By Rene Goscinny, Albert Uderzo
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The heterogeneity of thymine methyl group origin in DNA pyrimidine isostichs of developing sea urchin embryos. Proc Natl Acad Sci U S A 57 (1967), pp. 1394-400. Sullivan, J. and Joyce, P. Model selection in phylogenetics. Annual Review of Ecology, Evolution, and Systematics 36 (2005), pp. 445-466. Tavare, S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 17 (1986), pp. 57-86. , Chiaromonte, F. D. Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison.
Under normal circumstances the mutabilities of the protein coding regions is an oscillatory function with period 3 – what is the codon length. The third position in a codon is usually, due to the codon degeneracy, subjected to lower constraints than the other two positions and exhibits higher mutability. The replacements taking place at synonymous sites are neutral and the replacements at the nonsynonymous sites produce amino acid changes. It is not easy to detect the deviations of the expected mutational patterns that can indicate the presence of an accelerated evolution.
In Fig. 2 the pairs of A(t) matrix elements are plotted in such a way that the i <= j replacement counts are used as the x coordinate and the j <= i value as the y coordinate. The two points belonging to the same i,j pair are positioned symmetrically with respect to the y=x line and the distance between them represents the measure of the asymmetry. The dinucleotides connected by the strand symmetry are positioned approximately at the same place. The data plotted in Fig. 2 were extracted from the human/chimpanzee/rhesus (hpr) alignment.