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Post by Admin on Nov 19, 2017 19:10:30 GMT
Expected length of archaic tracts under admixture and ancestral population structure scenarios. Pigmentation In region p21.31 of chromosome 3, there is a 200kb haplotype of Neanderthal origin that has a high frequency (> 49%) in the East Asians sequenced as part of the 1000 Genomes Project7. The introgressed region shows very high LD and significantly high values of the iHS statistic49, which measures extended haplotype homozygosity and is a hallmark of a recent selective sweep. However, as mentioned before, it is unclear how the iHS score would be affected by admixture in the absence of selection. One of the most likely targets of selection is a nonsynonymous SNP in the gene HYAL2, involved in the cellular response to ultraviolet radiation. The SNP is absent in other non- African populations, so it appears to have been lost in the ancestors of Eurasians after migrating out of Africa, but was regained in East Asians via admixture with Neanderthals. The authors performed a bootstrapped phylogenetic analysis to support the shared ancestry of the haplotype with the Neanderthal sequence and obtained a significant p-value for the observed LD value compared to a null model without introgression. Its frequency distribution shows a weak latitudinal gradient, suggesting it was involved in the adaptive response to ultraviolet radiation as modern humans expanded throughout Asia7. A putative signal of adaptive introgression in East Asians in HYAL2 has also been identified using the CRF framework47. BNC2 seems to be a strong candidate for adaptive introgression, as shown in two genome-wide archaic ancestry analyses23, 47. Sankararaman et al.47 applied the CRF model to detect introgressed segments, and then inferred selection based on departures from a null model of neutrally introgressed alleles. Vernot and Akey23 also found the introgressed region using S*, then confirmed its ancestry by matching it with the Neanderthal genome, and finally inferred selection by observing that the region has high differentiation between Europeans and Asians, as measured by FST. A BNC2 SNP is associated with skin pigmentation76 and freckling in Europeans77, and the archaic haplotype is present at 70% frequency in Europeans, while it is absent in Asians. Interestingly both studies also found a strong adaptive introgression signal in a cluster of keratin genes on chromosome 12 in both Asians and Europeans23, 47. Two neighboring genes (POU2F3 and TMEM136) have significant evidence for adaptive introgression in East Asians only, again based on the two genome-wide archaic ancestry analyses23, 47 (see above). POU2F3 is a transcription factor that mediates keratinocyte differentiation and proliferation, and the archaic haplotype is at 66% frequency in East Asians but almost absent in Europeans. TMEM136 codes for a transmembrane protein, but little information is available about its function.47 Ding et al.78 identified an introgressed haplotype of Neanderthal origin in Eurasians carrying a loss-of-function variant (Val92Met) in the gene MC1R, which encodes a melanocyte stimulating hormone receptor. This gene is known to affect hair color in mice79 and is associated with red hair, freckles and type I/II fair skin type in humans80, 81. The region, however, shows no significant departures from neutrality at the introgressed region in Europeans or East Asians, using either Tajima’s D52, Fu and Li’s test82, or iHS49, presumably because the frequency of the archaic haplotype only ranges from 5–22%. In addition, the lossof- function mutation (Val92Met) is not actually seen in the high-coverage Neanderthal genome4, despite being almost exclusively observed within haplotypes inferred to be introgressed from Neanderthals in Eurasian populations. The variant is also present in 3 African HapMap samples83, which weakens the argument for introgression into Eurasians, unless the variant was later introduced into Africans via admixture from Eurasians. Intriguingly, the same variant is found at very high frequencies in Taiwanese aborigines (60–70%), but lack of extensive sequence data at this locus has prevented formal rejection of neutrality at the putatively introgressed haplotype in these populations78. Nat Rev Genet. 2015 Jun; 16(6): 359–371.
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Post by Admin on Dec 2, 2017 19:07:47 GMT
An international team of researchers has conducted a new test of Neanderthal remains found at Vindija Cave in Croatia and found them to be older than previous studies indicated. In their paper published in the Proceedings of the National Academy of Sciences, the team describes their dating technique and the possible implications of their findings. The Neanderthal remains were originally found in the cave approximately 40 years ago and have been tested for age several times. They have also been the subject of much speculation, as it was thought that the remains represented the last of the Neanderthals in that part of Europe and that they existed for a short period of time in close proximity to modern humans. Initial testing suggested the remains were approximately 28,000 to 29,000 years old. More recent tests have put them at 32,000 to 34,000 years old. Both time frames coincide with the arrival of modern humans into the area, keeping alive the theory that the two groups mixed, both physically and socially. But now, using what is being described as a more accurate technique, the group with this new effort has found that the remains are older than thought. The new technique, called ZooMS involves radiocarbon dating hydroxyproline—an amino acid taken from collagen samples found in bone remains. The team also purified the collagen to remove contaminants. The researchers report that the new technique indicates that the remains—all four samples—were approximately 40,000 years old. This new finding puts the Neanderthal in the cave well before the arrival of modern humans, thus, there could not have been mixing of the two. The researchers also studied other artifacts from the cave, including other animal bones, and found that the artifacts were a mixed bag, representing a timeline of thousands of years. The animal bones, they found, were from bears. This has led the team to conclude that the reason more modern artifacts were found with older artifacts is because of bears mixing them up. The researchers conclude by claiming their study has shown that the Neanderthals at the Vindija cave did not overlap in time with modern humans, and thus were not the final holdout that many have suggested. Abstract Previous dating of the Vi-207 and Vi-208 Neanderthal remains from Vindija Cave (Croatia) led to the suggestion that Neanderthals survived there as recently as 28,000–29,000 B.P. Subsequent dating yielded older dates, interpreted as ages of at least ∼32,500 B.P. We have redated these same specimens using an approach based on the extraction of the amino acid hydroxyproline, using preparative highperformance liquid chromatography (Prep-HPLC). This method is more efficient in eliminating modern contamination in the bone collagen. The revised dates are older than 40,000 B.P., suggesting the Vindija Neanderthals did not live more recently than others across Europe, and probably predate the arrival of anatomically modern humans in Eastern Europe. We applied zooarchaeology by mass spectrometry (ZooMS) to find additional hominin remains. We identified one bone that is Neanderthal, based on its mitochondrial DNA, and dated it directly to 46,200 ± 1,500 B.P. We also attempted to date six early Upper Paleolithic bone points from stratigraphic units G1, Fd/d+G1 and Fd/d, Fd. One bone artifact gave a date of 29,500 ± 400 B.P., while the remainder yielded no collagen. We additionally dated animal bone samples from units G1 and G1–G3. These dates suggest a co-occurrence of early Upper Paleolithic osseous artifacts, particularly split-based points, alongside the remains of Neanderthals is a result of postdepositional mixing, rather than an association between the two groups, although more work is required to show this definitively.
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Post by Admin on Dec 4, 2017 19:07:09 GMT
The period between ∼45,000 and 35,000 cal B.P. in Europe witnessed the so-called biocultural transition from the Middle to early Upper Paleolithic, when incoming anatomically modern humans displaced Neanderthal groups across the continent (1, 2). Significant questions still remain regarding the precise nature of this transition, the humans responsible for the various transitional early Upper Paleolithic industries, the degree of overlap between Neanderthals and modern humans, and the timing of the disappearance of the former. The European record for the transition retains its interest because it is the best-documented sequence for the disappearance of a hominin group available (3). The latest data, both radiometric and genetic, suggest Neanderthals and modern humans coexisted or overlapped for up to several thousand years in Europe until Neanderthal disappearance at around 40,000 cal B.P. (4, 5). Ascertaining the spatial attributes of Neanderthal and modern human populations in Europe is an area of active research, and a reliable chronology remains essential. Our understanding of the biocultural processes involved in the transition have been greatly influenced by improved accelerator mass spectrometry (AMS) dating methods and their application to directly dating the remains of late Neanderthals and early modern humans, as well as artifacts recovered from the sites they occupied. It has become clear that there have been major problems with dating reliability and accuracy across the Paleolithic in general, with studies highlighting issues with underestimation of the ages of different dated samples from previously analyzed sites (6). We have been working on redating some of the purported late-surviving Neanderthal sites from around Europe, which have included human and archaeological remains from sites such as Mezmaiskaya (Russia), where a previous directly dated Neanderthal infant yielded a radiocarbon age of ∼29,000 B.P. (7), and Zafarraya (Spain), which was thought to contain Neanderthal remains clustering in age around a small group of U-series–dated animal bones between 33,400 and 28,900 B.P. (8). At Mezmaiskaya, the AMS dates obtained for the Neanderthal excavated above the previously dated individual were substantially older (9). This, along with other AMS dates from cut-marked fauna from the same archaeological horizons, suggested the original date of 29,000 B.P. could not be correct. At Zafarraya, Wood et al. (10) showed that, when redated using ultrafiltration methods, the bones that produced ages of ∼33,000 B.P. were in fact beyond the radiocarbon limit, suggesting the Neanderthal remains were unlikely to be as young as previously thought. In both cases, revised radiocarbon dates produced with more robust chemical pretreatment methods have illustrated significant underestimates in the previous dates that cannot be reconciled with a hypothesis of late-surviving refugial Neanderthals. The Neanderthal fossil remains from level G1 of Vindija Cave in northern Croatia have remained in the literature as potentially late individuals. Given the evidence from the Peștera cu Oase specimen, which demonstrates a recent Neanderthal ancestry in a 40,000 cal B.P. modern human from the Danube corridor (5), the renewed dating of the Vindija remains is overdue. Two specimens, Vi-207 and Vi-208, were originally directly AMS dated in the late 1990s at the Oxford Radiocarbon Accelerator Unit (ORAU). Vi-207 is a right posterior mandible and Vi-208 is a parietal fragment, both showing Neanderthal-specific morphology (11, 12). The initial radiocarbon results were 29,080 ± 400 B.P. (OxA-8296) and 28,020 ± 360 B.P. (OxA-8295) (13). Higham et al. (14) attempted to redate these specimens by taking the very small amounts of collagen remaining from the original sample pretreatment and ultrafiltering the product before AMS dating. The revised measurements were 32,400 ± 1,800 B.P. (Vi-207: OxA-X-2089-07) and 32,400 ± 800 B.P. (Vi-208: OxA-X-2089-06), which indicated the previous dates were indeed too young. For sample Vi-208, after ultrafiltration, the C/N atomic ratio was 3.4, which indicates collagen of acceptable quality. However, for Vi-207, the >30-kDa fraction obtained produced a C/N ratio of 4.3, which indicates the presence of a high molecular weight contaminant. The radiocarbon date for this sample could therefore include a higher molecular weight noncollagenous contaminant, possibly cross-linked to the collagen. On the basis of the potential problems associated with the small size of the redated samples and the potential for remaining contaminants, OxA-X-2089-06 was considered to be a minimum age (14). If the dates are even approximately correct, however, it makes them the most recent known Neanderthals. This would imply a more extensive temporal overlap between Neanderthals and early modern humans in central Europe than has recently been documented (4). In addition to the Neanderthal remains, level G1 has yielded a small archaeological assemblage that contains techno-typologically Middle and Upper Paleolithic lithic artifacts plus several distinctively early Upper Paleolithic osseous points (12). It has been argued that the mix of Neanderthals, Middle Paleolithic tools, and Upper Paleolithic technology was the result of cryoturbation and Ursus spelaeus activity in level G1, with elements mixing into level G1 from both the Upper Paleolithic unit F above and the Middle Paleolithic level G3 below (15, 16). Zilhão (17) has suggested that the G1 lithic assemblage has parallels with the Szeletian technocomplex, and further, that there is a mixture of elements of Szeletian and Aurignacian I and II within the level [see also Svoboda (18)]. Karavanić and Smith (19) have suggested that the mixture of elements may represent the interaction and possible acculturation between modern humans and late Neanderthals. These alternatives are testable by selecting human and organic osseous points, as well as animal bones, for renewed AMS dating. This is what we have undertaken and describe here.
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Post by Admin on Dec 6, 2017 18:55:05 GMT
Fig. 1. (A) High-resolution photographs of the Vi-*28 Neanderthal bone found using ZooMS. The bone yields evidence for a probable cut and gauge marks (right upper part of the bone). The picture was taken after the bone had undergone sampling for ZooMS and before sampling for aDNA, radiocarbon, and stable isotope analysis. (B) MALDI-TOF mass spectrum of digested collagen from the Vi-*28 bone. All tagged peaks (A, B, C, D, and F) denote sequence-matched peptides observed in human collagen (27, 28). Results and Discussion ZooMS Collagen Fingerprinting. We used ZooMS to identify potential hominin bone fragments among the unidentified faunal remains from the G1 and G3 levels, as well as the stratigraphic unit G1–G3. The majority of the 383 samples we analyzed yielded poor collagen preservation, which prevented any identification to genus or taxon. Only 101 samples produced identifiable spectra; a summary of all taxa identified by ZooMS is shown in SI Appendix, Table S2. This assemblage is dominated by Ursus, and only six of the 27 taxa identified by morphological study of the bones in Miracle et al. (21) could be identified here. We identified a single hominin specimen (Fig. 1 A and B), which again highlights the use of applying such techniques to groups of unidentified Paleolithic bone samples. The bone was analyzed using ancient DNA techniques to enable a formal species identification. DNA Analysis of the Human Bones. Genomic analysis based on mitochondrial DNA revealed that all four human specimens fall into Neanderthal mitochondrial variation. Full mitochondrial genomes of Vi-207 and Vi-*28 were reconstructed with an average coverage of 103-fold and 257-fold, respectively. The mitochondrial DNA sequence of Vi-207 was identical to Vi-33.25 and Feldhofer 1 mitochondrial genomes, whereas Vi-*28 had an identical mitochondrial sequence to Vi-33.17 (SI Appendix, Fig. S2). Both Vi-33.25 and Vi-33.17 were found in layer I of Vindija Cave. As previously published, Vi-33.19 has the same mitochondrial sequence as Vi-33.16 (22). Because of lower endogenous DNA content in Vi-208, a full mitochondrial genome could not be reconstructed for the sample. However, from the limited amounts of mitochondrial sequences, we were able to trace most of the observed variants to variations found in previously sequenced Neanderthal mitochondrial genomes (SI Appendix, Fig. S3). Vi-208 and Vi-207 produced hydroxyproline dates of 42,700 ± 1,600 and 43,900 ± 2,000 B.P., respectively. These ages are significantly older than any of the dates obtained previously for these specimens using the AG (gelatinized filtered collagen) and AF (ultrafiltered collagen) procedures, and this strongly suggests that noncollagenous high molecular weight contaminants, probably crosslinked to the collagen, were still present in the sample previously dated. It is only by hydrolyzing the collagen and selecting the hydroxyproline that we were able to successfully remove these contaminants. Fig. 2. Bayesian age model showing the calibrated HYP ages of the four Neanderthal samples from Vindija Cave. The model is a simple phase model in OxCal 4.3 (47), in which all F14C determinations are assumed to have no relative order. “Start” and “End” correspond to the boundaries calculated by the model. The calibration curve of Reimer et al. (48) was used to calibrate the results. Details can be found in the SI Appendix. The AMS measurement of the third human bone from level G1 (Vi-*28), identified using the ZooMS method, gave a date of 46,200 ± 1,500 B.P. For these three HYP (extraction of hydroxyproline from hydrolyzed bone collagen) dates obtained on the Neanderthal bones from level G1, we performed a χ2 test using the modern fraction F14C and its error. The error weighted mean is 0.0038 ± 0.0005 with a t value of 2.57. If t is <5.99, the value for χ2, the error weighted mean is not significant. This shows that the results obtained on the three Neanderthal bones from level G1 are statistically in agreement. Vi-33.19 (level G3) was also dated using the hydroxyproline method and produced a date of 44,300 ± 1,200 B.P., which is a more precise date than the one obtained using the AF procedure (45,300 ± 2,300 B.P.). The AF determination had a low target current in the AMS (85% of normal current) and was imprecise for this reason. The fact that the two dates overlap suggests no significant contamination in this bone. Taken together, these dates show a significantly older occupation of the site by Neanderthals, suggesting the site cannot be considered to be a refugium for late-surviving Neanderthals (Fig. 2, code in SI Appendix). The two other dates obtained on samples Vi-33.26 and Vi-75, even if obtained with a method that can be less efficient in removing contamination, confirm the dating of level G is more than 42,000 B.P.
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Post by Admin on Dec 7, 2017 19:04:24 GMT
Only one bone point (Vi-3446–P41417) produced enough nitrogen during prescreening to warrant pretreatment chemistry. Less than 500 mg bone was available, so we applied an AG (gelatin) treatment to maximize the collagen yield. We obtained a date of 29,500 ± 400 B.P., which we consider to be a minimum age, as this pretreatment has been shown before to underestimate the age of ancient bones such as this (Table 3). To test possible perturbation in level G1, we also dated four faunal samples identified as originating from levels G1 and G1–G3, using ultrafiltration (AF). These samples produced dates that were all greater than or very close to the radiocarbon limit (Table 3). These samples are less likely to have been treated with conservation materials than the human bones, and therefore were not prepared using the HPLC method. Three of these faunal bones are from level G1 (Table 1). We see more variation that would be expected statistically if we combine the three Neanderthal bones and three faunal bones from level G1 for a χ2 test (error weighted mean, 0.0027 ± 0.0004; t = 22.52; χ2 = 11.07). This shows there is bone of variable radiocarbon age in the G1 level and suggests the possibility of postdepositional mixing and movement of material. In consequence, the bone tools cannot be associated with the Neanderthal remains unless further direct radiocarbon dating using the HYP approach is undertaken. Clearly, the low collagen content of the points appears to preclude this at this time. Conclusions Single-amino acid AMS dating of the Vindija Neanderthals has yielded results that are substantially older than the previous ages that were initially obtained. We have shown that the Neanderthals predate ∼44,000 cal B.P. The results suggest this group was not a late-surviving refugial Neanderthal population, as previously thought, and means the group almost certainly did not overlap with early anatomically modern humans in this part of Europe. Despite our best attempts, we were not able to date the bone industry associated with the archaeology of level G1. The one date we obtained from a later stratigraphic unit was younger than 30,000 B.P., but because the bone was not treated with the most rigorous pretreatment chemistry methods, it could potentially be older. The dating of other faunal materials from level G1 highlighted a significant range in age, which could indicate a perturbation of the general sequence. The question, then, of whether some of the points could have been produced by Neanderthals remains open; however, it is parsimonious to conclude that the split-based point at least must have a maximum age of 32,000–34,000 B.P. based on evidence for its association with the Aurignacian in other regions, and so it likely postdates the Vindija Neanderthals significantly. Bone points have been recovered throughout Eurasia with dates as early as ∼37,000 B.P. (e.g., from the Aurignacian site of Pes’ko and the Châtelperronian site of Arcy-sur-Cure) (6, 25, 26). It is therefore clear that both anatomically modern humans and Neanderthals produced bone points, with only split-based bone/antler points being diagnostic of the earlier facies of the former. Our perception of the biological transition between Neanderthals and modern humans has changed radically during the last decade. Evidence suggests interbreeding and a significant temporal overlap between the two from ∼44,000–40,000 cal B.P. On the basis of our hydroxyproline dates and the DNA results, the Vindija Neanderthals date before the period when the first modern humans arrived into Europe and interbred with Neanderthals. Published online before print September 5, 2017, doi: 10.1073/pnas.1709235114 PNAS October 3, 2017 vol. 114 no. 40 10606-10611
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