The genetic legacy of the expansion of Bantu-speaking peoples in Africa.

The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.

Potential biomarkers for southern African hunter-gatherer arrow poisons applied to ethno-historical and archaeological samples.

The detection of complex poison recipes applied to ancient hunting weapons has the potential to provide important insights into traditional pharmacological knowledge systems. Yet, recipes comprising many ingredients can be challenging to decipher, especially in older samples that have undergone biodegradation. We present the results of our attempt to analyze samples of poison collected from nineteenth and twentieth century arrowheads from southern Africa, and from a 1000-year-old archaeological bone point. The arrow poison residues and reference samples were analyzed by Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR FTIR) and Gas Chromatography Mass Spectrometry (GC-MS). The ATR FTIR analysis is primarily able to separate between different arrow poison binder recipes. The extractives identified by GC-MS analysis consist of a multitude of components from both binders and active substances, confirming and adding to the results from the ATR FTIR analyses. We discuss the results in terms of potential biomarkers for arrow poisons in organic residue analyses of archaeological artefacts; that residues of toxic cardiotonic glycosides can be detected on curated and excavated arrow tips of between about 1000 and 100 years old, serves as proof of concept for working with older materials in the future.

Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.

The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.

Did Pleistocene Africans use the spearthrower-and-dart?

Archeologists commonly suppose that among complex projectile weapons humans use as subsistence aids, the spearthrower-and-dart preceded bow-and-arrow use. And yet, neither ethnographic nor archeological records furnish any robust evidence for spearthrower-and-dart use in Africa. Instead, evidence grows apace for ever-more ancient bow-and-arrow use. Here we explore these findings and their implications for models of early Homo sapiens behavior.

Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.

Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry "Coloured" groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.

The skull from Florisbad: a paleoneurological report.

The Florisbad fossil cranium was found in South Africa in 1932. Different authors proposed a taxonomic affinity with early Homo sapiens, Neandertals or late Homo heidelbergensis. Here, we review its neurocranial morphology, to supply an updated perspective on its paleoneurological features. The curvature of the frontal squama is definitely within modern human variation, although the anterior cranial fossa is very broad, comparable to that of the Neandertals. In contrast, the parietal lobe and the vascular networks are more similar to the morphology observed in more archaic human species, such as Homo heidelbergensis. The endocranial anatomy of the Florisbad skull displays a mosaic of derived and plesiomorphic features, which makes this fossil compatible with distinct phylogenetic scenarios. None of these traits are, however, strictly diagnostic in terms of taxonomy. This specimen is central to the question on the possible anagenetic evolution from Homo heidelbergensis sensu lato to modern humans.

Where does the elephant come from? The evolution of causal cognition is the key.

Osiurak and Reynaud do not explain the evolutionary emergence and development of the elephant in the room, that is, technical cognition. We first argue that there is a tight correlation between the evolution of cumulative technological culture (CTC) and the evolution of reasoning about abstract forces. Second, intentional teaching plays a greater role in CTC evolution than acknowledged in the target article.

Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens.

The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.

The evolution of early symbolic behavior in Homo sapiens.

How did human symbolic behavior evolve? Dating up to about 100,000 y ago, the engraved ochre and ostrich eggshell fragments from the South African Blombos Cave and Diepkloof Rock Shelter provide a unique window into presumed early symbolic traditions of Homo sapiens and how they evolved over a period of more than 30,000 y. Using the engravings as stimuli, we report five experiments which suggest that the engravings evolved adaptively, becoming better-suited for human perception and cognition. More specifically, they became more salient, memorable, reproducible, and expressive of style and human intent. However, they did not become more discriminable over time between or within the two archeological sites. Our observations provide support for an account of the Blombos and Diepkloof engravings as decorations and as socially transmitted cultural traditions. By contrast, there was no clear indication that they served as denotational symbolic signs. Our findings have broad implications for our understanding of early symbolic communication and cognition in H. sapiens.

The people behind the samples: Biographical features of Past Hunter-Gatherers from KwaZulu-Natal who yielded aDNA.

PURPOSE: Skeletons sampled for ancient human DNA analysis are sometimes complete enough to provide information about the lives of the people they represent. We focus on three Later Stone Age skeletons, ca. 2000 B.P., from coastal KwaZulu-Natal, South Africa, whose ancient genomes have been sequenced (Schlebusch et al., 2017). METHODS: Bioarchaeological approaches are integrated with aDNA information. RESULTS: All skeletons are male. Dental development shows that the boy, with prominent cribra orbitalia, died at age 6-7 years. Two men show cranial and spinal trauma, extensive tooth wear, plus mild cribra orbitalia in one. CONCLUSIONS: Dental wear and trauma of the adults are consistent with hunter-gatherer lives. Even partial aDNA evidence contributes to sex determination. Parasitic infection such as schistosomiasis is the best-fit cause for the child's anemia in this case. CONTRIBUTION TO KNOWLEDGE: The convergence of genomic and bioarchaeological approaches expands our knowledge of the past lives of a boy and two men whose lives as hunter-gatherers included episodes of trauma and disease. LIMITATIONS: The skeletons are incomplete, in variable condition, and from poorly characterized local cultural contexts. SUGGESTIONS FOR FURTHER RESEARCH: Thorough osteobiographic analysis should accompany paleogenomic investigations. Such disciplinary collaboration enriches our understanding of the human past.

Causal Cognition, Force Dynamics and Early Hunting Technologies.

With this contribution we analyze ancient hunting technologies as one way to explore the development of causal cognition in the hominin lineage. Building on earlier work, we separate seven grades of causal thinking. By looking at variations in force dynamics as a central element in causal cognition, we analyze the thinking required for different hunting technologies such as stabbing spears, throwing spears, launching atlatl darts, shooting arrows with a bow, and the use of poisoned arrows. Our interpretation demonstrates that there is an interplay between the extension of human body through technology and expanding our cognitive abilities to reason about causes. It adds content and dimension to the trend of including embodied cognition in evolutionary studies and in the interpretation of the archeological record. Our method could explain variation in technology sets between archaic and modern human groups.

The role of play objects and object play in human cognitive evolution and innovation.

In this contribution, we address a major puzzle in the evolution of human material culture: If maturing individuals just learn their parental generation's material culture, then what is the origin of key innovations as documented in the archeological record? We approach this question by coupling a life-history model of the costs and benefits of experimentation with a niche-construction perspective. Niche-construction theory suggests that the behavior of organisms and their modification of the world around them have important evolutionary ramifications by altering developmental settings and selection pressures. Part of Homo sapiens' niche is the active provisioning of children with play objects - sometimes functional miniatures of adult tools - and the encouragement of object play, such as playful knapping with stones. Our model suggests that salient material culture innovation may occur or be primed in a late childhood or adolescence sweet spot when cognitive and physical abilities are sufficiently mature but before the full onset of the concerns and costs associated with reproduction. We evaluate the model against a series of archeological cases and make suggestions for future research.

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.

Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens 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.

Tracking the evolution of causal cognition in humans.

We suggest a seven-grade model for the evolution of causal cognition as a framework that can be used to gauge variation in the complexity of causal reasoning from the panin-hominin split until the appearance of cognitively modern hunter-gatherer communities. The intention is to put forward a cohesive model for the evolution of causal cognition in humans, which can be assessed against increasingly fine-grained empirical data from the palaeoanthropological and archaeological records. We propose that the tracking behaviour (i.e., the ability to interpret and follow external, inanimate, visual clues of hominins) provides a rich case study for tracing the evolution of causal cognition in our lineage. The grades of causal cognition are tentatively linked to aspects of the Stone Age/Palaeolithic archaeological record. Our model can also be applied to current work in evolutionary psychology and research on causal cognition, so that an inter-disciplinary understanding and correlation of processes becomes increasingly possible.

Still Bay Point-Production Strategies at Hollow Rock Shelter and Umhlatuzana Rock Shelter and Knowledge-Transfer Systems in Southern Africa at about 80-70 Thousand Years Ago.

It has been suggested that technological variations associated with Still Bay assemblages of southern Africa have not been addressed adequately. Here we present a study developed to explore regional and temporal variations in Still Bay point-production strategies. We applied our approach in a regional context to compare the Still Bay point assemblages from Hollow Rock Shelter (Western Cape) and Umhlatuzana Rock Shelter (KwaZulu-Natal). Our interpretation of the point-production strategies implies inter-regional point-production conventions, but also highlights variability and intra-regional knapping strategies used for the production of Still Bay points. These strategies probably reflect flexibility in the organisation of knowledge-transfer systems at work during the later stages of the Middle Stone Age between about 80 ka and 70 ka in South Africa.

The disappearing San of southeastern Africa and their genetic affinities.

Southern Africa was likely exclusively inhabited by San hunter-gatherers before ~2000 years ago. Around that time, East African groups assimilated with local San groups and gave rise to the Khoekhoe herders. Subsequently, Bantu-speaking farmers, arriving from the north (~1800 years ago), assimilated and displaced San and Khoekhoe groups, a process that intensified with the arrival of European colonists ~350 years ago. In contrast to the western parts of southern Africa, where several Khoe-San groups still live today, the eastern parts are largely populated by Bantu speakers and individuals of non-African descent. Only a few scattered groups with oral traditions of Khoe-San ancestry remain. Advances in genetic research open up new ways to understand the population history of southeastern Africa. We investigate the genomic variation of the remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published data sets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu speakers. Specifically, we found that the Lake Chrissie San are closely related to the current southern San groups (i.e., the Karretjie people). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. This study illustrates how genetic tools can be used to assess hypotheses about the ancestry of people who seemingly lost their historic roots, only recalling a vague oral tradition of their origin.

The Nature of Culture: an eight-grade model for the evolution and expansion of cultural capacities in hominins and other animals.

Tracing the evolution of human culture through time is arguably one of the most controversial and complex scholarly endeavors, and a broad evolutionary analysis of how symbolic, linguistic, and cultural capacities emerged and developed in our species is lacking. Here we present a model that, in broad terms, aims to explain the evolution and portray the expansion of human cultural capacities (the EECC model), that can be used as a point of departure for further multidisciplinary discussion and more detailed investigation. The EECC model is designed to be flexible, and can be refined to accommodate future archaeological, paleoanthropological, genetic or evolutionary psychology/behavioral analyses and discoveries. Our proposed concept of cultural behavior differentiates between empirically traceable behavioral performances and behavioral capacities that are theoretical constructs. Based largely on archaeological data (the 'black box' that most directly opens up hominin cultural evolution), and on the extension of observable problem-solution distances, we identify eight grades of cultural capacity. Each of these grades is considered within evolutionary-biological and historical-social trajectories. Importantly, the model does not imply an inevitable progression, but focuses on expansion of cultural capacities based on the integration of earlier achievements. We conclude that there is not a single cultural capacity or a single set of abilities that enabled human culture; rather, several grades of cultural capacity in animals and hominins expanded during our evolution to shape who we are today.

Lactase persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists.

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.

MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa.

BACKGROUND: The current San and Khoe populations are remnant groups of a much larger and widely dispersed population of hunter-gatherers and pastoralists, who had exclusive occupation of southern Africa before the influx of Bantu-speakers from 2 ka (ka = kilo annum [thousand years] old/ago) and sea-borne immigrants within the last 350 years. Here we use mitochondrial DNA (mtDNA) to examine the population structure of various San and Khoe groups, including seven different Khoe-San groups (Ju/'hoansi, !Xun, /Gui+//Gana, Khwe, ≠Khomani, Nama and Karretjie People), three different Coloured groups and seven other comparative groups. MtDNA hyper variable segments I and II (HVS I and HVS II) together with selected mtDNA coding region SNPs were used to assign 538 individuals to 18 haplogroups encompassing 245 unique haplotypes. Data were further analyzed to assess haplogroup histories and the genetic affinities of the various San, Khoe and Coloured populations. Where possible, we tentatively contextualize the genetic trends through time against key trends known from the archaeological record. RESULTS: The most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) that can be traced back in time to ~100 ka, found at high frequencies in Khoe-San and sampled Coloured groups. Furthermore, the L0d/k sub-haplogroups were differentially distributed in the different Khoe-San and Coloured groups and had different signals of expansion, which suggested different associated demographic histories. When populations were compared to each other, San groups from the northern parts of southern Africa (Ju speaking: !Xun, Ju/'hoansi and Khoe-speaking: /Gui+//Gana) grouped together and southern groups (historically Tuu speaking: ≠Khomani and Karretjie People and some Coloured groups) grouped together. The Khoe group (Nama) clustered with the southern Khoe-San and Coloured groups. The Khwe mtDNA profile was very different from other Khoe-San groups with high proportions of Bantu-speaking admixture but also unique distributions of other mtDNA lineages. CONCLUSIONS: On the whole, the research reported here presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the Khoe-San and Coloured populations of southern Africa.

The gripping nature of ochre: the association of ochre with Howiesons Poort adhesives and Later Stone Age mastics from South Africa.

This contribution provides direct evidence for the use of ochre in adhesive recipes during the Howiesons Poort of South Africa. Stone segments from two KwaZulu-Natal sites were microscopically analyzed to document ochre and resin microresidue occurrences. These microresidues show a clear distribution pattern on the tool portions that are associated with hafting. Results from a separate quartz and crystal-quartz sample may indicate that different adhesive recipes were applied to different raw materials. A possible functional application for ochre in association with Later Stone Age mastics is also explored. The evidence and suggestions presented here expand our understanding of the versatility, use, and value of pigmentatious materials in prehistory; it is not viewed as an alternative or replacement hypothesis for its possible symbolic role during the late Pleistocene.