Statistical binning enables an accurate coalescent-based estimation of the avian tree - Université Claude Bernard Lyon 1
Article Dans Une Revue Science Année : 2014

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Siavash Mirarab
  • Fonction : Auteur
Md. Shamsuzzoha Bayzid
  • Fonction : Auteur
Tandy Warnow
  • Fonction : Auteur

Résumé

Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although coalescent-based species tree estimation methods can have good accuracy in the presence of ILS, they are sensitive to gene tree estimation error. We propose a pipeline that uses bootstrapping to evaluate whether two genes are likely to have the same tree, then it groups genes into sets using a graph-theoretic optimization and estimates a tree on each subset using concatenation, and finally produces an estimated species tree from these trees using the preferred coalescent-based method. Statistical binning improves the accuracy of MP-EST, a popular coalescent-based method, and we use it to produce the first genome-scale coalescent-based avian tree of life.
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Dates et versions

hal-02045118 , version 1 (21-02-2019)

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Citer

Siavash Mirarab, Md. Shamsuzzoha Bayzid, Bastien Boussau, Tandy Warnow. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science, 2014, 346 (6215), pp.1250463. ⟨10.1126/science.1250463⟩. ⟨hal-02045118⟩
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