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Wiley InterScience

Evolution

Evolution

Volume 59 Issue 1, Pages 24 - 37

Published Online: 9 May 2007

© 2010, Society for the Study of Evolution



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GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS
James H. Degnan 1 , 2 Laura A. Salter 1 , 3
  1 Department of Mathematics and Statistics, MSC03 2150, University of New Mexico, Albuquerque, New Mexico 87131
Copyright 2005 The Society for the Study of Evolution
KEYWORDS
Coalescence • coalescent history • lineage Sorting • maximum likelihood • phylogenetics • species tree.

ABSTRACT

 Abstract

Under the coalescent model for population divergence, lineage sorting can cause considerable variability in gene trees generated from any given species tree. In this paper, we derive a method for computing the distribution of gene tree topologies given a bifurcating species tree for trees with an arbitrary number of taxa in the case that there is one gene sampled per species. Applications for gene tree distributions include determining exact probabilities of topological equivalence between gene trees and species trees and inferring species trees from multiple datasets. In addition, we examine the shapes of gene tree distributions and their sensitivity to changes in branch lengths, species tree shape, and tree size. The method for computing gene tree distributions is implemented in the computer program COAL.


Received June 18, 2004. Accepted October 8, 2004.

DIGITAL OBJECT IDENTIFIER (DOI)
10.1111/j.0014-3820.2005.tb00891.x About DOI

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