Reconstructing Denisovan Anatomy Using DNA Methylation Maps

  title={Reconstructing Denisovan Anatomy Using DNA Methylation Maps},
  author={David Gokhman and Nadav Mishol and Marc de Manuel and David Juan and Jonathan Shuqrun and Eran Meshorer and Tom{\'a}s Marqu{\`e}s-Bonet and Yoel Rak and Liran Carmel},
Differential DNA methylation of vocal and facial anatomy genes in modern humans
Comparing measured and reconstructed DNA methylation maps of present-day humans, archaic humans and chimpanzees are compared and it is found that genes that affect vocal tract and facial anatomy show methylation changes between archaic and modern humans.
Predicted Archaic 3D Genome Organization Reveals Genes Related to Head and Spinal Cord Separating Modern from Archaic Humans
Information on 3D genome organization is used to link ~70 out of the remaining 288 unassigned DMRs to genes, which reinforce the enrichment of these genes with vocal and facial anatomy, and additionally find significant enrichment with the spinal column, chin, hair, and scalp.
Harnessing epigenetics to study human evolution.
More arrows in the ancient DNA quiver: use of paleoepigenomes and paleomicrobiomes to investigate animal adaptation to environment.
It is proposed that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.
The cis-regulatory effects of modern human-specific variants
A massively parallel reporter assay is used in embryonic stem cells, neural progenitor cells and bone osteoblasts to investigate the regulatory effects of single-nucleotide modern human-specific variants, providing insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.
Quantitative Paleogenetics: what can ancient DNA tell us about complex trait evolution?
The advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodateAncient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations are discussed.
Ghost Introgression: Spooky Gene Flow in the Distant Past
  • Jente Ottenburghs
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2020
The increasing availability of high‐quality genome assemblies for non‐model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly reveal more cases of ghost Introgression, indicating that the Tree of Life is even more reticulated than assumed.
Human-derived alleles in SOST and RUNX2 3′UTRs cause differential regulation in a bone cell-line model
This study reports a set of genes with derived 3’UTR changes in either the Homo sapiens or the Neanderthal/Denisovan lineages and experimentally evaluates the impact of 3'UTR variants in four genes: E2F6, GLI3, RUNX2 and SOST.
Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution
Evidence of lineage-specific selection on the hedgehog signaling pathway is discovered, including a human-specific sixfold down-regulation of EVC2 (LIMBIN), a key hedgehog gene.


Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
Insight is provided into the epigenetic landscape of the authors' closest evolutionary relatives and a window is opened to explore the epigenomes of extinct species by harnessing the natural degradation processes of methylated and unmethylated cytosines.
A High-Coverage Genome Sequence from an Archaic Denisovan Individual
The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size, and illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
Neanderthal and Denisova tooth protein variants in present-day humans
The objective was to identify archaic-specific missense variants that may explain the dental morphostructural variability between extinct and modern humans, and to explore their putative impact on present-day dental phenotypes.
Inferring Past Environments from Ancient Epigenomes
The strategy presented here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals, by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers.
A fourth Denisovan individual
The view that Denisovans were likely to have been present in the vicinity of Denisova Cave over an extended time period is reinforced, and it is shown that the level of nuclear DNA sequence diversity found among Denisovan is within the lower range of that of present-day human populations.
Genetic history of an archaic hominin group from Denisova Cave in Siberia
A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.
It is shown that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains, laying the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics.
Archaic Adaptive Introgression in TBX15/WARS2
It is reported that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population.
Nuclear and mitochondrial DNA sequences from two Denisovan individuals
The number of Denisovan individuals known to three is extended to three, with the nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.
Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation
High coverage methylomes are reported that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence.