Dec 9, 2016

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

Genetics
Bo Xu, Ziheng Yang

Abstract

The multispecies coalescent (MSC) model has emerged as a powerful framework for inferring species phylogenies while accounting for ancestral polymorphism and gene tree-species tree conflict. A number of methods have been developed in the past few years to estimate the species tree under the MSC. The full likelihood methods (including maximum likelihood and Bayesian inference) average over the unknown gene trees and accommodate their uncertainties properly but involve intensive computation. The approximate or summary coalescent methods are computationally fast and are applicable to genomic datasets with thousands of loci, but do not make an efficient use of information in the multilocus data. Most of them take the two-step approach of reconstructing the gene trees for multiple loci by phylogenetic methods and then treating the estimated gene trees as observed data, without accounting for their uncertainties appropriately. In this article we review the statistical nature of the species tree estimation problem under the MSC, and explore the conceptual issues and challenges of species tree estimation by focusing mainly on simple cases of three or four closely related species. We use mathematical analysis and computer simulation to ...Continue Reading

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Mentioned in this Paper

Gene Polymorphism
Zone
Genome
Genes
Trees (plant)
Likelihood Functions
Phylogenetic Analysis
Morphologically Abnormal Structure (Morphologic Abnormality)
Genetic Pedigree
Phylogeny

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