populations, species, and evolution: an abridgment of animal species and evolution. Belknap Press of Harvard University Press, HarvardGoogle Scholar
  33. Mayr E (1974) The species problem. Arno Press, New YorkGoogle Scholar
  34. Milner Kumar M (2009) Multiparametric molecular phylogenetic trees in 3D. PhD thesis submitted to Department of zoology, Karnatak University, Dharwad, IndiaGoogle Scholar
  35. Milner Kumar M, Modak SP (2011) Estimating taxonomic fidelity of phylogenetic trees (manuscript submitted for publication)Google Scholar
  36. Milner Kumar M, Modak SP (2012) Multiparametric molecular phylogeny of eukaryotic mitochondrial polypeptides and taxonomic fidelity estimation (manuscript submitted for publication)Google Scholar
  37. Milner M, Patwardhan V, Bansode A, Nevagi SA, Kulkarni S, Kamakaka R, Modak SP (2003) Constructing 3D phylogenetic trees. Curr Sci 85:1471–1478Google Scholar
  38. Milner M, Bansode AG, Lawrence AL, Nevagi SA, Patwardhan V, Modak SP (2004) Molecular phylogeny in 3-D. Curr Issues Mol Biol 6:189–200PubMedGoogle Scholar
  39. Mount DW (2004) Bioinformatics: sequence and genome analysis. CSHL Press, New YorkGoogle Scholar
  40. Naylor GJP, Brown WM (1997) Structural biology and phylogenetic estimation. Nature 388:527–528PubMedCrossRefGoogle Scholar
  41. Nuin P, Wang Z, Tillier E (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7:471PubMedCrossRefGoogle Scholar
  42. Page RDM, Holmes EC (1998) Molecular evolution: a phylogenetic approach. Blackwell Publishing Limited, OxfordGoogle Scholar
  43. Patwardhan V (1992) Phylogeny of fish lens crystallins, pp 1–101. PhD thesis, University of Poona, Pune, IndiaGoogle Scholar
  44. Rannala B, Yang Z (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645–1656PubMedGoogle Scholar
  45. Rasmussen AS, Arnason U (1999) Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes within the tree of bony fishes. J Mol Evol 48:118–123PubMedCrossRefGoogle Scholar
  46. Rosbash M, Ford PJ, Bishop JO (1974) Analysis of the C-value paradox by molecular hybridization. Proc Natl Acad Sci U S A 71:3746–3750PubMedCrossRefGoogle Scholar
  47. Rzhetsky A, Nei M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073–1095PubMedGoogle Scholar
  48. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  49. Sokal RR, Michener CD (1958) A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 28:1409–1438Google Scholar
  50. Suthers RA (1970) Visual, olfaction and taste. In: Wimsatt WA (ed) Biology of bats, vol 1. Academic press, New York, pp 265–304Google Scholar
  51. Takezaki N, Gojobori T (1999) Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences. Mol Bio Evol 16:590–601CrossRefGoogle Scholar
  52. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCrossRefGoogle Scholar
  53. Woese C (1998) The universal ancestor. Proc Natl Acad Sci U S A 95:6854–6859PubMedCrossRefGoogle Scholar
  54. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74:5088–5090PubMedCrossRefGoogle Scholar
  55. Yang Z, Rannala B (1997) Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol Biol Evol 14:717–724PubMedCrossRefGoogle Scholar
  56. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New York, pp 97–166Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Sohan Prabhakar Modak
    • 1
    • 2
  • M. Milner Kumar
    • 1
    • 2
  • Rhishikesh Bargaje
    • 1
    • 2
    • 3
  1. 1.Open VisionPuneIndia
  2. 2.Computational Research Laboratories LimitedPuneIndia
  3. 3.Institute of Genomics and Integrative BiologyDelhiIndia

Personalised recommendations