|
Post by Admin on Feb 24, 2020 23:32:30 GMT
INTRODUCTION During the past decade, we have learned about interbreeding among hominin populations after 50 thousand years (ka) ago, when modern humans expanded into Eurasia (1–3). Here, we focus farther back in time, on events that occurred more than a half million years ago. In this earlier time period, the ancestors of modern humans separated from those of Neanderthals and Denisovans. Somewhat later, Neanderthals and Denisovans separated from each other. The paleontology and archaeology of this period record important changes, as large-brained hominins appear in Europe and Asia and Acheulean tools appear in Europe (4, 5). It is not clear, however, how these large-brained hominins relate to other populations of archaic or modern humans (6–9). We studied this period using genetic data from modern Africans and Europeans and from two archaic populations, Neanderthals and Denisovans. Figure 1 illustrates our notation. Uppercase letters refer to populations, and combinations such as XY refer to the population ancestral to X and Y. X represents an African population (the Yorubans), Y is a European population, N is Neanderthals, and D is Denisovans. S is an unsampled “superarchaic” population that is distantly related to other humans. Lowercase letters at the bottom of Fig. 1 label “nucleotide site patterns.” A nucleotide site exhibits site pattern xyn if random nucleotides from populations X, Y, and N carry the derived allele, but those sampled from other populations are ancestral. Site pattern probabilities can be calculated from models of population history, and their frequencies can be estimated from data. Our Legofit (10) software estimates parameters by fitting models to these relative frequencies. Fig. 1 A population network including four episodes of gene flow, with an embedded gene genealogy. Upper case letters (X, Y, N, D, and S) represent populations (Africa, Europe, Neanderthal, Denisovan, and superarchaic). Greek letters label episodes of admixture. d and xyn illustrate two nucleotide site patterns, in which 0 and 1 represent the ancestral and derived alleles. A mutation on the red branch would generate site pattern d. One on the blue branch would generate xyn. For simplicity, this figure refers to Neanderthals with a single letter. Elsewhere, we use two letters to distinguish between the Altai and Vindija Neanderthals. Nucleotide site patterns contain only a portion of the information available in genome sequence data. This portion, however, is of particular relevance to the study of deep population history. Site pattern frequencies are unaffected by recent population history because they ignore the within-population component of variation (10). This reduces the number of parameters we must estimate and allows us to focus on the distant past. The current data include two high-coverage Neanderthal genomes: one from the Altai Mountains of Siberia and the other from Vindija Cave in Croatia (11). Rather than assigning the two Neanderthal fossils to separate populations, our model assumes that they inhabited the same population at different times. This implies that our estimates of Neanderthal population size will refer to the Neanderthal metapopulation rather than to any individual subpopulation. The Altai and Vindija Neanderthals appear in site pattern labels as “a” and “v”. Thus, av is the site pattern in which the derived allele appears only in nucleotides sampled from the two Neanderthal genomes. Figure 2 shows the site pattern frequencies studied here. In contrast to our previous analysis (12), the current analysis includes singleton site patterns, x, y, v, a, and d, as advocated by Mafessoni and Prüfer (13). A simpler tabulation, which excludes the Vindija genome, is included as fig. S2. Fig. 2 Observed site pattern frequencies. Horizontal axis shows the relative frequency of each site pattern in random samples consisting of a single haploid genome from each of X, Y, V, A, and D, representing Africa, Europe, Vindija Neanderthal, Altai Neanderthal, Denisovan, and superarchaic. Horizontal lines (which look like dots) are 95% confidence intervals estimated by a moving blocks bootstrap (35). Data: Simons Genome Diversity Project (SGDP) (14) and Max Planck Institute for Evolutionary Anthropology (11). Greek letters in Fig. 1 label episodes of admixture. We label models by concatenating Greek letters to indicate the episodes of admixture they include. For example, model “αβ” includes only episodes α and β. Our model does not include gene flow from Denisovans into moderns because there is little evidence of such gene flow into Europeans (14, 15). Two years ago, we studied a model that included only one episode of admixture: α, which refers to gene flow from Neanderthals into Europeans (12). The left panel of Fig. 3 shows the residuals from this model, using the new data. Several are far from zero, suggesting that something is missing from the model (16). Fig. 3 Residuals from models α and αβγδ. Key: red asterisks, real data; blue circles, 50 bootstrap replicates. Recent literature suggests some of what might be missing. There is evidence for admixture into Denisovans from a superarchaic population, which was distantly related to other humans (2, 11, 17–19), and also for admixture from early moderns into Neanderthals (19). These episodes of admixture appear as β and γ in Fig. 1. Adding β and/or γ to the model improved the fit, yet none of the resulting models were satisfactory. For example, model αβγ implied (implausibly) that superarchaics separated from other hominins 7 million years (Ma) ago. To understand what might still be missing, consider what we know about the early middle Pleistocene, around 600 ka ago. At this time, large-brained hominins appear in Europe, along with Acheulean stone tools (4, 5). They were probably African immigrants, because similar fossils and tools occur earlier in Africa. According to one hypothesis, these early Europeans were Neanderthal ancestors (6, 7). Somewhat earlier—perhaps 750 ka ago [(8), table S12.2]—the “neandersovan” ancestors of Neanderthals and Denisovans separated from the lineage leading to modern humans. Neandersovans may have separated from an African population and then expanded into Eurasia. If so, then they would not have been expanding into an empty continent, for Eurasia had been inhabited since 1.85 Ma ago (20). Neandersovan immigrants may have met the indigenous superarchaic population of Eurasia. This suggests a fourth episode of admixture, from superarchaics into neandersovans, which appears as δ in Fig. 1.
|
|
|
Post by Admin on Feb 25, 2020 20:38:53 GMT
RESULTS We considered eight models, all of which include α, and including all combinations of β, γ, and/or δ. In choosing among complex models, it is important to avoid overfitting. Conventional methods such as Akaike’s information criterion (21) are not available because we do not have access to the full likelihood function. Instead, we use the bootstrap estimate of predictive error (bepe) (10, 22, 23). The best model is the one with the lowest value of bepe. When no model is clearly superior, it is better to average across several than to choose just one (24). For this purpose, we used bootstrap model averaging (booma) (10, 24). The booma weight of the ith model is the fraction of datasets (including the real data and 50 bootstrap replicates) in which that model “wins,” i.e., has the lowest value of bepe. The bepe values and booma weights of all models are in Table 1. The best model is αβγδ, which includes all four episodes of admixture. It has smaller residuals (Fig. 3, right), the lowest bepe value, and the largest booma weight. One other model, αβδ, has a positive booma weight, but all others have zero weight. To understand what this means, recall that bootstrap replicates approximate repeated sampling from the process that generated the data. The models with zero weight lose in all replicates, implying that their disadvantage is large compared with variation in repeated sampling. On this basis, we can reject these models. Neither of the two remaining models can be rejected. These results provide strong support for two episodes of admixture (β and δ) and qualified support for a third (γ). Not only does this support previously reported episodes of gene flow but it also reveals a much older episode, in which neandersovans interbred with superarchaics. Model-averaged parameter estimates, which use the weights in Table 1, are graphed in Fig. 4 and listed in table S1. Fig. 4 Model-averaged parameter estimates with 95% confidence intervals estimated by moving blocks bootstrap (35). Key: mα, fraction of Y introgressed from N; mβ, fraction of D introgressed from S; mγ, fraction of N introgressed from XY; mδ, fraction of ND introgressed from S; TXYNDS, superarchaic separation time; TXY, separation time of X and Y; TND, separation time of N and D; TN0, end of early epoch of Neanderthal history; TA, age of Altai Neanderthal fossil; TV, age of Vindija Neanderthal fossil; TD, age of Denisovan fossil; NS, size of superarchaic population; NXYND, size of populations XYND and XYNDS; NXY, size of population XY; NND, size of population ND; NN0, size of early Neanderthal population; NN1, size of late Neanderthal population. Parameters that exist in only one model are not averaged. Episode δ, which proposes gene flow from superarchaics into neandersovans, is a novel hypothesis. Before accepting it, we should ask whether the evidence in its favor could be artifactual, reflecting a bias in site pattern frequencies caused by sequencing error or somatic mutations. Sequencing error adds a positive bias to the frequency of each singleton site pattern proportional to the per-nucleotide error rate in the corresponding population (see the Supplementary Materials). Somatic mutations have a similar effect. These biases might explain evidence for episode δ, if it were true that larger values of mδ (the fraction of superarchaic admixture in neandersovans) imply larger frequencies of singleton site patterns. However, Table 2 shows that this is not the case. There is no consistent tendency for singleton frequencies to increase with mδ. Indeed, three of them decrease. Consequently, evidence that mδ > 0 cannot be the result of a positive bias in the frequencies of singleton site patterns. The evidence for δ admixture cannot be an artifact of sequencing error or somatic mutations. Table 2 Effect on singleton site pattern frequencies of gene flow (mδ) from superarchaics into neandersovans. Column 2 shows expected frequencies of singleton site patterns in a model in which mδ = 0, and all other parameters are as fitted under model αβγδ. In column 3, all parameters including mδ are as fitted under this model. Column 4 is obtained by subtracting column 2 from column 3. Expected site pattern frequencies were estimated using legosim with 107 iterations. Site pattern Frequency mδ = 0 mδ = 0.034 Difference x 0.15583 0.15174 −0.00409 y 0.15176 0.14778 −0.00398 v 0.04974 0.04942 −0.00032 a 0.03795 0.03798 0.00003 d 0.16051 0.16444 0.00393 The superarchaic separation time, TXYNDS, has a point estimate of 2.3 Ma ago. This estimate may be biased upward because our molecular clock assumes a fairly low mutation rate of 0.38 × 10−9 per nucleotide site per year. Other authors prefer slightly higher rates (25). Although this rate is apparently insensitive to generation time among the great apes, it is sensitive to the age of male puberty. If the average age of puberty during the past 2 Ma were halfway between those of modern humans and chimpanzees, the yearly mutation rate would be close to 0.45 × 10−9 [(26), Fig. 2B], and our estimate of TXYNDS would drop to 1.9 Ma, just at the origin of the genus Homo. Under this clock, the 95% confidence interval is 1.8 to 2.2 Ma. If superarchaics separated from an African population, then this separation must have preceded the arrival of superarchaics in Eurasia. Nonetheless, our 1.8 to 2.2 Ma interval includes the 1.85 Ma date of the earliest Eurasian archaeological remains at Dmanisi (20). Thus, superarchaics may descend from the earliest human dispersal into Eurasia, as represented by the Dmanisi fossils. On the other hand, some authors prefer a higher mutation rate of 0.5 × 10−9 per year (2). Under this clock, the lower end of our confidence interval would be 1.6 Ma ago. Thus, our results are also consistent with the view that superarchaics entered Eurasia after the earliest remains at Dmanisi. Parameter NS is the effective size of the superarchaic population. This parameter can be estimated because there are two sources of superarchaic DNA in our sample (β and δ), and this implies that coalescence time within the superarchaic population affects site pattern frequencies. Although this parameter has a broad confidence interval, even the low end implies a fairly large population of about 20,000. This does not require large numbers of superarchaic humans, because effective size can be inflated by geographic population structure (27). Our large estimate may mean that neandersovans and Denisovans received gene flow from two different superarchaic populations. Parameter TND is the separation time of Neanderthals and Denisovans. Our point estimate, 737 ka ago, is remarkably old. Furthermore, the neandersovan population that preceded this split was remarkably small: NND ≈ 500. This supports our previous results, which indicated an early separation of Neanderthals and Denisovans and a bottleneck among their ancestors (12). Because our analysis includes two Neanderthal genomes, we can estimate the effective size of the Neanderthal population in two separate epochs. The early epoch extends from TN0 = 455 ka to TND = 737 ka, and within this epoch, the effective size was large: NN0 ≈ 16,000. It was smaller during the later epoch: NN1 ≈ 3400. These results support previous findings that the Neanderthal population was large at first but then declined in size (2, 11).
|
|
|
Post by Admin on Feb 26, 2020 19:52:42 GMT
DISCUSSION This project began with a puzzle. We had argued in 2017 that Neanderthals and Denisovans separated early, that their neandersovan ancestors endured a bottleneck of population size, and that the postseparation Neanderthal population was large (12). That analysis omitted singleton site patterns. Mafessoni and Prüfer (13) pointed out that introducing singletons led to different results. In response, Rogers et al. (16) agreed, but also observed that the with-singleton analysis implied that the Denisovan fossil was only 4000 years old—a result that is plainly wrong. Furthermore, a residual analysis showed that neither of the models under discussion in 2017 fit the data very well (16). Something was apparently missing from both models—but what? The present paper provides an answer to that question.
Our results shed light on the early portion of the middle Pleistocene, about 600 ka ago, when large-brained hominins appear in the fossil record of Europe along with Acheulean stone tools. There is disagreement about how these early Europeans should be interpreted. Some see them as the common ancestors of modern humans and Neanderthals (28), others as an evolutionary dead end, later replaced by immigrants from Africa (29, 30), and others as early representatives of the Neanderthal lineage (6, 7). Our estimates are most consistent with the last of these views. They imply that by 600 ka ago, Neanderthals were already a distinct lineage, separate not only from the modern lineage but also from Denisovans.
These results resolve a discrepancy involving human fossils from Sima de los Huesos (SH). Those fossils had been dated to at least 350 ka ago and perhaps 400 to 500 ka ago (31). Genetic evidence showed that they were from a population ancestral to Neanderthals and therefore more recent than the separation of Neanderthals and Denisovans (9). However, genetic evidence also indicated that this split occurred about 381 ka ago [(2), table S12.2]. This was hard to reconcile with the estimated age of the SH fossils. To make matters worse, improved dating methods later showed that the SH fossils are even older, about 600 ka, and much older than the molecular date of the Neanderthal-Denisovan split (32). Our estimates resolve this conflict because they push the date of the split back well beyond the age of the SH fossils.
Our estimate of the Neanderthal-Denisovan separation time conflicts with 381 ka ago estimate discussed above (2, 13). This discrepancy results, in part, from differing calibrations of the molecular clock. Under our clock, the 381-ka date becomes 502 ka (12), but this is still far from our own 737-ka estimate. The remaining discrepancy may reflect differences in our models of history. Misspecified models often generate biased parameter estimates.
Our new results on Neanderthal population size differ from those we published in 2017 (12). At that time, we argued that the Neanderthal population was substantially larger than others had estimated. Our new estimates are more in line with those published by others (2, 11). The difference does not result from our new and more elaborate model because we get similar results from model α, which (as in our 2017 model) allows only one episode of gene flow (table S2). Instead, it was including the Vindija Neanderthal genome that made the difference. Without this genome, we still get a large estimate (NN1 ≈ 11,000), even using model αβγδ (table S3). This implies that the Neanderthals who contributed DNA to modern Europeans were more similar to the Vindija Neanderthal than to the Altai Neanderthal, as others have also shown (11).
Our results revise the date at which superarchaics separated from other humans. One previous estimate put this date between 0.9 and 1.4 Ma [(2), p. 47], which implied that superarchaics arrived well after the initial human dispersal into Eurasia around 1.9 Ma. This required a complex series of population movements between Africa and Eurasia [(33), pp. 66 to 71]. Our new estimates do not refute this reconstruction, but they do allow a simpler one, which involves only three expansions of humans from Africa into Eurasia: an expansion of early Homo at about 1.9 Ma ago, an expansion of neandersovans at about 700 ka ago, and an expansion of modern humans at about 50 ka ago.
Our results indicate that neandersovans interbred with superarchaics early in the middle Pleistocene, shortly after expanding into Eurasia. This is the earliest known admixture between hominin populations. Furthermore, the two populations involved were more distantly related than any pair of human populations previously known to interbreed. According to our estimates, neandersovans and superarchaics had been separate for about 1.2 Ma. Later, when superarchaics exchanged genes with Denisovans, the two populations had been separate even longer. By comparison, the Neanderthals and Denisovans who interbred with modern humans had been separate less than 0.7 Ma.
It seems likely that superarchaics descend from the initial human settlement of Eurasia. As discussed above, the large effective size of the superarchaic population hints that it comprised at least two deeply divided subpopulations, of which one mixed with neandersovans and another with Denisovans. We suggest that around 700 ka ago, neandersovans expanded from Africa into Eurasia, endured a bottleneck of population size, interbred with indigenous Eurasians, largely replaced them, and separated into eastern and western subpopulations—Denisovans and Neanderthals. These same events unfolded once again around 50 ka ago as modern humans expanded out of Africa and into Eurasia, largely replacing the Neanderthals and Denisovans.
Science Advances 20 Feb 2020: Vol. 6, no. 8, eaay5483
|
|
|
Post by Admin on Mar 8, 2020 19:45:29 GMT
Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia PNAS February 11, 2020 117 (6) 2879-2885; first published January 27, 2020 Significance Neanderthals once inhabited Europe and western Asia, spreading as far east as the Altai Mountains in southern Siberia, but the geographical origin and time of arrival of the Altai populations remain unresolved. Excavations at Chagyrskaya Cave in the Altai foothills have yielded 90,000 stone artifacts, numerous bone tools, 74 Neanderthal fossils, and animal and plant remains recovered from 59,000- to 49,000-year-old deposits. The Chagyrskaya Neanderthals made distinctive stone tools that closely resemble Micoquian artifacts from eastern Europe, whereas other Altai sites occupied by earlier Neanderthal populations lack such artifacts. This suggests at least two dispersals of Neanderthals into southern Siberia, with the likely ancestral homeland of the Chagyrskaya toolmakers located 3,000 to 4,000 kilometers to the west, in eastern Europe. Fig. 1. Chagyrskaya Cave. (A) Site location in the Altai region of southern Siberia. (B) View of the cave entrance, which faces north. (C) Plan of the cave interior showing the excavated area (in blue). (D and E) Stratigraphic profiles along the two transects (A–A′ and B–B′, respectively) shown in C. Abstract Neanderthals were once widespread across Europe and western Asia. They also penetrated into the Altai Mountains of southern Siberia, but the geographical origin of these populations and the timing of their dispersal have remained elusive. Here we describe an archaeological assemblage from Chagyrskaya Cave, situated in the Altai foothills, where around 90,000 Middle Paleolithic artifacts and 74 Neanderthal remains have been recovered from deposits dating to between 59 and 49 thousand years ago (age range at 95.4% probability). Environmental reconstructions suggest that the Chagyrskaya hominins were adapted to the dry steppe and hunted bison. Their distinctive toolkit closely resembles Micoquian assemblages from central and eastern Europe, including the northern Caucasus, more than 3,000 kilometers to the west of Chagyrskaya Cave. At other Altai sites, evidence of earlier Neanderthal populations lacking associated Micoquian-like artifacts implies two or more Neanderthal incursions into this region. We identify eastern Europe as the most probable ancestral source region for the Chagyrskaya toolmakers, supported by DNA results linking the Neanderthal remains with populations in northern Croatia and the northern Caucasus, and providing a rare example of a long-distance, intercontinental population movement associated with a distinctive Paleolithic toolkit. The period of existence of Neanderthals, their geographical range, and the timing of their dispersal and extinction are key issues in the study of human evolution and migration. Most Neanderthal remains and associated artifacts have been reported from Europe and western Asia, where they range in age from about 430,000 to 40,000 years ago (kiloannus, or ka) (1, 2). Further east, the unequivocal presence of Neanderthals prior to the last interglacial (which began around 130 ka) until about 50 ka is based on hominin remains (3) and DNA analyses of skeletal remains and sediments at three caves (Okladnikov, Denisova, and Chagyrskaya) in the Altai Mountains of southern Siberia (4⇓⇓–7). Additional evidence is required to support suggestions that Neanderthals had reached eastern and northern China by 125 to 105 and 45 ka, respectively (8, 9). Two genetically distinct Neanderthal populations inhabited the Altai region sometime during the Late Pleistocene (10), but the geographical origin of these populations and the timing of their migrations into the region remain unclear. On current evidence, Neanderthals were present at Denisova Cave between about 200 and 100 ka (11, 12). Chagyrskaya Cave (51°26′34.6′′ N, 83°09′18.0′′ E) is situated 19 m above the Charysh River in the western piedmont of the Altai Mountains (Fig. 1 and SI Appendix, Fig. S1), approximately 100 km west of Denisova Cave (13). The cave consists of two chambers, with a stratigraphic sequence up to 3.5 m thick (SI Appendix, sections S1 and S2, Figs. S2–S4, and Table S1). The dense basal deposit (layer 7) is archaeologically sterile and composed mainly of gravel and fine-grained sediments. An erosional contact (unconformity) separates it from overlying layers 6 and 5, which consist of poorly sorted sediments that contain approximately 90,000 Middle Paleolithic (MP) artifacts (including numerous bone tools), 74 Neanderthal specimens, about 250,000 animal fossils, and a range of plant remains (SI Appendix, section S3) (14 and 15). The sequence is capped by Bronze Age deposits, with no evidence of Upper Paleolithic (UP) occupation.
|
|
|
Post by Admin on Mar 9, 2020 18:34:31 GMT
Site Chronology and Environmental Reconstructions. Optical ages for 23 sediment samples indicate that layer 7 was deposited 329 ± 16 ka (weighted mean age of four samples) and that layers 6 and 5 accumulated sometime between 63 ± 4 and 48 ± 3 ka (weighted mean age of 54.0 ± 2.5 ka; total uncertainty at 1σ). The latter are consistent with the mostly infinite radiocarbon ages obtained for 20 bison (Bison priscus) remains (SI Appendix, section S4, Figs. S5 and S6, and Tables S2 and S3), but are younger than the DNA-based age estimate of 87 to 71 ka for the “Chagyrskaya Neanderthal” (Chagyrskaya 8) (16, 17), a distal manual phalanx retrieved from the sieved sediments of subunit 6b. This discrepancy may reflect a higher mutation rate in Neanderthals than in modern humans (18) that has not been taken into account and/or the omission of other uncertainties in the genetic age estimates, such as population size and generation interval. Chagyrskaya 8 and Denisova 3 (the youngest Denisovan fossil) share similar proportions of “missing” genetic mutations compared to present-day humans, which suggests that they are similar in age (16). Denisova 3 has been dated to between 76.2 and 51.6 ka (11, 12), an age range compatible with the optical ages for layers 6 and 5 at Chagyrskaya Cave. An overview of the human remains recovered from Chagyrskaya Cave is given in SI Appendix, section S5, Figs. S7–S9, and Table S4. The subunits of layer 6 have statistically indistinguishable ages, which indicate that these Neanderthal-associated MP deposits accumulated over a few millennia or less, during the final phase of marine isotope stage (MIS) 4 and/or the start of MIS 3. This was a period of cold climate (but warmer than during MIS 4), as indicated by pollen and mammal and bird remains from layer 6 compatible with a dry steppe environment and a rarity or lack of tundra species (SI Appendix, section S3) (13⇓–15). Layer 5 was deposited during a period of relatively warm and humid climate, characterized by steppe and forest-steppe vegetation. The main hominin occupation of Chagyrskaya Cave occurred during accumulation of subunit 6c, which represents the primary depositional context of the MP assemblage; subunits 6b and 6a and layer 5 include redeposited MP artifacts, bones, and sediments (SI Appendix, sections S1 and S2). Sedimentology and micromorphology analyses support these interpretations of cave use, site formation, and environmental conditions (ref. 13 and SI Appendix, sections S1 and S2). Neanderthal hunting activity was focused on bison (juveniles and females in particular) and may have been connected to the seasonal migration of bison herds to and from the mountain foothills (14). Other prey hunted to a lesser extent included horse, reindeer, Siberian ibex, and argali. Chagyrskaya Cave Lithic Assemblage. A total of 89,539 artifacts have been recovered from layer 6. Detailed lithic analysis of 4,249 artifacts from subunits 6a to 6c indicates that the assemblage represents a single technocomplex, with no marked differences between subunits (SI Appendix, section S6). Subunit 6c consists of two sublayers (6c/2 and 6c/1) with indistinguishable optical ages. Sublayer 6c/1 contains more artifacts than does sublayer 6c/2, which is preserved in only a few, spatially restricted, parts of the site. Accordingly, we focus here on the technological and typological characteristics of the 3,021 artifacts from sublayer 6c/1 and on the morphological variability of plano-convex bifacial tools (commonly retouched using bone; Fig. 2) and convergent scrapers in particular. Fig. 2. Stone artifacts from Chagyrskaya Cave, sublayer 6c/1. (A–C) Photographs, line drawings, and cross-sectional profiles of three plano-convex bifacial tools diagnostic of Micoquian Bocksteinmesser and Klausennischemesser types. (Scale bar, 5 cm.) The lithic assemblage consists of 25 raw materials, including high-quality jaspers, chalcedonites, and porphyrites, which were sourced as pebbles from the nearby riverbed. The assemblage is dominated by debris and chips, with the remaining artifacts characterized by a high proportion of tools and a few cores. Most of the flakes have asymmetrical trapezoidal and rectangular shapes and were manufactured on site using bifacial plano-convex, radial (Levallois centripetal), and orthogonal core-reduction flaking methods; blades occur in low numbers as occasional by-products. Scrapers dominate the toolkit, with a preference for trapezoidal and leaf shapes. Details of artifact production techniques, illustrations of artifacts, the proportions of different artifact types, and the variables used for statistical analysis are given in SI Appendix section S6, Figs. S10–S20, and Tables S5–S11. Fig. 3. Site map and principal component analysis of MP and UP lithic assemblages. (A) Location of sites with Levallois-Mousterian and Micoquian assemblages used for statistical comparison with Chagyrskaya Cave artifacts. (B) Scatterplot of the first two principal components for assemblages from Chagyrskaya Cave, three other Altai sites (Denisova Cave, Kara-Bom, Ust’-Karakol-1), and Obi-Rakhmat in central Asia (n = 40). (C) Scatterplot of the first two principal components for assemblages from Chagyrskaya and Micoquian sites in eastern Europe (Crimea, Donbass-Azoz, Caucasus) and central Europe (n = 26). (D) Scatterplot of the first two principal components for assemblages from Chagyrskaya Cave, Levallois-Mousterian sites in the Altai and central Asia, and European Micoquian sites (n = 67). The italic numbers correspond to the following sites and assemblages: 1, Chagyrskaya Cave (sublayer 6c/1); 2, Ust’-Karakol-1 (layers 17 to 13); 3, Ust’-Karakol-1 (layer 18); 4, Kara-Bom (layer MP2); 5, Kara-Bom (layer MP1); 6 to 8, Denisova Cave (entrance zone, layers 10 to 8, respectively); 9 to 13, Denisova Cave (main chamber, layers 22, 21, 19, 14, and 12, respectively); 14 to 19, Denisova Cave (east chamber, layers 15, 14, 12, and 11.4 to 11.2, respectively); 20, Strashnaya Cave; 21, Ust’-Kanskaya Cave; 22, Ust’-Karakol-1 UP (layer 11); 23, Kara-Bom UP (layers 6 and 5); 24, Kara-Bom UP (layers 4 to 1); 25, 26, Denisova Cave UP (entrance zone, layers 7 and 6, respectively); 27, Denisova Cave UP (main chamber, layer 11); 28, Denisova Cave UP (east chamber, layer 11.1); 29, Tumechin-1; 30, Tumechin-2; 31, Tumechin-4; 32 to 39, Obi-Rakhmat (layers 21.1, 20, 19.5 to 19.1, and 14.1, respectively); 40, Kulbulak, layer 23); 41 to 45, Kabazi V (subunits I/4A–II/7, III/1, III/1A, III/2, and III/5, respectively); 46, Karabai I (layer 4); 47, 48, Kabazi II (units IIA–III and V–VI, respectively); 49, Kiik-Koba (level IV); 50, Buran Kaya III (layer B); 51, Starosele (level 1); 52, Chokurcha I (unit IV); 53 to 59, Zaskalnaya V (units I, II, IIа, III/1–III/9–1, III/10–III/14, IIIA, and IV, respectively); 60 to 62, Sesselfelsgrotte (units G4–G2, respectively); 63, Antonovka I; 64, Antonovka II; 65, Barakaevskaya Cave; 66, 67, Mezmaiskaya Cave (layers 2B-4 and 3, respectively). Comparison with Other Altai MP Assemblages. The Chagyrskaya toolkit had been previously been grouped with the small artifact assemblage from Okladnikov Cave and named the Sibiryachikha variant (19). Only the remains of Neanderthals have been found in association with this variant, whereas the assemblages found at Denisova Cave and at the open-air sites of Kara-Bom and Ust’-Karakol-1 cannot be related unambiguously to a specific hominin species. Both Neanderthals and Denisovans (a genetically related group of archaic hominins) were present at Denisova Cave during the MP (11, 12), while Kara-Bom and Ust’-Karakol-1 have not yielded any hominin remains. These assemblages reflect the local development of Levallois-based industries with Mousterian features (20⇓–22), and they differ markedly from the Sibiryachikha variant, which is dominated by bifacial plano-convex, radial, and orthogonal flaking methods; bifacial tools; convergent scrapers and points; and the absence of Levallois preferential and Levallois convergent core reductions. Similarities between MP artifacts and associated hominin remains in the Altai, central Asia, and eastern Europe have been proposed (19, 23⇓⇓–26), but limitations in the archaeological and fossil records have precluded firm conclusions. We used a set of statistical methods (including hierarchical cluster analysis, nonmetric multidimensional scaling, and principal component analysis) to compare the technological and typological attributes of the Chagyrskaya artifacts with Levallois-Mousterian MP and UP assemblages in central Asia, and with Micoquian assemblages in central and eastern Europe. The analysis clearly distinguishes the Chagyrskaya assemblage from the central Asian Levallois-Mousterian MP and UP assemblages (Fig. 3 A and B and SI Appendix, section S7, Figs. S21A and S22A, and Tables S12–S19). Analysis of debitage that has been examined using a technological approach yields the same outcome (SI Appendix, Fig. S23 and Table S20). This suggests that the Chagyrskaya assemblage and that from Okladnikov Cave, the age of which is uncertain but is likely also younger than that of the Denisova Neanderthals (4, 19), constitute a separate and unique regional MP variant, technologically and typologically distinct from the Altai Levallois-Mousterian technocomplex.
|
|