The genomic prehistory of peoples speaking Khoisan languages

Pakendorf, Brigitte; Stoneking, Mark

doi:10.1093/hmg/ddaa221

Cited by 6 publications

(7 citation statements)

References 47 publications

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“…While ancient genomes are still scarce, the available data confirm inferences from modern populations suggesting that East African ancestry reached southern Africa and mixed with Khoisan-related ancestry before the arrival of Bantu-speaking groups (8,36). In particular, East African ancestry is absent from 2 ky South African hunter-gatherers but is evident in a 1.2 ky individual found in a herder context in the Western Cape who lacks West African-related ancestry (30).…”

Section: Spread Of Pastoralism From Eastern To Southern Africasupporting

confidence: 55%

“…Fossil, genetic, and archaeological evidence all strongly favor an African origin for our species; while very deep population relationships can still be found among present-day African hunter-gatherers, there are also high levels of genetic homogeneity across large areas that reflect expansions of food-producing groups (6)(7)(8). Domesticated animals from southwest Asia (Middle East) first spread into North Africa ~8,000 y ago, gradually moving south (9, 10) and entering eastern Africa ~5 kya and southern Africa ~2 kya (11)(12)(13).…”

Section: Africamentioning

confidence: 79%

“…By contrast, in southern Africa, Bantu-speaking groups show substantial amounts of autochthonous (Khoisanrelated) ancestry (identified from foraging and pastoralist groups of the Kalahari), and Khoisan-speaking groups show substantial amounts of Bantu-related ancestry, indicating considerable interactions between them (6,8)). These interactions were strongly sex biased, with primarily Khoisanrelated maternal lineages found in Bantu-speaking groups and Bantu-related paternal lineages found in Khoisanspeaking groups (31).…”

Section: Spread Of Pastoralism/farming Into North and East Africamentioning

confidence: 98%

“…Multiple genetic studies have found a signature of eastern African-related ancestry in southern African groups ( 8 , 13 , 18 ), which is usually attributed to the spread of pastoralism. However, Khoe-Kwadi groups have at most small amounts of East African ancestry, which is also found in other southern African groups ( 8 , 13 , 18 ), suggesting that the pastoral migrants extensively admixed with local hunter-gatherers, with genes flowing in both directions.…”

Section: Africamentioning

confidence: 99%

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Genomic perspectives on human dispersals during the Holocene

Stoneking

Arias

Liu

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. Here, we provide an overview of Holocene dispersals in the light of genomic evidence and conclude that they have a complex history. Even when there is a demonstrated connection between a demographic expansion of people, the spread of agriculture, and the spread of a particular language family, the outcome in the results of contact between expanding and resident groups is highly variable. Further research is needed to identify the factors and social circumstances that have influenced this variation and complex history.

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Section: Spread Of Pastoralism From Eastern To Southern Africasupporting

confidence: 55%

Section: Africamentioning

confidence: 79%

Section: Spread Of Pastoralism/farming Into North and East Africamentioning

confidence: 98%

Section: Africamentioning

confidence: 99%

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Genomic perspectives on human dispersals during the Holocene

Stoneking

Arias

Liu

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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“…However, more studies of whole genome sequences are needed for exact dating. For further review of the history of Khoe-San populations, see Pakendorf and Stoneking (2021) .…”

Section: Pervasive Admixture In Africa During the Past 10000 Yearsmentioning

confidence: 99%

Evolutionary Genetics and Admixture in African Populations

Pfennig

Petersen

Kachambwa

et al. 2023

Genome Biology and Evolution

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As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: they contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of African genetic variation and examine deep population structure within Africa, including evidence of ancient introgression from archaic “ghost” populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of African population genetic structure on health and disease and call for more ethically conducted studies of African genetic variation.

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Assessment and improvement of sex estimation standards for application in Holocene San and Khoekhoe populations

Malek

Sealy

Gibbon

2023

Intl J of Osteoarchaeology

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Accurate population‐specific sex estimation standards do not exist for southern African Holocene San and Khoekhoe populations. Due to markedly small stature, skeletal gracility, and physically active lifestyle, this population exhibits reduced sexual dimorphism, complicating application of standards developed elsewhere. The effectiveness of common sex estimation approaches were assessed and optimized for San and Khoekhoe populations. One‐hundred seventy‐five adult archaeological San and Khoekhoe skeletons were studied. Sex estimates from seven morphological traits (cranial and mandibular) and six metrical parameters (mandibular, humeral, and femoral) were compared with pelvic (Phenice) sex estimates to assess agreement. Results were analyzed using chi‐squared tests, univariate statistics, and cross‐validated discriminant function analysis. The effectiveness of individual cranial and mandibular traits varied: The mastoid process and mandibular shape produced the highest agreement rates with pelvic sex estimates (73% and 72%, respectively), while mental eminence and nuchal crest produced the lowest (both 53%). The nuchal crest exhibited a strong sex bias. All mandibular and long‐bone metrical parameters were sexually dimorphic; femoral and humeral vertical head diameter (FHD and HVHD) were the most discriminatory. The discriminant function equations showing the highest agreement with pelvic sex estimates were direct multivariate bicondylar breadth, FHD and HVHD (77%), univariate FHD (75%), and stepwise multivariate FHD and HVHD (73%). All variables were sexually dimorphic, but the reduced sexual dimorphism in this population necessitates careful choice of traits. Trait scores considered diagnostic of males and females may require adjustment to improve discriminating power. This study identified the most accurate areas to target for sex estimation and generated the first discriminant functions specific to archaeological San and Khoekhoe people.

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The genomic prehistory of peoples speaking Khoisan languages

Cited by 6 publications

References 47 publications

Genomic perspectives on human dispersals during the Holocene

Genomic perspectives on human dispersals during the Holocene

Evolutionary Genetics and Admixture in African Populations

Assessment and improvement of sex estimation standards for application in Holocene San and Khoekhoe populations

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