Siavash Mirarab, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow, 'Statistical Binning Enables an Accurate Coalescent-Based Estimation of the Avian Tree', Science (2014).
Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce accuracy of concatenation-based estimations of species trees. While 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 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 MPEST, a popular coalescent-based method, and we use it to produce the first genome-scale coalescent-based avian tree of life.