A genetic perspective on African prehistory

The various genetic systems (mitochondrial DNA, the Y-chromosome and the genome-wide autosomes) indicate that Africa is the most genetically diverse continent in the world and the most likely place of origin for anatomically modern humans. However, where in Africa modern humans arose and how the current genetic makeup within the continent was shaped is still open to debate. Here, we summarize the debate and focus especially on the maternally inherited mitochondrial DNA (mtDNA) and a recently revised chronology for the African mtDNA tree. We discuss the possible origin of modern humans in southern, eastern or Central Africa; the possibility of a migration from southern to eastern Africa more than 100 ka, carrying lineages within mtDNA haplogroup L0; the evidence for a climate-change-mediated population expansion in eastern Africa involving mtDNA haplogroup L3, leading to the “out-of-Africa” migration around 70–60 ka; the re-population of North Africa from the Near East around 40–30 ka suggested by mtDNA haplogroups U6 and M1; the evidence for population expansions and dispersals across the continent at the onset of the Holocene ; and the impact of the Bantu dispersals in Central, eastern and southern Africa within the last few millennia.

The social transition of risk factors for cardiovascular disease in the African region: evidence from three cross-sectional surveys in the Seychelles.

OBJECTIVES: To examine the association between socioeconomic status (SES) and several cardiovascular disease risk factors (CVRFs) and to assess whether this association has changed over a 15-year observation period. METHODS: Three independent population-based surveys of CVRFs were conducted in representative samples of all adults aged 25-64 years in the Seychelles, a small island state located east to Kenya, in 1989 (N=1081), 1994 (N=1067) and 2004 (N=1255). RESULTS: Among men, current smoking and heavy drinking were more prevalent in the low versus the high SES group, and obesity was less prevalent. The socioeconomic gradient in diabetes reversed over the study period from lower prevalence in the low versus the high SES group to higher prevalence in the low SES group. Hypercholesterolemia was less prevalent in the low versus the high SES group in 1989 but the prevalence was similar in the two groups in 2004. Hypertension showed no consistent socioeconomic pattern. Among women, the SES gradient in smoking tended to reverse over time from lower prevalence in the low SES group to lower prevalence in the high SES group. Obesity and diabetes were more common in the low versus the high SES group over the study period. Heavy drinking, hypertension and hypercholesterolemia were not socially patterned among women. CONCLUSION: The prevalence of several CVRFs was higher in low versus high SES groups in a rapidly developing country in the African region, and an increase of the burden of these CVRFs in the most disadvantaged groups of the population was observed over the 15 years study period.

The Distant neighbors — EU, Middle East, North Africa and the Euro-Mediterranean Partnership

The Barcelona Euro-Mediterranean Conference (1995) was intended to be a launching pad" for creating a new, innovative relationship between the EU-Fifteen and a selected set of non-member Middle Eastern and North African countries. The Barcelona Process was to become the European Union´s first attempt, of several, to create postmodern inclusive policy spheres as a way to deal with the post-enlargement problems of ´ins´ and outs´ in its immediate periphery. Nevertheless, in spite of geographical proximity, common problems and stated interest in creating amorphous EU borders in different sectors, the Euro-Mediterranean Partnership is today all but abandoned. This paper will examine some of the factors behind the current degeneration of the EU´s post-bipolar foreign policy strategy in the Mediterranean, by exploring the dialectic between the Union´s desire to expand its geopolitical, economic and cultural boundaries and the need to secure its territorial area (from migration, proliferation, social instability etc.). In the final part of the paper some suggestions for how to revive the relationship across the Mare Nostrum will be forwarded.

African signatures of recent positive selection in human FOXI1

Background: The human FOXI1 gene codes for a transcription factor involved in the physiology of the inner ear, testis, and kidney. Using three interspecies comparisons, it has been suggested that this may be a gene underhuman-specific selection. We sought to confirm this finding by using an extended set of orthologous sequences.Additionally, we explored for signals of natural selection within humans by sequencing the gene in 20 Europeans,20 East Asians and 20 Yorubas and by analysing SNP variation in a 2 Mb region centered on FOXI1 in 39worldwide human populations from the HGDP-CEPH diversity panel.Results: The genome sequences recently available from other primate and non-primate species showed that FOXI1divergence patterns are compatible with neutral evolution. Sequence-based neutrality tests were not significant inEuropeans, East Asians or Yorubas. However, the Long Range Haplotype (LRH) test, as well as the iHS and XP-Rsbstatistics revealed significantly extended tracks of homozygosity around FOXI1 in Africa, suggesting a recentepisode of positive selection acting on this gene. A functionally relevant SNP, as well as several SNPs either on theputatively selected core haplotypes or with significant iHS or XP-Rsb values, displayed allele frequencies stronglycorrelated with the absolute geographical latitude of the populations sampled.Conclusions: We present evidence for recent positive selection in the FOXI1 gene region in Africa. Climate mightbe related to this recent adaptive event in humans. Of the multiple functions of FOXI1, its role in kidney-mediatedwater-electrolyte homeostasis is the most obvious candidate for explaining a climate-related adaptation.

Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.

High blood pressure (BP) is more prevalent and contributes to more severe manifestations of cardiovascular disease (CVD) in African Americans than in any other United States ethnic group. Several small African-ancestry (AA) BP genome-wide association studies (GWASs) have been published, but their findings have failed to replicate to date. We report on a large AA BP GWAS meta-analysis that includes 29,378 individuals from 19 discovery cohorts and subsequent replication in additional samples of AA (n = 10,386), European ancestry (EA) (n = 69,395), and East Asian ancestry (n = 19,601). Five loci (EVX1-HOXA, ULK4, RSPO3, PLEKHG1, and SOX6) reached genome-wide significance (p < 1.0 × 10(-8)) for either systolic or diastolic BP in a transethnic meta-analysis after correction for multiple testing. Three of these BP loci (EVX1-HOXA, RSPO3, and PLEKHG1) lack previous associations with BP. We also identified one independent signal in a known BP locus (SOX6) and provide evidence for fine mapping in four additional validated BP loci. We also demonstrate that validated EA BP GWAS loci, considered jointly, show significant effects in AA samples. Consequently, these findings suggest that BP loci might have universal effects across studied populations, demonstrating that multiethnic samples are an essential component in identifying, fine mapping, and understanding their trait variability.

Risk factors of stroke mortality in the African region: a cohort study

Background: Population-based cohort studies of risk factors of stroke are scarce in developing countries and none has been done in the African region. We conducted a longitudinal study in the Seychelles (Indian Ocean, east of Kenya), a middle-income island state where the majority of the population is of African descent. Such data in Africa are important for international comparison and for advocacy in the region. Methods: Three examination surveys of cardiovascular risk factors were performed in independent samples representative of the general population aged 25-64 in 1989, 1994 and 2004 (n=1081, 1067, and 1255, respectively). Baseline risk factors data were linked with cause-specific mortality from vital statistics up to May 2007 (all deaths are medically certified in the Seychelles and kept in an electronic database). We considered stroke (any type) as a cause of death if the diagnosis was reported in any of the 4 fields in the death certificates for underlying and concomitant causes of death. Results. Among the 2479 persons aged 35-64 at baseline, 280 died including 56 with stroke during follow up (maximum: 18.2 years; mean: 10.2 years). In this age range, age-adjusted mortality rates (/100'000/year) were 969 for all cause and 187 for stroke; age-adjusted prevalence of high blood pressure (≥140/90 mmHg) was 48%. In multivariate Cox survival time regression, stroke mortality was increased by 18% and 35% for a 10-mmHg increase in systolic, respectively diastolic BP (p<0.001). Stroke mortality was also associated with age, smoking ≥5 cigarettes vs. no smoking (HR: 2.4; 95% CI: 1.2-4.8) and diabetes (HR: 1.9; 1.02-3.6) but not with sex, LDL-cholesterol intake, alcohol intake and professional occupation. Conclusion. This first population-based cohort study in the African region demonstrates high mortality rates from stroke in middle-aged adults and confirms associations with high BP and other risk factors. This emphasizes the importance of reducing BP and other modifiable risk factors in high risk individuals and in the general population as a main strategy to reduce the burden of stroke.

25-Hydroxyvitamin D in African-origin populations at varying latitudes challenges the construct of a physiologic norm.

BACKGROUND: The vitamin D-endocrine system is thought to play a role in physiologic processes that range from mineral metabolism to immune function. Serum 25-hydroxyvitamin D [25(OH)D] is the accepted biomarker for vitamin D status. Skin color is a key determinant of circulating 25(OH)D concentrations, and genes responsible for melanin content have been shown to be under strong evolutionary selection in populations living in temperate zones. Little is known about the effect of latitude on mean concentrations of 25(OH)D in dark-skinned populations. OBJECTIVE: The objective was to describe the distribution of 25(OH)D and its subcomponents in 5 population samples of African origin from the United States, Jamaica, Ghana, South Africa, and the Seychelles. DESIGN: Participants were drawn from the Modeling of the Epidemiologic Transition Study, a cross-sectional observational study in 2500 adults, ages 25-45 y, enrolled between January 2010 and December 2011. Five hundred participants, ∼50% of whom were female, were enrolled in each of 5 study sites: Chicago, IL (latitude: 41°N); Kingston, Jamaica (17°N); Kumasi, Ghana (6°N); Victoria, Seychelles (4°S); and Cape Town, South Africa (34°S). All participants had an ancestry primarily of African origin; participants from the Seychelles trace their history to East Africa. RESULTS: A negative correlation between 25(OH)D and distance from the equator was observed across population samples. The frequency distribution of 25(OH)D in Ghana was almost perfectly normal (Gaussian), with progressively lower means and increasing skewness observed at higher latitudes. CONCLUSIONS: It is widely assumed that lighter skin color in populations outside the tropics resulted from positive selection, driven in part by the relation between sun exposure, skin melanin content, and 25(OH)D production. Our findings show that robust compensatory mechanisms exist that create tolerance for wide variation in circulating concentrations of 25(OH)D across populations, suggesting a more complex evolutionary relation between skin color and the vitamin D pathway. This trial was registered at clinicaltrials.gov as NCT02111902.

Cross-hemispheric transport of Central African biomass burning pollutants: Implications for downwind ozone production

Pollutant plumes with enhanced concentrations of trace gases and aerosols were observed over the southern coast of West Africa during August 2006 as part of the AMMA wet season field campaign. Plumes were observed both in the mid and upper troposphere. In this study we examined the origin of these pollutant plumes, and their potential to photochemically produce ozone (O3) downwind over the Atlantic Ocean. Their possible contribution to the Atlantic O3 maximum is also discussed. Runs using the BOLAM mesoscale model including biomass burning carbon monoxide (CO) tracers were used to confirm an origin from central African biomass burning fires. The plumes measured in the mid troposphere (MT) had significantly higher pollutant concentrations over West Africa compared to the upper tropospheric (UT) plume. The mesoscale model reproduces these differences and the two different pathways for the plumes at different altitudes: transport to the north-east of the fire region, moist convective uplift and transport to West Africa for the upper tropospheric plume versus north-west transport over the Gulf of Guinea for the mid-tropospheric plume. Lower concentrations in the upper troposphere are mainly due to enhanced mixing during upward transport. Model simulations suggest that MT and UT plumes are 16 and 14 days old respectively when measured over West Africa. The ratio of tracer concentrations at 600 hPa and 250 hPa was estimated for 14–15 August in the region of the observed plumes and compares well with the same ratio derived from observed carbon dioxide (CO2) enhancements in both plumes. It is estimated that, for the period 1–15 August, the ratio of Biomass Burning (BB) tracer concentration transported in the UT to the ones transported in the MT is 0.6 over West Africa and the equatorial South Atlantic. Runs using a photochemical trajectory model, CiTTyCAT, initialized with the observations, were used to estimate in-situ net photochemical O3 production rates in these plumes during transport downwind of West Africa. The mid-troposphere plume spreads over altitude between 1.5 and 6 km over the Atlantic Ocean. Even though the plume was old, it was still very photochemically active (mean net O3 production rates over 10 days of 2.6 ppbv/day and up to 7 ppbv/day during the first days) above 3 km especially during the first few days of transport westward. It is also shown that the impact of high aerosol loads in the MT plume on photolysis rates serves to delay the peak in modelled O3 concentrations. These results suggest that a significant fraction of enhanced O3 in mid-troposphere over the Atlantic comes from BB sources during the summer monsoon period. According to simulated occurrence of such transport, BB may be the main source for O3 enhancement in the equatorial south Atlantic MT, at least in August 2006. The upper tropospheric plume was also still photochemically active, although mean net O3 production rates were slower (1.3 ppbv/day). The results suggest that, whilst the transport of BB pollutants to the UT is variable (as shown by the mesoscale model simulations), pollution from biomass burning can make an important contribution to additional photochemical production of O3 in addition to other important sources such as nitrogen oxides (NOx) from lightning.

Patterns of peristome reduction and ornamentation in African Entodontaceae

The Entodontaceae is characterised by erect capsules with inset and substantially reduced peristomes. Differences in peristome morphology and ornamentation delimit both genera and species within the family. The Entodontaceae, as presently recognised, consists of four genera, Entodon, Erythrodontium, Mesonodon and Pylaisiobryum, which show a variety of peristome ornamentation patterns, and exhibit differing levels of peristome reduction. This variation encompasses an unusual combination of structurally reduced peristomes, which retain massive exostome ornamentation, and residual peristome function. As part of a taxonomic revision of the family in Africa, generic patterns of peristome reduction and ornamentation are described. Inter- and intra-specific variation patterns of both the exostome and endostome have been investigated using detailed SEM studies of material from Africa and beyond. Structural reduction of the peristome is associated with high levels of intra-specific variation in peristome ornamentation patterns. Common trends in these patterns of variation are identified within the family. Putative hybrid sporophytes have been identified in Entodon, and the taxonomic implications of these observations are considered for a family where species delimitation has in the past often depended on minor variation in peristome structure or ornamentation patterns. (author abst.)

Child labour in African Artisanal Mining Communities: experiences from Northern Ghana

The issue of child labour in the artisanal and small-scale mining (ASM) economy is attracting significant attention worldwide. This article critically examines this ‘problem’ in the context of sub-Saharan Africa, where a lack of formal sector employment opportunities and/or the need to provide financial support to their impoverished families has led tens of thousands of children to take up work in this industry. The article begins by engaging with the main debates on child labour in an attempt to explain why young boys and girls elect to pursue arduous work in ASM camps across the region. The remainder of the article uses the Ghana experience to further articulate the challenges associated with eradicating child labour at ASM camps, drawing upon recent fieldwork undertaken in Talensi-Nabdam District, Upper East Region. Overall, the issue of child labour in African ASM communities has been diagnosed far too superficially, and until donor agencies and host governments fully come to grips with the underlying causes of the poverty responsible for its existence, it will continue to burgeon.

New Trypanosoma (Duttonella) vivax genotypes from tsetse flies in East Africa

Salivarian trypanosomes pose a substantial threat to livestock, but their full diversity is not known. To survey trypanosomes carried by tsetse in Tanzania, DNA samples from infected proboscides of Glossina pallidipes and G. swynnertoni were identified using fluorescent fragment length barcoding (FFLB), which discriminates species by size polymorphisms in multiple regions of the ribosomal RNA locus. FELLB identified the trypanosomes in 65 of 105 (61.9%) infected proboscides, revealing 9 mixed infections. Of 7 different FFLB profiles, 2 were similar but not identical to reference West African Trypanosoma vivax; 5 other profiles belonged to known species also identified in fly midguts. Phylogenetic analysis of the glycosomal glyceraldehyde phosphate dehydrogenase gene revealed that the Tanzanian T. vivax samples fell into 2 distinct groups, both outside the main chide of African and South American T. vivax. These new T. vivax genotypes were common and widespread in tsetse in Tanzania. The T. brucei-like trypanosome previously described from tsetse midguts was also found in 2 proboscides, demonstrating a salivarian transmission route. Investigation of mammalian host range and pathogenicity will reveal the importance of these new trypanosomes for the epidemiology and control of animal trypanosomiasis in East Africa.

Neoproterozoic geodynamic evolution of SW-Gondwana: a southern African perspective

Our current understanding of the tectonic history of the principal Pan-African orogenic belts in southwestern Africa, reaching from the West Congo Belt in the north to the Lufilian/Zambezi, Kaoko, Damara, Gariep and finally the Saldania Belt in the south, is briefly summarized. On that basis, possible links with tectono-stratigraphic units and major structures on the eastern side of the Rio de la Plata Craton are suggested, and a revised geodynamic model for the amalgamation of SW-Gondwana is proposed. The Rio de la Plata and Kalahari Cratons are considered to have become juxtaposed already by the end of the Mesoproterozoic. Early Neoproterozoic rifting led to the fragmentation of the northwestern (in today`s coordinates) Kalahari Craton and the splitting off of several small cratonic blocks. The largest of these ex-Kalahari cratonic fragments is probably the Angola Block. Smaller fragments include the Luis Alves and Curitiba microplates in eastern Brazil, several basement inliers within the Damara Belt, and an elongate fragment off the western margin, named Arachania. The main suture between the Kalahari and the Congo-So Francisco Cratons is suspected to be hidden beneath younger cover between the West Congo Belt and the Lufilian/Zambezi Belts and probably continues westwards via the Cabo Frio Terrane into the Goias magmatic arc along the Brasilia Belt. Many of the rift grabens that separated the various former Kalahari cratonic fragments did not evolve into oceanic basins, such as the Northern Nosib Rift in the Damara Belt and the Gariep rift basin. Following latest Cryogenian/early Ediacaran closure of the Brazilides Ocean between the Rio de la Plata Craton and the westernmost fragment of the Kalahari Craton, the latter, Arachania, became the locus of a more than 1,000-km-long continental magmatic arc, the Cuchilla Dionisio-Pelotas Arc. A correspondingly long back-arc basin (Marmora Basin) on the eastern flank of that arc is recognized, remnants of which are found in the Marmora Terrane-the largest accumulation of oceanic crustal material known from any of the Pan-African orogenic belts in the region. Corresponding foredeep deposits that emerged from the late Ediacaran closure of this back-arc basin are well preserved in the southern areas, i.e. the Punta del Este Terrane, the Marmora Terrane and the Tygerberg Terrane. Further to the north, present erosion levels correspond with much deeper crustal sections and comparable deposits are not preserved anymore. Closure of the Brazilides Ocean, and in consequence of the Marmora back-arc basin, resulted from a change in the Rio de la Plata plate motion when the Iapetus Ocean opened between the latter and Laurentia towards the end of the Ediacaran. Later break-up of Gondwana and opening of the modern South Atlantic would have followed largely along the axis of the Marmora back-arc basin and not along major continental sutures.

One, two or no record of late neoproterozoic glaciation in South-East Cameroon?

Severe climate changes culminating in at least three major glacial events have been recognized in the Neoproterozoic sedimentary record from many parts of the world Supportive to the global nature of these climatic shifts a considerable amount of data have been acquired from deposits exposed in Pan-African orogenic belts in southwestern and western Africa By comparison published data from the Pan-African belts in Central Africa are scarce We report here evidence of possibly two glacial events recorded in the Mintom Formation that is located on the margin of the Pan-African orogenic Yaounde belt in South-East Cameroon In the absence of reliable radiometric data only maximum and minimum age limits of 640 and 580 Ma respectively can at present be applied to the Mintom Formation The formation consists of two lithostratigraphic ensembles each subdivided in two members (i e in ascending stratigraphic order the Kol Metou Momibole and Atog Adjap Members) The basal ensemble exhibits a typical glacial to post-glacial succession It includes diamictites comprising cobbles and boulders in a massive argillaceous siltstone matrix and laminated siltstones followed by in sharp contact a 2 m-thick massive dolostone that yielded negative delta(13)C values (<-3 parts per thousand. V-PDB) similar to those reported for Marinoan cap carbonates elsewhere However uncertainty remains regarding the glacial influence on the siliciclastic facies because the diamictite is better explained as a mass-flow deposit and diagnostic features such as dropstones have not been seen in the overlying siltstones The Mintom Formation may thus provide an example of an unusual succession of non-glacial diamictite overlain by a truly glacial melt-related cap-carbonate We also report the recent discovery of ice-striated pavements on the structural surface cut in the Mintom Formation suggesting that glaciers developed after the latter had been deposited and deformed during the Pan-African orogeny Striations which consistently exhibit two principal orientations (N60 and N110) were identified in two different localities in the west of the study area on siltstones of the Kol Member and in the east on limestones of the Atog Adjap Member respectively N60-oriented striae indicate ice flow towards the WSW Assigning an age to these features remains problematical because they were not found associated with glaciogenic deposits Two hypotheses can equally be envisaged e either the striated surfaces are correlated (1) to the Gaskiers (or Neoproterozoic post-Gaskiers) glaciation and represent the youngest Ediacaran glacial event documented in the southern Yaounde belt or (2) to the Late Ordovician Hirnantian (Saharan) glaciation thereby providing new data about Hirnantian ice flows in Central Africa (C) 2010 Elsevier Ltd All rights reserved

Relics of eclogite facies assemblages in the Ceara Central Domain, NW Borborema Province, NE Brazil: Implications for the assembly of West Gondwana

The Borborema Province, in the NE of Brazil, is a rather complex piece in the Brazil-Africa puzzle as it represents the junction of the Dahomeyide/Pharusian, Central African, Aracuai and Brasilia fold belts located between the West-African/Sao Luis, Congo/Sao Francisco and Amazonas craton. The correlation between the Dahomeyides from W-Africa (Ghana, Benin, Togo, and Mali) and the Borborema Province involves the Medio Coreau and Central Ceara domains. The inferred continuation of the main oceanic suture zone exposed in the Dahomeyides of W Africa is buried beneath the Phanerozoic Parnaiba Basin in Brazil (northwest of the Medio Coreau domain) where some high density gravity anomalies may represent hidden remnants of an oceanic suture. In addition to this major suture a narrow, nearly continuous strip composed of mainly mafic pods containing relics of eclogite-facies assemblages associated with partially migmatized granulite-facies metapelitic gneisses has been found further east in the NW Borborema Province. These high pressure mafic rocks, interpreted as retrograded eclogites, are located between the Transbrasiliano Lineament and the Santa Quiteria continental arc and comprise primitive to evolved arc-related rocks with either arc- or MORB-type imprints that can indicate either deep subduction of oceanic lithosphere or roots of continental and oceanic magmatic arcs. Average peak P-T conditions under eclogite-facies metamorphism (T=770 degrees C and P = 17.3 kbar) were estimated using garnet-clinopyroxene thermometry and Jd content in clinopyroxene. Transition to granulite-facies conditions, as well as later widespread re-equilibration under amphibolite facies, were registered both in the basic and the metapelitic rocks and suggest a clockwise P-T path characterized by an increase in temperature followed by strong decompression. A phenomenon possibly related to the exhumation of a highly thickened crust associated with the suturing of the Medio Coreau and Central Ceara domains, two distinct crustal blocks separated by the Transbrasiliano Lineament. (C) 2009 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

African-Derived mitochondria in South American native cattle breeds (Bos taurus): Evidence of a new taurine mitochondrial lineage

This article reports the nucleotide diversity within the control region of 42 mitochondrial chromosomes belonging to five South American native cattle breeds (Bos taurus). Analysis of these data in conjunction with B. taurus and B. indicus sequences from Africa, Europe, the Near East, India, and Japan allowed the recognition of eight new mitochondrial haplotypes and their relative positions in a phylogenetic network. The structure of genetic variation among different hypothetical groupings was tested through the molecular variance decomposition, which was best explained by haplotype group components. Haplotypes surveyed were classified as European-related and African-related. Unexpectedly, two haplotypes within the African cluster were more divergent from the African consensus than the latter from the European consensus. A neighbor-joining tree shows the position of two haplotypes compared to European/African mitochondrial lineage splitting. This different and putatively ancestral mitochondrial lineage (AA) is supported by the calibration of sequence divergence based on the Bos-Bison separation. The European/African mitochondria divergence might be subsequent (67,100 years before present) to that between AA and Africans (84,700 years before present), also preceding domestication times. These genetic data could reflect the haplotype distribution of Iberian cattle five centuries ago.