title: Statistical binning enables an accurate coalescent-based estimation of the avian tree.
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.
authors.affiliation: Department of Computer Science, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: Siavash
authors.initials: S
authors.lastname: Mirarab
authors.affiliation: Department of Computer Science, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: Md Shamsuzzoha
authors.initials: MS
authors.lastname: Bayzid
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Université Lyon 1, 69622, Villeurbanne, France.
authors.forename: Bastien
authors.initials: B
authors.lastname: Boussau
authors.affiliation: Department of Computer Science, University of Texas at Austin, Austin, TX 78712, USA. Department of Bioengineering and Computer Science, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA. warnow@illinois.edu.
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
mesh_terms: D000818:Animals; D001717:Birds / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology; D016678:Genome; D016013:Likelihood Functions; D008322:Mammals / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment; D014714:Vertebrates / Q000145:classification / Q000235:genetics; D015003:Yeasts / Q000235:genetics