鸟类基因组及演化生物学研究

基于溯祖理论的构树方法

文章引用

Siavash Mirarab, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow, 'Statistical Binning Enables an Accurate Coalescent-Based Estimation of the Avian Tree', Science (2014).

英文摘要

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.

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