Inferring adaptive gene-flow in recent African history

Mapping Intimacies ◽

10.1101/205252 ◽

2017 ◽

Cited By ~ 3

Author(s):

George Busby ◽

Ryan Christ ◽

Gavin Band ◽

Ellen Leffler ◽

Quang Si Le ◽

...

Keyword(s):

Gene Flow ◽

African Ancestry ◽

The Gambia ◽

Sub Saharan Africa ◽

Histocompatibility Complex ◽

Genome Wide ◽

Genome Wide Data ◽

Multiple Regions ◽

Novel Method ◽

Sub Saharan

AbstractGene-flow from an ancestrally differentiated group has been shown to be a powerful source of selectively advantageous variants. To understand whether recent gene-flow may have contributed to adaptation among humans in sub-Saharan Africa, we applied a novel method to identify deviations in ancestry inferred from genome-wide data in 48 populations. Among the signals of ancestry deviation that we find in the Fula, an historically pastoralist ethnic group from the Gambia, are the region that encodes the lactose persistence phenotype, LCT/MCM6, which has the highest proportion of Eurasian ancestry in the genome. The region with the lowest proportion of non-African ancestry is across DARC, which encodes the Duffy null phenotype and is protective for Plasmodium vivax malaria. In the Jola from the Gambia and a Khoesan speaking group from Namibia we find multiple regions with inferred ancestry deviation including the Major Histocompatibility Complex. Our analysis shows the potential for adaptive gene-flow in recent human history.

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

Science ◽

10.1126/science.aaw6275 ◽

2019 ◽

Vol 365 (6448) ◽

pp. eaaw6275 ◽

Cited By ~ 24

Author(s):

Mary E. Prendergast ◽

Mark Lipson ◽

Elizabeth A. Sawchuk ◽

Iñigo Olalde ◽

Christine A. Ogola ◽

...

Keyword(s):

Iron Age ◽

Food Production ◽

Sub Saharan Africa ◽

Eastern Africa ◽

Multiphase Model ◽

Later Stone Age ◽

Genome Wide ◽

Genome Wide Data ◽

Sub Saharan ◽

Pastoral Neolithic

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African–related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African–related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

Admixture into and within sub-Saharan Africa

eLife ◽

10.7554/elife.15266 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 57

Author(s):

George BJ Busby ◽

Gavin Band ◽

Quang Si Le ◽

Muminatou Jallow ◽

Edith Bougama ◽

...

Keyword(s):

Gene Flow ◽

Geographic Region ◽

Sub Saharan Africa ◽

Genome Wide ◽

A Genome ◽

Depth Analysis ◽

Shared Ancestry ◽

Sub Saharan ◽

Linguistic Groups ◽

Insight Into

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

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

Science Advances ◽

10.1126/sciadv.aaz0183 ◽

2020 ◽

Vol 6 (24) ◽

pp. eaaz0183 ◽

Cited By ~ 2

Author(s):

Ke Wang ◽

Steven Goldstein ◽

Madeleine Bleasdale ◽

Bernard Clist ◽

Koen Bostoen ◽

...

Keyword(s):

Southern Africa ◽

Sub Saharan Africa ◽

The Past ◽

Genome Wide ◽

Movement Interaction ◽

Genome Wide Data ◽

Sub Saharan ◽

Population Interactions ◽

Eastern And Southern Africa ◽

Complex Trajectories

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.

The illusion of capitalism in contemporary Sub‐Saharan Africa: a case study of the Gambia

foresight ◽

10.1108/14636681111138767 ◽

2011 ◽

Vol 13 (3) ◽

pp. 50-63 ◽

Cited By ~ 3

Author(s):

Abdoulie Sallah ◽

Colin C. Williams

Keyword(s):

The Gambia ◽

Sub Saharan Africa ◽

Sub Saharan

Genome-wide data substantiate Holocene gene flow from India to Australia

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1211927110 ◽

2013 ◽

Vol 110 (5) ◽

pp. 1803-1808 ◽

Cited By ~ 71

Author(s):

I. Pugach ◽

F. Delfin ◽

E. Gunnarsdottir ◽

M. Kayser ◽

M. Stoneking

Keyword(s):

Gene Flow ◽

Genome Wide ◽

Genome Wide Data

Methylome-wide analysis reveals epigenetic marks associated with resistance to tuberculosis in HIV-infected individuals from East Africa

10.1101/2020.07.14.20153395 ◽

2020 ◽

Author(s):

Catherine Stein ◽

Penelope Bencheck ◽

Jacquelaine Bartlett ◽

Robert P Igo ◽

Rafal S Sobota ◽

...

Keyword(s):

Genome Wide Association Study ◽

Sub Saharan Africa ◽

Chromosome 1 ◽

Chromosome 2 ◽

Chromosome 5 ◽

Epigenetic Marks ◽

Genome Wide ◽

A Genome ◽

Immunodeficiency Virus ◽

Sub Saharan

Background: Tuberculosis (TB) is the most deadly infectious disease globally and highly prevalent in the developing world, especially sub-Saharan Africa. Even though a third of humans are exposed to Myocbacterium tuberculosis (Mtb), most infected immunocompetent individuals do not develop active TB. In contrast, for individuals infected with both TB and the human immunodeficiency virus (HIV), the risk of active disease is 10% or more per year. Previously, we identified in a genome-wide association study a region on chromosome 5 that was associated with resistance to TB. This region included epigenetic marks that could influence gene regulation so we hypothesized that HIV-infected individuals exposed to Mtb, who remain disease free, carry epigenetic changes that strongly protect them from active TB. To test this hypothesis, we conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania. Results: In 221 HIV-infected adults from Uganda and Tanzania, we identified 3 regions of interest that included markers that were differentially methylated between TB cases and LTBI controls, that also included methylation QTLs and associated SNPs: chromosome 1 (RNF220, p=4x10-5), chromosome 2 (between COPS8 and COL6A3 genes, p=2.7x10-5), and chromosome 5 (CEP72, p=1.3x10-5). These methylation results colocalized with associated SNPs, methylation QTLs, and methylation x SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. Conclusion: Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.

A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

10.1101/418509 ◽

2018 ◽

Cited By ~ 1

Author(s):

Veena Devi Ganeshan ◽

Stephen O. Opiyo ◽

Samuel K. Mutiga ◽

Felix Rotich ◽

David M. Thuranira ◽

...

Keyword(s):

Association Study ◽

Magnaporthe Oryzae ◽

Genome Wide Association Study ◽

Significant Snps ◽

Sub Saharan Africa ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Sub Saharan ◽

Genomic Regions

ABSTRACTThe fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.

Interaction between M. tuberculosis Lineage and Human Genetic Variants Reveals Novel Pathway Associations with Severity of TB

Pathogens ◽

10.3390/pathogens10111487 ◽

2021 ◽

Vol 10 (11) ◽

pp. 1487

Author(s):

Michael L. McHenry ◽

Eddie M. Wampande ◽

Moses L. Joloba ◽

LaShaunda L. Malone ◽

Harriet Mayanja-Kizza ◽

...

Keyword(s):

Genetic Variation ◽

Clinical Presentation ◽

Sub Saharan Africa ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Human Genomes ◽

Genome Wide ◽

Sub Saharan ◽

Cellular Replication

Tuberculosis (TB) remains a major public health threat globally, especially in sub-Saharan Africa. Both human and Mycobacterium tuberculosis (MTBC) genetic variation affect TB outcomes, but few studies have examined if and how the two genomes interact to affect disease. We hypothesize that long-term coexistence between human genomes and MTBC lineages modulates disease to affect its severity. We examined this hypothesis in our TB household contact study in Kampala, Uganda, in which we identified three MTBC lineages, of which one, L4.6-Uganda, is clearly derived and hence recent. We quantified TB severity using the Bandim TBscore and examined the interaction between MTBC lineage and human single-nucleotide polymorphisms (SNPs) genome-wide, in two independent cohorts of TB cases (n = 149 and n = 127). We found a significant interaction between an SNP in PPIAP2 and the Uganda lineage (combined p = 4 × 10−8). PPIAP2 is a pseudogene that is highly expressed in immune cells. Pathway and eQTL analyses indicated potential roles between coevolving SNPs and cellular replication and metabolism as well as platelet aggregation and coagulation. This finding provides further evidence that host–pathogen interactions affect clinical presentation differently than host and pathogen genetic variation independently, and that human–MTBC coevolution is likely to explain patterns of disease severity.

NATIONHOOD AND THE QUEST FOR NATIONAL DEVELOPMENT: THE GAMBIA’S EXPERIENCE UNDER THE SECOND REPUBLIC, 1994 – 2015

IJASOS- International E-journal of Advances in Social Sciences ◽

10.18769/ijasos.789467 ◽

2020 ◽

Vol 6 (17) ◽

pp. 665-673

Keyword(s):

Political Development ◽

National Development ◽

The Gambia ◽

Sub Saharan Africa ◽

Second Republic ◽

Nation States ◽

Ecological Resources ◽

Human Material ◽

Sub Saharan ◽

Fact Finding

The task of nation-building today in the world is that which carries along all well-meaning modern nation-states, with Gambia as no exemption. This paper examines the nationhood process and effort in the Gambia between 1994 and 2015. It focuses on national development efforts both in the first and second republics. The paper investigates how human, material and ecological resources are harnessed and deployed towards this noble goal, availing enabling policy-thrusts for effective implementation and goal attainments that attract sustainable socio-economic and political development. The paper beams searchlights on the redoubled efforts under the Yahya Jammeh regime and the pragmatic approaches taken to achieve more meaningfully goal-oriented national development strides that pave ways for practical development giants and strides. An inductive and deductive methods of research that are descriptive and fact-finding are employed for empirical and critical explorations. The paper posits that the strategies of the second republic government, which surpass the first republic’s conservatively-constructed approaches under Jawara served as impetus for the accomplishments recorded from 1994 to 2015 in making the Gambia an economic super power through industrialization of the agro-economic structures and processes of the small nation in the sub-Saharan Africa. Keywords: Nation, Nationhood, National Development, The Gambia, Second Republic, Independence.

Language-By-Radio in Sub-Saharan Africa

IALLT Journal of Language Learning Technologies ◽

10.17161/iallt.v16i2.9131 ◽

2019 ◽

Vol 16 (2) ◽

pp. 20-27

Author(s):

Edmun B. Richmond

Keyword(s):

United States ◽

Program Development ◽

Special Interest ◽

The United States ◽

The Gambia ◽

Sub Saharan Africa ◽

Foreign Languages ◽

Language Program ◽

Sub Saharan ◽

Radio Programs

In the summer of 1981, the author was engaged in pedagogicalresearch in language program development for the governments of Senegaland The Gambia. During that period, he further participated in an eight countrylanguage teaching survey throughout West, Central, and EastAfrica, under the sponsorship of the United States International CommunicationsAgency. Included in that survey was an analysis of the useof radio broadcasts as a means to teach foreign languages. This articlewill describe the language-by-radio programs in four countries, i.e.,Senegal, Burundi, Rwanda, and Kenya. Of special interest is the use ofradio to teach English.