Major expansion in the human niche preceded out of Africa dispersal In the format provided by the authors and unedited Nature | www.nature.com/nature Supplementary information https://doi.org/10.1038/s41586-025-09154-0 1 Major expansion in the human niche preceded out of Africa dispersal 1 2 3 Supplementary Information 4 5 6 Supplementary Information Guide 7 8 SI-1 Human Origins: Fossils and Archaeology brief overview 9 SI-2 Dispersals within and out of Africa 10 Supplementary Table 1 11 Supplementary Table 2 12 Supplementary Table 3 13 Supplementary Table 4 14 Supplementary References 15 16 17 SI-1 Human Origins: Fossils and Archaeology brief overview 18 Homo sapiens originated in Africa during the Middle Pleistocene (781-126 thousand years ago 19 or ka). This is supported by fossil, genetic, and archaeological evidence. In Africa, the later part 20 of the Middle Pleistocene corresponds to the archaeological period known as the Middle Stone 21 Age (MSA). The associated fossil record is somewhat sparse. At present the first appearance date 22 of “early or recent anatomically modern” H. sapiens106 is 315 ± 34 ka107 at Jebel Irhoud, 23 Morocco, in association with MSA technology. The Jebel Irhoud fossils have a modern human 24 facial and dental morphology, but a more archaic braincase morphology106. Hublin et al.106 25 suggest that by about 300 ka, the human facial morphology had been established, while the 26 braincase continued to evolve more recently in H. sapiens evolutionary history. The earliest H. 27 sapiens fossil that exhibits a modern braincase morphology was recently re-dated to a minimum 28 age of 233 ± 22 ka108 (previously 155-187 ka109) and was found in Ethiopia110-112. The Omo 29 Kibish 2 fossils include skull fragments and postcranial bones113-115. Similarly robust 30 anatomically modern human fossils dating to ~160 ka were also found at Herto, Middle Awash, 31 Ethiopia116. Anatomically modern human fossils have been directly dated at Qafzeh, Israel to 32 100±5 ka117. Additional anatomically modern human fragmented cranial and postcranial fossils 33 of a similar age have been recovered at Klasies River in South Africa118. The cranial and 34 mandibular remains from Klasies River fossils include gracile individuals119 as well as robust 35 individuals lacking a pronounced mental eminence120. The postcranial remains from Klasies 36 River suggest affinities with both archaic and recent human populations121. Cranial fragments of 37 anatomically modern human fossils have also been recovered in Ethiopia at Aduma and are dated 38 to ~100 ka122. All these fossils consist of a mix of different archaic and modern features123, and it 39 2 is not until between 100 and 40 ka that the full constellation of features that defines humans 40 today is found in single individuals124. 41 The archaeological record in Africa underwent a profound shift with the emergence of Middle 42 Stone Age (MSA) technology from around >300 ka. The shift in focus from shaping a block of 43 raw material to removing stone flakes from the block resulted in an explosion of new tool types, 44 not previously seen in the African record, and long thought to be a hallmark of modern 45 cognition125. The discovery of very early MSA technology with some of the earliest fossils of H. 46 sapiens at Jebel Irhoud has since indicated a link between the biological and behavioral 47 manifestations of MSA humans. Generic MSA technology is not dissimilar to Eurasian Middle 48 Palaeolithic technology in that basic elements include forms of scrapers, retouched points, and 49 denticulates often made using both Levallois and non-Levallois reduction methods. MSA 50 assemblages are generally characterized by featuring a higher frequency and morphological 51 variability of unifacial and bifacial points, as well as basally thinned pieces, which mark them 52 out from Middle Palaeolithic assemblages126. 53 The composition of the MSA flaked stone industries remained largely unchanged until about 130 54 ka, after which there is remarkable regional and temporal variability. The MSA is followed by 55 Later Stone Age (LSA) technologies, with the earliest evidence of this shift in some regions from 56 around 40 ka127, but perhaps as early as 67 ka128. The transition between the MSA and LSA over 57 Africa is spatio-temporally complex and not a uniform and parallel process (see Bader et al.129). 58 However, relatively brief periods of a marked increase in the frequency of complex material 59 culture and behavioral innovation within the MSA are evident in several regions of Africa, most 60 notably the northern and southern ends of the continent. Many of these innovations do not appear 61 to have had significant continuity and were used to greater and lesser degrees over time that 62 more reflect a complex mosaic rather than a cumulative process34. This notwithstanding, the 63 MSA witnessed a series of key developments, including the emergence of long-distance social 64 networks and the transport of exotic raw material48, bow and arrow technology130, traps and 65 snares131, water storage72, personal ornaments26,27,30,132,133, geometric engravings72,134, 66 drawings135, and stone tool technology that was regionally distinctive both in form136,137 and 67 methods of hafting138-140. 68 In southern Africa, a proliferation of traits associated with innovative MSA human behavior 69 appear first between ~100-70 ka. At Blombos Cave, an “ochre processing workshop” was 70 identified from deposits dated to 100 ka37, pierced shell beads were recovered from deposits 71 dated to ~75 ka27, by ~75 ka pressure flaked stone tools are present141, and bone tool technology 72 is present by ~100 ka at Klasies River Main site Cave 1A142 and occurs more regularly by ~72 ka 73 at Blombos Cave143,144 and at Sibudu Cave145. At Pinnacle Point 5-6, heat treatment of silcrete to 74 improve stone tool manufacture is present by ~72 ka36, microlithic technology is present by ~71 75 ka35, and dense shell middens146 are present in sediments dated to 70.6 ± 2.3 ka35. Regionally 76 distinct bone tools have been identified at Sibudu Cave and are from deposits dated to ~72 ka 77 3 and ~64-57 ka145,147. Long-term use of diverse marine resources and settlement of coastal 78 landscapes is well-established in southern but also northern Africa between at least ~160-50 79 ka148. 80 In northern Africa, innovative MSA technologies also appear beginning ~100 ka. The collection 81 and use of shells as personal ornaments (eg. Nassarius sp. and Tritia sp.) appear throughout 82 coastal and inland Morocco ~115 ka30. Pierced Nassarius sp. shell beads in situ have been 83 identified at Bizmoune and may date to ≥142 ka133, at Contrebandiers Cave dated to ~115-96 84 ka149-151, at El Harhoura 2 dated to ~116-100 ka152, at El Mnasra dated to 108-106 ka41,152, at Ifri 85 n’Ammar dated to ~83.3 ka132,153, and at Taforalt from deposits dated to ~82.5 ka26. A “bone 86 knife” tool from Dar es-Soltan I cave was identified in Aterian deposits dated to ~90 ka ago154, 87 and recently available chronologies at El Mnasra estimate the age of bone tool155-157-bearing 88 Aterian layers to be ~107 ka41. A worked bone industry was identified at Contrebandiers Cave in 89 deposits dated to 120-90 ka158. 90 In northern Africa, the region closest to the land route into Eurasia, cultural changes peaked 91 around the Last Interglacial, the time when early human fossils are also found in the Levant. The 92 basic Middle Palaeolithic (MP) technology in the Levant during this time was not substantially 93 different than the MSA in neighbouring regions of Africa159. Repeated humid episodes in the 94 Saharo-Arabian arid belt from around 125 ka likely facilitated these dispersals, as well as 95 widespread expansions within the Saharan region itself160 and now arid areas of the Arabian 96 Peninsula161,162. However, iconic innovations, such as Aterian tanged tools do not appear to cross 97 the Nile126. By the beginning of Marine Isotope Stage 4, (MIS 4, 71-57 ka), widespread 98 aridification appears to have driven the contraction or extirpation of many populations in this 99 region126. For example, Aterian tanged tool assemblages that had previously dominated vast 100 regions of northern Africa contract to the Mediterranean coast and the central Saharan 101 mountains, where they eventually disappear during this timeframe32. However by the end of MIS 102 4 and the beginning of MIS 3, multiple, if comparable, trajectories of technological change 103 within the MSA are observed in northeast Africa126, perhaps indicating a re-expansion of 104 populations shortly before dispersal out of Africa. At Haua Fteah in Libya, the MSA material 105 culture intermittently continues until about 46-41 ka and is then replaced by a completely 106 different and apparently unique blade-based industry, the so-called ‘Dabban’ around 39 ka85. The 107 Dabban post-dates the appearance of Upper Palaeolithic technologies in the Levant163, as well as 108 elsewhere in Europe164,165. 109 By MIS 3, Later Stone Age (LSA) assemblages begin to replace MSA assemblages. The oldest 110 examples of potential LSA technology come from eastern Africa, at Panga Ya Saidi in Kenya, 111 where relevant assemblages have been dated to MIS 4, at around ~67 ka128. While the profound 112 economic shift underlying the transition from the MSA to the LSA is not well understood, the 113 lifeways underpinning the LSA spread rapidly throughout MIS 3, until the MSA is all but 114 replaced in most of Africa by ~20 ka129,166-168 (but see Scerri et al. (2021)169). The LSA is usually 115 4 denoted by a significant reduction in the size of stone artefacts with a focus on microlithic tools, 116 sometimes appearing in standardized, geometric form, as well as a simplification of lithic 117 technology and an increase in non-lithic technologies127,170 . The LSA continued to dominate the 118 African record until the end of the Pleistocene171,172. While LSA populations clearly had different 119 practices than MSA populations and continued expanding into new regions and environments of 120 Africa, they remained hunter-gatherers without evidence for agriculture, animal husbandry or 121 sedentarism, and therefore shared many of the same vulnerabilities with Middle and earlier Late 122 Pleistocene humans. For these reasons, we explore the expansion of the human niche in our 123 study until the end of the Pleistocene. 124 125 SI-2 Dispersals within and out of Africa 126 127 The oldest MSA sites are found in eastern, southern, and north-eastern Africa42. Despite the 128 similarity of the technology, the few associated human fossils are diverse, as discussed above. It 129 seems likely that there wasn’t a single, geographically circumscribed ‘birthplace’ for H. sapiens1, 130 but that various morphs on the H. sapiens lineage may have been spread out in Africa. Whether 131 this includes most, or just parts, of Africa is currently not well understood. It is therefore difficult 132 to reconstruct within-Africa dispersals. However, the emergence of geographically discrete and 133 highly distinctive material cultures within the MSA, such as the Aterian and Howiesons Poort 134 technocomplexes, coupled with the diversity of the early H. sapiens fossil record, suggests that 135 mixing was not constant. 136 137 It has been suggested that some of these early populations may have left Africa relatively early. 138 Genetic studies have suggested that some very early H. sapiens, or populations on the lineage 139 leading to us, left Africa and replaced the Neanderthal mitochondrial genome, possibly before 140 270 kya173,174. Modern looking fossils from Apidima, Greece may also date to >210 ka15, while 141 fossil evidence at Misliya in Israel is dated to 177-194 ka14. Later human fossils from Skhul and 142 Qafzeh175-177 in the Mount Carmel of present-day Israel have yielded dates that suggest a 143 dispersal ~125-82 ka during Marine Isotope Stage 5. A human fossil from northern Arabia was 144 dated to the end of this range, at around 85 ka11. 145 146 5 It is currently very difficult to determine whether these lines of evidence indicate multiple early 147 dispersals, or just one or two10. Generally, these earlier dispersals are viewed as relating to 148 climatic windows81 in which Saharo-Arabia greened, thus permitting animals and humans to 149 cross the formerly impenetrable desert barrier into Eurasia. If the dates and taxonomic 150 identifications are correct for Apidima and Misliya, it would seem that dispersal took place 151 during interglacial MIS 7 to early glacial MIS 6. However, the age of fossil remains is not 152 necessarily the age of dispersal, which could have happened much earlier. Whatever the case, 153 these earlier incursions into Eurasia do not seem to have left any genetic legacy in living 154 Eurasian populations. One of the main lines of evidence for this is the Neanderthal ancestry 155 found in all present-day and ancient non-African modern human genomes that have been studied 156 to date. This ancestry is mostly consistent with originating from a single episode of 157 admixture2,3,6,7 which had mostly ceased by 50–60 ka4,178-180. 158 159 Supplementary Table 1. Database of radiometrically dated Pleistocene occupation layers 160 from archaeological sites in Africa used in this study. This database includes archaeological 161 layers that have published coordinates, radiometric dates, an error range less than or equal to 162 20,000 years, and a mean age ≤120,000 and ≥ 14,000 years. Bioclimatic variables for each 163 archaeological layer were accessed from Beyer et al. (2020)62 with added Heinrich events. 164 165 Supplementary Table 2. Calibration of 14C radiocarbon ages. This database includes the 166 number assigned to each archaeological site name and layer for Extended Data Figure 5, as well 167 as uncalibrated ages and errors, calibrated ages and 1σ errors that were used in the current study, 168 and calibrated ages and 1σ errors that were not used in the current study. 169 170 Supplementary Table 3. Tests of spatial autocorrelation in the residuals of the GAM with 171 Moran’s I values. This table includes estimates for Moran's I, the expected values and their 172 significance for both fixed-niche and changing-niche models. Each row represents a different 173 resampling of presences and pseudo-absences. 174 175 Supplementary Table 4. Biome classifications from Beyer et al (2020)62 with added 176 Heinrich events and from PCESM63,64. 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