Inscribed in their genomes, living natural systems have preserved a large part
of their evolutionary history. However, the reconstruction of this history
even on the level of nucleotide substitutions is quite a challenging task. For
vertebrates, this analysis is further complicated through the predominance of
the neighbor dependent CpG methylation deamination process. This CpG effect can
be included into the models of nucleotide substitutions in vertebrates. We
will use such models and exploit repetitive elements in the human genome as a
fossil record to measure regional (along chromosomes) and time-dependent (up to
250 Myr into the past) substitution pattern in the human genome. We discuss
difference of the substitutional patterns before and after the mammalian
radiation. Regions with enhanced substitutions from C:G to other nucleotides
are observed on all chromosomes. We investigate the correlations of those
mutational hot spot with other genomic features, and discuss a special
telomeric substitution pattern. We further introduce a new method for the
accurate reconstruction of ancestral sequences an the estimation of
substitution frequencies in a star phylogeny.