SUPPLEMENTARY INFORMATION

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1 doi: /nature06204 SUPPLEMENTARY INFORMATION Supplementary Information - Early human use of marine resources and pigment in South Africa during the Middle Pleistocene 1. Supplementary Figure(s) and Legend(s) Supplementary Figure 1. Non-georeferenced version of LC-MSA East Section shown in Figure 1 of the main text, and elsewhere in Supplementary Information. The orange scale is a balanced carpenter s level. 1

2 Supplementary Figure 2. Non-georeferenced version of LC-MSA North Section shown elsewhere in Supplementary Information. The orange scale is a balanced carpenter s level. 2

3 Supplementary Figure 3. Micromorphology slide of sample 46579A, flowstone overlying LC- MSA Upper and the contact between the two. The black arrows show sand grains along growth lines of flowstone. A is the second layer of flowstone, B is the aeolianite layer in between flowstone layers, C is the first layer of flowstone, and D is the upper LC-MSA sandstone (aeolianite). 3

4 Supplementary Figure 4. Micromorphology slide of sample 46579A, flowstone layers overlying LC-MSA Upper showing a discrete layer of aeolianite in between two layers of flowstone, and the contact between the flowstone and LC-MSA Upper. The black arrows show sand grains inside the flowstone laminae. A is the second layer of flowstone, B is the aeolianite layer in between flowstone layers, C is the first layer of flowstone (the contact with the underlying sandstone is erosional implying that cementation of the aeolianite preceded flowstone formation), and D is the LC-MSA Upper sandstone (aeolianite). 4

5 Supplementary Figure 5. A georeferenced photograph of the North section of the LC-MSA with the OSL samples plotted on the photograph. The orange scale is a balanced carpenter s level. 5

6 Supplementary Figure 6. A georeferenced photograph of the East section of the LC-MSA with the OSL samples plotted on the photograph. The orange scale is a balanced carpenter s level. 6

7 Supplementary Figure 7. A georeferenced photograph of the East section of the LC-MSA with all the plotted finds within 25 centimeters of the section shown. The orange scale is a balanced carpenter s level. 7

8 a b Supplementary Figure 8. The slope a and orientation b of plotted finds in the LC-MSA Lower. 8

9 Supplementary Figure 9. A georeferenced photograph of the North section of the LC-MSA with the plotted finds within 30 centimeters of the section plotted as slope lineations. This is accomplished by calculating the slope of each find and then projecting a line of set length displaying that slope. The orange scale is a balanced carpenter s level. 9

10 a b Supplementary Figure 10. The slope a and orientation b of plotted finds in the LC-MSA Middle. 10

11 Sample N = 36 Sample N = 42 Sample N = 40 Sample N = 40 Supplementary Figure 11. D e distributions for multi-grain aliquots of samples for which optical ages were based on multi-grain D e values. The radial plots display the individual D e values together with their associated measurement uncertainties. The grey shading in each plot denotes the two-sigma (95% confidence interval) band centered on the reference value, which is the weighted mean D e calculated using the central age model. 11

12 Sample N = 58 Sample N = ± 5% Sample N = ± 4% Sample N = ± 7% Sample N = ± 7% Sample N = ± 5% Supplementary Figure 12. D e distributions for individual grains of samples for which optical ages were based on single-grain D e values. For all samples, except , the finite mixture model was used to determine the number of dose components and their respective weighted mean D e values. The grey shading in each plot denotes the two-sigma (95% confidence interval) band centered on the weighted mean value of the dose 12

13 component represented by the highest proportion of D e values. The solid line shows the weighted mean D e value of the secondary component. The central age model was used to determine the weighted mean D e of sample

14 Supplementary Figure 13. Additional lithics from the LC-MSA not pictured in main text. a, quartzite blade with retouch b, silcrete bladelet c, quartzite blade d, quartzite dejeté flake e, quartzite flake with prepared platform f, quartz thumbnail scraper g, quartz endscraper on flake h, quartzite notched flake i, silcrete flake with discontinous retouch j, silcrete point, sidestruck, from prepared core k, quartz point l, quartzite point m, quartzite Levallois point n, silcrete point with acute retouch o, silcrete radial core fragment p, quartzite core with opposed platforms q, quartzite Levallois flaking core with cobble cortex r, quartzite core-on-flake. 14

15 2. Supplementary Methods U Series Dating Method 230 Th U dating was performed on 6 samples of speleothems using multicollector inductively coupled plasma mass spectrometer (MC-ICP-MS) Nu Instruments Ltd (UK) equipped with 12 Faraday cups and 3 ion counters. The sample was introduced to the MC-ICP-MS through an Aridus microconcentric desolvating nebuliser sample introducing system. The instrumental mass bias was corrected (using exponential equation) by measuring the 235 U/ 238 U ratio and correcting with the natural 235 U/ 238 U ratio. The calibration of ion-counters relative to Faraday cups was performed using several cycles of measurement with different collector configurations in each particular analysis. The age determination was possible due to the accurate determination of 234 U and 230 Th concentrations by isotope dilution analysis using the 236 U 229 Th spike. For 4 samples 230 Th/U ages were corrected for detrital 230 Th 35 assuming a 232 Th/ 238 U isotope atomic ratio of 3.8 (the mean crustal value) in the detrital components. The reproducibility of 234 U/ 238 U ratio was 0.11% (2σ). OSL Dating Method Optical dating provides a means of determining burial ages for sediments. The time elapsed since sediments were last exposed to sufficient heat or sunlight for grain bleaching can be estimated from measurements of the optically stimulated luminescence (OSL) signal and the radioactive content of the sample and the surrounding deposit Measuring the OSL signal from a sample of sediment, the equivalent dose (De) that represents the radiation dose to which sedimentary grains have been exposed in their burial environment, can be determined. Also estimated is the dose rate that represents the rate of exposure of grains to ionising radiation over the burial period. The burial age of initially well-bleached grains can then be calculated from the De divided by the dose rate. Nine sediment samples were collected from the LC-MSA in the North Area of Cave 13B (Supplementary Tab. 2). Five of the samples were collected from the LC-MSA Upper, of which two 15

16 (46447 and ) were from the upper dune sand and three (46467, and ) were from the lower dune sand (see supplementary discussion of stratigraphy for details). The other four sediment samples were collected from the LC-MSA archaeological sediments: sample from the LC- MSA Middle, and samples , and from the LC-MSA Lower sediments. We also collected one additional sample (111406) from the lowermost unexcavated LC-MSA sediments cemented to the south cave wall. We extracted quartz grains of μm diameter from all 10 samples, under dim red/orange illumination using standard procedures, including etching by HF acid to remove the external alphadosed layer and any feldspars 36. De values were estimated from multi-grain aliquots of all samples (~10 grains per aliquot), and 1000 individual grains of samples 20721, and were also measured. Multiple- and single-grain OSL data were obtained using the single-aliquot regenerative-dose protocol 40 and Risø TL/OSL-DA-20 (multi-grain aliquots) and TL/OSL-DA-15 (single grains) luminescence readers 41. Multi-grain aliquots were stimulated using 36 mw. cm-2 of blue (470 ± 30 nm) light for 40 s at 125 C, whereas single grains were stimulated using a focused 10 mw green (532 nm) laser for 1 s at 125 C. In both cases, the natural and regenerative doses were preheated at 240 C for 10 s, and the test doses (which are used to correct for any sensitivity changes) were preheated at 160 C for 5 s before optical stimulation. Because infrared-sensitive minerals (e.g., feldspars) could have been present either as remnant grains left after the HF etch and repeated sieving through a 180 μm-diameter sieve, or as inclusions internal to the quartz grains, their absence was checked for and confirmed using the OSL-IR depletion ratio test 42,43. The ultraviolet OSL emissions were detected using Electron Tubes Ltd 9635Q photomultiplier tubes fitted with 7.5 mm of Hoya U-340 filter, and laboratory doses were given using calibrated 90Sr/90Y beta sources. Multi-grain De values were determined from the first 0.8 s of OSL, using the final 8 s to measure the background. Single-grain De values were obtained from the first 0.1 s of OSL, using the 16

17 final 0.1 s of OSL as background. An instrumental reproducibility uncertainty of 0.5% (multi-grain aliquots) and 2% (single grains) (explicitly measured for the equipment used in this study) was added (in quadrature) to each OSL measurement error. Dose-response curves were fitted using a saturatingexponential-plus-linear function, with the standard error on the De value determined by Monte Carlo simulation 44. Tests of protocol performance were made for thermal transfer and test-dose sensitivitycorrection, and these reveal no significant problems for multi-grain aliquots; these routinely returned thermally-transferred signals <1% of the natural OSL at zero applied dose, and recycling ratios consistent with unity (at two standard deviations) for duplicate regenerative doses. In addition, dose recovery tests showed that correct dose estimates were obtained from multi-grain aliquots of sample that had been bleached by sunlight and then given a known laboratory dose, which was measured under the same experimental conditions as above (ratio of measured/given doses of 0.97 ± 0.04) 45,

18 3. Supplementary Table(s) Supplementary Table 1 Output of the multidimensional 3D GIS model showing age, relative sea level (RSL), and distance from PP13B. Age kyr RSL Distance from PP13B (km)

19

20 Supplementary Table 2 Dose rate data, D e values and optical ages for ten sediment samples from the LC-MSA. Sample Code Moisture Content Radionuclide concentrations a Dose rates (Gy kyr -1 ) Total dose rate b, c D e b, d Number of aliquots Over dispersi on f U TH K or grains e (%) (μg g -1 ) (μg g -1 ) (%) Beta Gamma Cosmic (Gy kyr -1 ) (Gy) (%) (kyr) LC-MSA Upper (Upper dune) ± ± ± ± ± ± ± ± 2 (M) 36 / ± 2 91 ± ± ± ± ± ± ± ± ± 2 (M) 42 / ± 2 90 ± 5 LC-MSA Upper (Lower dune) ± ± ± ± ± ± ± ± 3 (M) 40 / ± ± ± ± ± ± ± ± ± ± 2 (M) 43 / 48 7 ± ± ± ± ± ± ± ± ± ± 4 (M) 22 / ± ± ± 3 (S) 58 / ± ± 6 LC-MSA Middle ± ± ± ± ± ± ± ± 4 (M) 45 / ± ± 7 Optical age b LC-MSA Lower 122 ± 3 (S) 381 / ± ± ± ± ± ± ± ± ± ± 4 (M) 45 / ± ± ± 3 (S) 164 / 18 ± ± ± ± ± ± ± ± ± ± 3 (M) 41 / ± 2 91 ± ± 5 (S) 168 / ± ±

21 ± ± ± ± ± ± ± ± 5 (M) 42 / ± ± 12 LC-MSA Lower (South Wall) 119 ± 3 (S) 127 / ± ± ± ± ± ± ± ± ± ± 3 (M) 47 / ± ± ± 4 (S) 194 / ± ± 9 a Measurements made on sub-samples of dried, homogenised and powdered sample by thick source alpha counting (TSAC) (for U and Th) and a combination of TSAC and beta counting to obtain an estimate of 40 K. Dry dose rates calculated from these activities were adjusted for the water content (expressed as % of dry mass of sample). b c d Mean ± total uncertainty (68% confidence interval), calculated as the quadratic sum of the random and systematic uncertainties. Includes an assumed internal alpha dose rate of 0.03 Gy kyr -1, with an assigned relative uncertainty of ± 25%. Estimated using multi-grain aliquots (M) or single grains (S). All single-grain D e values were obtained using the finite mixture model to determine the D e for the dose component represented by the highest proportion of grains, except sample (for which the central age model was used). The total uncertainty includes a systematic component of ± 2% associated with laboratory beta-source calibration. e f Number of multi-grain aliquots or individual grains used for D e determination / total number of aliquots or grains analysed. Relative standard deviation of the D e distribution after allowing for measurement uncertainties. 21

22 Supplementary Table 3 Distribution of grouped NCS values (where n>3) between utilized and unutilized pigments. Utilized Unutilized Total Grouped NCS n mass n mass n mass (g.) (g.) (g.) Saturated very red Saturated reddishbrown Intermediate reddishbrown Total Mean NCS 4145 Y68R 3746 Y64R Supplementary Table 4 The basic lithic categories of the LC-MSA lithic sample. Detached Pieces Cores Cobbles Totals Upper LC-MSA Middle LC-MSA Lower LC-MSA Totals

23 Supplementary Table 5 Percentage of raw materials for all debitage in the LC-MSA lithic sample. Quartzite Quartz Silcrete Other Upper LC-MSA 70.3% 3.1% 15.7% 10.9% Middle LC-MSA 73.3% 10.5% 10.5% 5.7% Lower LC-MSA 77.8% 14.3% 4.8% 3.1% Totals 77.1% 13.5% 5.8% 3.6% Supplementary Table 6 The representation of major lithic classes in the LC-MSA plotted and 10mm lithic sample. Retouched Points Blades Bladelets Flakes and Totals Other Debitage Upper LC-MSA Middle LC-MSA Lower LC-MSA Totals additional bladelets in 3mm screen 23

24 4. Supplementary Discussion Discussion of Stratigraphy The initial LC-MSA excavations in 2000 involved a small test excavation of one roughly 50 cm by 50 cm quad into the exposed and eroded section. During the 2005 and 2006 field seasons we extended the excavations into the LC-MSA by excavating 2 more quads to the north of the quad excavated in The excavation into the LC-MSA was complicated by the cement-like calcareous horizon capping the archaeological horizons at the base of the LC-MSA Upper. We used an angle-grinder to cut through this capping, lifted it off, and it separated reasonably cleanly from the underlying archaeological sediment. This is clearly shown capping the eastern section (Fig. 1). We were able to excavate the semi-cemented archaeological horizons with a stratigraphic technique that included 3-D plotting of the finds. The LC-MSA Middle and Lower were only weakly cemented, and the sediments could be excavated quite easily. Initially, following the 2000 excavations we grouped the main part of the section into a single stratigraphic aggregate (the Lightly Consolidated MSA Facies =LC-MSA), despite the fact that it has multiple lenses of material that were excavated as separate stratigraphic units. This was done because the sample size of lithics was quite small and the short section (only 50 cm) provided little firm stratigraphic evidence. A micromorphology sample was taken from the entirety of this section (20249) in 2003, and has been studied. Like the other excavated areas, micromorphological observations fail to identify any significant bioturbation from burrowing insects or mammals. The 2005 and 2006 excavations provided us with a thicker and longer section from a much wider extent, and that, coupled with new stratigraphic observations, has allowed us to the refine our divisions of the stratigraphy as discussed in this paper. We now recognize the following stratigraphic aggregates, and provide an expanded discussion from that presented in the main text of this paper: 24

25 The Bedrock is at the base of the sediments as currently sampled. Much of it is rounded by water action. It is very likely the same boulder beach encountered at the base of the excavations in other excavation areas. We believe this represents the beach formed by high sea levels that cut the cave. The LC-MSA Lower (weighted mean OSL age of 164 ± 12 kyr) is the lowest set of sediments of the section and is the archaeologically richest of all. The LC-MSA Lower also occurs on the south wall of the cave and is dated by OSL sample (161.7 ± 17.2 kyr), consistent with the weighted mean age of the excavated northern area. This is the least cemented of all the layers in the LC-MSA. There are multiple lenses of carbonaceous material that appear heavily burnt. The presence of anthopogenically fire-altered material, which has a distinct mineral magnetic character, has also been documented by frequencydependent magnetic susceptibility analysis. This identifies ultra-fine-grained ferrimagnetic minerals formed during the heating process 47. Micromorphology shows that some of these are in situ combustion features, and some appear trampled. These are very fine in situ fires, with some hearth cleanout separating them. Micromorphology also shows that there is less ash in the LC-MSA Lower than in the LC- MSA Middle. Lithics and faunal remains are abundant throughout the LC-MSA Lower, both in these burnt lenses (Supplementary Fig. 7) and between them as well. There is a slight slope to the plotted finds, with most between 0 and 15 : however a substantial portion slope between 15 and 30, but with little or no dramatic or random changes to slope that would indicate intrusions or disturbances (Supplementary Fig. 8). The layers slope gently down from north to south, and where there is bedrock at the base of the sequence the layers dip and rise in concert with the rock surfaces. The distribution of plotted finds follows this grade. There is an observable change in the section, and also in the ash content and level of cementation, between the Lower and Middle LC-MSA. The contact between the Lower and Middle LC-MSA is abrupt in some areas. It appears likely that the contact represents slight erosion, lack of 25

26 deposition with exposure, or trampling of the top of the LC-MSA Lower. It does not indicate a major change in sedimentation. The LC-MSA Middle (weighted mean OSL age of 132 ± 12 kyr) includes multiple lenses of dark organic material that micromorphology shows have charcoal, and in situ hearths. Much of the deposit is ash. Micromorphology shows that there is evidence for trampling. Cobbles and roof fall are common. One of the main diagnostic features of the LC-MSA Middle is the presence of white pipes that penetrate into it and can be seen in cross-section in our section photographs (Supplementary Figs. 1 and 2). Micromorphology shows that these are the remnants of ancient roots that penetrated into this layer, disturbed the layer, and then were subsequently replaced with calcite. The slope line of the plotted finds shows that, while there is a general tendency for the finds to be rather parallel to the slope of the sediments, there are multiple examples of finds dipping abruptly down out of pattern with the surrounding finds suggesting some downward disturbance (Supplementary Fig. 9). The overall slope of finds shows a large spread in slope, with the majority of finds sloping between 5 and 25 degrees (Supplementary Fig. 10). The density of plotted finds is much lower than in the LC-MSA Lower (Supplementary Fig. 7). The penetration of the large roots terminates at the top of the LC-MSA Lower (Supplementary Fig. 1), while micromorphology shows that some smaller roots continue into the LSA-MSA Lower, suggesting the conditions of the LC-MSA Lower at the time of root formation were less agreeable to root formation. This could be due to increased water in the LC-MSA Lower, a very dense artifactual component, high organic content, or a combination of all three creating a supersaturated environment. The LC-MSA Upper caps the anthropogenic facies and is a heavily cemented zone composed of multiple layers. Micromorphological observations document several phases of cementation. The cementation events postdate the deposition of the layers in the LC-MSA. This cementation 26

27 stabilized and hardened both the LC-MSA deposits and the dune above. The surface of this cemented dune is clearly visible on the north wall of the cave as a steeply sloping remnant of the leeward face of the dune that sealed the cave (Supplementary Video 1). Within the LC-MSA Upper we recognize three layers: 1) A lower very hard sandy and silty layer that directly contacts and transitions into the richer archaeological deposits of the LC-MSA Middle. This layer includes multiple lenses of black to dark brown organic material. 2) A sandy horizon (weighted mean OSL age of 120 ± 7 kyr) with a lens of shellfish (Supplementary Fig. 5). This horizon is well preserved in the northern section, and in the northern area of the LC-MSA generally, but is eroded off the southern portion of the LC-MSA in the main area of excavation. It must have been deposited just prior to the sealing of the cave by the dune, and included significant organic activity as indicated by the black lenses. Micromorphology also documents the presence of small to larger fragments of shell, and some show slight rounding suggesting potential movement. 3) A dune formed against the cliff and sealed the cave (weighted mean OSL age of 90 ± 6 kyr) with sand spilling into the cave over the top of the LC-MSA deposits. The surface remnant of this dune is clearly evident on the northern cave wall (Supplementary Video 1), and there is a similarly reposed remnant in site 13A. Micromorphology shows that this dune was stabilized by a vegetative mat that eventually contributed to its cementation. The roots penetrate into the LC-MSA below. One way to explain this is that the dune formed, was vegetated and fixed, cemented, and then eroded. The cementation of the upper crust of the 13B dune is a result of the vegetative mat, not saturation of the entire dune. 27

28 The LC-MSA Flowstone drips from the cave wall and over the LC-MSA sequence where the LC- MSA abuts the cave wall. It grew between 92 and 39 kyr as dated by 6 U-series samples (Tab. 1 in text). The U-series ages provide a precise minimum age estimate for the sediment samples from below collected for optical dating from the LC-MSA. At its thickest the flowstone is about 5 cm of laminated brown to yellow flowstone, has a rough and wavy microscopically sharp boundary with the underlying LC-MSA Upper (Supplementary Fig. 3 and 4) and penetrates and seeps into it at various locations. Supplementary Figs. 3 and 4 of the micromorphology definitively document the LC-MSA Flowstone, and therefore the U-series ages, stratigraphically overlying the top of the LC- MSA Upper. Our excavations did not reach the area where the flowstone is present, so we core sampled approximately 50 cm to the north of the excavated area, pushing the core sufficiently deep to sample the entire sequence of sands and lenses in the LC-MSA Upper. This core was prepared into a micromorphology sample (46579), and study of this sample shows this flowstone cap on the aeolian sand of the LC-MSA Upper. The flowstone itself has two distinct periods of growth (Supplementary Fig. 4) separated by an increment of aeolian sand that is also cemented by organically produced calcite (roots, fungus etc). The two flowstone layers, however, laterally join again to form a compound layer. Each flowstone layer has multiple laminae with several growth lines of imperfect crystal coalescence. Along these growth lines, but also inside the laminae, are sand grains of aeolian origin. All grains have fresh outer surfaces so they cannot be derived from the already existing dune or aeolian deposits on which it grew since these were already cemented and thus their grains would have attached calcitic cement. This would suggest that sand was occasionally blowing inside the cave as the flowstone was forming. The very fact of the separation of the two layers by aeolian sand also suggests that sand was blowing inside the cave at that time. Laterally, the flowstone is sand-free but does contain growth lines and inclusions. This is most consistent with an area protected behind a hump of the dune (as preserved on the cave wall) that partially closed the cave, but surely made it uninhabitable (Supplementary Video 1). 28

29 Two micromorphology samples (46557 and 46552) were taken from carbonaceous layers cemented to the north wall since these resembled the LC-MSA. These are not archaeological, but have lots of gypsum and black organic phosphate rich material that is likely guano. This material formed after the cave was closed, so could represent use of the cave by bats. The presence of gypsum suggests the cave was damp but not wet at this time. The partially closed cave appears to have opened after about 39 kyr, when the flowstone stopped growing. Discussion of OSL dating For multi-grain aliquots the resulting De distributions are overdispersed by 7 23% (the relative spread in De values remaining after taking measurement uncertainties into account, which we calculated using the central age model 48. The upper and lower dune sands from the LC-MSA Upper showed less overdispersion (7 13%) than the archaeological sediments from the LC-MSA Middle and Lower units, and this amount of overdispersion is typical of that reported previously for multi-grain aliquots consisting of well-bleached quartz grains (which can have De distributions that are overdispersed by up to 20% Based on the physical appearance of the De distributions (Supplementary Fig. 11), restricted extent of overdispersion and results of the dose homogeneity test 52, the dune samples are thought to consist of grains that were emplaced during single depositional events and have since remained undisturbed. Accordingly, the optical ages for these samples were estimated from the weighted mean De values and associated standard errors, calculated using the central age model 48. The extent of dose overdispersion among the multi-grain aliquots of the archaeological samples (15 23%) is slightly higher than for the LC-MSA Upper dune sands. This may be a result of sediment mixing between adjacent younger or older sedimentary layers, the in situ disintegration of unbleached roof material, or reflect large variations in the beta dose received by individual grains; these phenomena have been observed previously at MSA sites in South Africa 53,54 and elsewhere 51,55. Although the calculated overdispersions are smaller than, or within error of, the 20% 29

30 value reported for some well-bleached sediments, the possibility of post-depositional mixing of grains cannot be discounted. As a result, individual grains of these samples were measured to investigate sediment mixing. A total of 6000 individual grains were measured: 1000 grains for sample (the lower dune sand in the LC-MSA Upper) and 1000 grains for each of the samples collected from the archaeological sediments in LC-MSA Middle (111402) and LC-MSA Lower (111403, , 20721, ). Not every grain measured resulted in usable OSL data and grains were rejected using the criteria described and tested elsewhere 56,57. The De values for the grains that were not rejected are displayed on radial plots in Supplementary Fig. 12. Fifty-eight single-grain De values were obtained for sample , which resulted in a De distribution that was overdispersed by only 5 ± 2%. The single-grain De distribution of this sample and its physical appearance (Supplementary Fig. 12) thus support the multi-grain results, which suggested that the upper and lower dune sands within the LC-MSA Upper stratigraphic aggregate had been well-bleached at burial and represent single depositional events, with no evidence for subsequent disturbance. A significantly larger number of De values (N = 381) were calculated for sample (LC-MSA Middle) and its De distribution showed larger overdispersion (25 ± 1%). This higher overdispersion, and the pattern of distribution of the De values when displayed on a radial plot (Supplementary Fig. 12), suggests that mixing has occurred within this sample. Similar mixing patterns (Supplementary Fig. 12) were also observed for the samples measured from the LC-MSA Lower, with overdispersion values ranging between 14 and 29% (Supplementary Tab. 11). In such instances, the results from multi-grain aliquots may under- or over-estimate the burial age of the primary sediments in these units, and the application of the central age model is inappropriate. Instead, we have applied the finite mixture model to the single-grain De distributions to distinguish the individual De components, determine the relative proportion of grains associated with each component, and estimate the weighted mean De value and associated standard error of each component 51,58,59. We used maximum log likelihood (llik) and the Bayes Information Criterion 30

31 (BIC) as statistical measures to estimate the optimum combination of number of dose components and the relative overdispersion 58. The latter varied from 10 to 12% for these samples, but the final model fits were not sensitive to substantial variations (5-25%) in this parameter. Application of the finite mixture model resulted in the recognition of two De components in each of the five mixed samples. To calculate the optical age for these samples (Supplementary Tab. 11), we used the weighted mean De and standard error for the dose component containing the greatest proportion of single grains (shown on Supplementary Fig. 12). The relative proportion of grains representing each of the single-grain De components in a sample (Supplementary Fig. 12) can be used to infer the degree of mixing. Sample , collected from the LC-MSA Middle, had 40% of its De values identified by the finite mixture model as being intrusive (that is, grains with De values that do not form part of the primary dose component). The slope of plotted finds showed the presence of areas of disturbance, and micromorphological investigations revealed the existence of ancient root casts (see supplementary discussion), within the LC-MSA Middle. Large roots penetrating through the LC-MSA Upper into the LC-MSA Middle could, therefore, potentially have been the mechanism responsible for introducing younger grains into the otherwise older underlying deposits. The degree of mixing observed for the samples from LC-MSA Lower is less significant, with only 11 17% of the grains being identified as intrusive for three of the four samples. This result may reflect the lack of penetration of large roots into these deeper deposits (as shown by micromorphology) and the rarity of steeply sloped plotted finds (Supplementary Figure 9). These independent lines of evidence confirm the absence of major post-depositional disturbance of the LC-MSA Lower, and support its stratigraphic integrity. The total dose rate for all 10 samples was calculated as the sum of the beta and gamma dose rates due to 238 U, 235 U, 232 Th (and their decay products) and 40 K. The concentrations of radioactive elements (Supplementary Tab. 2) were measured by Thick Source Alpha Counting (TSAC) and Risø GM-25-5 beta-counting. These values were converted to dose rates 60, making allowance for 31

32 beta-dose attenuation 61, HF etching 62 and sample moisture content 63. Account was also taken of the cosmic-ray contribution (adjusted for site altitude, geomagnetic latitude, cave configuration, and thickness and water content of the sediment overburden) 64,65 and the effective internal alpha dose rate. In situ gamma spectrometry was not possible at the site, but the gamma dose rates deduced from laboratory analysis of samples from the different sedimentary layers are very similar throughout the LC-MSA sequence and elsewhere in the cave (see Supplementary Tab. 2). We are confident, therefore, in our dose rate assessment except for sample , which has a total dose rate 52 59% larger than those of the other three samples from the same unit (LC-MSA Lower); hence we regard its anomalously high dose rate (and correspondingly young optical age) as unreliable. To calculate the optical ages, we assume that the measured radionuclide activities have prevailed throughout the period of sample burial. The De and dose rate information are presented in Supplementary Tab. 2, together with the optical ages for all samples. All ages (except that of ; see above) are in correct stratigraphic order. Given this stratigraphic consistency, and the reproducible OSL age estimates for each of the different levels, we calculated weighted mean ages of 164 ± 12 kyr (LC-MSA Lower), 132 ± 12 kyr (LC-MSA Middle), 120 ± 7 kyr (lower dune in LC-MSA Upper) and 90 ± 6 kyr (upper dune in LC- MSA Upper); the error on the weighted mean is reported at the 95% confidence interval. The occupational hiatus of 32 ± 14 kyr (at 95% CI) between the LC-MSA Lower and LC-MSA Middle supports the micromorphological observation of an erosional boundary and inferred depositional break between the two levels. Also, the optical age for the upper dune sand in LC-MSA Upper is concordant with the U-series age estimate (91.6 ± 1 kyr) for the overlying flowstone, which provides independent verification of the reliability of the OSL age determinations. Discussion of Pigments Fifty-seven pigment fragments (93.4g total, 92.8g came from LC-MSA Lower) have been studied from the LC-MSA (Supplementary Tab. 3). Seven are small (<10mm), identical, fragments. 32

33 Thirty-eight cases (88g) have a maximum dimension of 10mm. Twenty-nine cases were plotted; the remainder are from sieved material but only account for 9.45g of the total. Visual and physical identification was used to categorize 46 pigments as fine-grained sedimentary materials predominantly siltstone (29), followed by coarse siltstone (12) and shale (n=5). The remainder have seemingly undergone greater alteration and consist of 3 fine-sandstone, 2 medium-sandstone, 3 purer iron oxide and 1 other pigments. However, these materials may have derived from the same sedimentary contexts as the first group of material. By mass, the assemblage is dominated by coarse siltstone (38.7g), followed by shale (23.6g) and siltstone (15.1g). Fine sandstone and purer iron oxide make equal contributions (7.5g each). Siltstone is the most fragmented category (mean 0.5g, s.d. 0.9g); average weights for all other major categories are >1g. Attributes restricted to, or strongly associated with the fine-grained sedimentary forms include a tabular shape, lustrous appearance, and abundant very fine mica. The sandstone and purer iron oxide tends to be slightly harder than the fine-grained material. Most of the fine-grained sedimentary material had a pinkish-brown or reddish-brown surface colour; there was also a considerable proportion of pinkish-grey siltstone. Most of the purer iron oxides are black or dark brown. The Natural Colour System (NCS) was used to record streaks (n=53). NCS values were grouped along the dimensions of nuance and hue. Saturated nuances were those with the highest chroma values for given levels of blackness (7020, 6030, 5040, 4550, 4050, 3560, 3060, 2570, 2070, and 2060). Pastels had chroma values in the range of 10-25% for blackness values 20-50%, 10-15% for blackness 60%, and <10% for blackness 70%. Intermediate nuances fell between these two poles. The three hue groupings were yellow-brown (<50% red), reddish-brown (50%-74% red), and very red ( 75% red). The majority (n=31) are intermediate reddish-brown, followed by saturated reddish-brown (n=10), and saturated very red (n=7). There is a single pastel value (reddish-brown), and 3 values fall into the yellowish-brown category; however, the latter are all within 10% of the yellowishdoi: /nature06204 SUPPLEMENTARY INFORMATION 33

34 brown/reddish-brown cut-point. In sum, all the material could be subsumed under the general term red ochre. Nearly all the values with low (<32%) blackness are siltstone, as are nearly all cases with low (<60%) redness. The nearest possible terrestrial source of iron rich fine-grained sedimentary material that can be utilized as a pigment is an exposure of the Bokkeveld (shale and siltstone), about 5 km north of Pinnacle Point. However, with regressed sea levels it is possible that other sources were available. Ten pieces are definitely utilized (8 ground and 2 scraped) and 2 pieces are probably utilized (both ground). The definitely utilized pieces account for almost half (48.5%) the assemblage mass and 8 of the 10 pieces weigh >2g. They would account for 66.3% of assemblage mass but for one large piece of unutilized siltstone. Most ground pieces are moderately to intensively ground on one principal surface. There are no multi-facetted, intensively utilized pieces resembling crayons. Saturated very red values are disproportionately represented among utilized pieces, suggesting preferential use of the reddest, most chromatic pigments. Mineralogical analysis using X-ray diffraction and mineral magnetic characterization show that some of the pigments consist of hematite, magnetite, maghemite, or mixtures of the three. Some consist almost entirely of finegrained hematite. There are very few shelter/cave sites in South Africa currently thought to provide Middle Pleistocene MSA assemblages. Two of these (Peers Cave on the Cape Peninsula, and Cave of Hearths in Limpopo Province) are undated. Despite large lithic samples from both sites, no ochre is reported 33,66,67. Wonderwerk Cave (Northern Cape) has provided U-series age estimates between 78 and 220 kyr for the MSA 68, but no details on the pigments are available. At Border Cave (KwaZulu- Natal Province), the revised ESR chronology 69, indicates that the three oldest MSA stratigraphic units (6BS, 5WA, 5BS) are Middle Pleistocene. Pigment is scarcely detectable in the lowest units (6BS & 5WA), despite extensive excavation and large lithic samples. In 5BS, which has provided two dates within MIS6, there is a pronounced (fivefold) increase in the regularity of ochre use 67. The closest relevant site to Pinnacle Point is Blombos Cave. Regular use of ochre is evident 34

35 throughout the excavated and published sequence, at the base of which is a dune with an OSL age of 143 kyr ± Discussion of Shellfish Marine shell remains were identified wherever possible to generic or specific level whereupon minimum number of individuals (MNI) and weights were established. A total of at least fifteen categories of marine invertebrates were identified: four categories to species level (Perna perna, Choromytilus meridionalis, Scutellastra argenvillei and Turbo sarmaticus), five to genus level (Donax spp, Helcion sp, Oxystele spp, Nodilittorina spp, Burnupena spp), three to Family level (Mytilidae, Patellidae, and Turritellidae), one to Subphylum (shore barnacle as part of Crustacea), and two to a broad category of molluscs (whelks and chitons) to which, respectively, many Families and an entire Class belong. Specimens identified within the Family Mytilidae were the fragmentary adiagnostic remains of badly preserved bivalve shells that could be either P. perna or C. meridionalis. Shell remains classified as Patellidae are limpet remains that could belong to the Scutellastra genus or possibly also Cymbula. Species are divided into those collected as food and others which have been brought to the site because they are either common epibionts or cling often onto mussels, limpets, rocks and stones 70,71. P. perna (brown mussel) dominates throughout the LC-MSA sequence by way of mass and MNI, followed by T. sarmaticus (giant periwinkle), limpets (S. argenvillei and Patellidae), and small amounts of whelks. This species list is less diverse than the MSA at Klasies River Mouth (KRM) 72, although all species identified here are also present at KRM. This difference in diversity is most likely the result of a much larger sample size of marine shells recovered from KRM. Similar species were also exploited at Blombos Cave 73, although the proportion with which they appear is different. While we acknowledge that the samples of marine shellfish available for each sub-aggregate are small, there is a noticeable difference between LC-MSA Upper and the sub-units below it in that 35

36 brown mussels appear to be the overwhelmingly dominant species in this younger episode of occupation. This apparent pattern, however, would need to be tested with additional faunal material. With the exception of Donax spp (white mussel) and whale barnacle (Coronula spp), the vast majority of the shellfish species from the LC-MSA series were collected from rocky shores. Based on the current habitat of these species, people gathered shellfish from exposed to moderate rocky shores and also from tidal pools. The collection of these abundant, accessible and highly predictable resources would have been easily achieved during daily low tides and/or monthly spring-low tides. Based on the spatial distribution and micro-morphological evidence, empty shells were disposed of next to and close to the side cave walls. The fragment of a whale barnacle is tentatively identified as Coronula diadema 74, its presence pointing to another source of marine food, namely beached whales 75. Although several species of whales have been reported to host Coronula spp barnacles, the Humpback Whale (Megaptera novaeangliae) seems to be the best candidate as this species approaches the southern African shores in large numbers during migration and C. diadema is mostly found growing on this species. Whales were probably scavenged and/or processed at the beach with some parts taken back to the cave, like blubber with skin on which whale barnacles were attached. Whale barnacles have been reported for a modest number of Later Stone Age west coastal sites 75,76. Studies have shown that sites closest to the sea generally have the highest densities of shellfish remains and visa versa 72,77, with changes in quantities within one or two orders of magnitude. When the density of marine shells in LC-MSA is compared to that of samples from sites where distance to the coastline is known 77, it suggests that the coastline was within a few kilometers. This is consistent with the results suggested by the sea level model. Discussion of Lithics The vast majority (n=1575) of the 1836 lithic artifacts are from the LC-MSA Lower, and are the focus of description and analysis here (Supplementary Tab. 4). Detached pieces are the predominant form (1526), while the remainder of the assemblage is comprised of cores (n=20) or 36

37 unaltered or split cobbles (n=29). The assemblage is dominated by quartzite (77.8%) with smaller numbers of quartz (14.3%), silcrete (4.8%), and other raw materials (3.1%) (Supplementary Tab. 5). Although currently chemically unsourced, all classes of raw material are today available within 15 km of the cave 78. During the time of the formation of the LC-MSA Lower deposits an additional ~4.5 km of currently submerged coastal shelf would have been available for raw material exploitation, as reconstructed by the sea level model. Cortex amount and type was recorded for all pieces. When cortex is present it is nearly always water-worn cobble (98%). The use of locally available secondary deposits is common throughout the Cape MSA, especially on the coast. Based on flake and core morphology, the Levallois flaking technique and other prepared core technologies were used for the production of many of the larger products (points and blades, n=219). The Levallois technique is consistently present, although a preference between point and blade production is not marked. The smallest blade/bladelet products tend to have minimally prepared or plain platforms and the presence of small core rejuvenation flakes demonstrates continued maintenance of these cores. The regular production of small bladelets could signal composite technology, but confirmation of this awaits larger samples and study of microwear and/or residues. Expedient flaking of multiplatform cores is also present. The number of retouched pieces is small (n=12). Points (convergent flake-blades) (n=98) and blades (n=121) are common (Supplementary Tab. 6). 37

38 5. Supplementary Equation(s) None 6. Supplementary Notes (including notes clarifying statistical analyses, acknowledgements, grant or other numbers) We thank SAHRA and HWC for providing permits to conduct excavations at the selected sites and export specimens for analysis, and the Mossel Bay community for assisting during excavations and analyses. In particular we thank the staff of the Diaz Museum Complex, Mossel Bay Municipality, Cape Nature Conservation, Mr. Ricky van Rensberg for building our staircase, as well as the business community. This research was funded by the National Science Foundation (USA) (grants # BCS , BCS , and BCS to Marean), funding from the Huxleys, the Hyde Family Trust, the Institute for Human Origins, Arizona State University, the National Research Foundation (NRF): Division for Social Sciences and Humanities (DSSH) (South Africa) grant # 15/1/3/17/0053 to Nilssen, and a Wenner-Gren Dissertation Fieldwork Grant 6894 to Minichillo. Opinions expressed and conclusions arrived at, are those of the authors and are not to be attributed to any of these funding agencies. 38

39 7. Supplementary Video Legend(s) This movie shows a fly-in to Pinnacle Point cliffs, and then a fly-in and walk-around in Cave 13B. All imagery, polygons, and points are fully georeferenced. The models were created in ESRI ArcGlobe and ArcScene as discussed in the methods section above, and the animation is a recording of mouse movements. (Windows Media File; 28 MB). References from Supplementary Information 35. Kaufman, A. et al. U-Th isotope systematics from the Soreq cave, Israel and climatic correlations. Earth and Planet. Sci. Lett. 156, (1998). 36. Huntley, D. J., Godfrey-Smith, D. I. & Thewalt, M. L. W. Optical dating of sediments. Nature 313, (1985). 37. Aitken, M. J. Introduction to Optical Dating. (Oxford University Press, Oxford, 1998). 38. Bøtter-Jensen, L., McKeever, S. W. S. & Wintle, A. G. Optically Stimulated Luminescence Dosimetry. (Elsevier Science, Amsterdam, 2003). 39. Lian, O. B. & Roberts, R. G. Dating the Quaternary: progress in luminescence dating of sediments. Quaternary. Sci. Rev. 25, (2006). 40. Murray, A. S. & Wintle, A. G. Luminescence dating of quartz using an improved singlealiquot regenerative-dose protocol. Radiat. Meas. 32, (2000). 39

40 41. Bøtter-Jensen, L., Andersen, C. E., Duller, G. A. T. & Murray, A. S. Developments in radiation, stimulation and observation facilities in luminescence measurements. Radiat. Meas. 37, (2003). 42. Henshilwood, C. S. et al. Emergence of modern human behavior: Middle Stone Age engravings from South Africa. Science 295, (2002). 43. Duller, G. A. T. Distinguishing quartz and feldspar in single grain luminescence measurements. Radiat. Meas. 37, (2003). 44. Yoshida, H., Roberts, R. G. & Olley, J. M. Progress towards single-grain optical dating of fossil mud-wasp nests and associated rock art in northern Australia. Quaternary. Sci. Rev. 22, (2003). 45. Wintle, A. G. & Murray, A. S. A review of quartz optically stimulated luminescence characteristics and their relevance in single-aliquot regeneration dating protocols. Radiat. Meas. 41, (2006). 46. Jacobs, Z., Wintle, A. G. & Duller, G. A. T. Evaluation of SAR procedures for De determination using single aliquots of quartz from two archaeological sites in South Africa. Radiat. Meas. 41, (2006). 47. Herries, A. I. R. Archaeomagnetic evidence for climate change at Sibudu Cave. South. Afr. Humanit. 18, (2006). 40