Genetic structure and sex-biased gene flow in the history of southern African populations.

OBJECTIVES: We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y-chromosome haplogroup E1b1b (E-M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex-biased gene flow in southern Africa. MATERIALS AND METHODS: We analyzed previously published complete mtDNA genome sequences and ∼900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y-linked STR loci for samples assigned to haplogroup E1b1b. RESULTS: Our results support an eastern African origin for Y-chromosome haplogroup E1b1b (E-M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male-dominated expansion. Our finding of a significant increase in the intensity of the sex-biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time. CONCLUSIONS: Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex-biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

Strategic interactions: Games of the Ju|'hoan.

Three strategic games played by the Ju|'hoan-a board, a card, and a gesture game-complicate the rhetorics that suggest an evolutionary or psychological significance of play. They are mostly played by adults, although every individual adult does not necessarily engage in each game. The Ju|'hoan card and board game practices were transmitted through contact across large parts of Botswana and Namibia, while the gesture game n!àì has been known in other San communities. It suggests that the significance of strategic games is more likely found in its potential for social interaction (i.e., allowing to overcome cultural divides) than in evolution and psychology. Within the anthropological literature, strategy games were thought to be absent in egalitarian societies, such as that of the Ju|'hoan. Here, the roles of power, competition, and winning were thought to be disruptive and unwanted. A closer examination of the details behind the Ju|'hoan games shows that not only were strategy games adopted and adapted from neighboring societies but that the game of n!àì was developed by the Ju|'hoan into a competitive one. The evolutionary or psychological significance of play is informed by studies on individual play, children's play, and games with informal rules. When considering strategic games throughout history, it is their role of facilitator rather than the playing practice itself that makes games relevant across languages, cultural divides, and sociopolitical boundaries.

New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa.

Lactase persistence (LP), the ability to digest lactose into adulthood, is strongly associated with the cultural traits of pastoralism and milk-drinking among human populations, and several different genetic variants are known that confer LP. Recent studies of LP variants in Southern African populations, with a focus on Khoisan-speaking groups, found high frequencies of an LP variant (the C-14010 allele) that also occurs in Eastern Africa, and concluded that the C-14010 allele was brought to Southern Africa via a migration of pastoralists from Eastern Africa. However, this conclusion was based on indirect evidence; to date no study has jointly analyzed data on the C-14010 allele from both Southern African Khoisan-speaking groups and Eastern Africa. Here, we combine and analyze published data on the C-14010 allele in Southern and Eastern African populations, consisting of haplotypes with the C-14010 allele and four closely-linked short tandem repeat loci. Our results provide direct evidence for the previously-hypothesized Eastern African origin of the C-14010 allele in Southern African Khoisan-speaking groups. In addition, we find evidence for a separate introduction of the C-14010 allele into the Bantu-speaking Xhosa. The estimated selection intensity on the C-14010 allele in Eastern Africa is lower than that in Southern Africa, which suggests that in Eastern Africa the dietary changes conferring the fitness advantage associated with LP occurred some time after the origin of the C-14010 allele. Conversely, in Southern Africa the fitness advantage was present when the allele was introduced, as would be expected if pastoralism was introduced concomitantly.

Ontogenetic and static allometry in the human face: contrasting Khoisan and Inuit.

OBJECTIVES: Regional differences in modern human facial features are present at birth, and ontogenetic allometry contributes to variation in adults. However, details regarding differential rates of growth and timing among regional groups are lacking. We explore ontogenetic and static allometry in a cross-sectional sample spanning Africa, Europe and North America, and evaluate tempo and mode in two regional groups with very different adult facial morphology, the Khoisan and Inuit. MATERIALS AND METHODS: Semilandmark geometric morphometric methods, multivariate statistics and growth simulations were used to quantify and compare patterns of facial growth and development. RESULTS: Regional-specific facial morphology develops early in ontogeny. The Inuit has the most distinct morphology and exhibits heterochronic differences in development compared to other regional groups. Allometric patterns differ during early postnatal development, when significant increases in size are coupled with large amounts of shape changes. All regional groups share a common adult static allometric trajectory, which can be attributed to sexual dimorphism, and the corresponding allometric shape changes resemble developmental patterns during later ontogeny. DISCUSSION: The amount and pattern of growth and development may not be shared between regional groups, indicating that a certain degree of flexibility is allowed for in order to achieve adult size. In early postnatal development the face is less constrained compared to other parts of the cranium allowing for greater evolvability. The early development of region-specific facial features combined with heterochronic differences in timing or rate of growth, reflected in differences in facial size, suggest different patterns of postnatal growth.

The linguistic and genetic landscape of southern Africa.

The present-day diversity of southern African populations was shaped by the confluence of three major pre-historic settlement layers associated with distinct linguistic strata: i) an early occupation by foragers speaking languages of the Kx'a and Tuu families; ii) a Late Stone Age migration of pre-Bantu pastoralists from eastern Africa associated with Khoe-Kwadi languages; iii) the Iron Age expansion of Bantu-speaking farmers from West-Central Africa who reached southern Africa from the western and eastern part of the continent. Uniting data and methodologies from linguistics and genetics, we review evidence for the origins, migration routes and internal diversification patterns of all three layers. By examining the impact of admixture and sex-biased forms of interaction, we show that southern Africa can be characterized as a zone of high contact between foraging and food-producing communities, involving both egalitarian interactions and socially stratified relationships. A special focus on modern groups speaking languages of the Khoe-Kwadi family further reveals how contact and admixture led to the generation of new ethnic identities whose diverse subsistence patterns and cultural practices have long puzzled scholars from various disciplines.

Cross-Modality Information Transfer: A Hypothesis about the Relationship among Prehistoric Cave Paintings, Symbolic Thinking, and the Emergence of Language.

Early modern humans developed mental capabilities that were immeasurably greater than those of non-human primates. We see this in the rapid innovation in tool making, the development of complex language, and the creation of sophisticated art forms, none of which we find in our closest relatives. While we can readily observe the results of this high-order cognitive capacity, it is difficult to see how it could have developed. We take up the topic of cave art and archeoacoustics, particularly the discovery that cave art is often closely connected to the acoustic properties of the cave chambers in which it is found. Apparently, early modern humans were able to detect the way sound reverberated in these chambers, and they painted artwork on surfaces that were acoustic "hot spots," i.e., suitable for generating echoes. We argue that cave art is a form of cross-modality information transfer, in which acoustic signals are transformed into symbolic visual representations. This form of information transfer across modalities is an instance of how the symbolic mind of early modern humans was taking shape into concrete, externalized language. We also suggest that the earliest rock art found in Africa may constitute one of the first fossilized proxies for the expression of full-fledged human linguistic behavior.

Medicinal plants of the Kamiesberg, Namaqualand, South Africa.

ETHNOPHARMACOLOGICAL RELEVANCE: Qualitative and quantitative data is presented that gives a new perspective on the traditional medicinal plants of the Khoisan (Khoe-San), one of the most ancient of human cultures. The data is not only of considerable historical and cultural value, but allows for fascinating comparative studies relating to new species records, novel use records and the spatial distribution of traditional plant use knowledge within the Cape Floristic Region. AIM OF THE STUDY: A detailed documentation and quantitative analysis of medicinal plants of the Kamiesberg area (an important Khoisan and Nama cultural centre) and their traditional uses, which have hitherto remained unrecorded. MATERIALS AND METHODS: During four study visits to the Kamiesberg, semi-structured and structured interviews were conducted with 24 local inhabitants of the Kamiesberg, mostly of Khoisan decent. In addition to standard methodology, a newly developed Matrix Method was used to quantity medicinal plant knowledge. RESULTS: The Kamiesberg is an important center of extant Nama ethnomedicinal information but the knowledge is rapidly disappearing. Of a total of 101 medicinal plants and 1375 anecdotes, 21 species were recorded for the first time as having traditional medicinal uses and at least 284 medicinal use records were new. The relative importance, popularity and uses of the plants were quantified. The 97 newly documented vernacular names include 23 Nama (Khoekhoegowab) names and an additional 55 new variations of known names. The calculated Ethnobotanical Knowledge Index (EKI) and other indices accurately quantified the level of knowledge and will allow for future local, regional and even global comparisons. CONCLUSION: The results showed that the Kamiesberg is an important focal point of Khoisan (Nama) traditional knowledge but that the medicinal plants have not yet been systematically recorded in the scientific literature. There are numerous new use records and new species records that are in need of scientific study. Comparative data is now available for broader comparisons of the pattern of Khoisan plants use in southern Africa and the study represents another step towards a complete synthesis of Cape Herbal Medicine.

Characterization of the genetic variation present in CYP3A4 in three South African populations.

The CYP3A4 enzyme is the most abundant human cytochrome P450 (CYP) and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study was to identify genetic variation within CYP3A4 in three South African population groups comprising of 29 Khoisan, 65 Xhosa and 65 Mixed Ancestry (MA) individuals. To identify known and novel CYP3A4 variants, 15 individuals were randomly selected from each of the population groups for bi-directional Sanger sequencing of ~600 bp of the 5'-upstream region and all thirteen exons including flanking intronic regions. Genetic variants detected were genotyped in the rest of the cohort. In total, 24 SNPs were detected, including CYP3A4(*)12, CYP3A4(*)15, and the reportedly functional CYP3A4(*)1B promoter polymorphism, as well as two novel non-synonymous variants. These putatively functional variants, p.R162W and p.Q200H, were present in two of the three populations and all three populations, respectively, and in silico analysis predicted that the former would damage the protein product. Furthermore, the three populations were shown to exhibit distinct genetic profiles. These results confirm that South African populations show unique patterns of variation in the genes encoding xenobiotic metabolizing enzymes. This research suggests that population-specific genetic profiles for CYP3A4 and other drug metabolizing genes would be essential to make full use of pharmacogenetics in Southern Africa. Further investigation is needed to determine if the identified genetic variants influence CYP3A4 metabolism phenotype in these populations.