East African Populations Research Articles

Characterization of non-cytoplasmic incompatibility inducing Wolbachia in two continental African populations of Drosophila simulans.

Wolbachia is an endocellular bacterium infecting arthropods and nematodes. In arthropods, it invades host populations through various mechanisms, affecting host reproduction, the most common of which being cytoplasmic incompatibility (CI). CI is an embryonic mortality occurring when infected males mate with uninfected females or females infected by a different Wolbachia strain. This phenomenon is observed in Drosophila simulans, an intensively studied Wolbachia host, harbouring at least five distinct bacterial strains. In this study, we investigate various aspects of the Wolbachia infections occurring in two continental African populations of D. simulans: CI phenotype, phylogenetic position based on the wsp gene and associated mitochondrial haplotype. From the East African population (Tanzania), we show that (i) the siIII mitochondrial haplotype occurs in continental populations, which was unexpected based on the current views of D. simulans biogeography, (ii) the wKi strain (that rescues from CI while being unable to induce it) is very closely related to the CI-inducing strain wNo, (iii) wKi and wNo might not derive from a unique infection event, and (iv) wKi is likely to represent the same entity as the previously described wMa variant. In the West African population (Cameroon), the Wolbachia infection was found identical to the previously described wAu, which does not induce CI. This finding supports the view that wAu might be an ancient infection in D. simulans.

Tobacco smoking in Tanzania, East Africa: population based smoking prevalence using expired alveolar carbon monoxide as a validation tool

Objectives: To describe the prevalence of tobacco smoking in an urban East African population while using a simple validation procedure to examine the degree of under reporting in men and...

Distinct differences in a cyclin D1 single nucleotide polymorphism between ethnic groups

AbstractIntroduction Cyclin D1, encoded by the CCND1 gene, is a key regulator of the cell cycle at the G1/S phase checkpoint. A common A/G single nucleotide polymorphism (SNP) at nt870 of the CCND1 gene has been associated with outcome in patients with lung tumours and head and neck cancer. The aim of this study was to ascertain the genotype and allele frequency of the CCND1 polymorphism in five distinct ethnic populations.Methods Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis was carried out on genomic DNA from 505 subjects from five distinct ethnic populations (i.e. Caucasian, South‐west Asian, Ghanaian, Kenyan and Chinese subjects).Results Marked differences in genotype were apparent between the ethnic populations, with homozygosity for the G allele ranging from 13.6% in the Chinese subjects to 62.4% amongst Kenyan individuals (P < 0.001). Whereas the East and West African populations demonstrated almost identical allele frequencies, both populations differed significantly from each of the remaining populations. the allele frequencies for the South‐west Asian population fell between that of the Caucasian and Chinese populations but did not differ significantly from either, while the Caucasian and Chinese subjects displayed significant differences in CCND1 alleles (P = 0.003).Discussion These marked variations in SNP frequencies between ethnic groups may have a significant impact on prognosis of cancer in these populations, because the CCND1 genotype appears to influence prognosis in each tumour type examined to date.

Weaning, complementary feeding, and maternal decision making in a rural east African pastoral population.

A small-scale, prospective study of breastfeeding and weaning practices was conducted in a seminomadic pastoral population in northern Tanzania (Datoga of Mbulu District, Arusha Region). Focus group participants suggested that weaning patterns are strongly influenced by seasonal factors, and individual mothers often stated an intention to introduce adult staple foods and terminate breastfeeding at the end of the long rains. However, a combination of maternal self-perception, assessment of infant well-being, and indicators of household food supply influenced the actual progression of weaning for individual children. The results suggest that interventions to promote exclusive breastfeeding and improve complementary feeding practices in rural East African pastoral populations could build on maternal attention to infant-centered cues and address household-level constraints on caregivers making decisions about young child feeding.

Assessment of genetic diversity of East African goat populations using microsatellite DNA markers

Assessment of genetic diversity of East African goat populations using microsatellite DNA markers

Long term results of glaucoma surgery among participants in an east African population survey

AIMTo evaluate the long term results of glaucoma surgery among people in East Africa.METHODSParticipants in a population based survey of eye disease prevalence were offered glaucoma surgery using standardised criteria....

An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs

Genetic diversity in 31 individuals from 14 coconut populations across the entire geographic range (2–3 individuals per population) was assessed using sequence-tagged microsatellites (or simple sequence repeats, SSRs) and amplified fragment length polymorphism (AFLP). From the 39 SSR primer sets tested, only two gave patterns that could not be scored and used in the data analysis. The remainder included five SSRs that gave double-locus profiles in which one locus could still be scored separately. The 37 SSRs revealed between 2 and 16 alleles per locus and a total of 339 alleles in the 14 populations. Gene diversity (D = 1-Σpi 2) ranged from 0.47 to 0.90. Two of the four Dwarf populations were homozygous at all 37 loci, which is consistent with their autogamous (self-fertilising) reproduction. One Dwarf population was heterozygous at one locus but the other (Niu Leka Dwarf), which is known to be cross-pollinating, showed high levels of heterozygosity. Generally, diversity was higher in populations from the South Pacific and South East Asia. Three SSR loci (CNZ46, CN2A5, CN11E6) gave distinct genotypes for all but two populations. The East African populations had higher heterozygosities than those from West Africa, and the populations from Tonga and Fiji generally had distinct alleles from those of the South Pacific. AFLP analysis with 12 primer combinations gave a total of 1106 bands, of which 303 were polymorphic (27%). Similarity matrices were constructed from the two data sets using the proportion of shared alleles for SSRs and a Jaccard coefficient for AFLPs. In each case cluster and principal co-ordinates analyses were performed, with the resultant dendrograms and plots revealing similar relationships among the populations for both approaches. There was generally a good separation of populations, and phenetic relationships were in agreement with those previously shown by RFLPs. The use of SSRs and AFLPs in genetic-diversity analysis for the establishment of germplasm collections is discussed.

A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria.

Genetic variation in cytokine promoter regions is postulated to influence susceptibility to infection, but the molecular mechanisms by which such polymorphisms might affect gene regulation are unknown. Through systematic DNA footprinting of the TNF (encoding tumour necrosis factor, TNF) promoter region, we have identified a single nucleotide polymorphism (SNP) that causes the helix-turn-helix transcription factor OCT-1 to bind to a novel region of complex protein-DNA interactions and alters gene expression in human monocytes. The OCT-1-binding genotype, found in approximately 5% of Africans, is associated with fourfold increased susceptibility to cerebral malaria in large case-control studies of West African and East African populations, after correction for other known TNF polymorphisms and linked HLA alleles.

Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila.

Nucleotide sequence variation at the Acp29AB gene region has been surveyed in Drosophila melanogaster from Spain (12 lines), Ivory Coast (14 lines), and Malawi (13 lines) and in one line of D. simulans. The approximately 1.7-kb region studied encompasses the Acp29AB gene that codes for a male accessory gland protein and its flanking regions. Seventy-seven nucleotide and 8 length polymorphisms were detected. Nonsynonymous polymorphism was an order of magnitude lower than synonymous polymorphism, but still high relative to other non-sex-related genes. In D. melanogaster variation at this region revealed no major genetic differentiation between East and West African populations, while differentiation was highly significant between the European and the two African populations. Comparison of polymorphism and divergence at synonymous and nonsynonymous sites showed an excess of fixed nonsynonymous changes, which indicates that the evolution of the Acp29AB protein has been driven by directional selection at least after the split of the D. melanogaster and D. simulans lineages. The pattern of variation in extant populations of D. melanogaster favors a scenario where the fixation of advantageous replacement substitutions occurred in the early stages of speciation and balancing selection is maintaining variation in this species.

Analysis of mtDNA HVRII in several human populations using an immobilised SSO probe hybridisation assay.

Several populations were typed for the hypervariable region II (HVRII) of the mitochondrial DNA (mtDNA) control region using immobilised sequence-specific oligonucleotide (SSO) probes. A total of 16 SSO probes was used to type 1081 individuals from eight different ethnic groups (African Americans, Somali, US Europeans, US Hispanics, Bosnians, Finns, Saami and Japanese). Data was compared with already published sequence data by analysis of principal components, genetic distances and analysis of the molecular variance (AMOVA). The analyses performed group the samples in several clusters according to their geographical origins. Most of the variability detected is assigned to differences between individuals and only 7% is assigned to differences among groups of populations within and between geographical regions. Several features are patent in the samples studied: Somali, as a representative East African population, seem to have experienced a detectable amount of Caucasoid maternal influence; different degrees of admixture in the US samples studied are detected; Finns and Saami belong to the European genetic landscape, although Saami present an outlier position attributable to a strong maternal founder effect. The technique used is a rapid and simple method to detect human variation in the mtDNA HVRII in a large number of samples, which might be useful in forensic and population genetic studies.

Mitochondrial DNA population structure of roan and sable antelope: implications for the translocation and conservation of the species.

Mitochondrial DNA (mtDNA) control region sequences were analysed to determine the geographical genetic structure of Hippotragus niger (sable antelope) and H. equinus (roan antelope). Analyses by AMOVA, minimum evolution networks, parsimony, neighbour joining and maximum likelihood show that the roan antelope populations are geographically partitioned and that their phylogeography corresponds well with subspecific boundaries. In sharp contrast, however, our sequence data group all the sable antelope into two well-delineated maternal clades. One comprising specimens from the strictly east African H.n. roosevelti, and a second geographically diverse group which includes H.n. niger (South Africa, Zimbabwe), H.n. variani (Angola), and H.n. Kirkii (Zambia, Malawi). The differences in the genetic population structure suggest that distinct extrinsic and intrinsic factors have shaped the phylogeography of these two closely related antelope species. In the absence of obvious extrinsic barriers to gene flow, we suggest that behavioural differences may be responsible, at least in part, for the contrasting spatial patterns detected among geographical localities. Although our data reflect only the maternal phylogeny of these important game species, they nonetheless suggest that different management strategies should be applied. We recommend that roan antelope be translocated only within the currently defined subspecies boundaries, while in the case of sable antelope, conservation measures should focus on preserving the genetic integrity of the east African and southern African sable populations. Implicit in this is that translocations of animals between populations comprising these two distinct maternal genetic clades should be actively discouraged.

Molecular differences distinguish clonal lineages within East African populations of Fusarium oxysporum f.sp. cubense

Molecular approaches for the assessment of intraspecific diversity within an economically important plant pathogen were compared with traditional physiological methods (vegetative compatibility testing). The vegetative compatibility groups (VCGs) of 14 isolates of Fusarium oxysporum f.sp. cubense (FOC) from Kenya were first assessed using nitrate non-utilizing mutants. Nine of these isolates, from different areas of the country, were compatible with one or more of VCGs 0124, 0125, 0128 and 01220, i.e. they formed a single clonal lineage. Three isolates, all originating from the banana growing district of Kisii, were compatible with the VCG 01212 and formed a second distinct clonal lineage. Mutants could not be recovered from one isolate (62) and two isolates (27 and 30) were not vegetatively compatible with any of the VCG testers and may represent two novel VCGs. Polymerase chain reaction (PCR) fingerprinting, especially when using the M13 derived primer, was found to produce banding patterns that correlated with clonal lineage and also distinguished isolates 27 and 30 when analysed by unweighted pair group method analysis and principle co-ordinate analysis. This approach also distinguished FOC from F. oxysporum IMI350438 isolated from Triticum sp. and from isolates of Colletotrichum gloeosporioides. Total protein profiles were analysed by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and although clonal lineages were not separated, isolates 27 and 30 were again distinguishable and FOC produced a different profile to F. oxysporum (IMI 350438) and C. gloeosporioides.

Mitochondrial DNA differentiation among East and West African Nile tilapia populations

Mitochondrial DNA differentiation among East and West African Nile tilapia populations

Mitochondrial DNA differentiation among East and West African Nile tilapia populations

Variation of the ND5/6 mtDNA fragment was studied in six Nile tilapia populations using PCR and RFLP analysis. The observed variation allows a strict discrimination between eastern and western African populations.

Mitochondrial DNA Phylogeography and Comparative Cytogenetics of the Springhare, Pedetes capensis (Mammalia: Rodentia)

Variation in mitochondrial DNA (mtDNA) was used together with comparative cytogenetics to examine the evolutionary history and taxonomic status of an African hystricomorphous rodent, the springhare Pedetes capensis. The mtDNA phylogeographic structure showed that the majority of the southern African populations (P. c. capensis) are characterized by unique but closely related maternal lineages. Based on restriction endonuclease fragment analysis, the east African populations (P. c. surdaster) appear more structured and are distinguished from those in southern Africa by an average sequence divergence of 5.52% (±1.4%). This marked divergence is concordant with results of the cytogenetic study. Specimens from southern Africa have 2n = 38, and those from east Africa 2n = 40. The change in diploid number is due to a single centric fusion. It is suggested that the closure of the Brachystegia or “miombo” woodland (20,000–10,000 B.P.), which delimits contemporary springhare ranges, may have been too recent to account for the accumulated genetic differences that distinguish these taxa. While rifting and associated habitat changes in east Africa can be invoked to explain genetic structure in this region, the southern African springhare populations, which have a high incidence of locality-specific haplotypes, show a shallow phylogeographic structure, in keeping with a relatively recent range expansion from smaller source populations. Given the magnitude of genetic, morphological, and ethological differences between the two geographic isolates, we believe that there is strong support for the elevation of the east African and southern African springhare populations to full species status, thus supporting earlier taxonomic treatments of this rodent.

Current evidence for self-medication in primates: A multidisciplinary perspective

The study of self-medication in non-human primates sheds new light on the complex interactions of animal, plant and parasite. A variety of non-nutritional plant secondary compounds and nutrient-poor bark is found in the primate diet, but little is yet known about the possible medicinal consequences of their ingestion. Recent studies of the African great apes support a hypothesis in progress that the non-nutritional ingestion of certain plant species aid in the control of parasite infection and provide relief from related gastrointestinal upsets. Detailed behavioral, pharmacological and parasitological investigations of two such behaviors, bitter pith chewing and leaf swallowing, have been conducted on three East African chimpanzee populations, but they are now known to occur widely among all chimpanzee subspecies, as well as bonobos and lowland gorillas. For both bitter pith chewing and leaf swallowing, selection of the same plant species tends to occur among neighboring groups of same ape species. These local cultural traditions of plant selection may be transmitted when females of the same species transfer into non-natal groups. However, selection of the same plant species or species of related plant genera by two sympatric ape species or between regional populations of great ape subspecies strongly suggests a common criteria of medicinal plant selection. This and the intriguing observa- tion that the same medicinal plant is selected by apes and humans with similar illnesses provide insight into the evolution of medicinal behavior in modern humans and the possible nature of self-medication in early hominids. The occurrence of these and other specific self-medicative behaviors, such as fur rubbing and geophagy, in primates and other animal taxa suggest the existence of an underlying mechanism for the recognition and use of plants and soils with common medicinal or functional properties. Yrbk Phys Anthropol 40:171-200, 1997. r 1997 Wiley-Liss, Inc.

Allozyme variation in natural and cultured populations in two tilapia species: Oreochromis niloticus and Tilapia zillii

We investigated the electrophoretic polymorphism at 30 protein loci in 27 wild and cultured populations of two tilapia species, Tilapia zillii and Oreochromis niloticus. Single and joint segregations were analysed at 12 polymorphic loci in full-sib families. All the loci showed single segregation in agreement with the Mendelian expectations, and two nonrandom joint segregations were found. In total, 26 loci were polymorphic and 12 were diagnostic between the two species. A pronounced differentiation was observed between the Ivory Coast and Nilo-Sudanian T. zillii populations (average Nei's standard genetic distance = 0.13). Within the Nilo-Sudanian region, the level of variation observed in O. niloticus and T. zillii was rather low when compared with other freshwater species analysed at similar macrogeographical scales. The same pattern of geographical differentiation was found between the west and east African populations in both species suggesting that this structuring mainly reflected the same palaeo-geographical events. Most of the geographical variation observed in the Nile tilapia populations analysed here was present in the cultured stocks. In contrast to fish-farmed stocks analysed in other countries, those from the Ivory Coast and Niger displayed neither evidence of loss of genetic diversity nor any trace of introgression with other cultured tilapia species, indicating that these stocks have been properly managed.

96/00610 Techno-Economic analysis of a plastic cover solar air heater

We report four novel KIR2DL2 alleles and two novel KIR2DL3 alleles identified from an East African population using sequence-based typing. Sequencing and molecular cloning of exon 4 confirmed that the new 2DL2 alleles were identical to 2DL2*003, except for the following nucleotide differences: 2DL2*00601 had a difference at codon 16 (CGC→CCC), resulting in a coding change from arginine to proline; 2DL2*00602 also had this difference at codon 16, as well as a synonymous difference (GAT→GAC) at codon 31; 2DL2*00303 had a synonymous difference (AAA→AAG) at codon 61; and 2DL2*00304 had a synonymous difference (GGG→GGA) at codon 75. 2DL3*017 was identical to 2DL3*005 except at codon 11 (CGG→CTG, arginine→leucine) and exon 9, codons 297 (CAC→CGC, histidine→arginine) and 321 (TGA→AGA, stop codon→arginine). 2DL3*00104 was identical to KIR2DL3*001 except for a synonymous difference (GAG→GAA) at codon 54. Identification of novel killer cell immunoglobulin-like receptor (KIR) alleles is a testament to the genetic diversity in this population.

Comparative population structuring of molecular and allozyme variation ofDrosophila melanogaster Adhbetween Europe, West Africa and East Africa

Restriction enzyme molecular variation in Drosophila melanogaster Adh was compared between three natural populations from Europe, West Africa and East Africa. The frequency distribution of silent variation in the slow allele was compatible with the neutral model in all three samples. The number of haplotypes in East Africa was significantly higher than in the other two populations. The largest divergence, as measured by Fst, was between the East African population and a group made up from the West African, the European, and previously studied American populations. We suggest that a split first occurred within African populations at least 44000 years ago. European populations separated from West Africa more recently, between the last glacial maximum and the post-glacial optimum, 18,000 to 8,000 years ago. We suggest that this species was domesticated recently relative to human evolution, possibly with the advent of agriculture. Population differentiation with respect to the two allozymes, fast and slow, does not follow the geographical pattern of silent variation. It opposes European to both African populations, and probably results from selection for adaptation to alcohol in recent temperate populations.

Isotopic Tracking of Change in Diet and Habitat Use in African Elephants

The carbon, nitrogen, and strontium isotope compositions of elephants in Amboseli Park, Kenya, were measured to examine changes in diet and habitat use since the 1960s. Carbon isotope ratios, which reflect the photosynthetic pathway of food plants, record a shift in diet from trees and shrubs to grass. Strontium isotope ratios, which reflect the geologic age of bedrock, document the concentration of elephants within the park. The high isotopic variability produced by behavioral and ecological shifts, if it is representative of other East African elephant populations, may complicate the use of isotopes as indicators of the source region of ivory.