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Post by Admin on Jul 30, 2020 19:20:40 GMT
A new study of Neanderthal DNA suggests our species’ extinct relatives may have been particularly sensitive to pain, reports Ewen Callaway for Nature. Neanderthals disappeared some 40,000 years ago, but some humans living today retain bits of Neanderthal DNA—evidence that our species once interbred. Though they hunted large, dangerous animals—including bison, mammoths and cave bears—in frigid climes, Neanderthals may be the source of a genetic variant associated with increased sensitivity to pain in modern humans, accoring to the new research published last week in the journal Current Biology. Researchers looking to compare Neanderthals’ DNA to modern humans have historically only had a few low resolution genomes to choose from. But the team behind the new paper were able to produce three high-quality Neanderthal genomes from genetic material recovered from caves in Croatia and Russia, per Nature. Researchers found a mutation to a gene called SCN9A that encodes a protein involved in sending pain signals to the spinal cord and brain on both chromosomes of all the Neanderthal genomes. Its presence on both chromosomes of all three genomes suggests it was common in the Neanderthal population, according to Nature. The mutation to SCN9A codes for three amino acid differences compared to modern humans, researchers tell Brooks Hays of United Press International (UPI). "[The gene] is unusual in having three differences unique to Neandertals in the protein it encodes," Svante Pääbo, a geneticist at the Max Planck Institute for Evolutionary Anthropology and co-author of the study, tells UPI. Through experiments, the researchers determined that the Neanderthal mutation lowers the threshold required for the body’s nerves to send pain signals to the spinal cord and brain, which could also potentially make those sensations more painful, reports Emma Betuel for Inverse. “People have described it as a volume knob, setting the gain of the pain in nerve fibres,” Hugo Zeberg, the paper’s lead author and a researcher at the Max Planck Institute for Evolutionary Anthropology as well as the Karolinska Institutet, tells Nature. The researchers used a database of more than 362,944 genomes of British people to investigate whether this mutation was present in modern humans. Only 0.4 percent of Brits who responded to a questionnaire about their pain symptoms had a copy of the Neanderthal mutation to the SCN9A gene, per Inverse, but those who had the mutation were 7 percent more likely to report pain at least one pain symptom. Though its true older folks in the survey tended to report increased pain, the researchers found that people with the Neanderthal variant to SCN9A were reporting pain typical of someone about 8.5 years older than their actual age. In an emailed statement to Amy Woddyatt of CNN, Zeberg notes that other genetic variants impact people’s experience of pain that are unrelated to Neanderthal ancestry, and that not everyone with a low pain threshold could blame it on Neanderthals. "Whether Neandertals experienced more pain is difficult to say because pain is also modulated both in the spinal cord and in the brain," Pääbo says in a statement. "But this work shows that their threshold for initiating pain impulses was lower than in most present-day humans." Neuroscientist Cedric Boeckx of the Catalan Institute for Research and Advanced Studies tells Nature that, “this is beautiful work.” Boeckx, who was not involved in the research, says the paper shows how studying modern humans can illuminate facets of Neanderthal physiology. But Gary Lewin, a neuroscientist at the Max Delbrück Center for Molecular Medicine in Germany who was not involved in the research, tells Nature that the effect caused by the Neanderthal mutations to SCN9A is small, especially compared to other mutations associated with chronic pain. Lewin further wonders what adaptive advantage increased pain sensitivity might have conferred. "Pain is not necessarily a bad thing," Zeberg tells Inverse, noting that bad sensations help us avoid injury and survive.
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Post by Admin on Jul 31, 2020 20:37:51 GMT
A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans Published:July 23, 2020DOI:https://doi.org/10.1016/j.cub.2020.06.045 Summary The sodium channel Nav1.7 is crucial for impulse generation and conduction in peripheral pain pathways [1]. In Neanderthals, the Nav1.7 protein carried three amino acid substitutions (M932L, V991L, and D1908G) relative to modern humans. We expressed Nav1.7 proteins carrying all combinations of these substitutions and studied their electrophysiological effects. Whereas the single amino acid substitutions do not affect the function of the ion channel, the full Neanderthal variant carrying all three substitutions, as well as the combination of V991L with D1908G, shows reduced inactivation, suggesting that peripheral nerves were more sensitive to painful stimuli in Neanderthals than in modern humans. We show that, due to gene flow from Neanderthals, the three Neanderthal substitutions are found in ∼0.4% of present-day Britons, where they are associated with heightened pain sensitivity. Results and Discussion Neanderthals and their Asian relatives, Denisovans, evolved largely separately from the ancestors of present-day humans for about 500,000 years [2]. During that time, each group independently accumulated genetic changes that became frequent or fixed. However, late in their history, Neanderthals and Denisovans mixed with modern humans, which resulted in many genetic variants from Neanderthals and Denisovans being present in humans today [3, 4]. As several Neanderthal genomes of high quality are now available [2, 5, 6], it is possible to identify genetic changes that occurred in many or most Neanderthals, investigate their physiological effects, and assess their consequences when they occur in people today. Figure 1 Effects of Neanderthal-Derived Amino Acid Substitutions on Nav1.7 Inactivation Whereas most genetic differences between Neanderthals and modern humans that affect gene products occur singly in genes across the genome, genes that carry several such differences are of particular note. One such case is the gene SCN9A, which encodes the Nav1.7 protein, a voltage-gated sodium channel in which all Neanderthal genomes sequenced to date carry three amino acid substitutions relative to modern humans: M932L; V991L; and D1908G. At these positions, extant monkeys and apes share the modern human residues. Nav1.7 is the only ion channel carrying amino acid substitutions in Neanderthals that is highly expressed in peripheral nerves mediating pain sensation [7]. The channel allows for the passage of sodium ions across the membranes of neurons in response to changes in electrical membrane potential. In humans, loss-of-function mutations of SCN9A cause insensitivity to pain [8] and anosmia [9]. Gain-of-function mutations, on the other hand, are a leading cause of idiopathic small-fiber neuropathy [1], where patients present with sensory symptoms and pain, with pain as the dominant symptom [10]. To investigate the electrophysiological effects of the three substitutions seen in Neanderthals, we synthesized genes encoding the modern human and Neanderthal versions of Nav1.7, transcribed these in vitro, and injected the mRNAs into Xenopus laevis oocytes. We chose this system, rather than, for example, cultured murine dorsal root ganglion cells, in order to test the effects of the three amino acid substitutions when expressed together with relevant human subunits, which differ from those of rodents by 5–47 amino acids. In peripheral nerve endings, Nav1.7 forms complexes with the β3 subunit [11, 12, 13], encoded by SCN3B, which carries no amino acid differences between Neanderthals, Denisovans, and modern humans. When the β3 subunit is expressed together with Nav1.7 in the oocytes, the inactivation curve of the Neanderthal ion channel is shifted by ∼6.1 mV toward less negative values relative to the modern human channel (Figures 1A and 1B ; Table S1; p = 2.9 × 10−5; n = 26 and n = 31, respectively). This results in an increased availability of sodium channels for activation and increased probability that the sodium channel remains open for a longer time once activated and is expected to lower the threshold for the generation of an action potential (see computational model; Figures S1M and S1N). To examine which of the amino acid substitutions mediates the shift in the inactivation curve, we synthesized and injected mRNAs encoding each of the three amino acid substitutions singly (Figure S2). No single amino acid substitution had any effect on the inactivation of the ion channel (Figure 1E; Table S1). We next investigated the effect of the three possible combinations of two amino acid substitutions. Two of the combinations, M932L+D1908G and M932L+V991L, had no effect on the inactivation. However, V991L+ D1908G caused a shift in the inactivation curve, similar to that of the three substitutions (Figure 1F; Table S1; p = 2.4 × 10−5; n = 24). Thus, an epistatic interaction of the two substitutions V991L and D1908G, which are both located in the intracellular part of the protein, is necessary to elicit the electrophysiological effects. In contrast, M932L, which is located extracellularly, had no detectable effects. We note that the Denisovan genome carries the D1908G substitution in a homozygous form but lacks the other two substitutions. This 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. To test whether the effects of the Neanderthal substitutions are also seen in mammalian cells, we transfected human embryonic kidney (HEK) cells with vectors expressing the mRNAs encoding the modern human and the Neanderthal variants of Nav1.7 and the β3 subunit. As in the oocytes, we observe a depolarizing shift in inactivation for the Neanderthal variant of Nav1.7 (Figure 1C; Table S1; p = 9.1 × 10−3; n = 8 and n = 9, respectively). In addition, we observe a depolarizing shift of the activation curve (Figure S1C; Table S1; p = 1.1 × 10−3; n = 8 and n = 9, respectively). When investigated in a simple model of a human peripheral nerve, the depolarizing shift in the inactivation curve has an excitatory effect for suprathreshold stimuli, even in the presence of a depolarizing shift in activation (Figure S1N). Thus, we conclude that the shifts seen in both oocytes and HEK cells are likely to have an excitatory action. We next investigated whether any of the three SCN9A missense mutations (M932L, V991L, and D1908G) exist in present-day humans by examining 2,535 genomes available in the phase III 1000 Genomes (1000G) dataset (Figure 2A). We did not find any of the three variants in the African (N = 507) and European (N = 505) 1000G populations, but M932L and V991L occur in almost perfect linkage disequilibrium (R2 = 0.99) at frequencies of 0.9%–7.8% in Asia and 0.5%–23.8% in the Americas. In addition, D1908G occurs at a frequency of 0%–17.1% in Asia and 0.5%–52.9% in the Americas (Table S2) and tends to be in linkage disequilibrium with M932L+V991L (R2 = 0.26).
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Post by Admin on Aug 1, 2020 6:50:20 GMT
Figure 2 Geographical Distribution and Phylogenetic Relationships of SCN9A Variants These variants could have entered the present-day human population from a common ancestor shared with Neanderthals and Denisovans or by introgression from archaic hominins when these met modern humans some 40,000–60,000 years ago. In the latter case, the size of the archaic-like DNA segments on which the variants sit are expected to be substantially larger than if they were inherited from a common ancestor of the three groups, as meiotic recombination will have had less time to reduce their size. To estimate the size of these segments, we identified alleles in this genomic region that are absent in the 1000G Yoruba individuals but occur in homozygous form in the Neanderthal and/or Denisovan genomes and are likely to have entered modern human populations from archaic hominins. We identified one DNA segment (r2 > 0.8) of ∼26 kb around the M932L and V991L substitutions carrying 14 such alleles (chr2:167129256–167155131) and another segment (r2 > 0.8) of ∼110 kb around the D1908G substitution carrying 40 such alleles (chr2:167017315–167126999). Based on the sizes of the two DNA segments and their recombination rates, we concluded that these variants entered the modern human population by introgression from Neanderthals or Denisovans, rather than being inherited from a common ancestor of the groups (p = 0.059 for V991L and M932L; p = 7.8 × 10−16 for D1908G). We estimated the phylogenetic relationships of the two DNA segments overlapping M932L+V991L and D1908G to the corresponding present-day human and Neanderthal DNA segments. For both segments, one group of present-day human DNA sequences is most closely related to the Neanderthal segments (Figures 2B and 2C), and in both instances, these DNA sequences are found in Asia and the Americas. Figure 3 Pain Sensitivity among UK Biobank Individuals (n = 362,944) The amino acid substitutions M932L and V991L have previously been associated with increased pain sensitivity and small-fiber neuropathy in experimental and clinical studies in humans [1, 17]. To investigate whether the three introgressed Neanderthal variants affect pain sensitivity in the general human population, we selected 362,944 unrelated individuals of British ancestry in the UK Biobank (UKBB) [18] who had answered questions relating to their experience of pain (Table S3). Although no individual was homozygous for the Neanderthal variants, 1,327 individuals (0.4%) carried all three amino acid substitutions in a heterozygous form. Based on their answers to 19 pain-related questions, these carriers of the three Neanderthal substitutions had experienced one or more forms of pain more often than non-carriers (Figure 3; p = 0.0078; adjusted for age and sex). They also experienced more pain than carriers of only one or two of the Neanderthal substitutions, although these did not differ significantly from individuals carrying none of the Neanderthal substitutions (Figure 3). No individuals with the combination V991L and D1908G were found in the UKBB. Two other substitutions in Nav1.7 that have previously been reported to be associated with increased pain sensitivity are also genotyped in the UKBB and frequent enough to assess their phenotype (W1150R, n = 91,143; R185H, n = 1,369). Neither of these are associated with an increased probability to report pain (p = 0.82 and p = 0.72, respectively), suggesting that their effects are smaller than the Neanderthal-derived variants. Notably, sex did not affect the extent to which individuals in the UKBB report pain (p = 0.84; 198,047 females; 164,897 males), whereas age showed an approximately linear and positive correlation with reported pain between the ages of 40 and 70 (Figure S3; p = 4.6 × 10−282). Individuals who carried the three amino acid substitutions inherited from Neanderthals in heterozygous form are 7% more likely to report at least one form of pain compared to people without these substitutions. This corresponds to an increase of approximately 8.5 years in terms of pain reported. At the present time, we can only speculate about the consequences of having these substitutions in homozygous form, as was the case in the three Neanderthals genomes have been sequenced to high coverage. We note that Nav1.7 is expressed also in other cell types, for example, olfactory neurons, raising the possibility that the substitutions studied here might have additional effects beyond modulation of pain. However, given the electrophysiological effects of the 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.
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Post by Admin on Aug 3, 2020 18:40:19 GMT
The advent of DNA sequencing has given scientists a clearer insight into the interconnectedness of evolution and the web-like path that different organisms take, splitting apart and coming back together. Tony Capra, associate professor of biological sciences, has come to new conclusions about the influence of Neanderthal DNA on some genetic traits of modern humans. The article "Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations" was published in the journal Nature Ecology & Evolution on July 27. The ancestors of all modern humans lived across the African continent, until approximately 100,000 years ago when a subset of humans decided to venture further afield. Neanderthals, an extinct relative of modern humans, had been longtime residents of Europe and central and south Asia; their ancestors had already migrated there 700,000 years previously. The humans who moved into central Asia and the Middle East encountered and reproduced with Neanderthals. Neanderthal DNA is present in some modern humans, and now research shows that can sometimes be a good thing. "When Neanderthals split off from what became the human population 700,000 years ago, they took specific genetic variants along with them. Some of these genetic variants were later lost in human populations. We show that interbreeding with Neanderthals restored hundreds of thousands of previously lost genetic variants," said Capra. "These reintroduced genetic variants are more likely to have positive effects than genetic variants unique to Neanderthals." In practice these reintroduced variants might have helped to regulate negative traits associated with Neanderthal DNA including autoimmune and neuropsychiatric diseases and addiction risk. Connecting how genetics alter risk is essential to understanding the function and development of disease. "With this research we identify a unique set of very old genetic variants that predate Neanderthals, but that may have enabled segments of Neanderthal DNA to remain in the DNA of modern humans," said David Rinker, the first author of this research and postdoctoral scholar in the Capra Lab. "Pinpointing when those alleles (i.e., variant forms of genes) originated along the human timeline offers an evolutionary perspective on which genetic variants keep modern humans healthy, and has broad implications for how disease risk factors have evolved." Capra's lab worked with data from the 1000 Genomes Project and the Neanderthal Genome Project, two open initiatives that document genetic variation in detail. The researchers collaborated with Emily Hodges, assistant professor of biochemistry, to conduct a functional dissection of Neanderthal and human DNA to identify which variants have functional effects. "This analysis gives physical proof of our hypothesis," noted Capra. "It serves as a blueprint for doing analyses of this kind on a larger scale because we've proved the effect of these reintroduced genetic variants on a molecular level." Explore further How differences in the genetic 'instruction booklet' between humans and Neanderthals influenced traits More information: David C. Rinker et al. Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations, Nature Ecology & Evolution (2020). DOI: 10.1038/s41559-020-1261-z Abstract Neanderthal ancestry remains across modern Eurasian genomes and introgressed sequences influence diverse phenotypes. Here, we demonstrate that introgressed sequences reintroduced thousands of ancestral alleles that were lost in Eurasian populations before introgression. Our simulations and variant effect predictions argue that these reintroduced alleles (RAs) are more likely to be tolerated by modern humans than are introgressed Neanderthal-derived alleles (NDAs) due to their distinct evolutionary histories. Consistent with this, we show enrichment for RAs and depletion for NDAs on introgressed haplotypes with expression quantitative trait loci (eQTL) and phenotype associations. Analysis of available cross-population eQTLs and massively parallel reporter assay data show that RAs commonly influence gene expression independent of linked NDAs. We further validate these independent effects for one RA in vitro. Finally, we demonstrate that NDAs are depleted for regulatory activity compared to RAs, while RAs have activity levels similar to non-introgressed variants. In summary, our study reveals that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these RAs were more tolerated than NDAs. Thus, RAs and their distinct evolutionary histories must be considered when evaluating the effects of introgression.
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Post by Admin on Aug 4, 2020 6:54:14 GMT
Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations doi: doi.org/10.1101/533257ABSTRACT Neanderthal ancestry remains across modern Eurasian genomes, and introgressed sequences influence diverse phenotypes, including immune, skin, and neuropsychiatric diseases. Interpretation of introgressed sequences has focused on alleles derived in the Neanderthal lineage. Here, we demonstrate that introgressed Neanderthal haplotypes also carry hundreds of thousands of ancestral alleles that had been lost in Eurasian populations. These reintroduced alleles (RAs) exist exclusively on Neanderthal haplotypes in Eurasian populations. Illustrating the broad potential influence of these RAs, we find that over 70% of known phenotype associations with introgressed Neanderthal-derived alleles (NDAs) are equally associated with RAs. We also discover enrichment for RAs among introgressed eQTL in many tissues, including more than half of the brain tissues analyzed. Finally, combining expression quantitative trait loci (eQTL), massively parallel reporter assay (MPRA) data, and in vitro validation, we show that RAs can regulate gene expression independent of NDAs. In summary, our study reveals that Neanderthal introgression supplied Eurasians with many lost ancestral variants that may have restored lost regulatory functions. Thus, RAs should be considered when evaluating the effects of introgression. ONE SENTENCE SUMMARY Neanderthal interbreeding with anatomically modern humans restored thousands of ancient alleles that were previously lost in Eurasian populations. MAIN TEXT Modern Eurasian populations have significantly lower genetic diversity than modern African populations, despite having larger census population sizes (1, 2). This disparity reflects the genetic bottlenecks experienced by the direct ancestors of Eurasian anatomically modern humans (AMH) as they moved out of Africa approximately 50,000 years ago (2, 3). The effective population size of this ancestral Eurasian population is estimated to have been less than 20% of the size of the contemporaneous African populations (1, 4). As a result of this out of Africa (OOA) bottleneck and subsequent population dynamics, millions of ancient alleles were lost in the ancestors of modern Eurasian populations. More than 500,000 years prior to the Eurasian OOA bottleneck, members of other hominin groups in Africa, including the ancestors of Neanderthals and Denisovans, moved into Eurasia (5). The sequencing of ancient DNA from Neanderthal and Denisovan individuals has enabled reconstruction of their genomes (5–7). Comparing Neanderthal genomes to genomes of modern humans from around the world revealed that Eurasian AMHs interbred with Neanderthals approximately 50,000 years ago (5, 8). The legacy of this archaic introgression is reflected in the genomes of modern Eurasians, where ∼1–3% of individuals’ DNA sequences are of Neanderthal ancestry (9–12). Neanderthal introgression introduced many new alleles into Eurasian populations that were derived on the Neanderthal lineage. It has been hypothesized that some of these alleles were adapted to non-African environments and thus were beneficial to Eurasian AMH (9, 10, 13–18). However, Neanderthal interbreeding also likely came with a genetic cost due to accumulation of weakly deleterious alleles in their lineage, because of their lower effective population size compared to AMHs (19, 20). Indeed, the distribution of archaic ancestry across modern Eurasian genomes is non-random, with significant deserts of Neanderthal ancestry as well as many genomic regions in which Neanderthal ancestry is common. This distribution is generally attributed to the long term effects of positive and negative selection acting on introgressed Neanderthal alleles (9, 10, 21), with negative selection acting most strongly immediately after admixture (22). Introgressed alleles on Neanderthal haplotypes that remain in modern Eurasian populations are associated with diverse traits, including risk for skin, immune, and neuropsychiatric diseases (13, 14, 23–26). For example, an introgressed Neanderthal haplotype at the OAS1 locus is associated with innate immune response; however, this haplotype also contains an ancient hominin allele in high linkage disequilibrium (LD) with the Neanderthal alleles that could influence function (27). Thus, while most studies have focused on identifying and testing the effects of Neanderthal derived alleles in AMHs, archaic admixture may also have served as a route by which more ancient functional alleles reentered the genomes of Eurasians (27, 28). Here, we explore the hypothesis that Neanderthal introgression reintroduced previously lost ancestral alleles into Eurasian populations. To evaluate this hypothesis, we analyze archaic, modern, and simulated genomes to characterize the prevalence of the reintroduction of lost alleles to Eurasians. Given the conservation of many of these alleles in Africans and in closely related ape species, we evaluate and test whether the reintroduction of some of these variants may also have restored lost functions. We identify more than 200,000 ancient alleles that are only present on introgressed Neanderthal haplotypes in modern Eurasian populations. We discover enrichment for reintroduced alleles among introgressed haplotypes with gene regulatory effects in several tissues, including the brain. We demonstrate functional effects for reintroduced alleles using computational analyses, cross-population comparisons of eQTL, and MPRA data. Finally, we experimentally validate the gene regulatory effects of a reintroduced allele independent of associated Neanderthal alleles in the context of both African and Eurasian haplotypes. Taken together, our results demonstrate that Neanderthal populations served as reservoirs of functional ancestral alleles that were lost to the ancestors of Eurasians (and in some cases all modern humans), and that some of these alleles have functional effects in Eurasians after being reintroduced by Neanderthal admixture.
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