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
Chapter

Abstract

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.

Keywords

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.

Notes

Acknowledgments

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.

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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

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