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Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics
November/December 2011 (vol. 8 no. 6)
pp. 1667-1670
Tamir Tuller, Weizmann Institute of Science, Rehovot
Elchanan Mossel, Weizmann Institute of Science, Rehovot and University of California Berkeley, Berkeley
Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of orthologous sets of three fungi and their co-evolutionary relations, we demonstrate that co-evolutionary assumption may violate the Markov assumption. Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution.

[1] J. Felsenstein, “Evolutionary Trees from Dna Sequences: A Maximum Likelihood Approach,” J. Molecular Evolution, vol. 17, no. 6, pp. 368-376, 1981.
[2] M. Pagel, “Inferring the Historical Patterns of Biological Evolution,” Nature, vol. 401, no. 6756, pp. 877-884, 1999.
[3] J.P. Huelsenbeck and B. Rannala, “Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context,” Science, vol. 276, no. 5310, pp. 227-232, 1997.
[4] L.S. Jermiin, L. Poladian, and M.A. Charleston, “Evolution Is the “Big Bang” in Animal Evolution Real?,” Science, vol. 310, no. 5756, pp. 1910-1911, 2005.
[5] J.T. Bridgham, S.M. Carroll, and J.W. Thornton, “Evolution of Hormone-Receptor Complexity by Molecular Exploitation,” Science, vol. 312, no. 5770, pp. 97-101, 2006.
[6] E.C. Teeling et al., “A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record,” Science, vol. 307, no. 5709, pp. 580-584, 2005.
[7] C. Dieterich et al., “The Pristionchus Pacificus Genome Provides a Unique Perspective on Nematode Lifestyle and Parasitism,” Nature Genetics, vol. 40, no. 10, pp. 1193-1198, 2008.
[8] F. Delsuc, H. Brinkmann, and H. Philippe, “Phylogenomics and the Reconstruction of the Tree of Life,” Nature Rev. Genetics, vol. 6, no. 5, pp. 361-375, 2005.
[9] J.W. Thornton, “Resurrecting Ancient Genes: Experimental Analysis of Extinct Molecules,” Nature Rev. Genetics, vol. 5, no. 5, pp. 366-375, 2004.
[10] J.T. Chang, “Full Reconstruction of Markov Models on Evolutionary Trees: Identifiability and Consistency,” Math. Biosciences, vol. 137, no. 1, pp. 51-73, 1996.
[11] I. Elias and T. Tuller, “Reconstruction of Ancestral Genomic Sequences Using Likelihood,” J. Computational Biology, vol. 14, no. 2, pp. 216-237, 2007.
[12] T. Tuller et al., “Reconstructing Ancestral Gene Content by Coevolution,” Genome Research, vol. 20, no. 1, pp. 122-132, 2009.
[13] D. Juan, F. Pazos, and A. Valencia, “High-Confidence Prediction of Global Interactomes Based on Genome-Wide Coevolutionary Networks,” Proc. Nat'l Academy of Sciences USA, vol. 105, no. 3, pp. 934-939, 2008.
[14] M. Pellegrini et al., “Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles,” Proc. Nat'l Academy of Sciences USA, vol. 96, no. 8, pp. 4285-4288, 1999.
[15] C.H. Yeang and D. Haussler, “Detecting Coevolution in and among Protein Domains,” PLoS Computational Biology, vol. 3, no. 11, p. e211, 2007.
[16] S.W. Lockless and R. Ranganathan, “Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families,” Science, vol. 286, no. 5438, pp. 295-299, 1999.
[17] T. Tuller, Y. Felder, and M. Kupiec, “Discovering Local Patterns of Co-Evolution: Computational Aspects and Biological Examples,” BMC Bioinformatics, vol. 11, no. 43, p. 43, 2010.
[18] J.T. Chang, “Inconsistency of Evolutionary Tree Topology Reconstruction Methods when Substitution Rates Vary across Characters,” Math. Biosciences, vol. 134, no. 2, pp. 189-215, 1996.
[19] F.A. Matsen and M. Steel, “Phylogenetic Mixtures on a Single Tree Can Mimic a Tree of Another Topology,” Systematic Biology, vol. 56, no. 5, pp. 767-775, 2007.
[20] T. Tuller, M. Kupiec, and E. Ruppin, “Co-Evolutionary Networks of Genes and Cellular Processes across Fungal Species,” Genome Biology, vol. 10, no. 5, p. R48, 2009.
[21] T. Tuller et al., “An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation,” Cell, vol. 141, no. 2, pp. 344-354, 2010.
[22] T. Tuller et al., “Translation Efficiency Is Determined by Both Codon Bias and Folding Energy,” Proc. Nat'l Academy of Sciences USA, vol. 107, no. 8, pp. 3645-3650, 2010.
[23] M. Kellis et al., “Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Elements,” Nature, vol. 423, no. 6937, pp. 241-254, 2003.
[24] R.L. Tatusov et al., “The COG Database: An Updated Version Includes Eukaryotes,” BMC Bioinformatics, vol. 4, no. 41, p. 41, 2003.
[25] J.D. Thompson, T.J. Gibson, and D.G. Higgins, “Multiple Sequence Alignment Using Clustalw and ClustalX,” Current Protocols in Bioinformatics, vol. 2, no. 2, p. Unit 2.3, 2002.
[26] L.J. Jensen et al., “STRING 8-a Global View on Proteins and Their Functional Interactions in 630 Organisms,” Nucleic Acids Reseach, vol. 37 (Database issue), pp. D412-D416, 2009.
[27] D.A. Fitzpatrick et al., “A Fungal Phylogeny Based on 42 Complete Genomes Derived from Supertree and Combined Gene Analysis,” BMC Evolutionary Biology, vol. 6, no. 99, pp. 99-113, 2006.
[28] P.J. Waddell and M.A. Steel, “General Time-Reversible Distances with Unequal Rates across Sites: Mixing Gamma and Inverse Gaussian Distributions with Invariant Sites,” Molecular Phylogenetics and Evolution, vol. 8, no. 3, pp. 398-414, 1997.
[29] H.B. Fraser et al., “Evolutionary Rate in the Protein Interaction Network,” Science, vol. 296, no. 5568, pp. 750-752, 2002.

Index Terms:
Markov models, models of molecular evolution, co-evolution, phylogenetic reconstruction.
Citation:
Tamir Tuller, Elchanan Mossel, "Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 6, pp. 1667-1670, Nov.-Dec. 2011, doi:10.1109/TCBB.2010.124
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