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

Author:
Mirarab, Siavash, Bayzid, Md. Shamsuzzoha, Boussau, Bastien, Warnow, Tandy
Source:
Science 2014 v.346 no.6215 pp. 1250463
ISSN:
0036-8075
Subject:
birds, genes, phylogeny, trees
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.
Agid:
3129424