Genome-wide analysis of copy number variants and normal facial variation in a large cohort of Bantu Africans

Similarity in facial characteristics between relatives suggests a strong genetic component underlies facial variation. While there have been numerous studies of the genetics of facial abnormalities and, more recently, single nucleotide polymorphism (SNP) genome-wide association studies (GWASs) of normal facial variation, little is known about the role of genetic structural variation in determining facial shape. In a sample of Bantu African children, we found that only 9% of common copy number variants (CNVs) and 10-kb CNV analysis windows are well tagged by SNPs (r² ≥ 0.8), indicating that associations with our internally called CNVs were not captured by previous SNP-based GWASs. Here, we present a GWAS and gene set analysis of the relationship between normal facial variation and CNVs in a sample of Bantu African children. We report the top five regions, which had p values ≤ 9.35 × 10⁻⁶ and find nominal evidence of independent CNV association (p < 0.05) in three regions previously identified in SNP-based GWASs. The CNV region with strongest association (p = 1.16 × 10⁻⁶, 55 losses and seven gains) contains NFATC1, which has been linked to facial morphogenesis and Cherubism, a syndrome involving abnormal lower facial development. Genomic loss in the region is associated with smaller average lower facial depth. Importantly, new loci identified here were not identified in a SNP-based GWAS, suggesting that CNVs are likely involved in determining facial shape variation. Given the plethora of SNP-based GWASs, calling CNVs from existing data may be a relatively inexpensive way to aid in the study of complex traits.

Uncovering Tonal and Temporal Correlates of Phrasal Prominence in Medʉmba

Characterizing prosodic prominence relations in African tone languages is notoriously difficult, as typical acoustic cues to prominence (changes in F0, increases in intensity, etc.) can be difficult to distinguish from those which mark tonal contrasts. The task of establishing prominence is further complicated by the fact that tone, an important cue to syllable prominence and prosodic boundaries cross-linguistically, plays many roles in African languages: tones often signal lexical contrasts, can themselves be morphemes, and can also interact in key ways with prosody. The present study builds on phonological generalizations about tonal patterns in Medʉmba, a Grassfields Bantu language, and uses the speech cycling paradigm to investigate relative timing of syllables varying in phrase-level prominence. Specifically, we investigate timing asymmetries between syllables hypothesized to occur at the edge of a phonological phrase, which carry a high phrase accent, and those in phrase-medial position, which do not. Results indicate significant differences in the temporal alignment of accented versus non-accented syllables, with accented syllables occurring significantly closer to positions established as prominence-attracting in previous speech cycling research. We show that these findings cannot be attributed to differences in tone alone. Findings demonstrate the importance of relative temporal alignment as a correlate of prosodic prominence. Findings also point to increased duration as a phonetic property which distinguishes between syllables bearing phrasal prominence from those which do not.

Genome-wide copy number variations in a large cohort of bantu African children

BACKGROUND

Copy number variations (CNVs) account for a substantial proportion of inter-individual genomic variation. However, a majority of genomic variation studies have focused on single-nucleotide variations (SNVs), with limited genome-wide analysis of CNVs in large cohorts, especially in populations that are under-represented in genetic studies including people of African descent.

METHODS

We carried out a genome-wide copy number analysis in > 3400 healthy Bantu Africans from Tanzania. Signal intensity data from high density (> 2.5 million probes) genotyping arrays were used for CNV calling with three algorithms including PennCNV, DNAcopy and VanillaICE. Stringent quality metrics and filtering criteria were applied to obtain high confidence CNVs.

RESULTS

We identified over 400,000 CNVs larger than 1 kilobase (kb), for an average of 120 CNVs (SE = 2.57) per individual. We detected 866 large CNVs (≥ 300 kb), some of which overlapped genomic regions previously associated with multiple congenital anomaly syndromes, including Prader-Willi/Angelman syndrome (Type1) and 22q11.2 deletion syndrome. Furthermore, several of the common CNVs seen in our cohort (≥ 5%) overlap genes previously associated with developmental disorders.

CONCLUSIONS

These findings may help refine the phenotypic outcomes and penetrance of variations affecting genes and genomic regions previously implicated in diseases. Our study provides one of the largest datasets of CNVs from individuals of African ancestry, enabling improved clinical evaluation and disease association of CNVs observed in research and clinical studies in African populations.

An Acoustic Study of Sandhi Vowel Hiatus in Luganda

In Luganda (Bantu, Uganda), a sequence of vowels in successive syllables (V.V) is not allowed. If the first vowel is high, the two vowels are joined together in a diphthong (e.g., i + a → i͜a). If the first vowel is non-high, it is deleted with compensatory lengthening of the second vowel in the sequence (e.g., e + a → aː). This paper presents an acoustic investigation of inter-word V#V sequences in Luganda. It was found that the vowel interval in V#V sequences is longer than that in V#C sequences. When the first vowel in V#V is non-high, the formant frequency of the outcome is determined by the second vowel in the sequence. When the first vowel is high, on the other hand, the sequence is realized as a diphthong, with the transition between the two formant patterns taking up most of the duration. The durational patterns within these diphthongs provide evidence against the transcription-based claim that these sequences are reorganized so that the length lies in the second vowel (/i#V/ → [jVː]). The findings bring into question a canonical case of compensatory lengthening conditioned by glide formation.

Genetic structure and sex-biased gene flow in the history of southern African populations

Objectives

We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y‐chromosome haplogroup E1b1b (E‐M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex‐biased gene flow in southern Africa.

Materials and methods

We analyzed previously published complete mtDNA genome sequences and ∼900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y‐linked STR loci for samples assigned to haplogroup E1b1b.

Results

Our results support an eastern African origin for Y‐chromosome haplogroup E1b1b (E‐M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male‐dominated expansion. Our finding of a significant increase in the intensity of the sex‐biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

Conclusions

Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex‐biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

Association of urinary sodium excretion with blood pressure and risk factors associated with hypertension among Cameroonian pygmies and bantus: a cross-sectional study

Background

High salt intake increases blood pressure (BP) and hypertension risk. This study aimed to examine association of urinary sodium excretion with BP and hypertension correlates among Cameroonian pygmies under hunter-gatherer subsistence mode and Bantus, living in urban area under unhealthy behavioral habits.

Methods

In this cross-sectional cluster sampling study, we randomly enrolled rural pygmies living in Lolodorf and urban Bantus living in Douala. The World Health Organization steps questionnaire was used to collect socio-demographic and lifestyle data. Height, weight, BP and single overnight spot urine samples were obtained in all participants. BP was measured in triplicate. Urinary sodium and potassium excretion was determined by flame photometry. Data were recorded and analyzed using SPSS 16.0.

Results

We included 150 Pygmies and 150 Bantus aged 38 ± 12 years and 33 ± 11 years, respectively (p <  0.0001). Compare to Bantus, pygmy’s height and weight were respectively: 1.54 ± 0.09 m vs 1.72 ± 0.12 m; and 54.4 ± 9.2 kg vs 77.2 ± 14.8 kg, all p <  0.0001. Age-standardized prevalence of hypertension was 3.3% among Pygmies and 28% among Bantus (p <  0.0001). Age-adjusted systolic and diastolic BP were lower in Pygmies than in Bantus (107 ± 12 vs 119 ± 17 mmHg and 71 ± 11 vs 78 ± 13 mmHg respectively, all P <  0.0001). BP increased with age but to a lesser extent in Pygmies (all p <  0.01). Urinary sodium excretion was lower in Pygmies than in Bantus (46.9 ± 32.4 vs 121.5 ± 61.0 mmol/l, p <  0.0001). Systolic and diastolic BP were positively associated with urinary sodium excretion in Bantus (all p <  0.05). In the two groups, urinary potassium excretion was similar, and was not related to blood pressure. In the total study group and in Bantus taken separately, urinary sodium excretion was higher in hypertensive than in normotensive subjects. Multivariable logistic regression showed that urinary sodium excretion, Bantu status and age emerged as independent determinants of hypertension in the whole study group (OR (95%CI): 1.012 (1.005–1.018); 11.408 (3.599–36.165); 1.095 (1.057–1.135) respectively, p <  0.0001).

Conclusion

Hunter-gatherer pygmies exhibit low level of urinary sodium excretion related to low rate of hypertension and slower BP increase with age. Salt intake was a major driver of hypertension in our study population. Our findings highlight the need of efforts to implement nationwide prevention programs promoting risk factor screening and healthier lifestyles including reduction of dietary salt intake in Cameroonian.

Matriclans shape populations: Insights from the Angolan Namib Desert into the maternal genetic history of southern Africa

OBJECTIVES

Southern Angola is a poorly studied region, inhabited by populations that have been associated with different migratory movements into southern Africa. Apart from Kx'a-speaking San foragers and Bantu-speaking pastoralists, ethnographic and linguistic studies have suggested the existence of an enigmatic array of pre-Bantu communities, like the Kwepe (formerly Khoe-Kwadi speakers), Twa and Kwisi. Here, we evaluate previous peopling hypotheses by assessing the relationships between different southern Angolan populations, based on newly collected linguistic data and complete mtDNA genomes.

MATERIALS AND METHODS

We analyzed 295 complete mtDNA genomes and linguistic data from seven groups from the Namib Desert (Himba, Kuvale, Tjimba, Twa, Kwisi, Kwepe) and Kunene Province (!Xun), placing special emphasis on the evaluation of the genealogical consistency of the matriclanic system that characterizes most of these groups.

RESULTS

We found that the maternal genetic structure of all groups from the Namib Desert was strongly shaped by the consistency of their matriclanic system. The tracking of the maternal heritage enhanced population differentiation by genetic drift and is likely to have caused the divergent mtDNA profiles of the Kwepe, Twa, and Kwisi, who probably formed a single population within the spectrum of Bantu genetic variation. Model-based analyses further suggest that the dominant pastoral groups Kuvale and Himba may be grouped into a Bantu proto-population which also included the ancestors of present-day Tjimba and Herero, as well as the Khoe-Kwadi speaking Damara foragers from Namibia.

DISCUSSION

The view from southwestern Angola offers a new perspective on the populating history of southern Africa and the Bantu expansions by showing that social stratification and different subsistence patterns are not always indicative of remnant groups, but may reflect Bantu-internal variation and ethnogenesis.

Evaluation of the InnoTyper® 21 genotyping kit in multi-ethnic populations

We report the findings of the evaluation of the InnoTyper^® 21 genotyping kit for the use of human identification (HID) and paternity testing in South Africa. This novel forensic kit evaluates 20 retrotransposable elements (AC4027, MLS26, ALU79712, NBC216, NBC106, RG148, NBC13, AC2265, MLS09, AC1141, TARBP, AC2305, HS4.69, NBC51, ACA1766, NBC120, NBC10, NBC102, SB19.12 and NBC148) and the Amelogenin locus for sex determination. The evaluation of the genotyping performance showed no significant spectral pull-up for peak heights between 100 and 30,000 RFUs. All loci presented biallelic patterns except the triallelic RG148 locus resulting from a variant insertion allele, named RG148I-1, observed exclusively in the Bantu. The InnoTyper^® 21 kit was found to be highly discriminatory between the 507 unrelated individuals of the Afrikaaner, Asian Indian, Coloured, amaXhosa and amaZulu groups. The HID parameters: the CPD ranged between 0.99999987 and 0.9999999845, and the CMP between 1.0335×10^-7 and 1.5506×10^-8. The paternity parameters: the CPI ranged between 0.0202 and 0.3177, and the CPE between 0.9161 and 0.9749. There were no significant signs of deviations from HWE or linkage disequilibrium (LD) after applying a Bonferroni correction. This kit also showed minor levels of population structure which could differentiate between the African and non-African population groups. Finally, in challenging casework with severely degraded biological material, the InnoTyper^® 21 genotyping kit was compatible with GlobalFiler^® and Investigator DIPplex^® to increase the HID parameters.

On the Bantu expansion

Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups.

Phenotypic Diversity of Sickle Cell Disease in Patients with a Double Heterozygosity for Hb S and Hb D-Punjab

Phenotypic heterogeneity for sickle cell disease is associated to several genetic factors such as genotype for sickle cell disease, β-globin gene cluster haplotypes and Hb F levels. The coinheritance of Hb S (HBB: c.20A > T) and Hb D-Punjab (HBB: c.364G > C) results in a double heterozygosity, which constitutes one of the genotypic causes of sickle cell disease. This study aimed to assess the phenotypic diversity of sickle cell disease presented by carriers of the Hb S/Hb D-Punjab genotype and the Bantu [- + - - - -] haplotype. We evaluated medical records from 12 patients with sickle cell disease whose Hb S/Hb D-Punjab genotype and Bantu haplotype were confirmed by molecular analysis. Hb S and Hb D-Punjab levels were quantified by chromatographic analysis. Mean concentrations of Hb S and Hb D-Punjab were 44.8 ± 2.3% and 43.3 ± 1.8%, respectively. Painful crises were present in eight (66.7%) patients evaluated, representing the most common clinical event. Acute chest syndrome (ACS) was the second most prevalent manifestation, occurring in two individuals (16.7%). Three patients were asymptomatic, while another two exhibited greater diversity of severe clinical manifestations. Medical records here analyzed reported a significant clinical diversity in sickle cell disease ranging from the absence of symptoms to wide phenotypic variety. The sickle cell disease genotype, Bantu haplotype and hemoglobin (Hb) levels did not influence the clinical diversity. Thus, we concluded that the phenotypic variation in sickle cell disease was present within a specific genotype for disease regardless of the β-globin gene cluster haplotypes.

Food and pathogen adaptations in the Angolan Namib desert: Tracing the spread of lactase persistence and human African trypanosomiasis resistance into southwestern Africa

OBJECTIVES

We investigated the frequency distribution and haplotype diversity of human African trypanosomiasis (HAT) resistance and lactase persistence (LP) variants in populations from the Angolan Namib to trace the spread of these genetic adaptations into southwestern Africa.

MATERIALS AND METHODS

We resequenced two fragments of the LCT enhancer and the APOL1 gene and genotyped flanking short tandem repeat loci in six groups with different subsistence traditions living in the Angolan Namib, and in a comparative dataset including other populations from Africa and Europe. LP in the Angolan Namib is represented by the -14010*C allele, which is associated with a predominant haplotype that is shared with other southern and eastern African populations. While LP was found to be more frequent in foragers than in pastoralists, the frequencies of the two APOL1 variants associated with HAT-resistance (G1 and G2) did not differ between the two groups. The G1 allele is mostly associated with a single widespread haplotype. The G2 allele is linked to several haplotypes that are molecularly related to haplotypes found in other African Bantu-speaking populations. The putatively archaic G3 variant displayed more intra-allelic diversity in Africa than in Europe.

DISCUSSION

The LP adaptation was carried to southern Africa by non-Bantu speaking pastoralists from eastern Africa, but an obvious link between its presence in southern Angola and groups speaking languages of the Khoe-Kwadi family, as previously found in other areas, could not be confirmed. The presence of APOL1 variants G1 and G2 is linked to the Bantu expansions. Our results suggest that the G3 variant was retained in modern humans by incomplete lineage sorting.

Trends and challenges toward integration of traditional medicine in formal health-care system: Historical perspectives and appraisal of education curricula in Sub-Sahara Africa

The population residing Sub-Sahara Africa (SSA) continues to suffer from communicable health problems such as HIV/AIDS, malaria, tuberculosis, and various neglected tropical as well as non-communicable diseases. The disease burden is aggravated by shortage of medical personnel and medical supplies such as medical devices and minimal access to essential medicine. For long time, human beings through observation and practical experiences learned to use different plant species that led to the emergence of traditional medicine (TM) systems. The ancient Pharaonic Egyptian TM system is one of the oldest documented forms of TM practice in Africa and the pioneer of world's medical science. However, the medical practices diffused very fast to other continents being accelerated by advancement of technologies while leaving Africa lagging behind in the integration of the practice in formal health-care system. Challenging issues that drag back integration is the development of education curricula for training TM experts as the way of disseminating the traditional medical knowledge and practices imbedded in African culture. The few African countries such as Ghana managed to integrate TM products in the National Essential Medicine List while South Africa, Sierra Leone, and Tanzania have TM products being sold over the counters due to the availability of education training programs facilitated by research. This paper analyses the contribution of TM practice and products in modern medicine and gives recommendations that Africa should take in the integration process to safeguard the SSA population from disease burdens.

Bantu expansion shows that habitat alters the route and pace of human dispersals

Unlike most other biological species, humans can use cultural innovations to occupy a range of environments, raising the intriguing question of whether human migrations move relatively independently of habitat or show preferences for familiar ones. The Bantu expansion that swept out of West Central Africa beginning ∼5,000 y ago is one of the most influential cultural events of its kind, eventually spreading over a vast geographical area a new way of life in which farming played an increasingly important role. We use a new dated phylogeny of ∼400 Bantu languages to show that migrating Bantu-speaking populations did not expand from their ancestral homeland in a "random walk" but, rather, followed emerging savannah corridors, with rainforest habitats repeatedly imposing temporal barriers to movement. When populations did move from savannah into rainforest, rates of migration were slowed, delaying the occupation of the rainforest by on average 300 y, compared with similar migratory movements exclusively within savannah or within rainforest by established rainforest populations. Despite unmatched abilities to produce innovations culturally, unfamiliar habitats significantly alter the route and pace of human dispersals.

Phylogenetic reconstruction of Bantu kinship challenges Main Sequence Theory of human social evolution

Kinship provides the fundamental structure of human society: descent determines the inheritance pattern between generations, whereas residence rules govern the location a couple moves to after they marry. In turn, descent and residence patterns determine other key relationships such as alliance, trade, and marriage partners. Hunter-gatherer kinship patterns are viewed as flexible, whereas agricultural societies are thought to have developed much more stable kinship patterns as they expanded during the Holocene. Among the Bantu farmers of sub-Saharan Africa, the ancestral kinship patterns present at the beginning of the expansion are hotly contested, with some arguing for matrilineal and matrilocal patterns, whereas others maintain that any kind of lineality or sex-biased dispersal only emerged much later. Here, we use Bayesian phylogenetic methods to uncover the history of Bantu kinship patterns and trace the interplay between descent and residence systems. The results suggest a number of switches in both descent and residence patterns as Bantu farming spread, but that the first Bantu populations were patrilocal with patrilineal descent. Across the phylogeny, a change in descent triggered a switch away from patrifocal kinship, whereas a change in residence triggered a switch back from matrifocal kinship. These results challenge "Main Sequence Theory," which maintains that changes in residence rules precede change in other social structures. We also indicate the trajectory of kinship change, shedding new light on how this fundamental structure of society developed as farming spread across the globe during the Neolithic.

At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes

Here, we present 12 loci paternal haplotypes (Y-STR profiles) against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic) sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150) and Pygmy (B2b-M112) lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1) the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2) only traces of Khoisan (1.3%) and Pygmy (1.3%) markers persist in the Maputo Province Bantu gene pool, 3) the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4) the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west) may have impacted the paternal landscape of sub-Saharan Africa, 5) the admixture and assimilation processes of Bantu elements were both highly complex and region-specific.

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Maputo Bantus exhibit close affinities with other West and East African Bantus.

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Traces of Khoisan and Pygmy markers persist in the Maputo Province Bantus.

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R1a1a-M17/M198 in the Maputo Province may represent back or recent migration.

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Linguistic, cultural and genetic heritages are reflected in Maputo's gene pool.

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Admixture and assimilation processes of Bantu elements were region-specific.

Prevalence of the sickle cell trait in Gabon: a nationwide study

Sickle Cell Disease (SCD) is an important cause of death in young children in Africa, which the World Health Organization has declared a public health priority. Although SCD has been studied at the continental scale and at the local scale, a picture of its distribution at the scale of an African country has never been given. The aim of this study is to provide such a picture for the Republic of Gabon, a country where precisely the epidemiology of SCD has been poorly investigated. To this effect, 4250 blood samples from persons older than 15 were collected between June 2005 and September 2008 in 210 randomly selected villages from the nine administrative provinces of Gabon. Two methods were used to screen Sickle Cell Trait (SCT) carriers: isoelectric focusing (IEF) and high-performance liquid chromatography (HPLC). SCT prevalence in Gabon was 21.1% (895/4249). SCT prevalence was significantly larger for the Bantu population (21.7%, n=860/3959) than for the Pygmy population (12.1%, n=35/290), (p=0.00013). In addition, the presence of Plasmodium sp. was assessed via thick blood examination. Age was positively associated with SCT prevalence (odds-ratio for an increase of 10 years in age=1.063, p=0.020). Sex was not associated with SCT prevalence. The study reveals the absence of homozygous sickle-cell patients, and marked differences in SCT prevalence between the Gabonese provinces, and also between population groups (Bantu vs Pygmy). These findings could be used by the public health authorities to allocate medical resources and target prevention campaigns.