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Issue No.06 - November/December (2011 vol.8)
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.
Markov models, models of molecular evolution, co-evolution, phylogenetic reconstruction.
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, November/December 2011, doi:10.1109/TCBB.2010.124
[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.
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