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Hybrid Genetic Algorithm and Lasso Test Approach for Inferring Well Supported Phylogenetic Trees Based on Subsets of Chloroplastic Core Genes

  • Bassam AlKindy
  • Christophe Guyeux
  • Jean-François Couchot
  • Michel Salomon
  • Christian Parisod
  • Jacques M. Bahi
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9199)

Abstract

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of “problematic” genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained if the number of problematic genes is low, the problem being to determine the largest subset of core genes that produces the best supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, we propose an hybrid approach that embeds both genetic algorithms and statistical tests. Given a set of organisms, the result is a pipeline of many stages for the production of well supported phylogenetic trees. The proposal has been applied to different cases of plant families, leading to encouraging results for these families.

Keywords

Chloroplasts Phylogeny Genetic algorithms Lasso test 

Notes

Acknowledgement

Computations have been performed on the supercomputer facilities of the Mésocentre de calcul de Franche-Comté.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Bassam AlKindy
    • 1
    • 3
  • Christophe Guyeux
    • 1
  • Jean-François Couchot
    • 1
  • Michel Salomon
    • 1
  • Christian Parisod
    • 2
  • Jacques M. Bahi
    • 1
  1. 1.FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science DepartmentUniversity of Franche-ComtéBesançonFrance
  2. 2.Laboratory of Evolutionary BotanyUniversity of NeuchâtelNeuchâtelSwitzerland
  3. 3.Department of Computer ScienceUniversity of MustansiriyahBaghdadIraq

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