Statistical binning enables an accurate coalescent-based estimation of the avian tree - PubMed (original) (raw)
. 2014 Dec 12;346(6215):1250463.
doi: 10.1126/science.1250463. Epub 2014 Dec 11.
Affiliations
- PMID: 25504728
- DOI: 10.1126/science.1250463
Statistical binning enables an accurate coalescent-based estimation of the avian tree
Siavash Mirarab et al. Science. 2014.
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.
Copyright © 2014, American Association for the Advancement of Science.
Comment in
- Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".
Liu L, Edwards SV. Liu L, et al. Science. 2015 Oct 9;350(6257):171. doi: 10.1126/science.aaa7343. Science. 2015. PMID: 26450203 - Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".
Mirarab S, Bayzid MS, Boussau B, Warnow T. Mirarab S, et al. Science. 2015 Oct 9;350(6257):171. doi: 10.1126/science.aaa7719. Science. 2015. PMID: 26450204
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