Southern African Populations Research Articles

Adaptation to infectious disease exposure in indigenous Southern African populations.

Genetic analyses can provide information about human evolutionary history that cannot always be gleaned from other sources. We evaluated evidence of selective pressure due to introduced infectious diseases in the genomes of two indigenous southern African San groups-the ‡Khomani who had abundant contact with other people migrating into the region and the more isolated Ju|'hoansi. We used a dual approach to test for increased selection on immune genes compared with the rest of the genome in these groups. First, we calculated summary values of statistics that measure genomic signatures of adaptation to contrast selection signatures in immune genes and all genes. Second, we located regions of the genome with extreme values of three selection statistics and examined these regions for enrichment of immune genes. We found stronger and more abundant signals of selection in immune genes in the ‡Khomani than in the Ju|'hoansi. We confirm this finding within each population to avoid effects of different demographic histories of the two populations. We identified eight immune genes that have potentially been targets of strong selection in the ‡Khomani, whereas in the Ju|'hoansi, no immune genes were found in the genomic regions with the strongest signals of selection. We suggest that the more abundant signatures of selection at immune genes in the ‡Khomani could be explained by their more frequent contact with immigrant groups, which likely led to increased exposure and adaptation to introduced infectious diseases.

Genetic and Morphological Variation in Non-Polyphenic Southern African Populations of the Desert Locust

This study addresses geographic variation of body size and shape and of allele frequencies at 21 microsatellite loci in southern African populations of the desert locust, Schistocerca gregaria. These populations, which belong to the subspecies S. g. flaviventris, lack the capacity to change phase and to swarm relative to the northern populations of the nominate subspecies, S. g. gregaria. We reported overall genetic and morphological similarities among localities that cover most of the subspecies range. Of particular interest, the level of genetic diversity was moderately lower than in the swarming subspecies of the northern range. In addition, S. g. flaviventris populations were genetically homogeneous, such as observed in the northern range of the nominate subspecies. This result can be explained by north—southwest seasonal migration to follow rainfall.

Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.

Beta-globin gene haplotypes and selected Malaria-associated variants among black Southern African populations.

Partial carrier-resistance to Plasmodium falciparum malaria conferred by the sickle cell (HbS) mutation has resulted in the local amplification and positive selection of sickle cell disease (SCD) in malaria-endemic regions and particularly in sub-Saharan Africa (SSA). The present study investigated the β-globin gene haplotypes, and selected malaria-associated variants among three cohorts of Bantu-speaking individuals from Malawi, Zimbabwe and South Africa compared with reports with data from others SSA populations. The data suggest a south-ward frequency decrease of malaria-associated variants in SSA linked to the evolutionary dynamics of various African populations' genomes through selective pressure of malaria. These selected genomics differences, positive selection of SCD in malaria-endemic regions among 'Bantus' from various part of Africa emphasise the evidence of the dissociation between genetics, anthropology and culture. The present study also showed a relatively prevalent Benin haplotype, which is mostly found in West Africa, among Southern African Blacks and very low Bantu haplotype, which could suggest a major migration route, of Southern Africa Bantu, along the African west coast, post-occurrence of the Sickle cell mutation, which date remain to be fully elucidated.

Potential of Sugarcane in Modern Energy Development in Southern Africa

For more than half of the Southern African population, human development is limited by a lack of access to electricity and modern energy for cooking. Modern bioenergy merits consideration as one means to address this situation in areas where sufficient arable land is available. While numerous studies have concluded that Africa has significant biomass potential, they do not indicate by how much it can effectively reduce the use of traditional biomass and provide more accessible energy, especially at a country level. Here, we evaluate the potential of sugarcane to replace traditional biomass and fossil fuel, and enlarge the access to electricity in Southern Africa. By using its current molasses for ethanol production, Swaziland could increase electricity generation by 40% using bagasse, and replace 60% of cooking fuel or 30% of liquid fossil fuel. Sugarcane expansion over 1% of the pasture land in Angola, Mozambique, and Zambia could replace greater than 70% of cooking fuel. Bioelectricity generation from modest sugarcane expansion could be increased by 10% in Malawi, Mozambique and Zambia, and by 20% in Angola. Our results support the potential of sugarcane as a modern energy alternative for Southern Africa.

Restriction to gene flow is associated with changes in the molecular basis of pyrethroid resistance in the malaria vector Anopheles funestus

Resistance to pyrethroids, the sole insecticide class recommended for treating bed nets, threatens the control of major malaria vectors, including Anopheles funestus Effective management of resistance requires an understanding of the dynamics and mechanisms driving resistance. Here, using genome-wide transcription and genetic diversity analyses, we show that a shift in the molecular basis of pyrethroid resistance in southern African populations of this species is associated with a restricted gene flow. Across the most highly endemic and densely populated regions in Malawi, An. funestus is resistant to pyrethroids, carbamates, and organochlorides. Genome-wide microarray-based transcription analysis identified overexpression of cytochrome P450 genes as the main mechanism driving this resistance. The most up-regulated genes include cytochrome P450s (CYP) CYP6P9a, CYP6P9b and CYP6M7. However, a significant shift in the overexpression profile of these genes was detected across a south/north transect, with CYP6P9a and CYP6P9b more highly overexpressed in the southern resistance front and CYP6M7 predominant in the northern front. A genome-wide genetic structure analysis of southern African populations of An. funestus from Zambia, Malawi, and Mozambique revealed a restriction of gene flow between populations, in line with the geographical variation observed in the transcriptomic analysis. Genetic polymorphism analysis of the three key resistance genes, CYP6P9a, CYP6P9b, and CYP6M7, support barriers to gene flow that are shaping the underlying molecular basis of pyrethroid resistance across southern Africa. This barrier to gene flow is likely to impact the design and implementation of resistance management strategies in the region.

Kalahari vulture declines, through the eyes of meerkats

Vulture populations are experiencing rapid declines across the globe. While the declines have been most precipitous in Asia, recent reports suggest African populations are likewise imminently threatened. As the factors underlying these general population trends are multifaceted and will vary in their relative intensity spatially, it is imperative that monitoring data across different vulture populations is assimilated if targeted conservation action is to prove most effective. In this study, we highlight a medium-term decline in the African White-backed Vulture Gyps africanus population inhabiting the southern Kalahari, South Africa, using a long-term behavioural data set collected from a habituated population of meerkats Suricata suricatta. Meerkats emit an alarm call on sighting airborne vultures, which elicits a group-level response, such that the rates at which this behaviour is recorded in meerkats provides a high-resolution proxy for local vulture abundance. Although unconventional, this sampling method uncovered a steady decline over 17 years in White-backed Vulture numbers that mirrors the temporal decline recently documented in other southern African populations.

HTLV-1aA introduction into Brazil and its association with the trans-Atlantic slave trade

IntroductionHuman T-lymphotropic virus (HTLV) is an endemic virus in some parts of the world, with Africa being home to most of the viral genetic diversity. In Brazil, HTLV-1 is endemic amongst Japanese and African immigrant populations. Multiple introductions of the virus in Brazil from other epidemic foci were hypothesized. The long terminal repeat (LTR) region of HTLV-1 was used to infer the origin of the virus in Brazil, using phylogenetic analysis. MethodsLTR sequences were obtained from the HTLV-1 database (http://htlv1db.bahia.fiocruz.br). Sequences were aligned and maximum-likelihood and Bayesian tree topologies were inferred. Brazilian specific clusters were identified and molecular-clock and coalescent models were used to estimate each cluster's time to the most recent common ancestor (tMRCA). ResultsThree Brazilian clusters were identified with a posterior probability ranged from 0.61 to 0.99. Molecular clock analysis of these three clusters dated back their respective tMRCAs between the year 1499 and the year 1668. Additional analysis also identified a close association between Brazilian sequences and new sequences from South Africa. ConclusionOur results support the hypothesis of a multiple introductions of HTLV-1 into Brazil, with the majority of introductions occurring in the post-Colombian period. Our results further suggest that HTLV-1 introduction into Brazil was facilitated by the trans-Atlantic slave trade from endemic areas of Africa. The close association between southern African and Brazilian sequences also suggested that greater numbers of the southern African Bantu population might also have been part of the slave trade than previously thought.

The influence of ApoE genotype on the lipid profile and lipoproteins during normal pregnancy in a Southern African population.

Pregnancy is associated with increases in fasting triglycerides and total cholesterol.1 ApoE isoforms are known to influence the concentration of cholesterol, with apoE2 homozygosity lowering and apoE4 homozygosity raising the cholesterol concentration compared with E3 homozygosity.2 The lipid profiles ApoE status and prevalence of small dense LDL species were evaluated for subjects attending an antenatal clinic. Samples from 690 women aged between 16 and 42 years of age were analyzed during and after pregnancy. The fasting plasma triglyceride concentration (in mmol/L) was significantly higher in pregnancy (median = 1.5, IQR 1.0-2.0 vs median = 0.6, IQR 0.5-0.8 respectively, p < 0.0001). Similarly, the total cholesterol (in mmol/L) was increased during pregnancy (median=4.1, IQR 3.6-4.7 vs median 3.5, IQR 3.1-3.5, respectively p=0.0167). The median LDL cholesterol and HDL cholesterol did not change. Higher proportions of small density LDL species were seen during pregnancy compared to after pregnancy. The distribution of the LDL species during pregnancy and 6 weeks post-partum were significantly different p<0.0001 with the smaller species being much higher during pregnancy. ApoE4 genotype was associated with increased total cholesterol and LDL cholesterol concentrations during pregnancy. Pregnancy results in a reversible remodeling of LDL to smaller species, the significance of which is unknown but may indicate a predisposition to atherosclerosis.

Discontinuities in ethnographic time: A view from Africa

While there is evidence of discontinuities in the sequences of some archaeological sites that exhibit long-term occupation and use over time in southern Africa, there is less evidence of such discontinuity in the ethnographic record. Drawing on long-term interdisciplinary studies of southern African peoples in the Kalahari Desert, this paper examines the evidence of discontinuities in the historical and ethnographic records. Attention is focused primarily on two southern African San populations for which detailed diachronic data exist: (1) the Ju/’hoansi of northwestern Kalahari, and (2) the !Xóõ San of the southwestern Kalahari region of Botswana and Namibia. From an ethnographer’s perspective it might at first appear as though there was a fair amount of continuity in the Kalahari. It is shown, however, that there have been complex changes over time in the period from 1850 to the present, which occurred as a result of a combination of factors, including short-term and long-term ecological changes, in-migration and out-migration of various groups, cycles of population growth and decline, colonization, technological shifts, and implementation of development and conservation programs. The two cases illustrate the complex ways that activities, mobility, technology, land use, and demographic patterns can change over time as a result of both internal and external forces, resulting in discontinuities in the ethnographic record.

Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries.

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 ∼2000 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 >100 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, ∼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.

Food and pathogen adaptations in the Angolan Namib desert: Tracing the spread of lactase persistence and human African trypanosomiasis resistance into southwestern Africa.

We investigated the frequency distribution and haplotype diversity of human African trypanosomiasis (HAT) resistance and lactase persistence (LP) variants in populations from the Angolan Namib to trace the spread of these genetic adaptations into southwestern Africa. We resequenced two fragments of the LCT enhancer and the APOL1 gene and genotyped flanking short tandem repeat loci in six groups with different subsistence traditions living in the Angolan Namib, and in a comparative dataset including other populations from Africa and Europe. LP in the Angolan Namib is represented by the -14010*C allele, which is associated with a predominant haplotype that is shared with other southern and eastern African populations. While LP was found to be more frequent in foragers than in pastoralists, the frequencies of the two APOL1 variants associated with HAT-resistance (G1 and G2) did not differ between the two groups. The G1 allele is mostly associated with a single widespread haplotype. The G2 allele is linked to several haplotypes that are molecularly related to haplotypes found in other African Bantu-speaking populations. The putatively archaic G3 variant displayed more intra-allelic diversity in Africa than in Europe. The LP adaptation was carried to southern Africa by non-Bantu speaking pastoralists from eastern Africa, but an obvious link between its presence in southern Angola and groups speaking languages of the Khoe-Kwadi family, as previously found in other areas, could not be confirmed. The presence of APOL1 variants G1 and G2 is linked to the Bantu expansions. Our results suggest that the G3 variant was retained in modern humans by incomplete lineage sorting.

Approaches to Middle Stone Age landscape archaeology in tropical Africa

The Southern Montane Forest-Grassland mosaic ecosystem in the humid subtropics southern Rift Valley of Africa comprised the environmental context for a large area in which modern human evolution and dispersal occurred. Variable climatic conditions during the Late Pleistocene have ranged between humid and hyperarid, changing the character of the ecosystem and transforming it at different points in time into a barrier, a refuge, and a corridor between southern and eastern African populations. Alluvial fans presently blanket the areas adjacent to major river systems, which were key areas of prehistoric human habitation. These sets of variables have created conditions that are both challenging and advantageous to conduct archaeological research. Lateritic soil development has resulted in poor organic preservation and facilitated insect bioturbation, which has demanded an integrated micro-macro scale approach to building a reliable geochronology. An integrated field and analytical methodology has also been employed to identify the nature and degree of post-depositional movement in alluvial deposits, which preserve a wide range of spatial integrity levels in buried stone artifact assemblages between 47 and 30 ka in Karonga, northern Malawi. This paper describes the methodological advances taken toward understanding open-air Middle Stone Age archaeology in sub-tropical Africa, and explores the inferential potential for understanding Pleistocene human ecology in the important southern Rift Valley region.

Novel APOB missense variants, A224T and V925L, in a black South African woman with marked hypocholesterolemia

One genetic cause of markedly low plasma concentrations of apolipoprotein (apo) B and low density lipoprotein (LDL)-cholesterol is familial hypobetalipoproteinemia. We aimed to determine the molecular basis for the marked hypocholesterolemia consistent with heterozygous familial hypobetalipoproteinemia in a black female subject of Xhosa lineage. Coding regions of APOB, MTTP, PCSK9,ANGPTL3, SAR1B and APOC3 were sequenced, and APOE was genotyped. COS-7 cells were transfected with plasmids containing apoB variants. Western blotting was used to detect cellular and secreted apoB, and co-immunoprecipitation performed to assess binding with the microsomal triglyceride transfer protein (MTP). Sequence analysis of the APOB gene revealed her to be heterozygous for two novel variants, c.751G>A (A224T) and c.2854G>C (V925L). She was also homozygous for the APOEε2 allele, and did not carry a PCSK9 loss-of-function mutation. Although Ala(224) is within the postulated MTP binding region in apoB, it is not conserved among mammalian species. Subsequent genotyping showed that Ala224Thr is found in a southern African population (n=654) with an allele frequency of 1.15% and is not associated with plasma lipid levels. Val(925), like Ala(224), is within the N-terminal 1000 amino acids required for lipoprotein assembly, but was not found in the population screen. However, in vitro studies showed that apoB V925L did not affect apoB48 production or secretion nor have a deleterious effect on MTP interaction with apoB. Taken together, this suggests that the hypocholesterolemia in our case may be a result of being homozygous for APOEε2 with a low baseline cholesterol.

Phylogeography and genealogy of the tsetse fly Glossina pallidipes (Diptera: Glossinidae)

Glossina pallidipes, a widely but discontinuously distributed African savanna species, is one of the economically important tsetse flies because it is a vector of trypanosomiasis, a lethal disease of cattle and other domestic animals. DNA sequences of ribosomal (r16S2, 249 bp) and cytochrome oxidase I (COI, 421 bp) concatenated mitochondrial genes were analysed in 23 geographically diverse samples ofG. pallidipesfrom Ethiopia, Kenya, Tanzania, Zambia and Zimbabwe. Among 873 flies, we detected 181 composite haplotypes and found that their spatial diversities and frequency distributions were heterogeneous. Haplotype and nucleotide diversities were greatest in Ethiopia and least in southern Africa. We observed little haplotype and nucleotide diversity among regions, and detected severely limited maternal gene flow among the sampled populations (ΦST= 0.42). Tests for demographic stability and analysis of mismatch distributions revealed regionally contrasting demographic histories. The Ethiopian populations were phylogenetically the oldest and genetically the most diverse, and exhibited successive waves of contraction and expansion. The southern African populations were phylogenetically the youngest and genetically the least diverse, and showed only a single, recent expansion. Likely ecological correlates of historical tsetse fly demography include population suppression trials in East Africa and recurring rinderpest epizootics in southern Africa, beginning in the late nineteenth century that reduced host mammalian populations.

Large Scale Genetic Research on Neuropsychiatric Disorders in African Populations is Needed

Large Scale Genetic Research on Neuropsychiatric Disorders in African Populations is Needed

Implications of spatial genetic patterns for conserving African leopards

The leopard (Panthera pardus) is heavily persecuted in areas where it predates livestock and threatens human well-being. Attempts to resolve human–leopard conflict typically involve translocating problem animals; however, these interventions are rarely informed by genetic studies and can unintentionally compromise the natural spatial genetic structure and diversity, and possibly the long-term persistence, of the species. No significant genetic discontinuities were definable within the southern African leopard population. Analysis of fine-scale genetic data derived from mitochondrial and nuclear DNA revealed that the primary natural process shaping the spatial genetic structure of the species is isolation-by-distance (IBD). The effective gene dispersal (σ) index can inform leopard translocations and is estimated to be 82km for some South African leopards. The importance of adopting an evidence-based strategy is discussed for supporting the integration of genetic data, spatial planning and social learning institutions so as to promote collaboration between land managers, government agency staff and researchers.

Morphological variations in southern African populations of Myriophyllum spicatum: Phenotypic plasticity or local adaptation?

Variability in aquatic plant morphology is usually driven by phenotypic plasticity and local adaptations to environmental conditions experienced. This study aimed to elucidate which of these drivers is responsible for the morphological variation exhibited by three populations of Myriophyllum spicatum L. (Haloragaceae), a submerged aquatic plant whose status as native or exotic within southern Africa is uncertain. Individuals from three populations on the Vaal River (Northern Cape), Klipplaat River (Eastern Cape) and Lake Sibaya (KwaZulu-Natal) were grown under two nutrient treatments (high: 30mgN/kg sediment and low: sediment only), while all other variables were kept the same. Morphological characteristics were measured at the start of the experiment to obtain a baseline morphology, and again eight weeks later. By the end of the experiment, the individuals from each population had responded to the different growing conditions. In most cases, the individuals from each population were significantly larger under the high nutrient treatment (Stem diameter: F(5,86)=18.435, P<0.001, Internode length: F(5,86)=5.0747, P<0.001, Leaf length: F(5,86)=19.692, P<0.001). Despite these differences in nutrient treatments, the growth pattern of each population remained true to the original starting point indicated by the lack of overlap between populations in the PCA groupings. This suggests that local adaptations are responsible for the differences in morphology between populations of M. spicatum, but shows that phenotypic plasticity does play a role as evidenced by individual responses to the different nutrient conditions. The development of these local adaptations within southern Africa suggests that the populations have had a long evolutionary history in the region and are relatively isolated with little reproductive mixing.

Ecological Genetics and Host Range Expansion by Busseola fusca (Lepidoptera: Noctuidae).

The host plant range of pests can have important consequences for its evolution, and plays a critical role in the emergence and spread of a new pest outbreak. This study addresses the ecological genetics of the indigenous African maize stem borer, Busseola fusca (Fuller) (Lepidoptera: Noctuidae), in an attempt to investigate the evolutionary forces that may be involved in the recent host range expansion and establishment of this species in Ethiopian and southern African sugarcane. We used populations from Ethiopia, Zimbabwe, and South Africa to examine whether the host range expansion patterns shared by the Ethiopian and the southern African populations of B. fusca have evolved independently. Base-pair differences in the cytochrome oxidase I (COI) gene were used to characterize haplotype diversity and phylogenetic relationships. There were seven haplotypes among the 30 sequenced individuals collected on four host plant species from 17 localities in the four countries. Of the seven COI haplotypes identified, the two major ones occurred in both sugarcane and maize. Genetic analyses revealed no detectable genetic differentiation between southern African B. fusca populations from maize and sugarcane (FST = 0.019; P = 0.24). However, there was strong evidence of variation in genetic composition between populations of the pest from different geographic regions (FST = 0.948; P < 0.001). The main implication of these findings is that the B. fusca populations in maize in southern Africa are more likely to shift to sugarcane, suggesting that ecological opportunity is an important factor in host plant range expansion by a pest.

Understanding the Implications of Mitochondrial DNA Variation in the Health of Black Southern African Populations: The 2014 Workshop.

Understanding the Implications of Mitochondrial DNA Variation in the Health of Black Southern African Populations: The 2014 Workshop.