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

The genetic legacy of the expansion of Bantu-speaking peoples in Africa

The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.

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.

Complete mitochondrial DNA sequence tries to settle hitherto putative history of Kayastha population of India

OBJECTIVES

Indian caste system is unique as it has an inimitable type of class system where the social ordering is done based on birth. Within the caste system, there is a distinct endogamous population known as the Kayastha, who have had inconclusive stratification records due to unidentified historical records.

METHODS

To gain a more inclusive view on the history and genetic affinities of Kayastha people, complete mitochondrial genomes from 15 individuals of a Kayastha population from North-western India have been sequenced.

RESULTS

Interestingly, three novel sub-clades (U2b2a, M3d2, and M33a3b) have been identified that represent unique Kayastha motifs.

CONCLUSION

The haplotype-based analysis suggests that the Kayastha population shares genetic affinities with the Indo-European and Sino-Tibetan populations found in the trans-Himalayan region. The F_ST based population comparison and the MDS plot indicates that Kayastha people have close maternal genetic affinity with the available genetic database of Brahmins, Kashmiris, and Tharus. The maternal genetic lineages among Kayastha population shows deep in situ origin that emerged much before settled life developed on this sub-continent. Both mtDNA and Y-chromosome markers, trace the genetic lineages of Kayastha population with Tharus, who regard themselves Kshatriya, corroborated by the oral history of the Kayasthas for their Kshatriya affiliation. It also validates genetic heritage of earliest settlers of India in both indigenous tribal and caste populations.

Reconstructing 50,000 years of human history from our DNA: lessons from modern genomics

The advent of high throughput sequencing approaches and ancient DNA techniques have enabled reconstructing the history of human populations at an unprecedented level of resolution. The symposium from the French Academy of Sciences "50,000 ans d'épopée humaine dans notre ADN" has reviewed some of the latest contributions from the fields of genomics, archaeology, and linguistics to our understanding of >300,000 years of human history. DNA has revealed the richness of the human journey, from the deep divergences between human populations in Africa, to the first encounters of Homo Sapiens with other hominins on their way to Eurasia and the peopling of Remote Oceania. The symposium has also emphasized how migrations, cultural practices, and environmental pathogens have contributed to shape the genetic diversity of modern humans, through admixture, genetic drift or genetic adaptation. Finally, special attention was also given to how human behaviours have shaped the genome of other species, through the spreading of microbes and pathogens, as in the case of Yersinia Pestis, or through domestication, as elegantly demonstrated for dogs, horses, and apples. Altogether, this conference illustrated how the complex history of human populations is tightly linked with their contemporary genetic diversity that, in turn, has direct effects on their identity and health.

The Genes of Freedom: Genome-Wide Insights into Marronage, Admixture and Ethnogenesis in the Gulf of Guinea

The forced migration of millions of Africans during the Atlantic Slave Trade led to the emergence of new genetic and linguistic identities, thereby providing a unique opportunity to study the mechanisms giving rise to human biological and cultural variation. Here we focus on the archipelago of São Tomé and Príncipe in the Gulf of Guinea, which hosted one of the earliest plantation societies relying exclusively on slave labor. We analyze the genetic variation in 25 individuals from three communities who speak distinct creole languages (Forros, Principenses and Angolares), using genomic data from expanded exomes in combination with a contextual dataset from Europe and Africa, including newly generated data from 28 Bantu speakers from Angola. Our findings show that while all islanders display mixed contributions from the Gulf of Guinea and Angola, the Angolares are characterized by extreme genetic differentiation and inbreeding, consistent with an admixed maroon isolate. In line with a more prominent Bantu contribution to their creole language, we additionally found that a previously reported high-frequency Y-chromosome haplotype in the Angolares has a likely Angolan origin, suggesting that their genetic, linguistic and social characteristics were influenced by a small group of dominant men who achieved disproportionate reproductive success.

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.

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.

Along the Indian Ocean Coast: Genomic Variation in Mozambique Provides New Insights into the Bantu Expansion

The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using ∼1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a “late split” between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North–South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North–South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.

The Impacts of Conservation and Militarization on Indigenous Peoples : A Southern African San Perspective

There has been a long-standing debate about the roles of San in the militaries of southern Africa and the prevalence of violence among the Ju/'hoansi and other San people. The evolutionary anthropology and social anthropological debates over the contexts in which violence and warfare occurs among hunters and gatherers are considered, as is the "tribal zone theory" of warfare between states and indigenous people. This paper assesses the issues that arise from these discussions, drawing on data from San in Angola, Namibia, Botswana, and Zimbabwe. Utilizing cases of how San have been affected by military forces and wildlife conservation agencies in what became protected areas in southern Africa, this article shows that indigenous peoples have been treated differentially by state and nongovernmental organizations involved in anti-poaching, shoot-to-kill, and forced resettlement policies. Particular emphasis is placed on the !Xun and Khwe San of southern Angola and northern Namibia and the Tshwa San of western Zimbabwe and northern Botswana, who have been impacted by militarization and coercive conservation efforts since the late nineteenth century. Principal conclusions are that conservation and militarization efforts have led to a reduction in land and resources available to indigenous people, higher levels of poverty, increased socioeconomic stratification, and lower levels of physical well-being. San have responded to these trends by engaging in social activism, forming community-based institutions, and pursuing legal actions aimed at obtaining human rights and equitable treatment.

The evolutionary history of Southern Africa

The genomic variability of Southern African groups is characterized by an exceptional degree of diversity, which is the result of long-term local evolutionary history, migrations and gene-flow. Over the last few years several investigations have identified and described signatures related to these processes, revealing how ancient and more recent events have shaped the structure and ancestry composition of local populations. Here we discuss recent insights into the genetic history of the Southernmost part of the African continent provided by the analysis of modern and ancient genomes. Future work is expected to clarify the population dynamics associated with the emergence of Homo sapiens across Africa and the details of the process of dispersion and admixture associated with the arrival of Bantu-speaking groups in the region.

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.

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

Objectives

We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y‐chromosome haplogroup E1b1b (E‐M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex‐biased gene flow in southern Africa.

Materials and methods

We analyzed previously published complete mtDNA genome sequences and ∼900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y‐linked STR loci for samples assigned to haplogroup E1b1b.

Results

Our results support an eastern African origin for Y‐chromosome haplogroup E1b1b (E‐M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male‐dominated expansion. Our finding of a significant increase in the intensity of the sex‐biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

Conclusions

Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex‐biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.