Southern Africa is consistently placed as a potential region for the evolution of We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.

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The invention of the bow and arrow was a pivotal moment in the human story and its earliest use is a primary quarry of the modern researcher. Since the organic parts of the weapon – wood, bone, cord and feathers – very rarely survive, the deduction that a bow and arrow was in use depends heavily on the examination of certain classes of stone artefacts and their context. Here the authors apply rigorous analytical reasoning to the task, and demonstrate that, conforming to their exacting checklist, is an early assemblage from Sibudu Cave, KwaZulu-Natal, South Africa, which therefore suggests bow and arrow technology in use there 64 millennia ago.

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For various reasons increased effort has recently been made to detect the early use of mechanically-projected weaponry in the archaeological record, but little effort has yet been made to investigate explicitly what these tool sets could indicate about human cognitive evolution. Based on recent evidence for the use of bow-and-arrow technology during the Middle Stone Age in southern Africa by 64 kya, we use the method of generating and analysing cognigrams and effective chains to explore thought-and-action sequences associated with this technology. We show that, when isolated, neither the production of a simple bow, nor that of a stone-tipped arrow, can be reasonably interpreted to indicate tool behaviour that is cognitively more complex than the composite artefacts produced by Neanderthals or archaic modern Homo. On the other hand, as soon as a bow-and-arrow set is used as an effective group of tools, a novel cognitive development is expressed in technological symbiosis, i.e. the ability to conceptualize a set of separate, yet inter-dependent tools. Such complementary tool sets are able to unleash new properties of a tool, inconceivable without the active, simultaneous manipulation of another tool. Consequently, flexibility regarding decision-making and taking action is amplified. The archaeological evidence for such amplified conceptual and technological modularization implies a range of cognitive and behavioural complexity and flexibility that is basic to human behaviour today.

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The ability to digest milk into adulthood, lactase persistence (LP), as well as specific genetic variants associated with LP, is heterogeneously distributed in global populations. These variants were most likely targets of selection when some populations converted from hunter-gatherer to pastoralist or farming lifestyles. Specific LP polymorphisms are associated with particular geographic regions and populations; however, they have not been extensively studied in southern Africa. We investigate the LP-regulatory region in 267 individuals from 13 southern African populations (including descendants of hunter-gatherers, pastoralists, and agropastoralists), providing the first comprehensive study of the LP-regulatory region in a large group of southern Africans. The "East African" LP single-nucleotide polymorphism (SNP) (14010G>C) was found at high frequency (>20%) in a strict pastoralist Khoe population, the Nama of Namibia, suggesting a connection to East Africa, whereas the "European" LP SNP (13910C>T) was found in populations of mixed ancestry. Using genome-wide data from various African populations, we identify admixture (13%) in the Nama, from an Afro-Asiatic group dating to >1,300 years ago, with the remaining fraction of their genomes being from San hunter-gatherers. We also find evidence of selection around the LCT gene among Khoe-speaking groups, and the substantial frequency of the 14010C variant among the Nama is best explained by adaptation to digesting milk. These genome-local and genome-wide results support a model in which an East African group brought pastoralist practices to southern Africa and admixed with local hunter-gatherers to form the ancestors of Khoe people.