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Issue No. 06 - Nov.-Dec. (2012 vol. 9)
ISSN: 1545-5963
pp: 1558-1568
J. H. Degnan , Dept. of Math. & Stat., Univ. of Canterbury, Christchurch, New Zealand
N. A. Rosenberg , Dept. of Biol., Stanford Univ., Stanford, CA, USA
T. Stadler , Inst. of Integrative Biol., ETH Zurich, Zurich, Switzerland
Ranked gene trees, which consider both the gene tree topology and the sequence in which gene lineages separate, can potentially provide a new source of information for use in modeling genealogies and performing inference of species trees. Recently, we have calculated the probability distribution of ranked gene trees under the standard multispecies coalescent model for the evolution of gene lineages along the branches of a fixed species tree, demonstrating the existence of anomalous ranked gene trees (ARGTs), in which a ranked gene tree that does not match the ranked species tree can have greater probability under the model than the matching ranked gene tree. Here, we fully characterize the set of unranked species tree topologies that give rise to ARGTs, showing that this set contains all species tree topologies with five or more taxa, with the exceptions of caterpillars and pseudocaterpillars. The results have implications for the use of ranked gene trees in phylogenetic inference.
Genetics, Topology, History, Computational biology, Bioinformatics, Phylogeny

J. H. Degnan, N. A. Rosenberg and T. Stadler, "A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 6, pp. 1558-1568, 2013.
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