Bantu-speaker migration and admixture in southern Africa

Human Molecular Genetics ◽

10.1093/hmg/ddaa274 ◽

2020 ◽

Author(s):

Ananyo Choudhury ◽

Dhriti Sengupta ◽

Michele Ramsay ◽

Carina Schlebusch

Keyword(s):

Southern Africa ◽

Geographic Region ◽

Middle Stone Age ◽

East African ◽

Variant Discovery ◽

African Populations ◽

Sequencing Studies ◽

Anatomically Modern Humans ◽

Scale Population ◽

Novel Variant

Abstract The presence of Early and Middle Stone Age human remains and associated archaeological artefacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of southern Africa have largely been reshaped by three major sets of migrations over the last 2000 years. These migrations have led to a confluence of four distinct ancestries (San hunter-gatherer, East African pastoralist, Bantu-speaker farmer and Eurasian) in populations from this region. In this review, we have summarized the recent insights into the refinement of timelines and routes of the migration of Bantu-speaking populations to southern Africa and their admixture with resident southern African Khoe-San populations. We highlight two recent studies hinting at the emergence of fine-scale population structure within some South-Eastern Bantu-speaker groups. We also accentuate whole genome sequencing studies (current and ancient) that have both enhanced our understanding of the peopling of southern Africa and demonstrated a huge potential for novel variant discovery in populations from this region. Finally, we identify some of the major gaps and inconsistencies in our understanding and emphasize the importance of more systematic studies of southern African populations from diverse ethnolinguistic groups and geographic locations.

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Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1817678116 ◽

2019 ◽

Vol 116 (10) ◽

pp. 4166-4175 ◽

Cited By ~ 5

Author(s):

Laura B. Scheinfeldt ◽

Sameer Soi ◽

Charla Lambert ◽

Wen-Ya Ko ◽

Aoua Coulibaly ◽

...

Keyword(s):

Adaptive Landscape ◽

African History ◽

Common Ancestry ◽

East African ◽

Selective Pressures ◽

Genome Wide ◽

A Genome ◽

African Populations ◽

Anatomically Modern Humans ◽

Show Evidence

Anatomically modern humans arose in Africa ∼300,000 years ago, but the demographic and adaptive histories of African populations are not well-characterized. Here, we have generated a genome-wide dataset from 840 Africans, residing in western, eastern, southern, and northern Africa, belonging to 50 ethnicities, and speaking languages belonging to four language families. In addition to agriculturalists and pastoralists, our study includes 16 populations that practice, or until recently have practiced, a hunting-gathering (HG) lifestyle. We observe that genetic structure in Africa is broadly correlated not only with geography, but to a lesser extent, with linguistic affiliation and subsistence strategy. Four East African HG (EHG) populations that are geographically distant from each other show evidence of common ancestry: the Hadza and Sandawe in Tanzania, who speak languages with clicks classified as Khoisan; the Dahalo in Kenya, whose language has remnant clicks; and the Sabue in Ethiopia, who speak an unclassified language. Additionally, we observed common ancestry between central African rainforest HGs and southern African San, the latter of whom speak languages with clicks classified as Khoisan. With the exception of the EHG, central African rainforest HGs, and San, other HG groups in Africa appear genetically similar to neighboring agriculturalist or pastoralist populations. We additionally demonstrate that infectious disease, immune response, and diet have played important roles in the adaptive landscape of African history. However, while the broad biological processes involved in recent human adaptation in Africa are often consistent across populations, the specific loci affected by selective pressures more often vary across populations.

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Fine-scale human population structure in southern Africa reflects ecogeographic boundaries

10.1101/098095 ◽

2017 ◽

Author(s):

Caitlin Uren ◽

Minju Kim ◽

Alicia R. Martin ◽

Dean Bobo ◽

Christopher R. Gignoux ◽

...

Keyword(s):

Population Structure ◽

Southern Africa ◽

Population History ◽

Eastern Africa ◽

Fine Scale ◽

Kalahari Desert ◽

African Populations ◽

Scale Population ◽

Genetic Impact ◽

Northern Cape

AbstractRecent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until about 2,000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for more than one hundred South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu-speakers, approximately 14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.Data depositionData files are freely available on the Henn Lab website: http://ecoevo.stonybrook.edu/hennlab/data-software/SummaryDistinct, spatially organized ancestries demonstrate fine-scale population structure in southern Africa, implying a more complex history of the KhoeSan than previously thought. Southern KhoeSan ancestry in the Nama and ≠Khomani is shared in a rim around the Kalahari Desert. We hypothesize that there was recent migration of pastoralists from East Africa into southern Africa, independent of the Bantu-expansion, but the spread of pastoralism within southern Africa occurred largely by cultural diffusion.

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Fine-scale human population structure in southern Africa reflects ecological boundaries

10.1101/038729 ◽

2016 ◽

Cited By ~ 2

Author(s):

Caitlin Uren ◽

Minju Kim ◽

Alicia R Martin ◽

Dean Bobo ◽

Christopher R Gignoux ◽

...

Keyword(s):

Population Structure ◽

Southern Africa ◽

Population History ◽

Fine Scale ◽

Hunter Gatherers ◽

Kalahari Desert ◽

Genome Wide ◽

African Populations ◽

Scale Population ◽

Northern Cape

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until about 2,000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about population history within southern Africa. We examine new genome-wide polymorphism data and whole mitochondrial genomes for more than one hundred South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share recent ancestry with other Khoe-speaking forager populations that forms a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu-speakers, approximately 14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited impact from eastern African genetic diffusion.

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Genetic diversity of lactase persistence in East African populations

BMC Research Notes ◽

10.1186/s13104-015-1833-1 ◽

2016 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Hisham Y. Hassan ◽

Anke van Erp ◽

Martin Jaeger ◽

Hanan Tahir ◽

Marije Oosting ◽

...

Keyword(s):

Genetic Diversity ◽

Lactase Persistence ◽

East African ◽

African Populations

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Changing Patterns in the Late Pleistocene/Early Holocene Prehistory of Southern Africa as Seen from the Nelson Bay Cave Stone Artifact Sequence

Quaternary Research ◽

10.1016/0033-5894(78)90015-7 ◽

1978 ◽

Vol 10 (1) ◽

pp. 84-111 ◽

Cited By ~ 41

Author(s):

Janette Deacon

Keyword(s):

Southern Africa ◽

Sensu Stricto ◽

Middle Stone Age ◽

Stone Age ◽

Faunal Remains ◽

Later Stone Age ◽

Large Numbers ◽

Changing Patterns ◽

Selection Of ◽

Stone Artifact

The dating of the Stone Age sequence in southern Africa has been considerably revised over the last decade, and one of the anomalies which has resulted is that the Middle Stone Age, now dated to beyond 30,000 B.P., does not immediately precede the Later Stone Agesensu stricto. The excavation and analysis of occupation horizons dating between the most recent Middle Stone Age assemblages and the Holocene is therefore of particular interest. Nelson Bay Cave, situated on the southern coast of South Africa, contains deposits which partly fill the “gap” between the Middle and Later Stone Ages, and the occupation horizons dating between about 18,000 and 5000 years ago are described in this paper. Changes in the habitat in the vicinity of the site caused by sea-level and vegetation changes coincident with the amelioration of temperatures at the end of the Pleistocene are clearly marked in the faunal remains at the site. Largely correlated with the faunal changes (which includes the introduction of marine resources to the cave at about 12,000 B.P.) are changes in the stone artifact assemblages. Three industries are recognized in the sequence: the Robberg, characterized by microbladelets produced from bladelet cores and a few small scrapers and backed tools; the Albany, characterized by large scrapers and an absence of backed tools; and the Wilton, characterized by a variety of Formal Tools including relatively large numbers of small scrapers and backed tools. These changes in artifact-manufacturing traditions are interpreted as signaling adjustments to changing environmental conditions. An explanation for these adjustments is not sought in a simple cause-and-effect relationship between the environment and the cultural response; artifact changes are seen instead as the result of a twofold process, with the environment acting as an external stimulus to change, and the direction of the artifact change governed by the selection of a range of possibilities offered by the technology of the Later Stone Agesensu latothat was widespread in subequatorial Africa during the last 20,000 years.

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Increasing Behavioral Flexibility? An Integrative Macro-Scale Approach to Understanding the Middle Stone Age of Southern Africa

Journal of Archaeological Method and Theory ◽

10.1007/s10816-015-9254-y ◽

2015 ◽

Vol 23 (2) ◽

pp. 623-668 ◽

Cited By ~ 20

Author(s):

Andrew W. Kandel ◽

Michael Bolus ◽

Knut Bretzke ◽

Angela A. Bruch ◽

Miriam N. Haidle ◽

...

Keyword(s):

Southern Africa ◽

Behavioral Flexibility ◽

Middle Stone Age ◽

Stone Age ◽

Macro Scale

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The Archaeology of Archaic and Early ModernHomo Sapiens: An African Perspective

Cambridge Archaeological Journal ◽

10.1017/s0959774300000706 ◽

1993 ◽

Vol 3 (1) ◽

pp. 21-39 ◽

Cited By ~ 8

Author(s):

Philip Allsworth-Jones

Keyword(s):

Near East ◽

Middle Stone Age ◽

Stone Age ◽

Upper Palaeolithic ◽

Modern Humans ◽

Anatomically Modern Humans ◽

African Perspective ◽

Out Of Africa

Whereas in Europe the transition from Middle to Upper Palaeolithic and the replacement of Neanderthal by anatomically modern humans appear to be synchronous events, in Africa this is not the case. Neanderthals as such were not present in Africa, and if the ‘Out of Africa’ model is correct, the ancestors of anatomically modern humans must have made their appearance in a Middle Stone Age context before 100,000 years ago. Subsequently, it seems that they coexisted with Neanderthals for up to 70,000 years in the Near East. If a direct biological correlation can be ruled out, the question arises: what was the impetus for an Upper Palaeolithic ‘revolution’ and why should it have taken place at all?

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Gregariousness, foraging effort, and affiliative interactions in lactating bonobos and chimpanzees

Behavioral Ecology ◽

10.1093/beheco/araa130 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sean M Lee ◽

Gottfried Hohmann ◽

Elizabeth V Lonsdorf ◽

Barbara Fruth ◽

Carson M Murray

Keyword(s):

Social Interaction ◽

Travel Time ◽

Feeding Competition ◽

Wild Populations ◽

East African ◽

Foraging Effort ◽

African Populations ◽

Lactating Females ◽

Term Data

Abstract Fission–fusion dynamics have evolved in a broad range of animal taxa and are thought to allow individuals to mitigate feeding competition. While this is the principal benefit of fission–fusion, few studies have evaluated its costs. We compared gregariousness, foraging budgets, and social budgets between lactating bonobos and chimpanzees from wild populations to evaluate potential costs. Both species exhibit fission–fusion dynamics, but chimpanzees, particularly in East African populations, appear to experience higher feeding competition than bonobos. We expected lactating chimpanzees to be less gregarious than lactating bonobos; reduced gregariousness should allow lactating chimpanzees to mitigate the costs of higher feeding competition without requiring more foraging effort. However, we expected the reduced gregariousness of lactating chimpanzees to limit their time available for affiliative interactions. Using long-term data from LuiKotale bonobos and Gombe chimpanzees, we found that lactating chimpanzees were indeed less gregarious than lactating bonobos, while feeding and travel time did not differ between species. Contrary to our predictions, lactating females did not differ in social interaction time, and lactating chimpanzees spent proportionately more time interacting with individuals other than their immature offspring. Our results indicate that lactating chimpanzees can maintain social budgets comparable to lactating bonobos despite reduced gregariousness and without incurring additional foraging costs. We discuss potential explanations for why lactating bonobos are more gregarious.

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Prediction of peak expiratory flow rate in a Ugandan population

South African Respiratory Journal ◽

10.7196/sarj.2015.v21i4.36 ◽

2015 ◽

Vol 21 (4) ◽

pp. 96

Author(s):

Susan Kiwanuka Nakubulwa ◽

K Baisley ◽

J Levin

Keyword(s):

Lung Function ◽

Reference Values ◽

Regression Equations ◽

East African ◽

Cross Sectional ◽

African Populations ◽

Study Population ◽

Males And Females ◽

Western Uganda ◽

Ugandan Population

Background. Peak expiratory ow rate (PEFR) measurement is one of the commonly used methods for assessing lung function in general practice consultations. e reference values for use by this method are mainly from Caucasian populations; data for African populations are limited. e existence of ethnic and racial dierences in lung function necessitates further generation of PEFR reference values for use in African populations. Objective. To generate equations for predicting PEFR in a Ugandan population. Methods. e PEFR study was cross-sectional and based in rural south-western Uganda. Participants were aged 15 years or more, without respiratory symptoms and were residents of the study area. Multiple regression equations for predicting PEFR were tted separately for males and females. e model used for PEFR prediction was: logePEFR = intercept + a(age, y) + b(logeage) + c(1/height in cm), where a, b and c are the regression coecients. Results. e eligible study population consisted of 774 males and 781 females. Median height was 164 cm (males) and 155 cm (females). e majority of participants had never smoked (males 76.7%; females 98.3%). e equation which gave the best t for males was logePEFR = 6.188 – 0.019age + 0.557logeage – 199.945/height and for females: logePEFR = 5.948 – 0.014 age + 0.317logeage – 85.147/height. Conclusion. e curvilinear model obtained takes into consideration the changing trends of PEFR with increasing age from adolescence to old age. It provides PEFR prediction equations that can be applied in East African populations.

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