Southern Africans Research Articles

The Skeletal Phenotype of “Negritos” from the Andaman Islands and Philippines Relative to Global Variation among Hunter-Gatherers

The "negrito hypothesis" suggests that populations of small-bodied foragers in South and Southeast Asia who share common phenotypic characteristics may also share a common, ancient origin. The key defining characteristics of the "negrito" phenotype, small body size, dark skin, and tightly curled hair, have been interpreted as linking these populations to sub-Saharan Africans. The underlying assumption of this interpretation is that the observed phenotypic similarities likely reflect shared ancestry rather than phenotypic convergence. Current genetic evidence is inconclusive, as it both demonstrates that negrito populations have genetic affinities with neighboring populations but also rare and ancient variation that suggests considerable isolation. This study investigates the skeletal phenotype of Andaman Islanders and Aeta foragers from the Philippines in the context of the phenotypic variation among other hunter-gatherers globally, to test whether they show a common, unique physique apart from small body size. Particular emphasis is placed on the comparison of negrito phenotypes to African, Asian, and Australian hunter-gatherer diversity to investigate phenotypic similarities to other populations globally. The results demonstrate that despite sharing small adult stature, the Andaman Islanders and Aeta show variation in body dimensions. In particular, the Andaman Islanders share a pattern of narrow bi-iliac breadth and short upper limbs with the Khoisan (Later Stone Age Southern Africans), whereas the Aeta and Efé show broader bi-iliac breadths relative to lower limb lengths. Although general similarities in size and proportions remain between the Andamanese and Aeta, differences in humero-femoral indices and arm length between these groups and the Efé demonstrate that there is not a generic "pygmy" phenotype. Our interpretations of negrito origins and adaptation must account for this phenotypic variation.

KCNS1, but Not GCH1, Is Associated With Pain Intensity in a Black Southern African Population With HIV-Associated Sensory Neuropathy

KCNS1 and GCH1 were investigated for their association with pain intensity in black Southern Africans with HIV-associated sensory neuropathy. Previously associated single nucleotide polymorphisms (SNPs) were supplemented with population-specific tagSNPs. No SNPs in KCNS1 were individually associated with pain intensity. However, several haplotypes of population-specific tagSNPs correlated with pain intensity on univariate analysis and after correcting for age, gender, and CD4 T-cell count. This suggests that the haplotypes incorporate the causative SNP(s). No SNPs or haplotypes in GCH1 were associated with pain intensity. The study shows the importance of conducting association analyses in different ethnic groups, using population-based marker selection.

THE WEIGHT OF SUCCESS: THE BODY MASS INDEX AND ECONOMIC WELL-BEING IN SOUTHERN AFRICA.

We show that body mass increases with economic resources among most Southern Africans, although not all. Among Black South Africans the relationship is non-decreasing over virtually the entire range of incomes/wealth. Furthermore in this group other measures of "success" (e.g., employment and education) are also associated with increases in body mass. This is true in both 1998 (the Demographic and Health Survey) and 2008 (National Income Dynamics Survey). A similar relationship holds among residents of Lesotho, Swaziland, Mozambique, Malawi, and Namibia. This suggests that body mass can be used as a crude measure of well-being. This allows us to examine the vexed question in South African labor economics whether there is involuntary unemployment. The fact that the unemployed are lighter than the employed, even when we control for household fixed effects, suggests that they are not choosing this state.

Polymorphisms in uncoupling protein genes UCP2 and UCP3 are not associated with HIV‐associated sensory neuropathy in African individuals

Dear Editor,Human immunodeficiency virus-associated sen-sory neuropathy (HIV-SN), due to viral and/or drug-related toxicity, is the most common neurologicalcomplication of HIV (Sacktor, 2002) and causes sig-nificant suffering and reduced quality of life (Ellis et al.,2010). The neuropathy shares several features withdiabetic neuropathy, for example, both HIV-SN anddiabetic neuropathy are small-fibre, length-dependentneuropathies that are associated with mitochondrialdysfunction and intracellular calcium dysregulation(Verkhratsky and Fernyhough, 2008; Hoke et al., 2009;Lehmann et al., 2011).Recently, minor alleles in the genes encodingmitochondrial uncoupling proteins UCP2(rs659366*A,-866G

Extreme mobility in the Late Pleistocene? Comparing limb biomechanics among fossil Homo, varsity athletes and Holocene foragers

Descriptions of Pleistocene activity patterns often derive from comparisons of long bone diaphyseal robusticity across contemporaneous fossilized hominins. The purpose of this study is to augment existing understanding of Pleistocene hominin mobility patterns by interpreting fossil variation through comparisons with a) living human athletes with known activity patterns, and b) Holocene foragers where descriptions of group-level activity patterns are available. Relative tibial rigidity (midshaft tibial rigidity (J)/midshaft humeral rigidity (J)) was compared amongst Levantine and European Neandertals, Levantine and Upper Palaeolithic Homo sapiens, Holocene foragers and living human athletes and controls. Cross-country runners exhibit significantly (p < 0.05) greater relative tibial rigidity compared with swimmers, and higher values compared with controls. In contrast, swimmers displayed significantly (p < 0.05) lower relative tibial rigidity than both runners and controls. While variation exists among all Holocene H. sapiens, highly terrestrially mobile Later Stone Age (LSA) southern Africans and cross-country runners display the highest relative tibial rigidity, while maritime Andaman Islanders and swimmers display the lowest, with controls falling between. All fossil hominins displayed relative tibial rigidity that exceeded, or was similar to, the highly terrestrially mobile Later Stone Age southern Africans and modern human cross-country runners. The more extreme skeletal structure of most Neandertals and Levantine H. sapiens, as well as the odd Upper Palaeolithic individual, appears to reflect adaptation to intense and/or highly repetitive lower limb (relative to upper limb) loading. This loading may have been associated with bipedal travel, and appears to have been more strenuous than that encountered by even university varsity runners, and Holocene foragers with hunting grounds 2000–3000 square miles in size. Skeletal variation among the athletes and foraging groups is consistent with known or inferred activity profiles, which support the position that the Pleistocene remains reflect adaptation to extremely active and mobile lives.

The Skeletal Phenotype of “Negritos” from the Andaman Islands and Philippines Relative to Global Variation among Hunter-Gatherers

The “negrito hypothesis” suggests that populations of small-bodied foragers in South and Southeast Asia who share common phenotypic characteristics may also share a common, ancient origin. The key defining characteristics of the “negrito” phenotype, small body size, dark skin, and tightly curled hair, have been interpreted as linking these populations to sub-Saharan Africans. The underlying assumption of this interpretation is that the observed phenotypic similarities likely reflect shared ancestry rather than phenotypic convergence. Current genetic evidence is inconclusive, as it both demonstrates that negrito populations have genetic affinities with neighboring populations but also rare and ancient variation that suggests considerable isolation. This study investigates the skeletal phenotype of Andaman Islanders and Aeta foragers from the Philippines in the context of the phenotypic variation among other hunter-gatherers globally, to test whether they show a common, unique physique apart from small body size. Particular emphasis is placed on the comparison of negrito phenotypes to African, Asian, and Australian hunter-gatherer diversity to investigate phenotypic similarities to other populations globally. The results demonstrate that despite sharing small adult stature, the Andaman Islanders and Aeta show variation in body dimensions. In particular, the Andaman Islanders share a pattern of narrow bi-iliac breadth and short upper limbs with the Khoisan (Later Stone Age Southern Africans), whereas the Aeta and Efé show broader bi-iliac breadths relative to lower limb lengths. Although general similarities in size and proportions remain between the Andamanese and Aeta, differences in humero-femoral indices and arm length between these groups and the Efé demonstrate that there is not a generic “pygmy” phenotype. Our interpretations of negrito origins and adaptation must account for this phenotypic variation.

Genotyping and Molecular Characterization of Hepatitis B Virus from Human Immunodeficiency Virus-Infected Individuals in Southern Africa

Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) are hyperendemic in sub-Saharan Africa. The HBV genotypes prevailing in HIV-infected Africans are unknown. Our aim was to determine the HBV genotypes in HIV-infected participants and to identify clinically significant HBV mutations. From 71 HBV DNA+ve HIV-infected participants, 49 basic core promoter/precore (BCP/PC) and 29 complete S regions were successfully sequenced. Following phylogenetic analysis of 29 specimens in the complete S region, 28 belonged to subgenotype A1 and one to D3. Mutations affecting HBeAg expression at the transcriptional (1762T1764A), translational (Kozak 1809–1812, initiation 1814–1816, G1896A with C1858T), or post translational levels (G1862T), were responsible for the high HBeAg-negativity observed. The G1862T mutation occurred only in subgenotype A1 isolates, which were found in one third (7/21) of HBsAg−ve participants, but in none of the 18 HBsAg+ve participants (p<0.05). Pre-S deletion mutants were detected in four HBsAg+ve and one HBsAg−ve participant/s. The following mutations occurred significantly more frequently in HBV isolated in this study than in strains of the same cluster of the phylogenetic tree: ps1F25L, ps1V88L/A; ps2Q10R, ps2 R48K/T, ps2A53V and sQ129R/H, sQ164A/V/G/D, sV168A and sS174N (p<0.05). ps1I48V/T occurred more frequently in females than males (p<0.05). Isolates with sV168A occurred more frequently in participants with viral loads >200 IU per ml (p<0.05) and only sS174N occurred more frequently in HBsAg−ve than in HBsAg+ve individuals (p<0.05). Prior to initiation of ART, ten percent, 3 of 29 isolates sequenced, had drug resistance mutations rtV173L, rtL180M+rtM204V and rtV214A, respectively. This study has provided important information on the molecular characteristics of HBV in HIV-infected southern Africans prior to ART initiation, which has important clinical relevance in the management of HBV/HIV co-infection in our unique setting.

How to Do Things with Land: A Distributive Perspective on Rural Livelihoods in Southern Africa

Discussions on land use and land reform too often reduce the land question to the agrarian question. Yet a rich empirical literature in the region shows that producing agricultural goods is really only one of many, many ways in which land is used, and not necessarily the most important. This paper argues that many of the ways in which land is used (often labelled ‘social’ or ‘cultural’) are in fact best understood as part of processes of distribution that are a vital part of many poor Southern Africans' livelihoods. An exclusive focus on production as the problem, and more productive agriculture as the solution, blinds us both to most of the things that people, in fact, do with land, and to many of the most important issues facing low‐income rural people. Giving a more central place to processes of distribution may help us to see just how much is lost if we allow distribution to be treated as an afterthought to production – or the land question to be reduced to the agrarian question.

Genomic variation in seven Khoe-San groups reveals adaptation and complex African history.

The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ~2.3 million single-nucleotide polymorphisms in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but population structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response; potential adaptive introgression of protection from ultraviolet light; and selection predating modern human diversification, involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history.

Analysis of a Previously Identified “Pain-Protective” Haplotype and Individual Polymorphisms in the GCH1 Gene in Africans With HIV-Associated Sensory Neuropathy

We analyzed GTP cyclohydrolase 1 in symptomatic HIV-associated sensory neuropathy in Southern Africans including a "pain-protective" 3-SNP haplotype and 6 SNPs, analyzed individually and in a 6-SNP haplotype. The "pain-protective" 3-SNP haplotype and a 6-SNP haplotype containing these alleles associated with a reduced risk of pain. Another 3-SNP haplotype associated with increased presence of pain. Associations were lost after correction for age, gender, and CD4 T-cell count. Linkage disequilibrium differed between our cohort and Caucasians suggesting that these SNPs may not be ideal markers in Africans. Subsequently, the role of GTP cyclohydrolase 1 in painful HIV-associated sensory neuropathy remains possible.

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.

Northern Africa could also have housed the source population for living humans

Henn et al. (1) analyzed genetic diversity in extant African populations, including hunter-gatherers, and showed that indigenous hunter-gatherers in the Kalahari Desert have the longest population history, extending to 40,000 y ago or before. From this, Henn et al. (1) concluded that the source population for modern humans, including the group that expanded from Africa to Eurasia roughly 60,000 y ago, resided in southern Africa. There is the complication, however, that the dramatic climatic fluctuations of the late Pleistocene forced population redistributions, and this means that the ancestors of historic Kalahari hunter-gatherers could have lived elsewhere in Africa 60,000 y ago. They might subsequently have spread to replace preexisting southern Africans just as they spread to replace the Neanderthals and other preexisting Eurasians.

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-1angiotensin II receptor (AGTR1). We propose that the candidate genes identified in this study warrant further investigation as potential aetiological genes for salt-sensitive hypertension.

Humans: Bushmen have more diversity: Study of southern Africans finds genetic treasure trove

Science NewsVolume 177, Issue 6 p. 16-16 In The News Humans: Bushmen have more diversity: Study of southern Africans finds genetic treasure trove Tina Hesman Saey, Tina Hesman SaeySearch for more papers by this author Tina Hesman Saey, Tina Hesman SaeySearch for more papers by this author First published: 02 March 2010 https://doi.org/10.1002/scin.5591770615AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume177, Issue613 March 2010Pages 16-16 RelatedInformation

Complete Khoisan and Bantu genomes from southern Africa

The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.

What Can Archaeology Do for Society in Southern Africa?

In response to Barbara Little, I present a southern African perspective, sharing issues of mutual concern on how archaeology can be of service to society. How archaeology relates to indigenous communities, however defined, remains critical the world over, the main prob lem being archaeologists' treatment of cultural treasures including human remains of, or found in or among those communities. It is ironic that even here in southern Africa, South Africa in particular, archaeologists have failed to articulate the relevance of their own discipline to society, despite the region being replete with evidence for humanity's origins, and historical dynamics of social identities formed during the past half millennia. Archaeology still carries a bad image, often associated with desecration of sacred places including burials. To the majority of southern Africans, its usefulness is limited to knowledge production which only benefits archaeologists. Government authorities are distrustful of archae

Sexual networks and social capital: multiple and concurrent sexual partnerships as a rational response to unstable social networks

Multiple and concurrent sexual partnerships (MCP) are prevalent in southern Africa and have been identified as a primary cause of high HIV prevalence in this region. Sexual liaisons with multiple partners serve to increase the size and diversity of an individual's sexual—and social—network and therefore to increase their social capital. This maximisation of social capital may minimise the risk to relationship(s) at the cost of maximising the biological risk of HIV infection. Many sexually active individuals appear to neglect their biological risk of HIV infection in order to maximise their ‘social capital.’ This would seem to be irrational from the perspective of any individual actor, but on a larger social scale, this may give individuals better access to some social and economic goods. The article argues that people who are in unstable and less-connected parts of the sexual network are those most active in building their sexual networks, even where they are not especially promiscuous. However, such strategies may increase exposure to HIV infection in particular populations, such as intravenous drug users, sex workers, and men having sex with men, as well as in the general population of heterosexual southern Africans. What these high HIV-prevalence populations have in common is their participation in sexual-social networks in which individuals try to maximise their social capital by extending the diversity and density of their sexual networks. The discussion shifts analytic attention away from the notion of higher-risk sexual practices of individuals towards consideration for the structure and dynamics of social and sexual networks at a societal level.

Brief communication: The distribution of perikymata on Qafzeh anterior teeth

Recent studies have suggested that Neandertals and modern humans differ in the distribution of perikymata (enamel growth increments) over their permanent anterior tooth crowns. In modern humans, perikymata become increasingly more compact toward the cervix than they do in Neandertals. Previous studies have suggested that a more homogeneous distribution of perikymata, like that of Neandertals, characterizes the anterior teeth of Homo heidelbergensis and Homo erectus as well. Here, we investigated whether Qafzeh anterior teeth (N = 14) differ from those of modern southern Africans, northern Europeans, and Alaskans (N = 47-74 depending on tooth type) in the percentage of perikymata present in their cervical halves. Using the normally distributed modern human values for each tooth type, we calculated Z-scores for the 14 Qafzeh teeth. All but two of the 14 Qafzeh teeth had negative Z-scores, meaning that values equal to these would be found in the bottom 50% of the modern human samples. Seven of the 14 would be found in the lowest 5% of the modern human distribution. Qafzeh teeth therefore appear to differ from those of modern humans in the same direction that Neandertals do: with generally lower percentages of perikymata in their cervical regions. The similarity between them appears to represent the retention of a perikymata distribution pattern present in earlier members of the genus Homo, but not generally characteristic of modern humans from diverse regions of the world.

Writing in the San/d: Autoethnography among Indigenous Southern Africans. Keyan G. Tomaselli

<i>Writing in the San/d: Autoethnography among Indigenous Southern Africans</i>. Keyan G. Tomaselli

Remembering the Khoikhoi victory over Dom Francisco Almeida at the Cape in 1510

The general issue of how key moments of anti-colonial struggle are remembered in different colonial and postcolonial contexts is considered in relation to the specific case of the Khoikhoi victory over Viceroy Francisco Almeida in Table Bay on 1 March 1510. The contrasting literary and historical versions of the Khoikhoi victory are examined in three contexts: first, in the sixteenth-century Portuguese writings of the poet Luis Vaz de Camões and the chroniclers João de Barros, Fernão Lopez de Castanheda, Damião de Goís and Gaspar Correa; secondly, in the writings of British intellectuals of the period 1770–1830, including Robert Southey, William Julius Mickle and William Robertson; and thirdly, in the writings of nineteenth- and twentieth-century Southern Africans, including historian George McCall Theal, novelist André Brink and South African president Thabo Mbeki.