The genomic prehistory of peoples speaking Khoisan languages.

Peoples speaking so-called Khoisan languages-that is, indigenous languages of southern Africa that do not belong to the Bantu family-are culturally and linguistically diverse. They comprise herders, hunter-gatherers as well as groups of mixed modes of subsistence, and their languages are classified into three distinct language families. This cultural and linguistic variation is mirrored by extensive genetic diversity. We here review the recent genomics literature and discuss the genetic evidence for a formerly wider geographic spread of peoples with Khoisan-related ancestry, for the deep divergence among populations speaking Khoisan languages overlaid by more recent gene flow among these groups and for the impact of admixture with immigrant food-producers in their prehistory.

Bantu-speaker migration and admixture in southern Africa.

The presence of Early and Middle Stone Age human remains and associated archeological artifacts 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 has 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 providing evidence for 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.

Demographic history and admixture dynamics in African Sahelian populations.

The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.

Static and moving frontiers: the genetic landscape of Southern African Bantu-speaking populations.

A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.

Extensive population structure in San, Khoe, and mixed ancestry populations from southern Africa revealed by 44 short 5-SNP haplotypes.

The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter-gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Genetic studies [mitochondrial deoxyribonucleic acid (DNA) and Y-chromosome] conducted on San and Khoe groups revealed that they harbor some of the most divergent lineages found in living peoples throughout the world. Recently, high-density, autosomal, single-nucleotide polymorphism (SNP)-array studies confirmed the early divergence of Khoe-San population groups from all other human populations. The present study made use of 220 autosomal SNP markers (in the format of both haplotypes and genotypes) to examine the population structure of various San and Khoe groups and their relationship to other neighboring groups. Whereas analyses based on the genotypic SNP data only supported the division of the included populations into three main groups-Khoe-San, Bantu-speakers, and non-African populations-haplotype analyses revealed finer structure within Khoe-San populations. By the use of only 44 short SNP haplotypes (compiled from a total of 220 SNPs), most of the Khoe-San groups could be resolved as separate groups by applying STRUCTURE analyses. Therefore, by carefully selecting a few SNPs and combining them into haplotypes, we were able to achieve the same level of population distinction that was achieved previously in high-density SNP studies on the same population groups. Using haplotypes proved to be a very efficient and cost-effective way to study population structure.

HLA class-I diversity in Cameroon: evidence for a north-south structure of genetic variation and relationships with African populations.

HLA class I diversity (loci A, B and C) was analysed in four populations, two from North Cameroon (Podokwo and Uldeme) and two from South Cameroon (Ewondo and Bamileke). Northern and southern Cameroon populations show a substantial genetic diversity in terms of haplotype sharing and genetic distances, even despite the low percentage of variance due to differences among populations evidenced by analysis of molecular variance. The signals of differentiation among populations are consistent with their linguistic affiliation, and support previous evidence, based on autosomal microsatellites and protein loci, which has shown that the complex pattern of genetic variation of Cameroon can in part be described by contrasting the northern and southern part of the country. Looking at our results in the more general framework of HLA diversity in sub-Saharan Africa, it turns out that the Podokwo and Uldeme show some genetic links to populations of the southern western branch of the Sahel corridor, while their high frequency of A*02 and C*04 alleles is congruent with previously hypothesised introgression of non-sub-Saharan alleles. On the other hand, signals of shared ancestry between the Bamileke and Ewondo and the Bantu speakers from central and southern Africa were detected.

South Africans and Mexicans in Florida: intergroup conflict.

Newly arriving immigrants from Southern Africa and Mexicans do not get on well in the sunbelt state of Florida. A persistent theme emerging from discussions with South Africans on their relationship with Mexicans is that both sides perceive the other as culturally ethnocentric. The antagonistic relationship between both social groups is due to strong ethnic bonds and the clash of cultures.

Origin differences in self-reported health among older migrants living in France.

OBJECTIVES: Little is known about the health status of older migrants living in Europe. Using detailed data collected in 2003, this study investigated differences in health status by country of origin within the older immigrant population living in France using a self-rated health measure. STUDY DESIGN: The database used in this research was the Passage à la Retraite des Immigrés survey, conducted from November 2002 to February 2003 on a sample of 6211 migrants aged 45-70 years and living in France at the time of the survey. METHODS: A difficulty with a self-rated outcome is that it may not be comparable between different origin groups, particularly because of cultural and linguistic differences. Therefore, generalized ordered Probit models were estimated, and an indicator of health, net of cross-cultural effects was constructed for each respondent. RESULTS: This study found that male immigrants from southern Africa and Asia, and female immigrants from northern Europe, southern Africa and Asia are more likely to be in good health, while the health status is lower among immigrants from Eastern Europe living in France. CONCLUSION: The diversity in health status within the immigrant population is large in France. These results are helpful in order to target the more disadvantaged origin groups and to adjust the provision of health care.

The traditional use of southern African medicinal plants for the treatment of bacterial respiratory diseases: A review of the ethnobotany and scientific evaluations.

ETHNOPHARMACOLOGICAL RELEVANCE: Multiple plant species were used traditionally in southern Africa to treat bacterial respiratory diseases. This review summarises this usage and highlights plant species that are yet to be verified for these activities. AIM OF THE STUDY: This manuscript reviews the traditional usage of southern African plant species to treat bacterial respiratory diseases with the aim of highlighting gaps in the literature and focusing future studies. MATERIALS AND METHODS: An extensive review of ethnobotanical books, reviews and primary scientific studies was undertaken to identify southern African plants which are used in traditional southern African medicine to treat bacterial respiratory diseases. We also searched for southern African plants whose inhibitory activity against bacterial respiratory pathogens has been conmfirmed, to highlight gaps in the literature and focus future studies. RESULTS: One hundred and eighty-seven southern African plant species are recorded as traditional therapies for bacterial respiratory infections. Scientific evaluations of 178 plant species were recorded, although only 42 of these were selected for screening on the basis of their ethnobotanical uses. Therefore, the potential of 146 species used teraditionally to treat bacterial respiratory diseases are yet to be verified. CONCLUSIONS: The inhibitory properties of southern African medicinal plants against bacterial respiratory pathogens is relatively poorly explored and the antibacterial activity of most plant species remains to be verified.

Paradox of precision: bright tobacco as technology of transfer, 1880-1937.

This article compares two episodes of technology transfer in the 1890s: the movement of bright tobacco production technology to south-central Africa with the spread of the crop to eastern North Carolina and South Carolina. It finds similarities in the people who introduced the crop, but significant differences in the methods used to produce it. This is troubling because the type is defined by the cultivation and especially the curing techniques used to produce it; it is also often described in the historical literature as "Virginia tobacco," even when grown elsewhere. the technological differences are the product of different environments, which include not only the climate but also many elements of the technological system beyond immediate human control: the availability and organization of labor, differences in market structures and marketing institutions, and the government incentives provided to buyers. Therefore, this essay takes as its subject the paradox inherent in the official classification of tobacco types regulated by the USDA and argues that varietal types represent a form of market regulation disguised as botanical taxonomy.

Association between the MnSOD Ala-9Val polymorphism and development of schizophrenia and abnormal involuntary movements in the Xhosa population.

Reactive oxygen species (ROS)-mediated damage has been hypothesized to play a role in the development and poor outcome of schizophrenia, as well as the development of neuroleptic-induced abnormal involuntary movements. Recently, the functional polymorphism (Ala-9Val) in the manganese superoxide dismutase (MnSOD) gene (part of the antioxidant defense mechanism) was found to be associated with schizophrenia in a Turkish population. This study was aimed at replicating this finding in a Xhosa population. In addition, the role of Ala-9Val in abnormal involuntary movement and tardive dyskinesia development in the Xhosa population was also investigated. The schizophrenic patient group (n=286) and a healthy control group (n=243) were genotyped for the Ala-9Val polymorphism using heteroduplex-single stranded conformational polymorphism (HEX-SSCP) analysis. No significant difference in genotype or allele frequency could be observed between the schizophrenia and control group (P=0.294 and P=0.528 respectively). In addition no association could be found between the polymorphism and symptom severity (SANS and SAPS). The Xhosa schizophrenia patient group with abnormal involuntary movements (n=54) and a subgroup with tardive dyskinesia (n=30) was found to significantly differ in Ala-9Val genotype frequency (P=0.008 and P=0.011 respectively) compared to the Xhosa schizophrenia patient group without abnormal involuntary movements (n=204). However, no significant difference was found for the allele frequencies (P=0.955 and P=0.161). Further, using ANCOVA no association was found between AIMS score and genotype in the group with abnormal involuntary movements (P=0.1234). However, in the patient group with tardive dyskinesia an association was observed between genotype and AIMS score (P=0.0365). These results do not support a major role of the MnSOD Ala-9Val polymorphism in the development of schizophrenia or symptom severity in the Xhosa population. Yet it seems to be involved in the development of abnormal involuntary movements and tardive dyskinesia and may even modulate the severity of tardive dyskinesia.

Ethnobotany, therapeutic value, phytochemistry and conservation status of Bowiea volubilis: A widely used bulbous plant in southern Africa.

ETHNOPHARMACOLOGICAL RELEVANCE: Bowiea volubilis Harv. ex Hook.f. (Family: Asparagaceae) is a bulbous medicinal plant widely used against numerous ailments including headache, muscular pains, infertility, cystitis and venereal diseases in southern Africa. AIM OF THE REVIEW: To provide a critical and updated review of Bowiea volubilis with regards to its abundance, medicinal importance, conservation status and potential means to sustain its availability for future generations. METHODS: A comprehensive literature search using online databases such as Web of Science, Google Scholar, Scopus and Springerlink as well as ethnobotanical literature was done in order to obtain, collate, synthesize and critically analyze available information on Bowiea volubilis. RESULTS: On the basis of its wide distribution in many Provinces in South Africa, Bowiea volubilis has a long history of applications among the different ethnic groups. These applications include its uses as purgatives and for the treatment or relief of microbial infections, skin disorders, pains and inflammation. Scientific validation of its diverse uses in traditional medicine has been demonstrated via antimicrobial, anti-inflammatory and toxicity assays. Available results indicate a general poor antimicrobial activity especially with the bulb extracts while the anti-inflammatory activity appears promising. Phytochemical screenings revealed that Bowiea volubilis contains cardiac glycosides and related compounds while reports of other classes of compounds are unavailable. In line with its usage in traditional medicine, the majority of available studies on the species have focused on the use of different solvent extracts from the bulbs. The destructive harvesting of bulbs has led to a continuous decimation of wild populations. Consequently, there are increasing conservational concerns on the sustainability of this species for continuous supply to meet escalating demands. CONCLUSIONS: Bowiea volubilis remains a widely used medicinal plant and available but limited scientific evidence indicates its anti-inflammatory potential. The abundance of cardiac glycosides in its phytochemical composition provides an indication on the therapeutic potential. More research efforts including the application of different biotechnological techniques are still required in order to guarantee its sustainable use over time.

Merging pharmacopoeia: understanding the historical origins of incorporative pharmacopoeial processes among Xhosa healers in southern Africa.

This paper focusses on Xhosa healers and their pharmacopoeias in Southern Africa. Its preliminary aim is to show that Xhosa healers have incorporated Western pharmaceutical products into their traditional dispensaries. The primary aim of the paper is to explain the trend towards medicinal incorporation in terms of the historical development of health and health care in Xhosa-speaking regions. Finally, it is suggested that Xhosa healers utilise Western medicines for their symbolic value, allowing them to negotiate some of the historical precedents which have had the effect of marginalising their profession.

Extent of heterogeneity in mitochondrial DNA of sub-Saharan African populations.

Variation in the mitochondrial DNA (mtDNA) control region as detected by sequence-specific oligonucleotide (SSO) probes is described for 381 individuals from nine sub-Saharan African populations. Population diversity estimates for SSO types ranged from 0.23 to 0.97, while 102 SSO types were detected, none of these types was shared by more than four populations. Eighteen types occurred in > or = 10% of individuals in some populations; of these, 11 were population-specific. One type occurred in 15% of the total sample, but was shared among only three populations. African SSO types were characterized by high frequencies of blank variants, indicating that there was additional variation present at the nucleotide sequence level in regions where SSO probes hybridize. Analyses of molecular variance (AMOVA) incorporating genetic distances between SSO types showed that 30% of the total variation was due to differences among populations, indicating that there is statistically significant heterogeneity (p < 0.001). An AMOVA on mtDNA control region nucleotide sequence data from 12 populations showed that including all additional variation present at the sequence level increased the variance due to population subdivision to 34% (p < 0.001). Overall, when considering both the low diversity within some populations and high heterogeneity among populations, SSO typing of mtDNA may not be a desirable forensic DNA typing method for continental African populations. Further mtDNA sampling of African-derived populations of North America should be carried out to determine how much of the continental African mtDNA variation is of forensic significance. However, the existence of extensive mtDNA control region nucleotide sequence variation in African populations means that control region sequencing is still appropriate in forensic cases requiring mtDNA analysis.

Serum alpha-fetoprotein concentrations in urban and rural Southern African blacks with hepatocellular carcinoma.

The reason why only some hepatocellular carcinomas synthesize alpha-fetoprotein is not known. Both the frequency with which this foetal globulin is produced and the major aetiological associations of hepatocellular carcinoma vary between populations with high and low incidences of the tumour, raising the possibility that re-expression of the gene for alpha-fetoprotein is determined, or influenced by, the molecular genetic events that occur during hepatocellular carcinogenesis. This hypothesis could be tested by comparing serum alpha-fetoprotein concentrations in populations in which the major risk factors for hepatocellular carcinoma differ. Two such populations are urban and rural southern African blacks. We measured serum alpha-fetoprotein concentrations by radioimmunoassay in 234 southern African blacks with hepatocellular carcinoma: 78 of the patients were urban and they were age-matched with 156 patients born in rural areas, one-half of whom had remained in a rural environment (rural), whereas the others had migrated to the cities in adulthood (rural-urban). Urban patients were more likely than rural-born patients to have a normal serum alpha-fetoprotein value [23.1% (18/78) compared with 10.2% (16/156); p = 0.02]. There was no significant difference between the concentrations in rural and rural-urban patients. The absolute values of the raised serum alpha-fetoprotein values did not differ between urban (69,558 +/- 176,737 ng/ml; and rural-born patients (53,998 +/- 125,681 ng/ml), or between rural (69,207 +/- 159,975 ng/ml) and urban-rural patients (40,434 +/- 83,028 ng/ml). These findings are compatible with the hypothesis that re-expression of the alpha-fetoprotein gene in hepatocellular carcinoma is related to the aetiology or pathogenesis of the tumour.

An anatomical investigation of the coronary ostia and its relationship to the sinotubular junction within a select South African population

The coronary ostia (CO) lie within the left and right aortic sinuses, respectively; and are bound by the sinotubular junction (STJ) superiorly. The high frequency of cardiac procedures that require catheterization has necessitated the reappraisal of the anatomy of the origin of the coronary arteries. Therefore, this study aimed to describe the CO by recording its diameter, shape, and relation to the sinotubular junction in a select South African population.The present study included the gross dissection of 50 formalin fixed, adult cadaveric hearts. The average diameter of the right coronary ostium (RCO) was 3.29mm and the left coronary ostium (LCO) was 3.87mm. With regard to the shape of the ostia, the RCO was described as circular in 52% (26/50), horizontally ellipsoid in 24% (12/50) and vertically ellipsoid in 24% (12/50) of cases. The LCO was circular in 30% (15/50), horizontally ellipsoid in 60% (30/50) and vertically ellipsoid in 10% (5/50) of cases. The RCO was located below the STJ in 88% (44/50) and at the level of the STJ in 12% (6/50) of cases. The LCO was recorded below the STJ in 64% (32/50), at the level of the STJ in 32% (16/50) and above the STJ in 4% (2/50) of cases. Multiple ostia arising from a single aortic sinus was recorded in 14% (7/50) of cases. In 2% (1/50) of cases, the RCO was located in the non-coronary sinus. In addition, the RCO arose from the left aortic sinus in 2% of cases. The results of the present study correlate with those of previous studies. Anomalous CO, although asymptomatic has been linked to myocardial infarction and sudden cardiac death. It is, therefore, imperative for the clinician to be aware of variant CO anatomy, which may alert them to the predisposition of cardiac risks

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Different cranial ontogeny in Europeans and Southern Africans.

Modern human populations differ in developmental processes and in several phenotypic traits. However, the link between ontogenetic variation and human diversification has not been frequently addressed. Here, we analysed craniofacial ontogenies by means of geometric-morphometrics of Europeans and Southern Africans, according to dental and chronological ages. Results suggest that different adult cranial morphologies between Southern Africans and Europeans arise by a combination of processes that involve traits modified during the prenatal life and others that diverge during early postnatal ontogeny. Main craniofacial changes indicate that Europeans differ from Southern Africans by increasing facial developmental rates and extending the attainment of adult size and shape. Since other studies have suggested that native subsaharan populations attain adulthood earlier than Europeans, it is probable that facial ontogeny is linked with other developmental mechanisms that control the timing of maturation in other variables. Southern Africans appear as retaining young features in adulthood. Facial ontogeny in Europeans produces taller and narrower noses, which seems as an adaptation to colder environments. The lack of these morphological traits in Neanderthals, who lived in cold environments, seems a paradox, but it is probably the consequence of a warm-adapted faces together with precocious maturation. When modern Homo sapiens migrated into Asia and Europe, colder environments might establish pressures that constrained facial growth and development in order to depart from the warm-adapted morphology. Our results provide some answers about how cranial growth and development occur in two human populations and when developmental shifts take place providing a better adaptation to environmental constraints.

Computational analysis of candidate disease genes and variants for salt-sensitive hypertension in indigenous Southern Africans.

Multiple factors underlie susceptibility to essential hypertension, including a significant genetic and ethnic component, and environmental effects. Blood pressure response of hypertensive individuals to salt is heterogeneous, but salt sensitivity appears more prevalent in people of indigenous African origin. The underlying genetics of salt-sensitive hypertension, however, are poorly understood. In this study, computational methods including text- and data-mining have been used to select and prioritize candidate aetiological genes for salt-sensitive hypertension. Additionally, we have compared allele frequencies and copy number variation for single nucleotide polymorphisms in candidate genes between indigenous Southern African and Caucasian populations, with the aim of identifying candidate genes with significant variability between the population groups: identifying genetic variability between population groups can exploit ethnic differences in disease prevalence to aid with prioritisation of good candidate genes. Our top-ranking candidate genes include parathyroid hormone precursor (PTH) and type-1 angiotensin II receptor (AGTR1). We propose that the candidate genes identified in this study warrant further investigation as potential aetiological genes for salt-sensitive hypertension.