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Post by Admin on Oct 17, 2018 18:19:01 GMT
Figure 7 Enrichments in Adaptive Introgression from Neanderthals to Modern Humans among Gene Ontology Annotations Over-represented or Not Over-represented in VIPs The enrichments of VIPs in IS represent statistical associations, and more evidence is required to demonstrate causality. One particular worry is that host biological functions that are significantly enriched among VIPs might also be enriched in adaptive IS independently of their interactions with viruses. In such a case, the observed enrichment of adaptive introgression at VIPs would not be due to interactions with viruses but would be due, instead, to the uneven representation of diverse host functions between VIPs and non-VIPs. Consider a hypothetical example in which genes that have the biological Gene Ontology (GO) function “cell cycle” tend to be enriched in IS independently of their interactions with viruses. If the genes with this function are also enriched among VIPs, this could by itself lead to the enrichment of VIPs in the IS. We test this possibility by assessing if the biological functions over-represented among VIPs (≥1.5 enrichment, permutation test p ≤ 0.05) are enriched within IS overall or within particularly long and/or frequent IS (Figure 7). If they are not—as schematically shown in Figure 7A—then this is an unlikely explanation for our results. If they are—as schematically shown in Figure 7B—then this would be worrisome and would require us to carry out additional analyses to control for this bias. Figures 7C–7F show no evidence that biological functions enriched in VIPs show any biased signals (Wilcoxon rank sum test p > 0.05 in all cases) in their presence in IS. Assuming that viruses were responsible for the observed enrichments, we then asked whether VIPs in IS tend to possess any particular functions. We used a permutation test to estimate the over-representation of GO annotations of biological functions at VIPs inside IS compared to VIPs outside IS (STAR Methods). We used IS of at least the length and the frequency where we first started observing highly significant (bootstrap test p < 10−3 both in Europe and East Asia) enrichments in IS at VIPs (longer than 50 kb and at frequencies higher than 5%; Figure 3). In line with a possible causal role of viruses, multiple functions related to immune response or to crucial steps of the viral replication cycle were significantly over-represented among VIPs within IS in Europe, although not in East Asia (Table S6). This pattern was particularly pronounced when using only the manually curated LT-VIPs (Table S6), which may reflect the fact that LT-VIPs are better annotated. For example, the GO annotation “immune effector process” was one of the most strongly over-represented in Europe (all VIPs: 57 VIPs versus 34 expected by chance, permutation test p = 5 × 10−4; LT-VIPs: 49 versus 27.5 expected by chance, p = 10−4). Importantly, the “immune effector process” function was not over-represented among non-VIPs within IS (permutation test p > 0.05 for all GO annotations in Table S6).
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Post by Admin on Oct 18, 2018 18:17:01 GMT
Discussion Here, we presented evidence that a substantial proportion of IS from Neanderthals to modern humans and vice versa are strongly enriched for proteins interacting with viruses. We further detected a particularly strong signal for VIPs interacting with RNA viruses in Europeans. The more comprehensive annotations of host-virus interactions we used as well as the controls for multiple genomic factors explain why such signals were not noticed in previous functional analyses of IS (STAR Methods). Altogether, our results suggest that adaptive introgression in response to viruses might have been more prevalent than previously known based on the small number of published examples (Abi-Rached et al., 2011, Dannemann et al., 2016, Mendez et al., 2012, Mendez et al., 2013, Nedelec et al., 2016, Quach et al., 2016, Sams et al., 2016). Indeed, we estimate that out of all long (≥100 kb) and high-frequency (≥15%) IS from Neanderthals to modern humans, 32% (54 of 171) in Asians and 25% (27 of 105) in Europeans might have been positively selected in response to viruses. Note that we specifically tested the model of positive directional selection of IS soon after interbreeding which is expected to drive long IS of Neanderthal ancestry to high frequency into the population. However, we do not exclude the possibility that the IS were subsequently maintained by balancing selection or frequency-dependent selection of some kind. This is an intriguing possibility especially if the increased genetic variability introduced by introgression was advantageous in variable environments. Overall, these results provide preliminary support for the “poison-antidote” hypothesis under which the interactions between modern humans and Neanderthals exposed each species to novel viruses while gene flow between the species afforded a measure of resistance by allowing VIPs that were already adapted to the presence of specific viruses in the donor species to cross species boundaries and provide adaptive function in the recipient species. In this respect, the finding that the greater enrichment of Neanderthal ancestry at RNA VIPs is restricted to Europe is particularly interesting. Several authors have concluded that multiple pulses of interbreeding occurred between Neanderthals and modern humans, with at least one pulse before the split of Asian and European modern populations and multiple independent pulses after the split of these populations (Kim and Lohmueller, 2015, Vernot and Akey, 2015, Villanea and Schraiber, 2018). The strong enrichment at RNA VIPs in Europe but not in East Asia then suggests that this difference arose due to the pulses of interbreeding after the split between Asians and Europeans. Whether adaptive introgression at DNA VIPs in East Asians compensated for a previous bias toward RNA VIPs still visible in Europeans, or adaptive introgression at RNA VIPs occurred specifically after an independent pulse of interbreeding in Europe, remains an open question. Despite the strong statistical signals, we believe that the evidence gathered in favor of the poison-antidote scenario is preliminary. Indeed, although the enrichments we describe are rigorously defined, they represent only statistical associations. We believe that more functional work will be required to establish the causal impact of the virus-host interactions on the detected patterns of adaptive introgression. Intriguingly, such evidence is beginning to accumulate. Quach et al. (2016) recently found that regulatory variants that affect host gene expression during IAV infection are particularly strongly enriched in Neanderthal ancestry in Europeans. Furthermore, Sams et al. (2016) recently found that flaviviruses—a class of RNA viruses that include HCV, Dengue, and other viruses—might have been driving selection at the adaptively introduced Neanderthal haplotype at the OAS1 locus. The analysis presented here opens the door for more functional studies of this kind. Our own cursory look at the functional data revealed some tantalizing patterns. For instance, several of the RNA virus VIPs that have a low FDR for adaptive introgression are known to affect specific steps of the viral replication cycle, and in some cases, introgression increased the frequency of specific functional variants that plausibly confer increased resistance against viruses. For example, the IAV VIP PPIE (also known as cyclophilin E) has been shown to inhibit the formation of the viral ribonucleoprotein complex required for IAV RNA replication (Wang et al., 2011b). Introgression at the PPIE locus in Europeans has increased the frequency of allelic variants of expression quantitative trait loci (eQTL) SNPs that are associated with very high expression of PPIE across many tissues, including the lungs (GTEx Consortium, 2015). It is possible that such an increased expression results in greater inhibition of the viral ribonucleoprotein complex and thus increased viral resistance. Another noteworthy example is Toll-like receptor 2 TLR2, a HIV VIP where introgression increased the frequency of alleles at multiple linked eQTL SNPs associated with higher TLR2 expression in many tissues (GTEx Consortium, 2015). HIV protein ENV has been shown to bind and inhibit TLR2 activity (Reuven et al., 2014), suggesting that increased TLR2 expression might have at least partially prevented such inhibition for related lentiviruses. Furthermore, it will be interesting to study whether the presence of Neanderthal ancestry at VIPs still leads to variable susceptibility to modern viruses in modern humans. Interestingly, the C-type lectin receptor CD209/DCSIGN, one of the five virion attachment HCV VIPs found to be highly enriched in IS in Europe (Crucial Immune and Proviral VIPs Are Over-Represented in Introgressed Segments, in Results), interacts with HCV and Dengue virus. Introgression from Neanderthals at this locus has affected the frequency of alleles at a well-known variant (rs4804803) within the promoter of DCSIGN with a documented effect on CD209/DCSIGN expression and on HCV and dengue virus infection severity (Ryan et al., 2010, Wang et al., 2011a). Cell, VOLUME 175, ISSUE 2, P360-371.E13, OCTOBER 04, 2018
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Post by Admin on Nov 14, 2018 18:19:44 GMT
New research published today in Nature is finally setting the record straight, showing that Neanderthals and Upper Paleolithic modern humans experienced similar levels of head trauma. Yes, life was tough for Neanderthals—but the new research suggests life wasn’t any less tougher or violent for contemporaneous Homo sapiens. Fig. 1: Neanderthal and Upper Palaeolithic modern human sites. Neanderthals are commonly depicted as leading dangerous lives and permanently struggling for survival. This view largely relies on the high incidences of trauma that have been reported1,2 and have variously been attributed to violent social behaviour3,4, highly mobile hunter-gatherer lifestyles2 or attacks by carnivores5. The described Neanderthal pattern of predominantly cranial injuries is further thought to reflect violent encounters with large prey mammals, resulting from the use of close-range hunting weapons1. These interpretations directly shape our understanding of Neanderthal lifestyles, health and hunting abilities, yet mainly rest on descriptive, case-based evidence. Quantitative, population-level studies of traumatic injuries are rare. Here we reassess the hypothesis of higher cranial trauma prevalence among Neanderthals using a population-level approach—accounting for preservation bias and other contextual data—and an exhaustive fossil database. We show that Neanderthals and early Upper Palaeolithic anatomically modern humans exhibit similar overall incidences of cranial trauma, which are higher for males in both taxa, consistent with patterns shown by later populations of modern humans. Beyond these similarities, we observed species-specific, age-related variation in trauma prevalence, suggesting that there were differences in the timing of injuries during life or that there was a differential mortality risk of trauma survivors in the two groups. Finally, our results highlight the importance of preservation bias in studies of trauma prevalence. Fig. 2: Predicted cranial trauma prevalence in skeletal elements from Neanderthals and Upper Palaeolithic modern humans. This idea, that Neanderthals led brutal lives, was largely predicated on injuries observed in the bones and skulls left behind by Neanderthals. When comparing trauma in Neanderthals to those seen in anatomically modern humans, scientists observed higher levels of head and neck injuries in Neanderthals, which was attributed to their lifestyle. Neanderthals, it was argued, engaged in violent social behavior; lived a mobile hunter-gatherer lifestyle in perilous Ice Age environments where opportunities for accidents were in steady supply; were prone to attacks by dangerous carnivores such as bears and cave hyenas; and, as hunters, relied on close-range weapons—such as stabbing implements and thrusting spears—to subdue their prey, which required them to come into close contact with large animals. Katerina Harvati, the lead author of the new study and an archaeologist at the University of Tübingen in Germany, said these earlier studies were based on a descriptive approach, focusing on just injured individuals and evaluating trauma patterns across skeletons rather than injury rates. Recent efforts have tried to be more systematic and quantitative in their approach, but Harvati said these studies were limited in scope and thus inconclusive. Fig. 3: Predicted cranial trauma prevalence in individual cranial specimens from Neanderthal and Upper Palaeolithic modern humans. “Our study is the first to address the question of population-level rates of head injuries in Neanderthals and Upper Paleolithic Europeans by examining both injured and non-injured individuals, and using the largest dataset currently available that we compiled from the literature,” Harvati explained to Gizmodo. “We used sophisticated statistical modeling, taking into account preservation bias and other factors. As such our study is the first that addresses the question of head injury rates in Neanderthal and Upper Paleolithic modern human populations.” For the study, the University of Tübingen researchers documented incidents of skull trauma, sex, age at death, degree of skeleton preservation, and the geographical location of each sample. Frequency of head trauma was evaluated for the two groups. In total, 836 cranial elements were analyzed from 204 individuals. Looking at the data, no differences could be detected in the injury rates between Neanderthals and contemporaneous humans. “What we know now that we did not know before is that the prevalence of cranial injury at the population level is comparable between ‘classic’ Neanderthals and early Upper Paleolithic modern humans, suggesting that Neanderthal lives were not more dangerous than those of the latter group,” Harvati told Gizmodo. “This has potential implications for previous hypotheses about Neanderthal behavior developed on the basis of the assumption of high levels of Neanderthal trauma, such as those regarding dangerous hunting practices or high levels of interpersonal violence.”
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Post by Admin on Jan 27, 2019 18:25:35 GMT
The study, published in Scientific Reports, examined the performance of replicas of the 300,000 year old Schöningen spears -- the oldest weapons reported in archaeological records -- to identify whether javelin throwers could use them to hit a target at distance. Dr Annemieke Milks (UCL Institute of Archaeology), who led the study, said: "This study is important because it adds to a growing body of evidence that Neanderthals were technologically savvy and had the ability to hunt big game through a variety of hunting strategies, not just risky close encounters. It contributes to revised views of Neanderthals as our clever and capable cousins." The appearance of weaponry - technology designed to kill - is a critical but poorly established threshold in human evolution. It is an important behavioural marker representing evolutionary changes in ecology, cognition, language and social behaviours. While the earliest weapons are often considered to be hand-held and consequently short-ranged, the subsequent appearance of distance weapons is a crucial development. Projectiles are seen as an improvement over contact weapons, and are considered by some to have originated only with our own species in the Middle Stone Age and Upper Palaeolithic. Despite the importance of distance weapons in the emergence of full behavioral modernity, systematic experimentation using trained throwers to evaluate the ballistics of thrown spears during flight and at impact is lacking. This paper addresses this by presenting results from a trial of trained javelin athletes, providing new estimates for key performance parameters. Overlaps in distances and impact energies between hand-thrown spears and spearthrowers are evidenced, and skill emerges as a significant factor in successful use. The results show that distance hunting was likely within the repertoire of hunting strategies of Neanderthals, and the resulting behavioural flexibility closely mirrors that of our own species. Figure 1 Results: Velocity In total thirty-six throws, or recorded events (REs), were captured on HSV. Release velocities ranged from 11.8–20.11 m/s (Table 1). Impact velocities for aimed throws ranged from 13.5–21.7 m/s. Impact velocities analysed by distance for all throws show overall an even distribution across the distances (Fig. 1). However, those at the 20 m distance are high in relation to those at other distances, and two outliers also occur at longer distances. Of the distance throws that could be analysed, impact velocities ranged from 12.7–33.3 m/s, with the highest velocity relating to a distance throw of 23.2 m, and the spear landing point first. Impact velocity data show variability by participant (Supplementary Information Fig. 6). For example, the participant with the least number of years’ experience (P5) also produced the lowest impact velocities. The two participants (P1 and P4) with the highest percentage of ‘hits’ (Supplementary Information Table S3) also produced the highest impact velocities. Figure 2 Removing an outlier with a large increase, the remaining 17 REs demonstrate a trend for an overall slight increase in velocity from the point of release to the point of impact (Fig. 3). The rate of change from release to impact velocities ranged from −1.51 m/s to 1.84 m/s (Table 1). Both slight decreases and increases occurred across the range of distances, with the largest increase occurring at a distance of 20 m (Fig. 3). Gravitational acceleration (9.81 m/s2) in part explains the increases with acceleration from point of release to impact. Some velocity is gained through gravitational acceleration for all throws including parabolic trajectories because the release height of the spears was >1.5 m while impact velocity was measured at or near ground level (see Supplementary videos 2 and 4, and Supplementary Information for detailed explanation and equations). Spears thrown in a parabolic trajectory are affected by multiple forces during flight, and tail winds such as those experienced during this experiment can also increase velocity by increasing the horizontal velocity as well as affecting lift (see Supplementary Information Section 1.3 and Supplementary Information Fig. 1)72,73. Figure 3 Results: Kinetic Energy and momentum The KE from the trial ranges from 71 to 179 J (Table 1) for aimed throws. The mean KE of aimed throws (107.6 J) exceeds the maximum of complex projectiles due to the mass of the spears (Supplementary Information Table S3; Supplementary Information Fig. 5) further underscoring the significance of mass for hand-delivered weaponry. The range for all combined throws in this study is greater than for aimed throws, from 65 to 444 J. Although many of the distance impacts did not fall point first, the highest value of 444 J related to a point-first impact (RE 28). Momentum follows much the same pattern, ranging from 10–17 kg*m/s for aimed throws, with the lowest value for hand-thrown spears exceeding even the highest values for complex projectiles (Supplementary Information Table S3).
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Post by Admin on Jan 27, 2019 21:11:40 GMT
Figure 4 Results: Distance and accuracy Of the 102 aimed throws, 25 hit the target (25%) (Fig. 4) while 77 (75%) missed entirely. A breakdown of the hit/miss data by distance confirms the correlation between target distance and accuracy (Table 2). When combining the data of all throws at 10 m, the percentage of hits follows a clear descending pattern by distance (Fig. 5). The additional hits performed at 10 m with increase in target height target greatly increased the number of hits: 17% of throws were hits at 10 m with the hay bale horizontal on the ground, while 33% resulted in hits when vertical, which is an increase of 16%. Hit rates at other distances may have been similarly improved with a higher target, meaning taller or standing prey may be easier to hit than prey closer to the ground. Participants showed variability in their ability to hit the target. The percentage of total hits by participant ranges from 11% to 33% (Supplementary Information Table S7). The participant with the fewest years’ throwing experience (P5) had the lowest percentage of hits, and the lowest impact velocities underscoring the significance of training. Participants with 5 years experience had the best hit rate. However, body mass also appears to have a role (Supplementary Information Fig. 7), with a relatively strong correlation between body mass and successful hit rate. Participant height did not have a clear correlation. Distance throws ranged from 19.4 m to 31.2 m (mean = 26.33 m; SD = 3.981 m). The most experienced participant (P2) who is accustomed to stiff distance-rated javelins achieved the farthest distance, while the one with least experience (P5) performed the poorest. Results: Flight trajectories Throughout the experiment, two types of flight trajectories were observed. Flight paths for throws at 5 m had a downward-directed flat flight trajectory. Participants adjusted the angle of release according to each distance, with a maximum upward angle of release for the farthest distances (Supplementary Videos 1 and 2). At 5 m distance throws, the angle of release and impact fall within –0.20 and –0.40 radians (rad), corresponding to between −11° and −23° (Supplementary Information Figs 11 and 12). At 10 m release angles were near to zero, with impact angles being negative, beginning an increasing trend towards parabolic throws. From 10 m and beyond angles increase upwards in relation to the ground at release, and decrease by impact. These results demonstrate a correlation between release and impact angles and reflect the shift from flat flight trajectories at the closest distances to parabolic trajectories at the farther distances. The maximum release angle is 0.55 rad, which is a 35° angle, corresponding to a 25 m throw. Impact angles ranged from −0.57 to −0.22 rad, translating to impacts between −33° and −13°. Spears oscillated (vibrated) along the long axis of the spear in flight and flexed upon impact (Supplementary Videos 3 and 4). Spears also spun in flight (Supplementary Video 4), a result of the throwers intentionally imparting spin, which improves stability73. Of the 25 suitable target impact videos (including both hits and misses), 84% (n = 21) landed point first, 12% (n = 3) landed rear first and 4% (n = 1) landed flat. In distances 20 m and beyond, both for target and distance throws, several examples of the spear yawing and stalling in flight were observed. For the distance throws, spears rarely landed point first (n = 3), typically landing with the proximal (back) of the spear first, which are failed landings. Yawing and stalling are influenced by release conditions, spear design, and conditions during flight including both wind and the orientation of the spear in relation to the flight trajectory, and it is likely that a combination of these factors contributed to these suboptimal flight behaviours (see Supplementary Information). Figure 5 Discussion The mean impact velocity in this experiment provides data for replication studies, and while it largely confirms existing estimates of prehistoric spear throwing25,74, the spear replicas used in this study were of a higher mass, demonstrating that in skilled hands, such masses are not a limiting factor. According to the principle that the greater the mass of an object, the greater the work to propel that mass75, objects with lighter mass, such as those thrown by inexperienced throwers used for the calculations elsewhere25 would be expected to be thrown with significantly higher velocities by skilled throwers than those achieved in the present study using heavier spears. This is supported by the higher release velocities achieved with lighter thrown objects such as balls and sticks by skilled throwers (Supplementary Information Table S1). The range of velocities in the present study overlaps with velocities recorded for spearthrowers. The lack of a trend to drop in impact velocity from release differs from lighter and fletched projectiles such as arrows and darts, which experience more drag than a heavier unfletched spear (see Supplementary Information for further explanation). Overall the data from this experiment demonstrate that at short ranges in field conditions there is not a demonstrable loss in velocity and therefore KE or momentum from release to impact for spears such as those from Schöningen, and therefore the hypothesis that this is a significant limitation of the weapon is not supported. With different wind conditions and/or at greater distance throws there may be more significant velocity losses, though a recent javelin study also shows that loss in velocity from release to impact over longer distances can also be slight76. Further experimentation on this question would be useful. Hand-thrown spears can impact with KE and momentum values that are suggested to be sufficient to hunt large prey77. Considering that it is impact energy, not just velocity, that influences penetration and fracture mechanics, these results are significant for those seeking to identify prehistoric weaponry delivery systems in the Pleistocene archaeological record using systematic mechanical projection. In addition to KE and momentum, other variables such as tip material and morphology affect penetration, influencing ability to cut through hide, muscle and bone, depth of penetration, and wound morphology. The spears used in this experiment have wide diameters in comparison with most complex projectiles, and do not have a stone tip. This study focuses on the external and terminal ballistics of the spears and does not address penetration and wounding capabilities, or overall effectiveness of these weapons, something that requires systematic experimentation. The primary purpose of this paper was to replace problematic estimates of the external and terminal ballistics of hand-thrown spears by reviewing the existing evidence and collecting empirical data. The data support hypotheses that early spears, such as the double-tapered examples from Schöningen, function as throwing weapons both for flat and parabolic trajectories at distances up to 20 m. Our results underscore the importance of using trained participants if launching weapons manually in experimental research79 whether the aim be to further evaluate performance parameters or for replication work. In experimental work using human throwers, recording of impact velocities, accuracy data, and physical attributes and skill level of throwers will help fill in knowledge gaps. Unlike for spear thrusting, controlled mechanical replication of hand-thrown velocities is straightforward, but experimenters should carefully consider potential masses of hand-thrown spears as this affects external, terminal and wound ballistics. Replicating a mean statistic for weapon performance parameters while ignoring the range creates problems for comparing and identifying delivery systems. In particular replicating mean impact velocity and by extension KE and momentum rather than the range superficially suppresses human and technological variability, masks overlaps with other weapon systems, and may create false taxonomies. The results imply that robust, highly-trained and habitual throwers could throw spears with more power and at least twice as far as has been widely argued for in the literature. The extension to a 20 m accuracy limit from this experiment implies greater flexibility in hunting strategies than the previous distance estimates. The larger ethnographic distances discussed would put hand-thrown spears on par with spearthrowers. In hunter-gatherer societies, the skills involved in hunting take decades to master, beginning in early childhood78. With both skill, strength and potentially a larger body size needed to use spears effectively as thrown weapons, we can theorize that only hominins that combined relatively large brains with robust physiques could have employed them as part of a successful subsistence strategy. These effective costs are high when compared to later complex projectiles that may have offered a relaxation on time and energy budgets required to learn and effectively use these ‘simple’ hunting technologies. The importance of skill in weapon use has been discussed elsewhere31,70,80, with an interesting hypothesis proposing that hand-delivered weapons are not inferior in terms of energy, but rather that part of their disadvantage relates to a high investment in training31. Understanding and explaining the development and persistence of hand-thrown weapons in the human past is complex and requires approaches from multiple disciplines. It is not the case that hand-thrown spears are universally replaced by complex projectiles, as they continued to be used, most typically alongside other weapon systems, through to the ethnographic present. Moreover we can compare this performance data with those from experiments demonstrating the potential of these weapons as thrusting spears, in order to consider the likelihood that they were routinely thrown at all. Understanding the fine detail of the situations, ecologies, and strategies in which hand-thrown spears were considered preferable to more complex weapons may now provide a useful avenue for understanding the context in which these weapons emerged in the first place. Scientific Reportsvolume 9, Article number: 820 (2019)
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