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Some people flinch at a needle prick faster than others. One possible reason, at least in a very specific experimental setting, may be old very old DNA. In a 2023 paper published in Communications Biology, researchers linked three Neanderthal-derived variants in the gene SCN9A to a lower threshold for one kind of pain test in modern humans: a skin-pricking test performed after the area had been sensitized with mustard oil…….Continue reading….
By: Tim Newcomb
Source: Popular Mechanics
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Critics:
Genetic studies on Neanderthal ancient DNA became possible in the late 1990s. In July 2006, the Max Planck Institute for Evolutionary Anthropology and 454 Life Sciences announced that they would sequence the Neanderthal genome over the next two years. It was hoped the comparison would expand understanding of Neanderthals, as well as the evolution of humans and human brains.
They published the full sequence Neanderthal mitochondrial DNA (mtDNA) in 2008. Svante Pääbo noted that, “Contamination was indeed an issue,” and they eventually realised that 11% of their mtDNA sample was modern human DNA. Since then, more of the preparation work has been done in clean areas and 4-base pair ‘tags’ have been added to the DNA as soon as it is extracted so the Neanderthal DNA can be identified.
The first Neanderthal genome sequence was published in 2010, and strongly indicated interbreeding between Neanderthals and early modern humans. This was based on three specimens in Vindija Cave, Croatia, which contained almost 4% archaic DNA (allowing for near complete sequencing of the genome). However, there was approximately 1 error for every 200 letters (base pairs) based on the implausibly high mutation rate, probably due to the preservation of the sample.
In 2012, British-American geneticist Graham Coop hypothesised that they instead found evidence of a different archaic human species interbreeding with modern humans, which was disproven in 2013 by the sequencing of a high-quality Neanderthal genome preserved in a 50,000 year old toe (phalanx) bone from Denisova Cave, Siberia. A visualisation map of the reference modern-human containing the genome regions with high degree of similarity or with novelty according to a 50,000 year old Neanderthal from the Siberian Altai Mountains has been built by Pratas et al.
Neanderthal genomes sequenced include those from Denisova Cave including an offspring of a Neanderthal and a Denisovan, from Chagyrskaya Cave, from Vindija Cave, Mezmaiskaya cave, Les Cottés cave, Goyet Caves and Spy Cave, Hohlenstein-Stadel and Scladina caves Galería de las Estatuas and Gibraltar. Neanderthal mtDNA (which is passed on from mother to child) is absent in modern humans. This is evidence that interbreeding occurred mainly between Neanderthal males and modern human females.
According to Svante Pääbo, it is not clear that modern humans were socially dominant over Neanderthals, which may explain why the interbreeding occurred primarily between Neanderthal males and modern human females. Furthermore, even if Neanderthal women and modern human males did interbreed, Neanderthal mtDNA lineages may have gone extinct if women who carried them only gave birth to sons.
There is considerably less Neanderthal ancestry on the X-chromosome compared to the autosomal chromosomes, which similarly suggests that admixture with modern humans was primarily the result of mating between modern human females and Neanderthal males. Other authors have suggested that this may be due to negative selection against Neanderthal alleles, but these two proposals are not mutually exclusive.
A 2023 study confirmed that the low level of Neanderthal ancestry on the X-chromosomes is best explained by sex bias in the admixture events, and these authors also found evidence for negative selection on archaic genes. The lack of Neanderthal-derived Y-chromosomes in modern humans (which is passed on from father to son), has also inspired the suggestions that the hybrids that contributed ancestry to modern populations were predominantly females, or that the Neanderthal Y-chromosome was not compatible with modern humans and became extinct.
Based on nuclear DNA (nDNA), Neanderthals and Denisovans share a more recent last common ancestor (LCA) than to modern humans. However, Neanderthals and modern humans share a more recent mitochondrial LCA (observable by studying mtDNA) and Y chromosome LCA. This likely resulted from an interbreeding event subsequent to the Neanderthal/Denisovan split. This involved either introgression coming from an unknown archaic human into Denisovans, or introgression from an earlier unidentified modern human wave from Africa into Neanderthals.
Several Neanderthal-like fossils in Eurasia from a similar time period are often grouped into H. heidelbergensis, of which some may be relict populations of earlier humans, which could have interbred with Denisovans. This is also used to explain an approximately 124,000-year-old German Neanderthal specimen with mtDNA that diverged from other Neanderthals (except for Sima de los Huesos) about 270,000 years ago, while its genomic DNA indicated divergence less than 150,000 years ago.
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