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

Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry

Ancient DNA studies reveal the genetic structure of Africa before the expansion of Bantu-speaking agriculturalists; however, the impact of now extinct hunter-gatherer and herder societies on the genetic makeup of present-day African groups remains elusive. Here, we uncover the genetic legacy of pre-Bantu populations from the Angolan Namib Desert, where we located small-scale groups associated with enigmatic forager traditions, as well as the last speakers of the Khoe-Kwadi family's Kwadi branch. By applying an ancestry decomposition approach to genome-wide data from these and other African populations, we reconstructed the fine-scale histories of contact emerging from the migration of Khoe-Kwadi-speaking pastoralists and identified a deeply divergent ancestry, which is exclusively shared between groups from the Angolan Namib and adjacent areas of Namibia. The unique genetic heritage of the Namib peoples shows how modern DNA research targeting understudied regions of high ethnolinguistic diversity can complement ancient DNA studies in probing the deep genetic structure of the African continent.

Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe

BACKGROUND

While the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood. To gain better insights into the general composition of the microbiome on a global scale, the characterization of microbiomes from a broad range of populations, including non-industrialized societies, is needed. Here, we used the portion of non-human reads obtained through an expanded exome capture sequencing approach to characterize the saliva microbiomes of 52 individuals from eight ethnolinguistically diverse southern African populations from Angola (Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, !Xun) and Zimbabwe (Tshwa), including foragers, food-producers, and peripatetic groups (low-status communities who provide services to their dominant neighbors).

RESULTS

Our results indicate that neither host genetics nor livelihood seem to influence the oral microbiome profile, with Neisseria, Streptococcus, Prevotella, Rothia, and Porphyromonas being the five most frequent genera in southern African groups, in line with what has been shown for other human populations. However, we found that some Tshwa and Twa individuals display an enrichment of pathogenic genera from the Enterobacteriaceae family (i.e. Enterobacter, Citrobacter, Salmonella) of the Proteobacteria phylum, probably reflecting deficient sanitation and poor health conditions associated with social marginalization.

CONCLUSIONS

Taken together, our results suggest that socio-economic status, rather than ethnolinguistic affiliation or subsistence mode, is a key factor in shaping the salivary microbial profiles of human populations in southern Africa.

Advances in Low-Lactose/Lactose-Free Dairy Products and Their Production

With increasing health awareness worldwide, lactose intolerance has become a major concern of consumers, creating new market opportunities for low-lactose/lactose-free dairy foods. In recent years, through innovating processes and technologies, dairy manufacturers have significantly improved the variety, and functional and sensory qualities of low-lactose and lactose-free dairy products. Based on this, this paper first covers the pathology and epidemiology of lactose intolerance and market trends. Then, we focus on current advantages and disadvantages of different lactose hydrolysis technologies and improvements in these technologies to enhance nutritional value, and functional, sensory, and quality properties of lactose-free dairy products. We found that more and more cutting-edge technologies are being applied to the production of lactose-free dairy products, and that these technologies greatly improve the quality and production efficiency of lactose-free dairy products. Hopefully, our review can provide a theoretical basis for the marketing expansion and consumption guidance for low-lactose/lactose-free dairy products.

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.

The Evolutionary History of Human Skin Pigmentation

Skin pigmentation is a complex, conspicuous, highly variable human trait that exhibits a remarkable correlation with latitude. The evolutionary history and genetic basis of skin color variation has been the subject of intense research in the last years. This article reviews the major hypotheses explaining skin color diversity and explores the implications of recent findings about the genes associated with skin pigmentation for understanding the evolutionary forces that have shaped the current patterns of skin color variation. A major aspect of these findings is that the genetic basis of skin color is less simple than previously thought and that geographic variation in skin pigmentation was influenced by the concerted action of different types of natural selection, rather than just by selective sweeps in a few key genes.

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx'a, Khoe-Kwadi, and Bantu languages. Although present-day Bantu speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been thought to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the male-specific region of the Y chromosome (MSY) from 170 individuals with previously reported mitochondrial DNA (mtDNA) genomes, to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun), and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu MSY lineages among Bantu-speaking groups, except for small amounts of "Khoisan" introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for MSY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.

Matriclans shape populations: Insights from the Angolan Namib Desert into the maternal genetic history of southern Africa

OBJECTIVES

Southern Angola is a poorly studied region, inhabited by populations that have been associated with different migratory movements into southern Africa. Apart from Kx'a-speaking San foragers and Bantu-speaking pastoralists, ethnographic and linguistic studies have suggested the existence of an enigmatic array of pre-Bantu communities, like the Kwepe (formerly Khoe-Kwadi speakers), Twa and Kwisi. Here, we evaluate previous peopling hypotheses by assessing the relationships between different southern Angolan populations, based on newly collected linguistic data and complete mtDNA genomes.

MATERIALS AND METHODS

We analyzed 295 complete mtDNA genomes and linguistic data from seven groups from the Namib Desert (Himba, Kuvale, Tjimba, Twa, Kwisi, Kwepe) and Kunene Province (!Xun), placing special emphasis on the evaluation of the genealogical consistency of the matriclanic system that characterizes most of these groups.

RESULTS

We found that the maternal genetic structure of all groups from the Namib Desert was strongly shaped by the consistency of their matriclanic system. The tracking of the maternal heritage enhanced population differentiation by genetic drift and is likely to have caused the divergent mtDNA profiles of the Kwepe, Twa, and Kwisi, who probably formed a single population within the spectrum of Bantu genetic variation. Model-based analyses further suggest that the dominant pastoral groups Kuvale and Himba may be grouped into a Bantu proto-population which also included the ancestors of present-day Tjimba and Herero, as well as the Khoe-Kwadi speaking Damara foragers from Namibia.

DISCUSSION

The view from southwestern Angola offers a new perspective on the populating history of southern Africa and the Bantu expansions by showing that social stratification and different subsistence patterns are not always indicative of remnant groups, but may reflect Bantu-internal variation and ethnogenesis.

APOL1 renal risk variants have contrasting resistance and susceptibility associations with African trypanosomiasis

Reduced susceptibility to infectious disease can increase the frequency of otherwise deleterious alleles. In populations of African ancestry, two apolipoprotein-L1 (APOL1) variants with a recessive kidney disease risk, named G1 and G2, occur at high frequency. APOL1 is a trypanolytic protein that confers innate resistance to most African trypanosomes, but not Trypanosoma brucei rhodesiense or T.b. gambiense, which cause human African trypanosomiasis. In this case-control study, we test the prevailing hypothesis that these APOL1 variants reduce trypanosomiasis susceptibility, resulting in their positive selection in sub-Saharan Africa. We demonstrate a five-fold dominant protective association for G2 against T.b. rhodesiense infection. Furthermore, we report unpredicted strong opposing associations with T.b. gambiense disease outcome. G2 associates with faster progression of T.b. gambiense trypanosomiasis, while G1 associates with asymptomatic carriage and undetectable parasitemia. These results implicate both forms of human African trypanosomiasis in the selection and persistence of otherwise detrimental APOL1 kidney disease variants.

DOI:http://dx.doi.org/10.7554/eLife.25461.001

African-Americans have a greater risk of developing chronic kidney disease than Americans with European ancestry. Much of this increased risk is explained by two versions of a gene called APOL1 that are common in people with African ancestry. These two versions of the gene, known as G1 and G2, suddenly became much more common in people in sub-Saharan Africa in the last 10,000 years. One theory for their rapid spread is that they might protect against a deadly parasitic disease known as African sleeping sickness. This disease is caused by two related parasites of a species known as Trypanosoma brucei, one of which is found in East Africa, while the other affects West Africa.

Laboratory studies have shown that blood from individuals who carry the G1 and G2 variants is better at killing the East African parasites. However, it is not clear if these gene versions help people living in the rural communities, where African sleeping sickness is common, to fight off the disease.

Now, Cooper, Ilboudo et al. show that G1 and G2 do indeed influence how susceptible individuals in these communities are to African sleeping sickness. Individuals with the G2 version were five-times less likely to get the disease from the East African parasite. Neither version could protect individuals from infection with the West African parasite, but infected individuals with the G1 version had fewer parasites in their blood and were less likely to become severely ill. The ability of the G1 version to control the disease and prolong life could explain why this gene version has become so common amongst people in West Africa.

Unexpectedly, the experiments also revealed that people with the G2 version were more likely to become severely unwell when they were infected by the West African parasite. This indicates that whether this gene variant is helpful or harmful depends on where an individual lives. The next step following on from this work will be to investigate exactly how the G1 version reduces the severity of the West African disease. This may aid the development of new drugs for African sleeping sickness and kidney disease.

DOI:http://dx.doi.org/10.7554/eLife.25461.002