In the last two decades, remarkable evidence from (in particular) Pinnacle Point and Blombos Cave at the southern Cape of South Africa has accumulated for signs of symbolic behaviour stretching back more than 150 ka. This evidence includes an intensification of selection of red ochre for potentially ritual-based body decoration, sophisticated technological operations such as heat-treatment of lithic raw materials, optimising shell-fishing by tracking lunar phases, and use of shell beads for ornamentation35,45,50,62,63 (and references therein). Most recently, Blombos has yielded the earliest evidence for drawing32. These activities initially appeared sporadically, rather than as a package. However, it has been argued that the southern Cape was a refuge throughout the glacial Marine Isotope Stage 6, and a greater intensity seems evident after the end of Stage 6, and especially after 90 ka, as parts of southern Africa likely became wetter and more hospitable and the southern coasts were settled64,65,66. As a result, some have suggested that all later modern humans must, in some sense, descend from a small refugial population of modern humans who lived in southern Africa during Marine Isotope Stage 6, ~200–130 ka67,68.

The deep genetic division between Khoe-San groups and other extant humans shows that the idea of a southern refuge is highly plausible – but also that it was not a major genetic source for the rest of humankind. Genetically, present-day modern humans do not descend primarily from southern Africans who lived before ~70 ka – modern African diversity has much deeper roots. In particular, extant mtDNA diversity coalesces around the transition from the inter-glacial Marine Isotope Stage 7 and the glacial Marine Isotope Stage 6, at ~190 ka, and comprises two deep branches, both dating to ~150 ka, one of which arose amongst the ancestors of present-day hunter–gatherer/herder (“Khoe-San”) southern Africans and the other amongst the ancestors of present-day central and eastern Africans. These two deep branches separated between ~190–150 ka, and the northern cluster then split further into a central and an eastern branch. It is from the eastern branch that much African (and all ancient non-African) diversity descends, in the wake of unprecedented demographic expansions, which fuelled dispersals of mtDNA haplogroup L3 both across Africa and out of Africa, after ~70–60 ka28. Thus, at least two Stage 6 refuges contributed to modern human mtDNA diversity, but by far the larger contribution was from eastern Africa.

It is widely agreed that the Homo sapiens inhabitants of both of these regions would have been cognitively modern – in other words, they would not seem out of place if they were raised in any twenty-first century society. Shea69 has argued, for example, that early MSA eastern Africans were as behaviourally flexible as other MSA population where symbolic activities are more evident. It nevertheless remains intriguing that the most impressive evidence for symbolic activities and technological complexity is seen in southern Africa before ~70 ka, and appears in eastern Africa only after 70 ka. This was the time at which microlithic technology appears in both regions almost simultaneously, and was also the only time in the last 135 ka that the climate was simultaneously humid across the whole of the sub-Saharan Africa, so that dispersals became more feasible between what had generally been isolated regions8, following the end of the “megadrought” that had kept the tropics largely arid since ~135 ka44. Did the southern refuge somehow play a role in the dramatic expansions that led to the peopling of the world?

If this was the case, contact between the two regions at this time may have left a trace in a migration from south to east. Here, indeed, we have described the discovery of a small stream of migrants who moved from southern to eastern Africa around 70–60 ka, during precisely the window of opportunity provided by the climate. Our results suggest it was only during this pan-African wet phase that connections were finally established between southern and eastern Africa with dispersals from south to east.

Signals of MSA migrations between ~135 ka and 70 ka are very scarce in the genetic record. One exception involves the movement of a likely ancestor of haplogroup L2 from eastern to central/western Africa at ~100–85 ka26 (Fig. 1A). This represents the most ancient migration detected on the female line of descent following the establishment of specific sub-regional diversities after ~150 ka5,6. The dispersal we detect at ~70–60 ka is the next signal that is evident in the mtDNA record, and the first to connect southern and eastern Africa. Aside from a possible later migration that brought L0d3 into Tanzania after 25 ka, it may be the only episode of gene flow between these two regions until the Holocene5,6.

While this migration from south to north is clearly visible in the mtDNA record, we do not detect any genome-wide signal. This may be due to the very nature of genome-wide data. In an ADMIXTURE-type analysis of present day individuals70, any component arriving ~60 ka would most likely have long since been diluted through recombination into the sink regions’ indigenous components, as suggested by ADMIXTURE analyses of Eurasian aDNA dating to before 20 ka71. Even more sophisticated methodologies, such as TreeMix72, are unlikely to provide further insight, despite the available resolution of over 1.5 million genome-wide SNPs.

Such deep admixture events would be most readily detected in regions that did not undergo large-scale recombination, and this is where the non-recombining mtDNA and Y-chromosome variation come into their own. Detailed high-resolution genomic Y-chromosome data for eastern Africa and southern Khoe-San populations are still lacking, although we must note that, in any case, Y-chromosome results will not necessarily match mtDNA patterns, as males and females can have very different populations histories – and deep ancestry seems to be more often over-written on the male line of descent, further exacerbating the problem of limited sampling73. Nevertheless, despite the inability of the genome-wide analyses to detect the deep migratory events, the early separations and dispersals established a deep genome-wide African population structure that closely matches the mtDNA phylogeography and the split of human diversity into three major groups (southern African, central/western African, and eastern African/non-African). This supports the deep L0 southern African ancestry and, consequently, the presence of more recent L0 subclades in eastern Africa can only be explained by gene flow from southern to eastern Africa.

Several archaeologists have proposed that developments during the Still Bay and Howiesons Poort phase of the MSA maybe have contributed to the out-of-Africa expansions31,47,74. It is therefore tempting to speculate that the migrants at 70–60 ka might have transmitted innovations developed in the southern refuge, such as microlithic technology or even novel symbolic activities, to eastern Africa – innovations that may have had a role in the subsequent unprecedented expansions of eastern African populations. The number of migrants from the south was probably not very large, as reflected in the present-day frequencies of L0 in eastern Africa of 5–15% on average5. Technologies and culture are readily transmitted horizontally, and a relatively minor genetic influx (involving several thousand individuals at most) may have sufficed to transmit the cultural innovations to eastern Africans ~70–60 ka, and seed the populations that migrated outside the continent. In genetic terms, the earliest out-of Africa populations might even have carried a low level of southern African ancestry, but the out-of-Africa bottleneck was very drastic, with the maternal lineage of all humans outside Africa eventually deriving from a single (and likely random) eastern African sequence, the root of haplogroup L3, and any hypothetical genome-wide South African ancestry was diluted through recombination.

It is possible that both the dispersal south to north and the out-of-Africa expansion are independent by-products of the shift in climate after 70 ka, and that the simultaneous appearance of the microliths is a coincidence or an artefact of the scanty archaeological evidence in eastern Africa. On the other hand, if the connections were causal, it would imply that a seemingly minor re-evaluation of the mtDNA tree in Africa may have significant implications for the evolution of Homo sapiens. A cluster of Homo sapiens populations, living in a glacial refuge area on the southern coast of Africa, developed a sophisticated repertoire of complex technological and symbolic behaviours over many tens of thousands of years75,76. This was already evident ~165 ka at Pinnacle Point and reached a zenith at sites such as Blombos by ~80–70 ka. These developments were far from unique (with even some indications amongst other hominin species such as Neanderthals37,38): similar developments took place at other sites across the range of early Homo sapiens in North Africa and the Near East, who likely had similar cognitive capacities. However, these were lost or dispersed southwards due to the onset of harsher climatic conditions in the north after 75 ka39,40,41 – there may even have been a “corridor” connecting these regions via the eastern African coastline prior to this time66. Populations may well have moved rather than simply becoming extinct – indeed, population shifts seem to characterise the MSA66. At the same time, however, favourable climate conditions in the tropics and the south and demographic expansion led to the innovations that emerged in southern Africa being fixed in an expanding population, resulting in them being transmitted to other human groups in, ultimately, eastern Africa. Thus demography likely played a critical role, re-shaping cognitive capacities that may have been in place for perhaps half a million years37.

Thus the use of beads, incised ochre, heat treatment and possibly microlithic technologies, might then potentially have been transmitted to eastern Africa after 70 ka, when – even considering a sampling bias for previous periods – some of these elements become more common in the archaeological record43. As well as the appearance of microlithic tools, the earliest bead in a 78,000 year-long archaeological record in Kenya appears at ~67–63 ka alongside a shift in toolkits44. This migration from southern to eastern Africa after 70 ka was closely followed by a major demographic expansion that is clearly visible in both the genetic and archaeological records77, marked by the decreasing reliance on diagnostic MSA technologies characteristic of the MSA–LSA transition. While the microlithic evidence for a southern source into eastern Africa can be contested on statistical grounds, the putative scenario described for the migration of people and behavioural elements from southern to eastern Africa at the 70–60 ka time frame would be consistent with the concomitant transmission of a technology which clearly appears in both regions at this time. This spread likely involved a small group of migrants from southern Africa, leading not to population replacement or an immediate acculturation across indigenous eastern African populations after 70 ka, but creating a patchwork distribution in both time and space, consistent with the heterogeneity of the archaeological record44.

By 60,000 years ago, however, a fully “syntactic” language akin to those used today74 must have been widespread across both southern and eastern Africa, and have been carried out of Africa. The inference from various aspects of the record to “symbol use” and from there to “fully syntactical language” is far from straightforward63,74. However, the fact that a phenomenon is imperfectly understood does not mean it should be dismissed78, especially when it as potentially significant as charting the emergence of people who potentially were beginning to communicate in ways approaching present-day humans. Indeed, linguists and archaeologists have begun to address the theoretical challenges63,74, and it is possible to sketch out plausible trajectories from courtship rituals shaped by sexual selection into symbolic activity and language, over a likely timeframe of hundreds of thousands of years79,80,81.

Even so, there has been growing scepticism amongst archaeologists in recent years against the possibility that human symbolic behaviour radiated outwards from a single source in southern Africa at such a recent date. By providing novel genetic evidence for a dispersal at this time, we show that a transmission mechanism existed. If symbolic behaviour first gained a foothold primarily in the south, this dispersal could have transmitted it to the rest of Africa by migration and subsequent acculturation.

The populations in eastern Africa that resulted from the arrival of new groups from the south were the starting point for the greatest expansion ever undergone by modern humans, not only back across Africa but also out of Africa, along the Indian Ocean into South Asia, Southeast Asia and Australasia, and ultimately to the rest of the globe. Interpreted in this way, the archaeological and genetic evidence concur that southern Africa is a plausible candidate for the cradle of modern humankind.