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.