Abstract
Replying to T. Yonezawa & M. Hasegawa Nature 468, 10.1038/nature09482 (2010)
Yonezawa and Hasegawa1 provide an example from two apparently unrelated families of nucleic acid coding sequences for which an Akaike information criterion (AIC) model selection test, similar to mine2, chooses a common origin hypothesis. Although this may seem surprising, the coding sequences in this example were aligned in the same reading frame. The constraints of the genetic code are expected to induce correlations between these sequences (and among all coding sequences) that are not due to common ancestry. For instance, owing to codon bias and the structure of the genetic code, in these sequences the second codon position is biased towards T (about twofold over average), whereas the third position is usually an A (∼50%) and rarely a G (∼4%).
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References
Yonezawa, T. & Hasegawa, M. Was the universal common ancestry proved? Nature 468, 10.1038/nautre09482 (2010)
Theobald, D. L. A formal test of the theory of universal common ancestry. Nature 465, 219–222 (2010)
Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997)
Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003)
Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E. & Stanhope, M. J. Universal trees based on large combined protein sequence data sets. Nature Genet. 28, 281–285 (2001)
Stewart, C. B., Schilling, J. W. & Wilson, A. C. Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330, 401–404 (1987)
Omelchenko, M. V., Galperin, M. Y., Wolf, Y. I. & Koonin, E. V. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol. Direct 5, 31 (2010)
Andreeva, A. et al. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36, D419–D425 (2008)
Cheng, H., Kim, B. H. & Grishin, N. V. Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. J. Mol. Biol. 377, 1265–1278 (2008)
Cheng, H., Kim, B. H. & Grishin, N. V. MALISAM: a database of structurally analogous motifs in proteins. Nucleic Acids Res. 36, D211–D217 (2008)
Povolotskaya, I. S. & Kondrashov, F. A. Sequence space and the ongoing expansion of the protein universe. Nature 465, 922–926 (2010)
Steel, M. & Penny, D. Origins of life: Common ancestry put to the test. Nature 465, 168–169 (2010)
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Theobald, D. Theobald reply. Nature 468, E10 (2010). https://doi.org/10.1038/nature09483
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DOI: https://doi.org/10.1038/nature09483
