Gene tree incongruence resulting from incomplete lineage sorting (ILS) can
    make standard species tree estimation methods, such as concatenation, have poor
    accuracy. While coalescent-based methods can accurately estimate species trees in the
    presence of ILS, these methods can be less accurate than concatenation when estimated
    gene trees are insufficiently accurate. We present a new “statistical binning”
    technique to address this challenge: we use a statistical test for combinability and a
    graph-theoretic optimization to bin genes into subsets, estimate trees on each subset
    using concatenation, and then combine the “supergene” trees using the preferred
    coalescent-based method. We show that statistical binning dramatically improves the
    accuracy of MP-EST, a leading coalescent-based method, and we use statistical binning
    to produce the first genome-scale coalescent-based avian tree of life.