African papers dump

 Dump of papers on Sub Saharan Africa. A quick summary of all studies on Africa so far.

• Genetics and the African Past

Summary

Africa harbors the greatest human genetic diversity on the planet, a fact that has inspired extensive investigation of the population structure found across the continent and the demographic processes that shaped observed patterns of genetic variation. Since the 1980s, studies of the DNA of living people have repeatedly demonstrated that Africa is the cradle of human origins, in agreement with fossil and archaeological evidence. Since the first ancient human genome was published in 2010, ancient DNA (aDNA) has contributed additional possibilities for exploring population history, providing a direct window into genetic lineages that no longer exist or are barely discernible. Genetic data from both living and ancient people—when integrated with available archaeological, bioarchaeological, historical linguistic, and written or oral historical data—are important tools for contextualizing African genetic diversity and understanding the biological and cultural processes that have shaped it over time. While most studies to date have focused on humans, aDNA can also be obtained from plant and animal remains, sediments, and some artifacts, all of which can enable a more comprehensive understanding of human lives.

Genetic research on the African past often focuses on human origins and Pleistocene population structure, as well as on the origins, directionality, and tempo of demographic changes that accompanied Holocene transitions to herding and farming. The rise of cosmopolitan cities and states in the past two millennia has been examined with genetic evidence to a very limited extent, but this is a potentially rich vein of research. Increasingly, forced migrations of enslaved Africans and the development of the diaspora are the subjects of genetic study as well. Yet to date, Africa remains vastly understudied relative to parts of the world such as Eurasia, in terms of both ancient and present-day DNA. This shapes not only the study of the past but also medical innovations and public health.

While the bulk of published African genomes come from present-day people, there are problems with relying solely on this data to reconstruct the past, given the continent’s long and complex demographic history. Increasingly, aDNA is providing novel perspectives on a past largely invisible in the genomes of people living in the 20th and 21st centuries due to recent demographic shifts. A surge in African aDNA studies since 2015 has also renewed longstanding debates about the ethics of genetic research on people, both living and deceased. Researchers working in Africa today must consider ethical issues including stakeholder engagement, informed consent, and control of biological samples and data; in aDNA studies, descendant communities, museum curators, bioarchaeologists, and geneticists, among others, play critical roles in these discussions.

 

•  Genetic substructure and complex demographic history of South African Bantu speakers

Abstract

South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa. 

• Clarifying distinct models of modern human origins in Africa 

Accumulating genomic, fossil and archaeological data from Africa have led to a renewed interest in models of modern human origins. However, such discussions are often discipline-specific, with limited integration of evidence across the different fields. Further, geneticists typically require explicit specification of parameters to test competing demographic models, but these have been poorly outlined for some scenarios. Here, we describe four possible models for the origins of Homo sapiens in Africa based on published literature from paleoanthropology and human genetics. We briefly outline expectations for data patterns under each model, with a special focus on genetic data. Additionally, we present schematics for each model, doing our best to qualitatively describe demographic histories for which genetic parameters can be specifically attached. Finally, it is our hope that this perspective provides context for discussions of human origins in other manuscripts presented in this special issue.

 

• African population history: an ancient DNA perspective

The history of human populations in Africa is complex and includes various demographic events that influenced patterns of genetic variation across the continent. Through genetic studies of modern-day, and most recently, ancient African genetic variation, it became evident that deep African history is captured by the relationships among hunter-gatherers. Furthermore, it was shown that agriculture had a large influence on the distribution of current-day Africans. These later population movements changed the demographic face of the continent and descendants of farming groups today form the majority populations across Africa. Ancient DNA methods are continually evolving, and we see evidence of this in how research has advanced in the last decade. With the increased availability of full genomic data from diverse sets of modern-day and prehistoric Africans we now have more power to infer human demography. Future ancient DNA research promises to reveal more detailed stories of human prehistory in Africa.

• Reconstructing Prehistoric African Population Structure

Summary

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.

• Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

Abstract

Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.

• Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa 

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5× coverage ancient genome of an Ethiopian male (“Mota”) who lived approximately 4500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4000 years earlier.