scholarly journals Demographic history and admixture dynamics in African Sahelian populations

2020 ◽  
Author(s):  
Viktor Černý ◽  
Cesar Fortes-Lima ◽  
Petr Tříska
Keyword(s):  
Demographic History ◽  
Distribution Patterns ◽  
Human Populations ◽  
African Region ◽  
Genetic Studies ◽  
Genomic Studies ◽  
History Of ◽  
Sub Saharan ◽  
High Degree ◽  
The Impact

Abstract The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterised by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure as well as the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity, and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.

scholarly journals Discovery of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

2018 ◽  
Author(s):  
Quentin D. Sprengelmeyer ◽  
Suzan Mansourian ◽  
Jeremy D. Lange ◽  
Daniel R. Matute ◽  
Brandon S. Cooper ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
Historical Context ◽  
Model Organism ◽  
Widespread Species ◽  
Wilderness Areas ◽  
Genomic Studies ◽  
History Of ◽  
Sub Saharan ◽  
Improved Model

A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster, a globally widespread species [1] which “has invariably appeared to be a strict human commensal” [2]. In spite of its sub-Saharan origins, this species has never been reported from undisturbed wilderness environments that might reflect its pre-commensal niche [3]. Here, we document the collection of 288 D. melanogaster individuals from African wilderness areas in Zambia, Zimbabwe, and Namibia. After sequencing the genomes of 17 flies collected from Kafue National Park, Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these new genomes with prior data enabled us to gain novel insights into the history of this species’ geographic expansion. Our demographic estimates indicated that an expansion from southern Africa began approximately 10,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,400 years ago. This improved model of demographic history will provide a critical resource for future evolutionary and genomic studies of this key model organism. Our results add historical context to the species’ human association, and the opportunity to study wilderness populations opens the door for future studies on the biological basis of its adaptation to human environments.

scholarly journals Genetics and Southern African History

2018 ◽  
Author(s):  
Francesco Montinaro ◽  
Cristian Capelli
Keyword(s):  
Demographic History ◽  
Complete Characterization ◽  
Human Populations ◽  
Cultural Groups ◽  
Population Movements ◽  
Common View ◽  
Genomic Variability ◽  
European Colonization ◽  
History Of ◽  
High Degree

Southern Africa’s past is constellated by a series of demographic events tracing back to the dawn of our species, approximately 300,000 years ago. The intricate pattern of population movements over the millennia contributed to creating an exceptional level of diversity, which is reflected by the high degree of genomic variability of southern African groups. Although a complete characterization of the demographic history of the subcontinent is still lacking, several decades of extensive research have contributed to shed light on the main events. Genetic and archaeological researches suggest that modern humans may have emerged as the result of admixture between different African groups, possibly including other Homo populations, challenging the common view of a unique origin of our species. Although details are still unknown, surveys suggest that long term resident populations (related to Khoe-San speakers) of the subcontinent may have emerged hundreds of thousand years ago, and have inhabited the area for at least five millennia. Population movements, and the introduction of new cultural features, characterize the history of southern Africa over the last five millennia and have had a dramatic impact on subcontinental genetic variability. Traces of these migrations can be identified using different genetic systems, revealing a complex history of adaptation to new selective pressures and sex-biased admixture. The historical events of the European colonization and the slave trade of the last millennium, and the emergence of new cultural groups, further increased the genomic variability of human populations in this region, one of the most genetically diverse in the world.

scholarly journals Estimating the burden of cardiovascular risk in community dwellers over 40 years old in South Africa, Kenya, Burkina Faso and Ghana

2021 ◽  
Vol 6 (1) ◽  
pp. e003499
Author(s):  
Ryan G Wagner ◽  
Nigel J Crowther ◽  
Lisa K Micklesfield ◽  
Palwende Romauld Boua ◽  
Engelbert A Nonterah ◽  
...  
Keyword(s):  
Risk Factors ◽  
Risk Factor ◽  
South African ◽  
Sub Saharan Africa ◽  
African Countries ◽  
Cvd Risk ◽  
Genomic Studies ◽  
Sub Saharan ◽  
Context Specific ◽  
The Impact

IntroductionCardiovascular disease (CVD) risk factors are increasing in sub-Saharan Africa. The impact of these risk factors on future CVD outcomes and burden is poorly understood. We examined the magnitude of modifiable risk factors, estimated future CVD risk and compared results between three commonly used 10-year CVD risk factor algorithms and their variants in four African countries.MethodsIn the Africa-Wits-INDEPTH partnership for Genomic studies (the AWI-Gen Study), 10 349 randomly sampled individuals aged 40–60 years from six sites participated in a survey, with blood pressure, blood glucose and lipid levels measured. Using these data, 10-year CVD risk estimates using Framingham, Globorisk and WHO-CVD and their office-based variants were generated. Differences in future CVD risk and results by algorithm are described using kappa and coefficients to examine agreement and correlations, respectively.ResultsThe 10-year CVD risk across all participants in all sites varied from 2.6% (95% CI: 1.6% to 4.1%) using the WHO-CVD lab algorithm to 6.5% (95% CI: 3.7% to 11.4%) using the Framingham office algorithm, with substantial differences in risk between sites. The highest risk was in South African settings (in urban Soweto: 8.9% (IQR: 5.3–15.3)). Agreement between algorithms was low to moderate (kappa from 0.03 to 0.55) and correlations ranged between 0.28 and 0.70. Depending on the algorithm used, those at high risk (defined as risk of 10-year CVD event >20%) who were under treatment for a modifiable risk factor ranged from 19.2% to 33.9%, with substantial variation by both sex and site.ConclusionThe African sites in this study are at different stages of an ongoing epidemiological transition as evidenced by both risk factor levels and estimated 10-year CVD risk. There is low correlation and disparate levels of population risk, predicted by different risk algorithms, within sites. Validating existing risk algorithms or designing context-specific 10-year CVD risk algorithms is essential for accurately defining population risk and targeting national policies and individual CVD treatment on the African continent.

scholarly journals An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa

2020 ◽  
Vol 12 (4) ◽  
pp. 407-412 ◽  
Author(s):  
Iain Mathieson ◽  
Federico Abascal ◽  
Lasse Vinner ◽  
Pontus Skoglund ◽  
Cristina Pomilla ◽  
...  
Keyword(s):  
Southern Africa ◽  
Nonhuman Primates ◽  
Demographic History ◽  
Structured Populations ◽  
Human Populations ◽  
Papio Ursinus ◽  
Anthropological Research ◽  
Population Continuity ◽  
High Degree

Abstract Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa—indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

scholarly journals Efficient phasing and imputation of low-coverage sequencing data using large reference panels

2020 ◽  
Author(s):  
S. Rubinacci ◽  
D.M. Ribeiro ◽  
R. Hofmeister ◽  
O. Delaneau
Keyword(s):  
Paradigm Shift ◽  
Rare Variants ◽  
Association Studies ◽  
Cost Effective ◽  
Human Populations ◽  
Sequencing Data ◽  
Snp Arrays ◽  
Genomic Studies ◽  
Low Coverage ◽  
The Impact

AbstractLow-coverage whole genome sequencing followed by imputation has been proposed as a cost-effective genotyping approach for disease and population genetics studies. However, its competitiveness against SNP arrays is undermined as current imputation methods are computationally expensive and unable to leverage large reference panels.Here, we describe a method, GLIMPSE, for phasing and imputation of low-coverage sequencing datasets from modern reference panels. We demonstrate its remarkable performance across different coverages and human populations. It achieves imputation of a full genome for less than $1, outperforming existing methods by orders of magnitude, with an increased accuracy of more than 20% at rare variants. We also show that 1x coverage enables effective association studies and is better suited than dense SNP arrays to access the impact of rare variations. Overall, this study demonstrates the promising potential of low-coverage imputation and suggests a paradigm shift in the design of future genomic studies.

scholarly journals Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

2019 ◽  
Vol 37 (3) ◽  
pp. 627-638 ◽  
Author(s):  
Quentin D Sprengelmeyer ◽  
Suzan Mansourian ◽  
Jeremy D Lange ◽  
Daniel R Matute ◽  
Brandon S Cooper ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
Central Africa ◽  
Model Organism ◽  
Sub Saharan Africa ◽  
Wilderness Areas ◽  
Southern Central ◽  
History Of ◽  
Sub Saharan ◽  
Improved Model

Abstract A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that could reflect its precommensal niche. Here, we document the collection of 288 D. melanogaster individuals from multiple African wilderness areas in Zambia, Zimbabwe, and Namibia. The presence of D. melanogaster in these remote woodland environments is consistent with an ancestral range in southern-central Africa, as opposed to equatorial regions. After sequencing the genomes of 17 wilderness-collected flies collected from Kafue National Park in Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these genomes with existing data, we probed the history of this species’ geographic expansion. Demographic estimates indicated that expansion from southern-central Africa began ∼13,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,800 years ago. This improved model of demographic history will provide an important resource for future evolutionary and genomic studies of this key model organism. Our findings add context to the history of D. melanogaster, while opening the door for future studies on the biological basis of adaptation to human environments.

scholarly journals The demography of the Canary Islands from a genetic perspective

2020 ◽  
Author(s):  
Rosa Fregel ◽  
Alejandra C Ordóñez ◽  
Javier G Serrano
Keyword(s):  
Canary Islands ◽  
Demographic History ◽  
American Continent ◽  
North African ◽  
European Colonization ◽  
History Of ◽  
The Impact ◽  
First Time ◽  
Canarian Archipelago ◽  
North African Origin

Abstract The establishment of European colonies across the world had important demographic consequences because it brought together diverse and distant civilizations for the first time. One clear example of this phenomenon is observed in the Canary Islands. The modern Canarian population is mainly the result of the admixture of natives of North African origin and European colonizers. However, additional migratory flows reached the islands due to the importation of enslaved Africans to cultivate sugarcane and the intense commercial contact with the American continent. In this review, we evaluate how the genetic analysis of indigenous, historical, and current populations has provided a glimpse into the Canary Islands’ complex genetic composition. We show that each island subpopulation’s characterization is needed to fully disentangle the demographic history of the Canarian archipelago. Finally, we discuss what research avenues remain to be explored to improve our knowledge of the impact that the European colonization had on its native population.

scholarly journals An Analysis of Public-Private Partnerships in East Africa

2020 ◽  
Vol 11 (5) ◽  
pp. 152
Author(s):  
Lukamba Muhiya Tshombe ◽  
Thekiso Molokwane ◽  
Alex Nduhura ◽  
Innocent Nuwagaba
Keyword(s):  
Developed Countries ◽  
Public Private Partnerships ◽  
Infrastructure Development ◽  
East African ◽  
African Region ◽  
African Countries ◽  
Scientific Discussion ◽  
East African Region ◽  
Sub Saharan ◽  
The Impact

The impact of the implementation of public-private partnerships (PPPs) in the Sub-Saharan African region on infrastructure and services is becoming increasingly perceptible. A considerable number of African countries have embraced PPPs as a mechanism to finance large projects due to a constrained fiscus. At present, many financial institutions, such as the World Bank, the International Monetary Fund and the African Development Bank, which finance some of the projects, have established a department or unit that mainly focuses on infrastructure development in developing countries. The private sector in Africa is equally seen as a significant partner in the development of infrastructure. African governments need to tap into private capital to invest in infrastructure projects. This scientific discussion provides an analysis of PPPs in the East African region. This article selected a number of countries to illustrate PPP projects in the sub-region. The analysis of this study illustrates that the East African region represents unique and valuable public-private partnership lessons in different countries. This study also traces the origins of PPPs to more than a century ago where developed countries completed some of their projects using the same arrangement. This paper further demonstrates that the application of PPPs is always characterised by three factors, namely a country, a sector and a project. Experts in the field often refer to these elements as layers, which usually precede any successful PPP.

scholarly journals Early estimates of COVID-19 infections in small, medium and large population clusters

2020 ◽  
Vol 5 (9) ◽  
pp. e003055
Author(s):  
Amir Siraj ◽  
Alemayehu Worku ◽  
Kiros Berhane ◽  
Maru Aregawi ◽  
Munir Eshetu ◽  
...  
Keyword(s):  
Large Population ◽  
Face Mask ◽  
Sub Saharan Africa ◽  
Contact Tracing ◽  
Local Context ◽  
African Region ◽  
Social Distancing ◽  
Population Sizes ◽  
Sub Saharan ◽  
The Impact

IntroductionSince its emergence in late December 2019, COVID-19 has rapidly developed into a pandemic in mid of March with many countries suffering heavy human loss and declaring emergency conditions to contain its spread. The impact of the disease, while it has been relatively low in the sub-Saharan Africa (SSA) as of May 2020, is feared to be potentially devastating given the less developed and fragmented healthcare system in the continent. In addition, most emergency measures practised may not be effective due to their limited affordability as well as the communal way people in SSA live in relative isolation in clusters of large as well as smaller population centres.MethodsTo address the acute need for estimates of the potential impacts of the disease once it sweeps through the African region, we developed a process-based model with key parameters obtained from recent studies, taking local context into consideration. We further used the model to estimate the number of infections within a year of sustained local transmissions under scenarios that cover different population sizes, urban status, effectiveness and coverage of social distancing, contact tracing and usage of cloth face mask.ResultsWe showed that when implemented early, 50% coverage of contact tracing and face mask, with 33% effective social distancing policies can bringing the epidemic to a manageable level for all population sizes and settings we assessed. Relaxing of social distancing in urban settings from 33% to 25% could be matched by introduction and maintenance of face mask use at 43%.ConclusionsIn SSA countries with limited healthcare workforce, hospital resources and intensive care units, a robust system of social distancing, contact tracing and face mask use could yield in outcomes that prevent several millions of infections and thousands of deaths across the continent.

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