scholarly journals Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes

2015 ◽  
Author(s):  
Brenna M. Henn ◽  
Laura R Botigue ◽  
Stephan Peischl ◽  
Isabelle Dupanloup ◽  
Mikhail Lipatov ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Allele Frequencies ◽  
Sub Saharan Africa ◽  
Human Populations ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
High Coverage ◽  
Deleterious Alleles ◽  
Out Of Africa ◽  
Sub Saharan

The Out-of-Africa (OOA) dispersal ~50,000 years ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from 7 geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

scholarly journals Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

2015 ◽  
Vol 113 (4) ◽  
pp. E440-E449 ◽  
Author(s):  
Brenna M. Henn ◽  
Laura R. Botigué ◽  
Stephan Peischl ◽  
Isabelle Dupanloup ◽  
Mikhail Lipatov ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Allele Frequencies ◽  
Sub Saharan Africa ◽  
Human Populations ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
High Coverage ◽  
Deleterious Alleles ◽  
Out Of Africa ◽  
Sub Saharan

The Out-of-Africa (OOA) dispersal ∼50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

Interactions between ecological and socio-economic drivers of Buruli ulcer burden in Sub-Saharan Africa: opportunities for an improved control

2018 ◽  
Author(s):  
Andes Garchitorena ◽  
Matthew H. Bonds ◽  
Jean-Francois Guégan ◽  
Benjamin Roche
Keyword(s):  
Socioeconomic Factors ◽  
Disease Transmission ◽  
Access To Health Care ◽  
Buruli Ulcer ◽  
Mycobacterium Ulcerans ◽  
Sub Saharan Africa ◽  
Aquatic Environments ◽  
Human Populations ◽  
Complex Interactions ◽  
Sub Saharan

This chapter provides an overview of the complex interactions between ecological and socioeconomic factors for the development and control of Buruli ulcer in Sub-Saharan Africa. We review key ecological and evolutionary processes driving the environmental persistence and proliferation of Mycobacterium ulcerans, the causative agent, within aquatic environments, as well as transmission processes from these aquatic environments to human populations. We also outline key socioeconomic factors driving the economic and health burden of Buruli ulcer in endemic regions, revealed by reciprocal feedbacks between poverty, disease transmission from exposure aquatic environments and disease progression to severe stages owing to low access to health care. The implications of such insights for disease control, both in terms of limitations of current strategies and directions for the future, are discussed.

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Sub Saharan Africa ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes

Abstract Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

scholarly journals Nonpaternity and Half-Siblingships as Objective Measures of Extramarital Sex: Mathematical Modeling and Simulations

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Ryosuke Omori ◽  
Nico Nagelkerke ◽  
Laith J. Abu-Raddad
Keyword(s):  
Sexual Behavior ◽  
Pearson Correlation ◽  
Demographic Data ◽  
Reliability And Validity ◽  
Correlation Coefficients ◽  
Sub Saharan Africa ◽  
Objective Measures ◽  
Human Populations ◽  
Extramarital Sex ◽  
Sub Saharan

Background. Understanding the epidemiology of HIV and other sexually transmitted infections (STIs) requires knowledge of sexual behavior, but self-reported behavior has limitations. We explored the reliability and validity of nonpaternity and half-siblings ratios as biomarkers of current and past extramarital sex. Methods. An individual-based Monte Carlo simulation model was constructed to describe partnering and conception in human populations with a focus on Sub-Saharan Africa (SSA). The model was parameterized with representative biological, behavioral, and demographic data. Results. Nonpaternity and half-siblings ratios were strongly correlated with extramarital sex, with Pearson correlation coefficients (PCC) of 0.79 (95% CI: 0.71–0.86) and 0.77 (0.68–0.84), respectively. Age-specific nonpaternity ratios correlated with past extramarital sex at time of conception for different scenarios: for example, PCC, after smoothing by moving averages, was 0.75 (0.52–0.89) in a scenario of steadily decreasing nonmarital sex and 0.39 (0.01–0.73) in a scenario of transient drops in nonmarital sex. Simulations assuming self-reported levels of extramarital sex from Kenya yielded nonpaternity levels lower than global nonpaternity data, suggesting sizable underreporting of extramarital sex. Conclusions. Nonpaternity and half-siblings ratios are useful objective measures of extramarital sex that avoid limitations in self-reported sexual behavior.

Assessing the Monophyly of Alectra and its Relationship to Melasma (Orobanchaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 561-569 ◽  
Author(s):  
Jeffery J. Morawetz ◽  
Andrea D. Wolfe
Keyword(s):  
Dna Sequences ◽  
Sub Saharan Africa ◽  
African Species ◽  
Widespread Species ◽  
Tropical America ◽  
Agricultural Weed ◽  
The Subject ◽  
Out Of Africa ◽  
Sub Saharan ◽  
India And China

Alectra (Orobanchaceae) consists of primarily hemiparasitic herbaceous species distributed mainly in sub-Saharan Africa, with two species native to tropical America, and two widespread species extending out of Africa into India and China. Despite containing an economically important noxious agricultural weed, Alectra has never been the subject of a phylogenetic analysis. The monophyly of Alectra was assessed using DNA sequences from the nuclear (internal transcribed spacer) and chloroplast (rpl16, trnT-L) genomes, including 11 of 12 species. One of two holoparasitic species, Alectra alba, was placed outside of Alectra, supported as sister to a lineage containing the Asian holoparasitic genera Aeginetia + Christisonia. Two highly supported lineages of Melasma were revealed: one containing the two included African species, and the other comprising the tropical American Melasma rhinanthoides and the single accession of the tropical American Escobedia. The placement of the Madagascan endemic Alectra fruticosa was shown to be unresolved in relationship to the remaining Alectra species and the two lineages containing Melasma. The monophyly of the remaining species of Alectra was highly supported.

scholarly journals Aflatoxin Exposure in Developing Countries: The Critical Interface of Agriculture and Health

2007 ◽  
Vol 28 (2_suppl2) ◽  
pp. S372-S380 ◽  
Author(s):  
Christopher Paul Wild
Keyword(s):  
West Africa ◽  
Relevant Literature ◽  
Intervention Strategies ◽  
Sub Saharan Africa ◽  
Farm Animals ◽  
Human Populations ◽  
Growth Faltering ◽  
Sub Saharan ◽  
Underlying Mechanisms ◽  
Agricultural Setting

Background Aflatoxins are common contaminants of staple foods in sub-Saharan Africa. These toxins are human liver carcinogens, especially in combination with chronic infection with hepatitis B virus. However, in an agricultural setting, the effects on growth, immune status, and susceptibility to infectious disease in farm animals are also well recognized. These latter effects have been far less explored in human populations. Objectives To review some of the more recent work on aflatoxins where the health outcomes seen in the agricultural setting, including growth impairment and immune suppression, have been investigated in human populations. The paper draws largely on examples from West Africa. The paper also sets out how knowledge gained about aflatoxins in the agricultural setting can be used to design intervention studies in human populations. Methods A review of the relevant literature. Results Human exposure to aflatoxins begins early in life, and recent studies in West Africa have demonstrated an association between exposure and growth faltering, particularly stunting, in young children. At present the underlying mechanisms for the latter effects are unknown but may include impairment of immunity and increased susceptibility to infections. Simple postharvest intervention strategies were successful in reducing aflatoxin exposure in a subsistence farm setting, providing a rationale for prevention of aflatoxin-related disease. Conclusions There are potential benefits to public health from intervention strategies combining expertise in the agricultural and health settings to address the aflatoxin problem.

scholarly journals First Case of COVID-19-Associated Collapsing Glomerulopathy in Sub-Saharan Africa

2020 ◽  
Vol 2020 ◽  
pp. 1-5
Author(s):  
Yannick M. Nlandu ◽  
Jean-Robert R. Makulo ◽  
Nestor M. Pakasa ◽  
Ernest K. Sumaili ◽  
Clarisse N. Nkondi ◽  
...  
Keyword(s):  
Coming Out ◽  
Negative Impact ◽  
Kidney Injury ◽  
Sub Saharan Africa ◽  
Collapsing Glomerulopathy ◽  
First Case ◽  
Out Of Africa ◽  
Sub Saharan ◽  
Glomerular Involvement ◽  
New Onset

Although the lungs remain the main target of SARS-CoV-2, other organs, such as kidneys, can be affected, which has a negative impact on the outcomes of COVID-19 patients. Although previous studies of kidney disease in COVID-19 reported mainly SARS-CoV-2-induced tubular and interstitial injury, there is growing evidence coming out of Africa of glomerular involvement, especially collapsing glomerulopathy seen particularly in people of African descent. We report a case of collapsing glomerulopathy revealed by acute kidney injury and a new onset of full blown nephrotic syndrome in a black Congolese patient coinfected with COVID-19 and malaria.

scholarly journals Evolution of cultural traits occurs at similar relative rates in different world regions

2014 ◽  
Vol 281 (1795) ◽  
pp. 20141622 ◽  
Author(s):  
Thomas E. Currie ◽  
Ruth Mace
Keyword(s):  
Cultural Change ◽  
Purifying Selection ◽  
Sub Saharan Africa ◽  
Rates Of Change ◽  
World Regions ◽  
The Pacific ◽  
General Rules ◽  
Cultural Traits ◽  
Sub Saharan ◽  
Patterns And Processes

A fundamental issue in understanding human diversity is whether or not there are regular patterns and processes involved in cultural change. Theoretical and mathematical models of cultural evolution have been developed and are increasingly being used and assessed in empirical analyses. Here, we test the hypothesis that the rates of change of features of human socio-cultural organization are governed by general rules. One prediction of this hypothesis is that different cultural traits will tend to evolve at similar relative rates in different world regions, despite the unique historical backgrounds of groups inhabiting these regions. We used phylogenetic comparative methods and systematic cross-cultural data to assess how different socio-cultural traits changed in (i) island southeast Asia and the Pacific, and (ii) sub-Saharan Africa. The relative rates of change in these two regions are significantly correlated. Furthermore, cultural traits that are more directly related to external environmental conditions evolve more slowly than traits related to social structures. This is consistent with the idea that a form of purifying selection is acting with greater strength on these more environmentally linked traits. These results suggest that despite contingent historical events and the role of humans as active agents in the historical process, culture does indeed evolve in ways that can be predicted from general principles

scholarly journals Economic inequality caused by feedbacks between poverty and the dynamics of a rare tropical disease: the case of Buruli ulcer in sub-Saharan Africa

2015 ◽  
Vol 282 (1818) ◽  
pp. 20151426 ◽  
Author(s):  
Andrés Garchitorena ◽  
Calistus N. Ngonghala ◽  
Jean-Francois Guegan ◽  
Gaëtan Texier ◽  
Martine Bellanger ◽  
...  
Keyword(s):  
Neglected Tropical Diseases ◽  
Economic Status ◽  
Buruli Ulcer ◽  
Population Level ◽  
Sub Saharan Africa ◽  
Human Populations ◽  
Tropical Diseases ◽  
Sub Saharan ◽  
Low Incidence ◽  
Heath Community

Neglected tropical diseases (NTDs) have received increasing attention in recent years by the global heath community, as they cumulatively constitute substantial burdens of disease as well as barriers for economic development. A number of common tropical diseases such as malaria, hookworm or schistosomiasis have well-documented economic impacts. However, much less is known about the population-level impacts of diseases that are rare but associated with high disability burden, which represent a great number of tropical diseases. Using an individual-based model of Buruli ulcer (BU), we demonstrate that, through feedbacks between health and economic status, such NTDs can have a significant impact on the economic structure of human populations even at low incidence levels. While average wealth is only marginally affected by BU, the economic conditions of certain subpopulations are impacted sufficiently to create changes in measurable population-level inequality. A reduction of the disability burden caused by BU can thus maximize the economic growth of the poorest subpopulations and reduce significantly the economic inequalities introduced by the disease in endemic regions.

scholarly journals Frequent infection of Hylobates pileatus (pileated gibbon) with species-associated variants of hepatitis B virus in Cambodia

2005 ◽  
Vol 86 (2) ◽  
pp. 333-337 ◽  
Author(s):  
A. A. Sall ◽  
S. Starkman ◽  
J. M. Reynes ◽  
S. Lay ◽  
T. Nhim ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
East Asia ◽  
Genetic Relationships ◽  
Sub Saharan Africa ◽  
Human Populations ◽  
South East Asia ◽  
B Virus ◽  
Hylobates Pileatus ◽  
Sub Saharan

As well as being distributed widely in human populations, hepatitis B virus (HBV) infections occur frequently in chimpanzee, gibbon and other ape populations in sub-Saharan Africa and South-East Asia. To investigate the frequency and genetic relationships of HBV infecting gibbons in Cambodia, pileated gibbons (Hylobates pileatus) that were originally wild-caught were screened for surface antigen. Twelve of 26 (46 %) were positive, of which 11 were positive for HBV DNA. Phylogenetic analysis of complete genome sequences revealed two distinct genetic groups in the gibbon/orangutan clade. Three were similar to previously described variants infecting H. pileatus in Thailand and eight formed a distinct clade, potentially representing distinct strains of HBV circulating in geographically separated populations in South-East Asia. Because of the ability of HBV to cross species barriers, large reservoirs of infection in gibbons may hamper ongoing attempts at permanent eradication of HBV infection from human populations in South-East Asia through immunization.

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