From Networks to Trees

  • Marco Alves
  • Joãd Alves
  • Rui Camacho
  • Pedro Soares
  • Luísa Pereira
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 154)

Abstract

Phylogenetic networks are a useful way of displaying relationships between nucleotide or protein sequences. They diverge from phylogenetic trees as networks present cycles, several possible evolutionary histories of the sequences analysed, while a tree presents a single evolutionary relationship. Networks are especially useful in studying markers with a high level of homoplasy (same mutation happening more than once during evolution) like the control region of mitochondrial DNA (mtDNA), where the researcher does not need to compromise with a single explanation for the evolution suggested by the data. However in many instances, trees are required. One case where this happens is in the founder analysis methodology that aims at estimating migration times of human populations along history and prehistory. Currently, the founder analysis methodology implicates the creation of networks, from where a probable tree will be extracted by hand by the researcher, a time-consuming process, prone to errors and to the ambiguous decisions of the researcher. In order to automate the founder analysis methodology an algorithm that extracts a single probable tree from a network in a fast, systematic way is presented here.

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References

  1. 1.
    Alves, M.: Biblioteca de programas para análise de genética populacional. Master’s thesis, University of Porto (2011)Google Scholar
  2. 2.
    Bandelt, H.J., Forster, P., Sykes, B., Richards, M.: Mitochondrial portraits of human populations using median networks. Genetics 141(2), 743–753 (1995)Google Scholar
  3. 3.
    Bandelt, H.J., Forster, P., Röhl, A.: Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16, 37–48 (1999)Google Scholar
  4. 4.
    Dijkstra, E.W.: A note on two problems in connexion with graphs. Numerische Mathematik 1, 269–271 (1959)MathSciNetMATHCrossRefGoogle Scholar
  5. 5.
    Jarník, V.: O jistém problému minimálním [about a certain minimal problem]. Práce Moravské Přírodovědecké Společnosti 6, 57–63 (1930)Google Scholar
  6. 6.
    Ltd FT: Network 4.6 user guide (2011), http://www.fluxus-engineering.com/Network4600_user_guide.pdf
  7. 7.
    Prim, R.C.: Shortest connection networks and some generalizations. Bell System Technical Journal 36, 1389–1401 (1957)Google Scholar
  8. 8.
    Richards, M.B., Macaulay, V., Hickey, E., Vega, E., Sykes, B., Guida, V., Rengo, C., Sellitto, D., Cruciani, F., Kivisild, T., Villems, R., Thomas, M., Rychkov, S., Rychkov, O., Rychkov, Y., Gölge, M., Dimitrov, D., Hill, E., Bradley, D., Romano, V., Calì, F., Vona, G., Demaine, A., Papiha, S., Triantaphyllidis, C., Stefanescu, G., Hatina, J., Belledi, M., Rienzo, A.D., Novelletto, A., Oppenheim, A., Ren Nørby, S., Al-Zaheri, N., Santachiara-Benerecetti, S., Scozzari, R., Torroni, A., Bandelt, H.J.: Tracing european founder lineages in the near eastern mtdna pool. The American Journal of Human Genetics 67, 1251–1276 (2000)Google Scholar
  9. 9.
    Soares, P., Ermini, L., Thomson, N., Mormina, M., Rito, T., Röhl, A., Salas, A., Oppenheimer, S., Macaulay, V., Richards, M.: Correcting for purifying selection: an improved human mitochondrial molecular clock. American Journal of Human Genetics 84, 740–759 (2009)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Marco Alves
    • 1
  • Joãd Alves
    • 2
  • Rui Camacho
    • 3
  • Pedro Soares
    • 4
  • Luísa Pereira
    • 5
  1. 1.DEI & Faculdade de Engenharia & IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto)Universidade do PortoPortoPortugal
  2. 2.DEI & Faculdade de EngenhariaUniversidade do PortoPortoPortugal
  3. 3.DEI & Faculdade de Engenharia & LIAAD-INESC Porto L.A. (Laboratory of Artificial Intelligence and Decision Support)Universidade do PortoPortoPortugal
  4. 4.IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto)Universidade do PortoPortoPortugal
  5. 5.IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto) & Faculdade de MedicinaUniversidade do PortoPortoPortugal

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