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Issue No.06 - Nov.-Dec. (2012 vol.9)
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,population genetics, Anomalous gene trees, coalescent, genealogies, phylogenetics
J. H. Degnan, N. A. Rosenberg, T. Stadler, "A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, no. 6, pp. 1558-1568, Nov.-Dec. 2012, doi:10.1109/TCBB.2012.110
[1] M. DeGiorgio and J.H. Degnan, “Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples,” Molecular Biology and Evolution, vol. 27, pp. 552-569, 2010.
[2] J.H. Degnan, M. DeGiorgio, D. Bryant, and N.A. Rosenberg, “Properties of Consensus Methods for Inferring Species Trees from Gene Trees,” Systematic Biology, vol. 58, pp. 35-54, 2009.
[3] J.H. Degnan and N.A. Rosenberg, “Discordance of Species Trees with Their Most Likely Gene Trees,” PLoS Genetics, vol. 2, pp. 762-768, 2006.
[4] J.H. Degnan and N.A. Rosenberg, “Gene Tree Discordance, Phylogenetic Inference, and the Multispecies Coalescent,” Trends in Ecology and Evolution, vol. 24, pp. 332-340, 2009.
[5] J.H. Degnan, N.A. Rosenberg, and T. Stadler, “The Probability Distribution of Ranked Gene Trees on a Species Tree,” Math. Biosciences, vol. 235, pp. 45-55, 2012.
[6] J.H. Degnan and L.A. Salter, “Gene Tree Distributions under the Coalescent Process,” Evolution, vol. 59, pp. 24-37, 2005.
[7] G.B. Ewing, I. Ebersberger, H.A. Schmidt, and A. von Haeseler, “Rooted Triple Consensus and Anomalous Gene Trees,” BMC Evolutionary Biology, vol. 8, article 118, 2008.
[8] E.M. Jewett and N.A. Rosenberg, “iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees,” J. Computational Biology, vol. 19, pp. 293-315, 2012.
[9] L. Liu and S.V. Edwards, “Phylogenetic Analysis in the Anomaly Zone,” Systematic Biology, vol. 58, pp. 452-460, 2009.
[10] L. Liu, L. Yu, D.K. Pearl, and S.V. Edwards, “Estimating Species Phylogenies Using Coalescence Times Among Sequences,” Systematic Biology, vol. 58, pp. 468-477, 2009.
[11] E. Mossel and S. Roch, “Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 7, no. 1, pp. 166-171, Jan.-Mar. 2010.
[12] P. Pamilo and M. Nei, “Relationships between Gene Trees and Species Trees,” Molecular Biology and Evolution, vol. 5, pp. 568-583, 1988.
[13] N.A. Rosenberg, “The Probability of Topological Concordance of Gene Trees and Species Trees,” Theoretical Population Biology, vol. 61, pp. 225-247, 2002.
[14] N.A. Rosenberg, “Counting Coalescent Histories,” J. Computational Biology, vol. 14, pp. 360-377, 2007.
[15] N.A. Rosenberg and R. Tao, “Discordance of Species Trees with Their Most Likely Gene Trees: The Case of Five Taxa,” Systematic Biology, vol. 57, pp. 131-140, 2008.
[16] T. Stadler and J.H. Degnan, “A Polynomial Time Algorithm for Calculating the Probability of a Ranked Gene Tree Given a Species Tree,” Algorithms for Molecular Biology, vol. 7, article 7, 2012.
[17] N. Takahata, “Gene Genealogy in Three Related Populations: Consistency Probability between Gene and Population Trees,” Genetics, vol. 122, pp. 957-966, 1989.
[18] S. Tavaré, “Line-of-Descent and Genealogical Processes, and Their Applications in Population Genetics Models,” Theoretical Population Biology, vol. 26, pp. 119-164, 1984.
[19] C.V. Than and N.A. Rosenberg, “Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences,” J. Computational Biology, vol. 18, pp. 1-15, 2010.
[20] Y. Wang and J.H. Degnan, “Performance of Matrix Representation with Parsimony for Inferring Species From Gene Trees,” Statistical Applications in Genetics and Molecular Biology, vol. 10, article 21, 2011.
[21] Y. Wu, “Coalescent-Based Species Tree Inference from Gene Tree Topologies under Incomplete Lineage Sorting by Maximum Likelihood,” Evolution, vol. 66, pp. 763-775, 2012.
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