|
|
Post by Admin on Jan 2, 2018 19:06:31 GMT
 Fig. 6. Marginal sampling distributions of legofit estimates, based on 50 simulated datasets. Simulation parameters (shown as red crosses) equal the estimates from the YRI.CEU analysis in Figs. 4 and 5. These simulations also show that estimates of mNmN and 2NN2NN are not as well behaved as those of the other parameters. They exhibit broad confidence intervals in real data (Figs. 4 and 5). In simulations (Fig. 6), they exhibit broad sampling distributions and bias. Presumably this reflects the association seen in Fig. 3. It is difficult to choose between parameter values that lie along the regression line. Our base model (Fig. 1A) omits several forms of gene flow that are known or suspected, and these omissions may have introduced bias. We therefore fitted four alternative models, as described in Section S3. None of these explains the surprising features of our estimates. We have found no way to explain these features as artifacts of a misspecified model.  Fig. 7. Poor fit of two constrained models. Horizontal axis shows deviation of fitted from observed site-pattern frequencies under two constraints: 2NND=10,0002NND=10,000 (blue circles) and TND=17,318TND=17,318 generations (red crosses). Horizontal bars show 95% confidence intervals. Both analyses use the YRI.CEU data. Our estimate of the Neanderthal–Denisovan separation time is surprisingly old. The most recent whole-genome estimate of this parameter is 381 kya (ref. 14, table S12.2), which corresponds to 502 kya or 17,318 generations under our molecular clock. To determine the cause of this inconsistency, we fitted a model in which TNDTND is fixed at 17,318 generations. The red crosses in Fig. 7 show the difference between fitted and observed site-pattern frequencies under this constrained model. The constrained model predicts too much ndnd but too little xndxnd and yndynd. The predicted points lie well outside the confidence intervals. This, along with the smaller discrepancies seen elsewhere in Fig. 7, refutes the hypothesis that Neanderthals and Denisovans separated as recently as 17,318 generations ago. |
|
|
|
Post by Admin on Jan 3, 2018 19:14:52 GMT
Discussion
These results contradict current views about Neanderthal population history. For example, Prüfer et al. (14) estimate that the Neanderthal population was very small—declining toward extinction. This view receives additional support from research showing elevated frequencies of nonsynonymous (and presumably deleterious) mutations among Neanderthals (22⇓–24). This abundance of deleterious alleles implies that drift was strong and thus that population size was small. Yet our estimate of Neanderthal population size is large—in the tens of thousands.
To reconcile these views, we suggest that the Neanderthal population consisted of many small subpopulations, which exchanged mates only rarely. In such a population, the effective size of the global population can be large, even if each local population is small (25). A sample from a single subpopulation would show a misleading signal of gradual population decline, even if the true population were constant (26). Furthermore, there is direct evidence of large genetic differences among Neanderthal populations (22, 27). Finally, the rich and widespread fossil record of Neanderthals is hard to reconcile with the view that their global population was tiny. We suggest that previous research has documented the small size of local Neanderthal populations, whereas our own findings document the large effective size of the metapopulation that contributed genes to modern humans.
This interpretation implies that at least some of the Neanderthals who contributed to the modern gene pool were distant relatives of the Altai Neanderthal. On the other hand, there is also evidence of gene flow from moderns into the Altai Neanderthal (28). This suggests contact between modern humans and at least two groups of Neanderthals: one that was ancestral to the Altai fossil and one or more others whose relationship to Altai was distant.
As discussed above, our results also disagree with previous estimates of the Neanderthal–Denisovan separation time. On the other hand, Meyer et al. (29) show that 430 ky-old fossils from Sima de los Huesos, Spain are more closely related to Neanderthals than to Denisovans. This implies an early separation of the two archaic lineages. Our own estimate—25,660 generations, or 744 ky—is earlier still. It is consistent with the results of Meyer et al. (29) but not with those of Prüfer et al. (14), as discussed above. The cause of this discrepancy is unclear. Prüfer et al. use the pairwise sequentially Markovian coalescent (PSMC) method (30), which may give biased estimates of separation times in subdivided populations (ref. 26, p. 6).
Our results shed light on the large-brained hominins who appear in Europe early in the Middle Pleistocene. Various authors have suggested that these were African immigrants (1, 2). This story is consistent with genetic estimates of the separation time of archaics and moderns (14). Our own results imply that, by the time these hominins show up in European archaeological sites, they had already separated from Denisovans. This agrees with Meyer et al. (29), who show that the hominins at Sima de los Huesos were genetically more similar to Neanderthals than to Denisovans. It also agrees with Hublin (4, 5), who argues that Neanderthal features emerged gradually in Europe, over an interval that began 500–600 kya.
PNAS, vol. 114 no. 37, Alan R. Rogers, 9859–9863, doi: 10.1073/pnas.1706426114
|
|
|
|
Post by Admin on Jan 5, 2018 19:20:48 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). |
|
|
|
Post by Admin on Jan 7, 2018 19:17:21 GMT
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.  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). 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). |
|
|
|
Post by Admin on Jan 9, 2018 19:16:58 GMT
 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. 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. 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.  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. Thibaut Devièse, doi: 10.1073/pnas.1709235114 |
|
