Over the past decade, genetic archeology has revealed two branches of the human family tree, one known since the 19th Century (the Neanderthals) and the other more recently discovered (the Denisovans, an Asian relative of the Neanderthal population). These populations evolved without genetic intermingling with Homo sapiens sapiens for about 500,000 years, which resulted in the accumulation of genetic variants specific for these populations. But the migration of modern human populations out of Africa and throughout the world resulted in interbreeding between humans and Neanderthals or Denisovans about 60,00-40,000 years ago, and as a result there are genetic sequences inherited from them in modern human DNA that can be distinguished on the basis of these population-specific genetic alterations (see, e.g., Inherited Neanderthal Gene Encodes Genetic Risk for COVID-19).
Recent work* has found a cluster of genetic alterations ultimately inherited by modern humans from Neanderthals in a paper entitled "A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans," published in Cell Current Biology 30: P3465-69. These alterations were found in a Neanderthal version of a gene, the SCN9A gene, that encodes Nav1.7 voltage-gated sodium ion channel involved in nerve transmission in peripheral nerves and implicated in pain sensation. In modern humans, mutations in this gene causing a "loss of function" phenotype (inactivation of this gene) are associated with pain insensitivity and anosmia, while "gain of function" mutations (increased activity) are associated with idiopathic small-fiber neuropathy and increased sensitivity to pain.
The Neanderthal-specific alleles reported in this paper contained three amino acid variants (M932L, V991L, and D1908G) compared with the gene found in modern humans; alleles containing all three of these variant amino acids are not found in any living primate other than humans (see below). These researchers performed a series of experiments to determine the physiological effects of these variants assessed alone, in pairs, and in the presence of all three variant amino acids. These experiments involved synthesizing messenger RNAs (mRNAs) corresponding to each species of variant and introducing them into Xenopus laevis oocytes (which provided a more easily manipulated experimental platform for establish the effects) and then human cells. The oocyte experiments, which involved co-expression with a human gene encoding a protein (termed the "β3 subunit") that forms a functional complex with Nav1.7 protein, evaluated the electrophysiological function of the channel and showed a shift compared to the human gene product indicating increased sensitivity. Physiologically, the channel having the Neanderthal variants remained "open" for a longer time and, the researchers wrote, "is expected to lower the threshold for the generation of an action potential" (i.e., activate the physiological mediator of nerve activity that can be perceived as pain).
When tested individually and in combinations (M932L+V991L, V991L+D1908G, M932L+D1908G, and M932L, V991L, and D1908G), none of the single amino acid variant-containing species showed any differential effect on function. When tested in pairs, two of the variants (M932L+D1908G and M932L+V991L) also showed no effect. However the third combination (V991L+D1908G) showed the same type of shift detected in the triple variant. When these amino acids were mapped to the protein (shown below) the V991L and D1908G residues were found on the intracellular portion of the protein while the M932L residue was found extracellularly, perhaps indicating a need for an interaction prevented by the intervening cell membrane for the M932L variant. The D1908G variant (but not the other two) is also found in Denisovan DNA and can be inherited homozygously; as the authors speculate, "[t]his suggests that the D1908G substitution occurred in the common ancestor of Neanderthals and Denisovans but that it may have had a functional effect only in Neanderthals, where also the V991L substitution occurred."
Similar experiments were performed using human embryonic kidney cells, where similar results were obtained for these variant Nav1.7 protein species.
The authors next reported the results of their investigations of whether any of these variants are found in DNA from present-day humans, examining 2,535 genomes in the 1000 Genomes database. None of these variants were found in DNA from African or European populations, but the M932L and V991L variants were found in Asian and American populations at low frequencies (0.9-7.8% and 0.5-23.8%, respectively) but in a pattern indicting co-inheritance (termed "linkage disequilibrium"). The D1908G variant was also detected in these populations, at frequencies of 0-17.1% in Asia and 0.5-52.9% in America; where present this variant is in linkage disequilibrium with the M932L and V991L variants.
These researchers also tested whether these variants were inherited from a common ancestor to Neanderthals, Denisovans, and modern humans or whether they arose in ancient Neanderthal and Denisovan populations and were introduced later by cross-breeding with Homo sapiens sapiens. The genetic signal providing the assay was the size of the genetic element in which these variants are found, which were expected to be larger if the introduction was more recent than a common ancestor because the "genetic reshuffling" caused by meiotic recombination would not have had as long a time to disrupt co-inheritance. Indeed this was the found to be the case, when a comparison was made between DNA fragments from Yoruba individuals and ones from Neanderthal and Denisovan samples containing alleles likely to have been co-inherited. The researchers found one ~26 kilobasepair (kb) fragment containing the M932L and V991L variants and another ~110 kb fragment containing the D1908G variant whose inheritance patterns were consistent with later introgression of these variants from interbreeding between the different populations.
The M932L and V991L variants have also been associated in modern populations with increased sensitivity to pain, and small-fiber neuropathy, consistent with the experimental results reported in this paper. A survey of 362,944 unrelated "individuals of British ancestry" revealed none that while were homozygous for the three variants, 1,327 (0.4%) carried an allele bearing all three variants in heterozygous form. And their genetic makeup correlated to their responses to questions about their sensitivity to pain, which was that they "had experienced one or more forms of pain more often than non-carriers." However, there were no individuals in this dataset having both V991L and D1908G variants. And while gender was not a factor, age seemed to be, with "an approximately linear and positive correlation with reported pain between the ages of 40 and 70."
The authors conclude with reasoned speculation on the significance of their findings:
[G]iven the electrophysiological effects of the [amino acid] substitutions, nociception, i.e., the input to the central nervous system from peripheral nerves in response to harmful or potentially harmful stimuli, is likely to have been higher in Neanderthals than in modern humans. The translation of such input into the conscious perception of pain is modulated both at the level of the spinal cord and the brain. Thus, it is not possible to conclude that Neanderthals necessarily experienced more pain than modern humans do. Yet the input from Neanderthal peripheral nerve endings would have allowed Neanderthals to be more sensitive to stimuli, as suggested by the observations in present-day people heterozygous for the Neanderthal Nav1.7 variant.
*H. Zeberg, M. Dannemann, K. Sahlholm, K. Tsuo, T. Maricic, V. Wiebe, W. Hevers, H. Robinson, J. Kelso, and S. Pääbo
