Phylo-Epigenetic Conservation and CpG Erosion in OCT4, SOX2, and hTERT Intragenic CpG Islands: A Waddingtonian Perspective on Mammalian Developmental Evolution

<b>Background/Objectives:</b> Developmental biologist Conrad Waddington proposed that evolution is shaped not only by genetic mutations and natural selection but also by environmentally responsive developmental mechanisms. Building on this premise, the epigenetic regulation of three master genes central to mammalian embryogenesis-<i>OCT4</i>, <i>SOX2</i>, and <i>hTERT</i>-focusing on their intragenic CpG islands (iCpGIs), which are crucial for transcriptional control and chromatin state modulation, were investigated. <b>Methods:</b> By performing a phylo-epigenetic comparison across 12 primate species, strong conservation of CpG-rich regions, punctuated by lineage-specific CpG transitions, particularly CpG→TpG and CpG→CpA was identified. <b>Results:</b> These mutational patterns align with methylation-dependent deamination mechanisms and highlight iCpGIs as evolutionarily constrained, epigenetically plastic elements. Notably, CpG variation alone recapitulated known primate phylogenies, suggesting that methylation-sensitive sites within iCpGIs encode both developmental and evolutionary information. <b>Conclusions:</b> It is proposed that such sites are prone to Environmentally Determined Epimutations (EDEMs)-methylation-driven, nutrition-sensitive changes that persist across generations and modulate gene regulatory capacity. This integrative framework advances Waddington's concept of canalization by providing a molecular mechanism through which environmental factors can reshape developmental trajectories and contribute to evolutionary innovation.