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

Siavash Mirarab, Md Shamsuzzoha Bayzid, Bastien Boussau, Tandy Warnow

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Article number1250463
JournalScience
Volume346
Issue number6215
DOIs
StatePublished - Dec 12 2014

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Statistical binning enables an accurate coalescent-based estimation of the avian tree. / Mirarab, Siavash; Bayzid, Md Shamsuzzoha; Boussau, Bastien; Warnow, Tandy.

In: Science, Vol. 346, No. 6215, 1250463, 12.12.2014.

Research output: Contribution to journalArticle

Mirarab, Siavash ; Bayzid, Md Shamsuzzoha ; Boussau, Bastien ; Warnow, Tandy. / Statistical binning enables an accurate coalescent-based estimation of the avian tree. In: Science. 2014 ; Vol. 346, No. 6215.
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