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Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci
January-March 2010 (vol. 7 no. 1)
pp. 166-171
Elchanan Mossel, UC Berkeley, Berkeley
Sebastien Roch, Microsoft Research, Redmond
We introduce a simple computationally efficient algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our technique is statistically consistent under standard stochastic assumptions, that is, it returns the correct tree given sufficiently many unlinked loci. We also show that it can tolerate moderate estimation errors.

[1] J.H. Degnan and N.A. Rosenberg, "Discordance of Species Trees with Their Most Likely Gene Trees," PLoS Genetics, vol. 2, no. 5, May 2006.
[2] V.E. Scott, L. Liu, and D.K. Pearl, "High-Resolution Species Trees without Concatenation," Proc. Nat'l Academy of Sciences USA, vol. 104, no. 14, pp. 5936-5941, 2007.
[3] P.L. Erdös, M.A. Steel, L.A. Székely, and T.A. Warnow, "A Few Logs Suffice to Build (Almost) All Trees (Part 1)," Random Structure and Algorithms, vol. 14, no. 2, pp. 153-184, 1999.
[4] J. Felsenstein, Inferring Phylogenies. Sinauer, 2004.
[5] J. Hey and C.A. Machado, "The Study of Structured Populations— New Hope for a Difficult and Divided Science," Nature Rev. Genetics, vol. 4, no. 7, pp. 535-543, July 2003.
[6] J. Hein, M.H. Schierup, and C. Wiuf, Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory. Oxford Univ. Press, Feb. 2005.
[7] L.S. Kubatko and J.H. Degnan, "Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence," Systematic Biology, vol. 56, no. 1, pp. 17-24, Feb. 2007.
[8] J.F.C. Kingman, "On the Genealogy of Large Populations," J. Applied Probability, special vol. 19A, Essays in Statistical Science, pp. 27-43, 1982.
[9] L.L. Knowles, "The Burgeoning Field of Statistical Phylogeography," J. Evolutionary Biology, vol. 17, no. 1, pp. 1-10, 2004.
[10] L.L. Knowles and W.P. Maddison, "Statistical Phylogeography," Molecular Ecology, vol. 11, no. 12, pp. 2623-2635, 2002.
[11] W.P. Maddison, "Gene Trees in Species Trees," Systematic Biology, vol. 46, no. 3, pp. 523-536, 1997.
[12] W. Maddison and L. Knowles, "Inferring Phylogeny Despite Incomplete Lineage Sorting," Systematic Biology, vol. 55, no. 1, pp. 21-30, Feb. 2006.
[13] R. Nichols, "Gene Trees and Species Trees Are Not the Same," Trends in Ecology & Evolution, vol. 16, no. 7, pp. 358-364, July 2001.
[14] M. Nordborg, "Coalescent Theory," Handbook of Statistical Genetics, D.J. Baldingand, M.J. Bishop, and C. Cannings, eds., pp. 179-212, John Wiley & Sons, 2001.
[15] P. Pamilo and M. Nei, "Relationships between Gene Trees and Species Trees," Molecular Biology and Evolution, vol. 5, no. 5, pp. 568-583, Sept. 1988.
[16] N.A. Rosenberg, "The Probability of Topological Concordance of Gene Trees and Species Trees," Theoretical Population Biology, vol. 61, no. 2, pp. 225-247, Mar. 2002.
[17] M. Steel and A. Rodrigo, "Maximum Likelihood Supertrees," Systematic Biology, vol. 57, no. 2, pp. 243-250, 2008.
[18] C. Semple and M. Steel, "Phylogenetics," Mathematics and Its Applications Series 22, Oxford Univ. Press, 2003.
[19] N. Takahata, "Gene Genealogy in Three Related Population: Consistency Probability between Gene and Population Trees," Genetics, vol. 122, pp. 957-966, 1989.
[20] S. Tavaré, "Line-of-Descent and Genealogical Processes, and Their Applications in Population Genetics Models," Theoretical Population Biology, vol. 26, no. 2, pp. 119-164, Oct. 1984.
[21] S. Tavaré, "Ancestral Inference in Population Genetics," Lectures on Probability Theory and Statistics, Lecture Notes in Mathematics 1837, pp. 1-188, Springer, 2004.

Index Terms:
Incomplete lineage sorting, coalescent process, topological concordance, statistical consistency.
Elchanan Mossel, Sebastien Roch, "Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 1, pp. 166-171, Jan.-March 2010, doi:10.1109/TCBB.2008.66
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