An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees

BMC Bioinformatics

Research

Lawrence H. Uricchio¹  Noah A. Rosenberg¹  Tandy Warnow² 

[1] Department of Biology, Stanford University, Stanford, CA, USA;Departments of Computer Science & Bioengineering, University of Illinois, Urbana-Champaign, IL, USA;

关键词: Bipartitions;    Coalescent;    Gene trees;    Species trees;   

DOI  :  10.1186/s12859-016-1266-4

来源: Springer

【 摘 要 】

BackgroundMany methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify “sufficiently large”.ResultsUsing the multispecies coalescent model, we report a general analytical upper bound on the number of gene trees n required such that with probability q, each bipartition of a species tree is represented at least once in a set of n random gene trees. This bound employs a formula that is straightforward to compute, depends only on the minimum internal branch length of the species tree and the number of taxa, and applies irrespective of the species tree topology. Using simulations, we investigate numerical properties of the bound as well as its accuracy under the multispecies coalescent.ConclusionsOur results are helpful for conservatively bounding the number of gene trees required by the ASTRAL inference method, and the approach has potential to be extended to bound other properties of gene tree sets under the model.

【 授权许可】

CC BY   
© The Author(s) 2016

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