Epigenetics explains Neanderthal and Human differences better than Neo-Darwinism

Article:”Unveiling the Epigenetic Landscape of Our Closest Extinct Relatives: A Tale of Neanderthal and Denisovan DNA Methylation,” by Nobel Laureate Svante Pääbo, Science (4/14)

The realm of epigenetics, a relatively young branch of genetics, delves into the intricate interplay between genes and their environment, deciphering how factors beyond DNA sequence influence gene expression. DNA methylation, a key epigenetic mechanism, involves the addition of a methyl group to cytosine bases, altering gene activity. By unraveling ancient DNA methylation patterns, scientists have gained unprecedented insights into the epigenetic landscape of our long-lost relatives – the Neanderthals and Denisovans.

Harnessing the power of computational methods, researchers have ingeniously reconstructed the DNA methylation maps of Neanderthals and Denisovans, capitalizing on the natural degradation processes of methylated and unmethylated cytosines in ancient DNA. By comparing these methylation maps to those of modern humans, a treasure trove of differentially methylated regions (DMRs) has been unearthed. These DMRs represent genomic regions where methylation patterns have diverged between present-day humans and their archaic counterparts.

Intriguingly, a subset of these DMRs resides within genes implicated in crucial biological processes, including development, immunity, and cognition. This observation suggests that methylation-driven gene regulation may have played a pivotal role in shaping the phenotypic traits that distinguished Neanderthals, Denisovans, and modern humans.

Neanderthal shares 98% of human DNA so the question arises how they can look so different? The answer is in the epigenetics of their Junk DNA.

They Reconstructed of the DNA methylation maps of the Neandertal and the Denisovan, two extinct human species. This is the first time that the epigenetic landscape of these species has been studied. The researchers found that there are about 2,000 differentially methylated regions (DMRs) between Neanderthals, Denisovans, and present-day humans. DMRs are regions of DNA that are methylated in one population but not in another. Methylation is a chemical modification that can affect gene expression.

The researchers found that some of the DMRs are located in genes that are involved in development, such as the HOXD cluster. Hox genes account for the body plans. This suggests that epigenetic changes may have played a role in the evolution of some of the anatomical differences between Neanderthals, Denisovans, and present-day humans. Epigenetics turned on and off the Hox genes to cause different body plans without neo Darwinism.

The researchers also found that DMRs are more likely to be associated with diseases than non-DMRs. This suggests that epigenetic changes may also have played a role in the development of some diseases. For instance it's believed Neanderthal had a higher rate of schizophrenia than humans.

This study is a significant advance in our understanding of human development. It provides the first insights into the epigenetic landscape of our extinct relatives and opens up new avenues for research into the development  of human disease.

A closer examination of Neanderthal methylation has revealed striking differences in brain-related genes compared to Denisovans. This divergence hints at potential cognitive disparities between these two groups of archaic humans.

Furthermore, the study of Neanderthal and Denisovan methylation has shed light on the genetic underpinnings of human disease. DMRs have been found to be significantly more prevalent in regions associated with various diseases, implying a potential role of methylation alterations in disease susceptibility.

The reconstruction of Neanderthal and Denisovan DNA methylation maps represents a landmark achievement in our understanding of human development. It has unveiled the epigenetic tapestry of our closest extinct relatives, providing valuable insights into their biology and potential links to human diseases. As research in this field continues to flourish, we anticipate further revelations about the epigenetic landscape that has shaped our developmental trajectory.

This research has also raised some challenges for neo-Darwinian evolutionary theory.

DNA methylation is a chemical modification that can affect gene expression without changing the underlying DNA sequence as per neo darwinism. Methylation can either turn genes on or off, and it is thought to play an important role in development, disease, and other biological processes.

The researchers found that the DNA methylation patterns of the Neandertal and the Denisovan were different from those of modern humans. They also found that these differences were associated with genes that are involved in development, disease, and other biological processes.

Neo-Darwinian states that evolution is driven by natural selection on random mutations, which is the process by which organisms with traits that make them better adapted to their environment are more likely to survive and reproduce.

The reconstruction of the DNA methylation maps of the Neandertal and the Denisovan suggests that epigenetic changes plays a more important role in evolution than previously thought. This is because epigenetic changes can occur very quickly, without the need for changes in the underlying DNA sequence as with neo darwinism. This could allow for rapid adaptation to new environments.

In addition, the finding that the DNA methylation patterns of the Neandertal and the Denisovan were different from those of modern humans suggests that there may be more genetic diversity among human species than previously thought. This is because epigenetic changes are not always heritable, so they can be different even between individuals of the same species.

This research is a significant step forward in our understanding of human development and disease.