Other changes accompanying the major shifts

This methylation/CpG transition deserves a more detailed discussion. An analysis of the data presented in Part 5 indicates that (i) two positive correlations hold between the 5mC and GC levels of the genome of fishes/amphibians and mammals/birds, respectively (see Fig. 5.13) (ii) the higher methylation of fishes and amphibians is not related to the higher amounts of repetitive DNA sequences (see Fig. 5.14) and (iii) the 5mC and CpG observed/ expected values show no overlap between the two groups of vertebrates and suggest the existence of two equilibria in 5mC and CpG levels (see Fig. 11.14). Several important questions then arise concerning (i) the two equilibria in methylation and CpG shortage (ii) the transition between the two equilibria and (iii) the causes of the methylation/CpG transition. 

Concerning the methylation/CpG levels changes, the results available so far suggest that reptiles are characterized by a lower methylation level, compared to fishes and amphibians, close to those of mammals and birds placing the methylation transition at the appearance of the common ancestor of reptiles and mammals, namely at the appearance of amniotes. 

One should, however, keep in mind that the number of reptilian DNAs analysed so far is small, that rather different levels were found in the few reptiles investigated and that no estimate is available for the CpG shortage. Under these circumstances, the question as to whether the low methylation level is present in all or only in some reptiles is still open. Therefore, two possibilities should be considered, namely, that either the common reptilian ancestor of mammals and birds had already undergone a decrease in methylation which was then transmitted by descent to extant reptiles, mammals and birds or that the methylation change occurred independently in reptiles (possibly, only in some of them), in mammals and in birds. 

As far as the causes for the methylation/CpG transition are concerned, they will be discussed in Part 12, along with the causes for the major shifts. 

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