Paleogenetics becomes paleoepigenetics

By Kate Allen

Excerpt: “More than anything else, the study opens up new avenues of inquiry. Paleogenetics, itself a newfound discipline, may soon be joined by paleoepigenetics, says Carmel.”
My comment: DNA methylation is the paleoepigenetic link to the physical landscape of DNA in the organized genomes of archaic and modern humans. The current publication makes this clearer than the mouse to human model of epigenetically-effected methylation and amino acid substitutions linked to morphological and behavioral phenotypes in mice and a modern human population that arose in what is now central China during the past ~30,000 years. Others seem to have realized that the disappearance of the Neanderthals at about that same time is more readily linked to diet and methylation than to inbreeding or mutations.
Their current results support the claim that nutrient-uptake and the metabolism of nutrients to species-specific pheromones, which control the physiology of reproduction, is clearly the link to species diversity in all genera. Ecological variation leads to ecological adaptation, nutrient-dependent changes in base pairs and in intracellular signaling, and to methylation that facilitates amino acid substitutions and the de novo creation of olfactory receptor genes linked to targeted expression of testis genes in mammals. See for example, the sequence in bats:
1) “A Cluster of Olfactory Receptor Genes Linked to Frugivory in Bats” links the epigenetic landscape from food odors to the physical landscape of DNA in their organized genomes.
2) “Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats” links food odors to targeted gene expression in testis genes.
3) “SELECTION FOR MECHANICAL ADVANTAGE UNDERLIES MULTIPLE CRANIAL OPTIMA IN NEW WORLD LEAF-NOSED BATS” links frugivory, microRNAs, and  de novo creation of olfactory receptor genes to targeted gene expression in testis genes. It completes the ecological link from variation to adaptation via odor-driven nutrient-dependent pheromone-controlled differences in the most morphologically diverse family of mammals.
In bats, a rapid increase in the rate of species diversification and significant slowing of the rate of evolution of cranial morphology occurs that can be linked to rapid changes in human cranial morphology and to across-species differences in morphological and behavioral phenotypes.
Claims that
4) “DNA Methylation Maps of the Neandertal and the Denisovan…“… uncover the epigenetic basis for phenotypic differences between present-day and archaic humans…” follow from what has already been detailed in the context of
5) nutrient-dependent pheromone-controlled ecological adaptations in species from yeasts to insects to vertebrates.
That explains why serious scientists, including Svante Paabo, no longer frame their experimental results in the context of evolutionary theory. Simply put, ideas from others about constraint-breaking mutations and natural selection of anything other than food, which then somehow results in the increased organismal complexity manifested in species diversity, are ideas that have been abandoned by anyone who has learned anything about molecular epigenetics since our 1996 review From Fertilization to Adult Sexual Behavior.
We may unknowingly have initiated the change from a paleogenetic approach to a paleoepigenetic approach with our details of molecular epigenetics that linked conserved molecular mechanisms of individual diversity and species diversity in species from microbes to man. If so, it would be nice to learn if anyone else acknowledges our seminal work. In any case, however, theories about mutations, natural selection and evolution are now rapidly being replaced by accurate representations of biophysically constrained cause and effect (i.e, methylation and ecological adaptation).