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In Silico AFLP: An Application to Assess What Is Needed to Resolve a Phylogeny

  • María Jesús García-Pereira
  • Armando Caballero
  • Humberto Quesada
Conference paper
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 74)

Abstract

We examined the effect of increasing the number of scored AFLP bands to reconstruct an accurate and well-supported AFLP-based phylogeny. In silico AFLP was performed using simulated DNA sequences evolving along a symmetric tree with ancient radiation. The comparison of the true tree to the estimated AFLP trees suggests that moderate numbers of AFLP bands are necessary to recover the correct topology with high bootstrap support values (i.e > 70%). However, branch length estimation is rather unreliable and does not improve substantially after a certain number of bands are sampled.

Keywords

AFLP phylogeny bootstrap support simulation accuracy 

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References

  1. 1.
    Meudt, H.M., Clark, A.C.: Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant. Sci. 12, 106–117 (2007)CrossRefGoogle Scholar
  2. 2.
    García-Pereira, M.J., Caballero, A., Quesada, H.: Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets. Mol. Biol. Evol. (in press, 2010)Google Scholar
  3. 3.
    Rambaut, A., Grassly, N.C.: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235–238 (1997)Google Scholar
  4. 4.
    Swofford, D.L.: PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts (1999)Google Scholar
  5. 5.
    Soria-Carrasco, V., Talavera, G., Igea, J., Castresana, J.: The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics 23, 2954–2956 (2007)CrossRefGoogle Scholar
  6. 6.
    Robinson, D.F., Foulds, L.R.: Comparison of phylogenetic trees. Math. Biosci. 53, 131–147 (1981)zbMATHCrossRefMathSciNetGoogle Scholar
  7. 7.
    Simmons, M.P., Webb, C.T.: Quantification of the success of phylogenetic inference in simulations. Cladistics 22, 249–255 (2006)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • María Jesús García-Pereira
    • 1
  • Armando Caballero
    • 1
  • Humberto Quesada
    • 1
  1. 1.Departamento de Bioquímica, Genética e Inmunología, Facultad de BiologíaUniversidad de VigoVigoSpain

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