Hominin activity in the Denisova Cave microstratigraphic record

Hominin fossils and aDNA have been recovered from the sediments preserved at Denisova Cave1,2,3,9,10,11,12, as well as significant numbers of stone artefacts and faunal remains, specimens of which show signs of human modification6,7,8,9,12,16,17. Optical ages9 indicate slow rates of net sedimentation, with periods of non-deposition or erosion, resulting in the accumulation of up to ~4.5 m of Pleistocene deposit in DCM and DCE since ~300 ka (excluding unconformities). Unequivocal signs of hominin activity in the sediments at the field scale are limited, including evidence for fire-use18,19,20,21,22,23 in the Middle Palaeolithic deposits that form the majority of the sequence.

We sought microscopic evidence of hominin activity in the sediments, where diagnostic features invisible to the naked eye might be recognised. While we do not identify intact combustion features—common elements of Palaeolithic cave sites—we do observe disassembled combustion bi-products, including micro-charcoal, charcoal fragments and occasional localised ashes. Micromorphological descriptions of all samples examined in this study are provided in Supplementary Information (Table S1), together with a selection of photomicrographs of the thin sections (Fig. S1) and flatbed scans of the sediment blocks (Fig. S2).

In DCM (Fig. 3a), we observe micro-charcoal in the basal region within layer 20 (which contains early Middle Palaeolithic artefacts and finished accumulating 170 ± 19 ka), at the interface with overlying layer 19, and as a distinct band within layer 19 (which contains middle Middle Palaeolithic artefacts and started accumulating 151 ± 17 ka). (Archaeological phases and ages, with uncertainties expressed at the 95.4% confidence interval, are from ref.9 (Fig. 3 and Extended Data Table 1) and shown here in Fig. 3 and Table S1.) This micro-charcoal is most likely a taphonomic concentration of combustion bi-products, given the undulating topography of this part of the cave produced by deformation, the truncation of layer 22 by low-energy colluviation, and the localised concentrations of fine charcoal. Layer 19 has produced a total of 1,925 stone artefacts9, so clearly hominins were present at this time. Given the slow sedimentation rate, the artefact assemblage may perhaps represent the product of periodic visitations over many millennia. Site conditions would not have been attractive for hominin occupation during the deposition of these lower layers, owing to the irregular surfaces and occasionally humid conditions in the cave. Higher up the DCM sequence, layers 11.4 and 11.2 also contain charcoal, with larger fragments recorded in layer 11.4 and much finer charcoal powder in layer 11.2. Both layers are associated with the Initial Upper Palaeolithic9.

Figure 3 Summary stratigraphic logs of the sequences exposed in (a) DCM and (b) DCE, showing the locations of the micromorphological samples and key microstratigraphic features. To the right of each log, optical ages (in ka, with uncertainties at 95.4% probability) are shown for the major boundaries between lithological units in the thin sections, together with the associated archaeological phases (from ref.9). Full size image

In DCE (Fig. 3b), we record trace quantities of fine charcoal fragments and flecks closely associated with crushed charcoal and bone fragments in layer 16, and more commonly in layer 15—the earliest layer containing artefacts (early Middle Palaeolithic)9 and also Denisovan DNA10. This indicates fire use and trampling occurring tentatively from 259 ± 28 ka and certainly from 203 ± 14 ka, but we cannot unequivocally and directly link the manufacturers of the stone tools with fire-use because these fine combustion products are highly mobile. In layer 14, which yielded Neanderthal DNA and early Middle Palaeolithic artefacts and was deposited between 193 ± 12 and 187 ± 14 ka, there is a marked increase in micro-charcoal that imparts a dark colouration, and also a small piece (3–4 mm) of angular chert debitage in our sample.

We identify large charcoal fragments (>4–5 mm) in layers 11.4 and 11.3 in DCE, which were deposited between 120 ± 11 and 70 ± 8 ka and contain middle Middle Palaeolithic artefacts. A Neanderthal toe phalanx (Denisova 5) was recovered from layer 11.4, but we cannot confidently associate this and other similarly small and isolated hominin fossils with elements of the sedimentary matrix, given the possibility of displacement9,12. In thin section, we observe sediment movement in the form of micro-faulting and slippage features in these layers, presumably associated with the aforementioned post-depositional subsidence. However, such deformation processes do not necessarily promote the translocation or mixing of fine material across lithological boundaries. Our sample location was close to the rear of DCE, where the chamber tapers to a narrow slot (~1 m wide), a locale unlikely to have been conducive to human occupation—especially the lighting of a fire—given the confined space. Evidence of sediment compaction does suggest compressive forces, however, so animals that are represented in the faunal record may have been present in this restricted space.

Ashes are present in very low quantities in the Denisova Cave microstratigraphy. Nevertheless, we cannot rule out ash dissolution as the biasing factor, given the mobility of calcite and decalcification recorded locally in some layers. Could fire have been used at Denisova Cave more extensively by hominins, but with the associated evidence subsequently removed from the stratigraphic record? Bearing in mind the rate of cave sedimentation, erosional (chronological) gaps and the evidence for bioturbation in some parts of the sequence—mostly parts of the upper layers of DCE—reworking and redistribution of combustion bi-products may have occurred, although it is unlikely that all micro-traces would have been completely removed. The reworking of previously in situ fire residues is supported by the absence of structured combustion features that would signify the presence of intact hearths. Furthermore, stone tools do not exhibit signs of thermal alteration24, which might be expected should fire-use have been common—or even present—in these confined spaces, and other indicators of fire, such as thermally altered clays, were not evident in our samples. Although fire may not have been used extensively within the sampled areas of the cave, the lack of an obvious pyrotechnology need not preclude the use of a site by hominins, even during glacial periods25. Elsewhere in the Altai, the site of Kara-Bom contains well-preserved hearths in the Initial Upper Palaeolithic deposits26, but no clear evidence of fire-use has been found in the region beyond about 50–40 ka27.

Overall, the microstratigraphic record for Denisova Cave indicates that human activity was intermittent over the past three glacial–interglacial cycles represented by the Pleistocene sedimentary infill (>300 ka to ~20 ka). The stone artefact assemblages indicate long-term hominin occupation of the site during both warm climates and cold conditions, when the foothills of the Altai Mountains likely served as a refugium28.

Other animal users of Denisova Cave: the fossil coprolites

Coprolites are common biogenic components of the cave sediments, often present in dense concentrations, suggesting that animals visited the site for much of its depositional history. The coprolites can be grouped into a number of recurring types throughout the sequence, presumably reflecting the use of the site by a variety of animals, and potentially associated with a range of preservation states. We recognise four main coprolite types (CT-1 to CT-4), described in Table 1 and shown in Fig. 4. Although we cannot confidently attribute all of these droppings to a specific animal, we assign CT-1 to Crocuta crocuta spelaens (cave hyena), based on consistency with published results describing the morphology and optical properties of this material in thin section29,30,31; this supports the faunal evidence of regular use of the cave by these animals6,7,8,9. We tentatively attribute CT-2 to wolf (Canis lupus), based on the similarity between these coprolite fragments and dog coprolites recorded at Vanguard Cave, Gibraltar32, as well as other published data31. The coprolite fragments (CT-3) in our thin section of layer 12.2 in DCM are consistently larger and darker than CT-1 and CT-2. This layer contains very high proportions of these coprolites, and the chaotic arrangement of the coarse limestone gravel, with long axes in a vertical to sub-vertical alignment, suggests disturbance of these sediments, possibly by a large animal such as a cave bear. We cannot assign CT-3 or CT-4 to a specific species.

Table 1 Coprolite types identified in the Denisova Cave microstratigraphic record. Full size table

Figure 4 Examples of coprolites identified in the Denisova Cave microstratigraphic record (see Table 1 for coprolite descriptions). (a–c) Type CT-1 originating from cave hyena occurs through much of the sampled sequence; (d–f) Type CT-2 has a much darker matrix, possibly related to wolf; (g,h) Type CT-3 is highly weathered; (i) Type CT-4 has a distinctive red matrix. Types CT-3 and CT-4 cannot be linked to specific animals. Scale bars: red, 800 µm; green, 500 µm; yellow, 1 mm; blue, 2 mm. Full size image

Coprolite fragments commonly occur in layers that also contain stone artefacts. Given that hominins and hyenas will not cohabitate7,33, this indicates that specific occupation events will be extremely challenging—if not impossible—to tease out at Denisova Cave, with the slow sedimentation rates effectively precluding the identification of alternating hominin–carnivore occupations, should they exist. The lack of defined stratigraphy within layers (e.g., buried surfaces) may be due, at least in part, to carnivore denning or other animal burrowing activities in parts of the deposit. At Bois Roche in France, for example, stone tools accumulated by local movement (e.g., by gravity) in areas that functioned primarily as carnivore dens34. The DCE faunal record includes the remains of a number of large cave-dwelling mammals recovered in relatively high numbers, including hyena, wolf, red fox and, to a lesser extent, bear9,35. As these animals are unlikely to have cohabitated, either with each other or with hominins, the co-occurrence of their remains likely reflects the scale of resolution (time averaging) of the sedimentological, chronological and hominin occupation records at Denisova Cave.

The presence of coprolites in layers from which hominin remains and aDNA have been recovered implies that large carnivores might be an accumulating agent for these materials, particularly in areas of the site where evidence for hominin activity is scarce (e.g., the farthest recesses of DCE). Specific areas of the site might have been designated as waste dumps for lithic debitage and food detritus, for example, which in turn attracted scavengers such as the cave hyena when hominins were absent from the site. Interestingly, we record in thin section only a few examples of bone fragments that exhibit characteristic etching related to digestion in the gut of a carnivore, although etched bones are common in the faunal record35.

In the field, rodent burrows (krotovinas36) are clearly visible in the Holocene deposits of DCE, and in fewer numbers in DCM. Disturbance of the sediments by bioturbation is also evident in thin section. Parts of layer 12 and much of layer 13 in DCM display a chaotic arrangement of limestone clasts within finer material, consistent with disturbance by large animals such as bears, wolves or hyenas. This accords with field observations of layer 13 being a hyena lair9. Thin sections of layers 9.2 and 9.3 in DCM and layers 9.1, 11.3 and 11.4 in DCE display abundant, loosely arranged aggregates and irregular vughs typical of bioturbation37. These small, mm-size features are typical of smaller soil fauna, such as worms, spring-tails (Collemboles) and isopods. We note that these fine crumb structures occur essentially in the uppermost Pleistocene strata in DCE (i.e., layer 9), which accumulated after 38 ± 9 ka and may represent milder conditions that enabled these fauna to flourish.

Diagenesis and the completeness of the archaeological record

Chemical alteration features are rare in Denisova Cave. Where present, they take the form of carbonate dissolution and phosphatisation, such as that reported for the uppermost Pleistocene and Holocene layers in DCE38. In thin section, we observe phosphatic rinds around limestone clasts, a common occurrence in prehistoric caves when calcite reacts to phosphate-rich solutions39,40,41,42,43,44. This is expressed as reaction rims around individual clasts (Fig. 5), resulting in replacement of the original birefringent calcite by isotropic phosphate, generally apatite (dahllite). We also record the etching of calcite sand and decalcification of the surrounding matrix (e.g., in layer 13 in DCE), indicating the dissolution of calcium carbonate.

Figure 5 Phosphate rind around limestone grain in sample DCM-MM2B. (a) Macroscan of thin section of this sample; (b) Inset showing limestone fragment, with green rectangle indicating the location of qualitative maps collected using energy-dispersive X-ray (EDS) spectroscopy. EDS maps showing the relative distribution of (c) calcium and (d) phosphorus, in which higher colour intensities represent greater concentrations of each element. Full size image

Animals are the most likely source of phosphate in an archaeological cave sequence40. Although some layers are richer than others in phosphates, including coprolites, none of those examined in thin section stands out as being excessively phosphatised. Bat and bird guano is also a possible source of cave phosphates and associated diagenetic transformations21,38,40,41,42,43,44,45,46,47,48,49,50,51. We did not record guano directly in thin section, but acidic water percolating through guano—in combination with coprolite-rich sediments—can dissolve calcite21, including the fine calcareous fraction of limestone grains and the outer surface of larger limestone fragments, to produce apatite (dahllite) rims. Bat remains occur in relatively high numbers in some layers9,35. Although bats do not commonly occupy caves at the same time as hominins, small populations could, nonetheless, have supplied a persistent supply of guano to maintain phosphatisation processes.

Common diagenetic cave minerals (e.g., taranakite, leucophosphite, crandallite, brushite and ardealite)48,52,53,54,55 have been recorded in the Holocene deposits and in layer 11.1 in DCE38. The diagenesis occurred during the Holocene and affected only the upper parts of the underlying Pleistocene sediments. We do not observe these minerals in our thin sections of the Pleistocene deposits, underscoring Denisova Cave as a depositional environment where persistently cold conditions have afforded exceptional preservation of organic materials—including lipid micro-residues on Middle Palaeolithic stone tools in DCE56—and minimal diagenesis.

Cold-climate indicators and implications for cave use

We record platy microstructures in thin section for layers 12.2 (70 ± 8 to 58 ± 6 ka) and 11.4/11.2 (44 ± 5 to 38 ± 3 ka) in DCM, and for layers 13 (156 ± 15 to 146 ± 11 ka) and 11.1/9.1 (49 ± 8 to after 38 ± 9 ka) in DCE. These features, together with the presence of rounded grains and granostriated b-fabrics, which are indicative of grain rotation, indicate incipient cryoturbation. This modification of the sediment structure is most likely associated with seasonal frost, with the thinner bands in layer 9.1 of DCE possibly associated with repeated ice lensing as a result of soil creep during thaw57. The limestone clasts in these parts of the stratigraphy are generally angular and fresh, and lack signs of phosphatisation that would reflect diagenetic transformations of calcite. We therefore correlate these platy structures with the occurrence of low temperatures in the cave and relatively few freeze-thaw cycles58.

In DCM, these platy microstructures are associated with sediments that contain unequivocal signs of hominin occupation (charcoal and closely associated bone fragments; Fig. 6). We do not know the vertical extent of these post-depositional features, however, so it is not clear how these signatures correlate. They may penetrate down into the underlying, older layers, but the sediments immediately above and adjacent to these samples are not affected in this way. Given the slow rate of sedimentation in the cave, we cannot rule out later over-printing of the sediments by these cold-climate indicators.

Figure 6 Evidence of freezing conditions in the microstratigraphy at Denisova Cave. (a,b) Two thin-section scans from layers 11.4 and 11.4/11.2 in DCM, respectively; (c) Photomicrograph showing detail of the platy structures relating to frost heave; (d) Photomicrograph showing the excellent state of preservation of bone (asterisk) and charcoal with preserved plant cellular structure (red arrow). Full size image

At the present day, thin (mm-thick) vertical cracks filled with ice have sometimes been observed within the Holocene deposits in the South Chamber. These would not, however, account for the horizontal ice lensing observed in our thin sections of layers 11.2 and 11.4 in DCM, and we see no such analogous vertical fissures in any of our thin sections. It is not clear why such platy structures and signs of incipient cryoturbation are not more common in the Pleistocene sequences at Denisova Cave, but this may relate to the enclosed cave environment mitigating extremes in temperature through restricted airflow. The South Chamber is better ventilated than are DCM and DCE, which may explain their modern occurrence there.