Kenyan Population Research Articles

Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant’s gazelles

The intraspecific phylogeography of Grant’s gazelles Nanger granti was assessed with mitochondrial DNA control region sequences. Samples of 177 individuals from 17 Kenyan and Tanzanian populations were analysed. Three highly divergent, reciprocally monophyletic lineages were found, with among group net nucleotide distances of 8–12%. The three lineages—notata, granti and petersii—grouped populations according to their geographic origin, encompassing populations in the north, southwest, and east, respectively. The mtDNA lineages reflected distinct evolutionary trajectories, and the data are discussed in reference to the four currently recognised subspecies. We suggest Grant’s gazelles be raised to the superspecies Nanger (granti) comprising three taxonomic units corresponding to the three mtDNA lineages. There was no evidence of gene flow between the notata and granti lineages, despite their geographic proximity, suggesting reproductive isolation. These constitute evolutionary significant units within the adaptive evolutionary framework. Due to its restricted geographic distribution and genetic and morphological distinctiveness, we suggest the petersii lineage be raised to the species Nanger (granti) petersii within the Grant’s gazelles superspecies.

Antiretroviral Durability and Tolerability in HIV-Infected Adults Living in Urban Kenya

Insufficient data exist on the durability and tolerability of first-line antiretroviral therapy (ART) regimens provided by HIV treatment programs implemented in developing countries. Longitudinal observation of clinical, immunologic, and treatment parameters of all HIV-infected adult patients initiated on ART was performed at Saint Mary's Mission Hospital in Nairobi, Kenya from September 2004 until August 2006. A total of 1286 patients were analyzed (59.1% female). Initial ART regimens were primarily stavudine, lamivudine, and nevirapine (62.1%). Median ART duration was 350 days (11.6 months). Significant improvements in clinical and immunologic status were noted after 12 months of therapy. ART switches occurred in 701 (54.5%) patients. The cumulative incidence of ART switch at 12 months was 78.4%. Concurrent ART-related toxicities (40.6%) and tuberculosis treatment interactions (28.1%) were the most frequent reasons for ART switch. Baseline AIDS symptoms (hazard rate [HR]=1.59, 95% confidence interval [CI]: 1.28 to 1.98; P<0.01) and a CD4 count<or=100 cells/mm3 (HR=1.20, CI: 1.01 to 1.43; P=0.04) were independent predictors of ART switch. ART-related clinical toxicity occurred in 341 (26.5%) patients. Peripheral neuropathy was reported most frequently (20.7%). A CD4 count<or=100 cells/mm3 was an independent predictor of clinical toxicity. Excellent clinical and immunologic responses to ART were observed in this urban Kenyan population; however, frequent switches in ART among medication classes because of toxicity or drug interactions may limit the durability of these responses.

Towards a spatially disaggregated material-based hardship index for the cities of developing nations: Nairobi, Kenya

Gauging the nature, location and extent of poverty in the cities of developing nations is a necessary prelude to remedial intervention. A proper measure would acknowledge poverty's demography, multidimensionality, geographic contextuality and causal precursors. Poverty indices are generally unreliable due to the nature, paucity and intermittency of available data. Most rely on measures of income, and hence buying power, which are inappropriate in mixed economies. We aim in contrast to examine the physical conditions that underpin poverty in 110 sub-locations of Nairobi, Kenya using the 1999 Kenyan housing and population census, augmented by survey data assembled in 2002 by UN-Habitat and the Kenyan government. Principal components analysis exposes the essential parameters of a material-based hardship index. Cross-sectional regression analysis then identifies its most important determinants. Implications of this study for poverty indexing, and for local area-based policy interventions in cities of the deve...

Acceptability and suitability of six fruit fly species (Diptera: Tephritidae) for Kenyan strains of Psyttalia concolor (Hymenoptera: Braconidae)

Host acceptability and suitability Psyttalia concolor (Szépligeti) is a koinobiont, larval parasitoid of tephritid fruit flies. Individuals of P. concolor were field-collected from coffee in the central highlands of Kenya, and cultured initially on Mediterranean fruit fly (medfly), Ceratitis capitata (Wiedemann). They were then examined for their ability to oviposit in and develop on five other tephritid species that are pests in Kenya. In addition to the medfly, acceptability for oviposition and suitability for development were tested against the mango fruit fly, Ceratitis cosyra (Walker), the Natal fruit fly, Ceratitis rosa Karsch, Ceratitis fasciventris (Bezzi), Ceratitis anonae Graham and the melon fruit fly, Bactrocera cucurbitae (Coquillett). Ceratitis capitata and C. cosyra were accepted as hosts significantly more often than the other species. Superparasitism was recorded only from C. capitata and C. cosyra. Two days after oviposition, parasitoid eggs in C. fasciventris and B. cucurbitae were encapsulated, whereas those in C. rosa and C. anonae were encapsulated, and often melanized. Ceratitis capitata was the most suitable host for Kenyan populations of Psyttalia concolor in terms of progeny production, and proportion of female progeny.

Genetic diversity within Sclerocarya birrea populations in Kenya

Knowledge on genetic diversity is important for the successful conservation and domestication of a species. In order to determine the genetic diversity within different populations of Sclerocarya birrea (A. Rich.) Hochst. (Anacardiaceae) (marula) in Kenya, leaf morphological characteristics and random amplified polymorphic DNA (RAPD) profiles from 92 and 61 trees, respectively, collected from six Kenyan stands and two reference populations from Tanzania, were investigated. Leaf blade lengths were measured, and whether leaf margins were serrated or entire was recorded. RAPD analysis was applied to genomic DNA using 10 primers of 10 base pairs each. Both leaf morphology and DNA analysis clustered the eight populations of S. birrea into three groups. Group 1 (two populations) consisted of plants with small sized leaves (average leaf blade length <3 cm) that had entire or serrated leaf margins. Group 2 (two populations) comprised plants with large sized leaves (average leaf blade length >3 cm) that, again, had entire or serrated leaf margins. Group 3 (four populations) consisted of plants with large sized leaves (average leaf blade length >3 cm) but had entire leaf margins only. RAPD analysis suggested that two Kenyan populations had particularly high genetic diversity; these two stands could be of particular conservation and genetic improvement value.

Kenya: Population Growth in the Light of Its Adopted Policies

This article, part of a wider study on fertility dynamics in Kenya, attempts to synthetically reconstruct the evolution of the Kenyan population structure over the past 60 years, following the development of population policies adopted by the Kenyan government. It emphasizes the importance and the necessity of political participation in order to restrain the population growth that, in a country such as Kenya, aggravates the existing deficiencies in the field of nutrition and hygiene. The article also takes a brief look at the future prospects of Kenya.

Genetic variation in the threatened medicinal tree Prunus africana in Cameroon and Kenya: Implications for current management and evolutionary history

Listed as vulnerable under Appendix II of CITES, populations of the commercially valuable African highland medicinal tree Prunus africana are threatened by over-exploitation in a number of countries. Here, random amplified polymorphic DNA (RAPD) analysis was used to assess patterns of genetic variation in the species in Cameroon and Kenya, two countries where exploitation has been particularly high and where information on genetic structure is a crucial input for developing the national management plans that are a requirement of CITES listing. Analysis of molecular variance (AMOVA), which employed 39 RAPD markers, indicated that a significantly greater proportion of total country variation partitioned among eight stands in Kenya than among nine stands in Cameroon (values of 55% and 24%, respectively), with important implications for conservation strategies. Kenyan stands appear to represent a particularly diverse resource for conservation, evaluation and domestication, although possible human movement of germplasm during cultivation raises integrity concerns. Data also shed light on the evolutionary history of P. africana stands. A genetic disjunction between western and central Kenyan populations was observed, with individuals from western Kenya more similar to geographically distant stands from Cameroon (>2000 km) than to central Kenya (<400 km). In the context of present-day floristic distributions and the historical data available, this disjunction appears more consistent with genetic exchange between east and west African highlands via migration (associated with climate change) than via long distance seed dispersal. Data suggested that conservation strategies for P. africana should place relatively more emphasis than currently on the status of surrounding phytochoria.

Contrasting signatures of selection on the Plasmodium falciparum erythrocyte binding antigen gene family

Erythrocyte binding antigens of Plasmodium falciparum are involved in erythrocyte invasion, and may be targets of acquired immunity. Of the five eba genes, protein products have been detected for eba-175, eba-181 and eba-140, but not for ψeba-165 or ebl-1, providing opportunity for comparative analysis of genetic variation to identify selection. Region II of each of these genes was sequenced from a cross-sectional sample of parasites in an endemic Kenyan population, and the frequency distributions of polymorphisms analysed. A positive value of Tajima's D was observed for eba-175 ( D = 1.13) indicating an excess of intermediate frequency polymorphisms, while all other genes had negative values, the most negative being ebl-1 ( D = −2.35) followed by ψeba-165 ( D = −1.79). The eba-175 and ebl-1 genes were then studied in a sample of parasites from Thailand, for which a positive Tajima's D value was again observed for eba-175 ( D = 1.79), and a negative value for ebl-1 ( D = −1.85). This indicates that eba-175 is under balancing selection in each population, in strong contrast to the other members of the gene family, particularly ebl-1 and ψeba-165 that may have been under recent directional selection. Population expansion simulations were performed under a neutral model, further supporting the departures from neutrality of these genes.

Mitochondrial DNA Lineages and Haplotype Diversity of Elite Kenyan Athletes

Mitochondrial DNA (mtDNA) codes for elements of the mitochondrial respiratory chain. The maternal inheritance of mtDNA has enabled construction of detailed phylogenies. Analysis of key polymorphisms from these phylogenies allows mtDNA to be assigned to haplogroups. Recently, it has been shown that certain mtDNA haplogroups differ in frequency between elite Finnish endurance and sprint athletes (Niemi et al. Eur J Hum Genet 13(8):965–9, 2005), although we have previously shown that mtDNA haplogroups were not associated with elite Ethiopian athlete status (Scott et al. Comp Biochem Physiol A Mol Integr Physiol 140(3):497–503, 2005). PURPOSE: To compare the frequencies of mtDNA haplogroups found in elite Kenyan athletes with haplogroup frequencies in the general Kenyan population. METHODS: DNA samples were obtained, with ethics approval, from 221 national level Kenyan athletes (N), 70 International Kenyan athletes (I), and 85 members of the general Kenyan population (C). mtDNA was classified into haplogroups by sequencing 340 bases of hypervariable sequence (HVS I), and by genotyping known restriction sites (3592 HpaI, 10394 DdeI, and 10397 A luI). Frequency differences between groups were assessed using contingency chi-square tests. RESULTS: All groups displayed similar high levels of haplotype diversity, based on HVS I haplotypes (C = 0.99, N = 0.99, I = 0.99). However, the haplogroup distribution of International athletes differed significantly from Controls (P = 0.027), with International athletes showing a greater proportion of L0 haplogroups (C = 15%, N = 18%, I = 30%) and a lower proportion of L2 haplogroups (C = 18%, N = 10%, I = 7%) relative to Controls. Although a disproportionately high number of International athletes originated from the Rift Valley province, this province did not differ in haplogroup distribution from other regions (P = 0.715). Haplogroup distribution did not differ between Bantu and Nilote language speakers (P = 0.193). CONCLUSIONS: International athletes, consisting of many of the most successful athletes in Kenyan athletic history, differed in their mtDNA haplogroup distribution relative to the general Kenyan population. They displayed an overrepresentation of L0 haplogroups, and an under-representation of L2 haplogroups. This may suggest that certain mtDNA haplogroups are influential in elite Kenyan distance running, although population stratification cannot be ruled out. Despite the over-representation of L0 haplogroups relative to controls, only 30% of Kenyan international athletes belonged to this haplogroup, highlighting the complexity of the elite athlete phenotype.

Psychiatric morbidity among leprosy patients in Teso and Busia districts of Western Kenya

To establish the magnitude of psychiatric disorders among leprosy patients in western Kenya. A cross-sectional descriptive study. Busia and Teso districts in western Kenya. A sample of 152 male and female, adult leprosy patients. The prevalence of psychiatric morbidity (PM) was 53.29%. The PM was positively correlated with physical disability and marital status but not with age, sex, education, type of leprosy, or duration of the illness. The prevalence of psychiatric morbidity was lower among Kenyan leprosy patients compared to studies carried out in India (56% to 78%). It was high compared to the rate of psychiatric morbidity in those seeking medical help in primary health care centres in Kenya, which was recently estimated to be 10%. The prevalence of PM in leprosy patients in western Kenya was lower than that in studies carried out in India. This could be attributed to de-institutionalisation and re-integration of leprosy sufferers back into their local communities. Since the rate was more than double that in the general Kenyan population and seemed to be related to presence of physical disability, an appraisal of psychiatric services offered to these patients is needed.

Demographic characteristics of elite Kenyan endurance runners

Kenyan athletes have dominated international distance running in recent years. Explanations for their success include favourable physiological characteristics, which could include favourable genetic endowment, and advantageous environmental conditions. The aim of this study was to compare the demographic characteristics of elite Kenyan runners with those of the general Kenyan population. Questionnaires, administered to 404 elite Kenyan runners specializing in distances ranging from the 800 m to the marathon and 87 Kenyan controls, obtained information on place of birth, language, and distance and method of travel to school. Athletes were separated into two groups according to athletic success: those who competed in international competition and those who competed in national competition. The athletes differed from controls in regional distribution, language, and distance and method of travel to school; athletes also differed from each other with the exception of method of travel to school. Most national and international athletes came from the Rift Valley province (controls 20%, national athletes 65%, international athletes 81%), belonged to the Kalenjin ethnic group (controls 8%, national athletes 49%, international athletes 76%) and Nandi sub-tribe (controls 5%, national athletes 25%, international athletes 44%), and spoke languages of Nilotic origin (controls 21%, national athletes 60%, international athletes 79%). A higher proportion of all athletes ran to school each day (controls 22%, national athletes 73%, international athletes 81%) and covered greater distances. In conclusion, Kenyan runners are from a distinctive environmental background in terms of geographical distribution, ethnicity and travelled further to school, mostly by running. These findings highlight the importance of environmental and social factors in the success of Kenyan runners.

The ties that bind: genetic relatedness predicts the fission and fusion of social groups in wild African elephants.

Many social animals live in stable groups. In contrast, African savannah elephants (Loxodonta africana) live in unusually fluid, fission-fusion societies. That is, 'core' social groups are composed of predictable sets of individuals; however, over the course of hours or days, these groups may temporarily divide and reunite, or they may fuse with other social groups to form much larger social units. Here, we test the hypothesis that genetic relatedness predicts patterns of group fission and fusion among wild, female African elephants. Our study of a single Kenyan population spans 236 individuals in 45 core social groups, genotyped at 11 microsatellite and one mitochondrial DNA (mtDNA) locus. We found that genetic relatedness predicted group fission; adult females remained with their first order maternal relatives when core groups fissioned temporarily. Relatedness also predicted temporary fusion between social groups; core groups were more likely to fuse with each other when the oldest females in each group were genetic relatives. Groups that shared mtDNA haplotypes were also significantly more likely to fuse than groups that did not share mtDNA. Our results suggest that associations between core social groups persist for decades after the original maternal kin have died. We discuss these results in the context of kin selection and its possible role in the evolution of elephant sociality.

Fisherfolk are among groups most at risk of HIV: cross-country analysis of prevalence and numbers infected

HIV prevalence in some fishing communities in low and middle-income countries is known to be high relative to national average seroprevalence rates. Most of the studies supporting this claim refer to the men involved in fish-catching operations (fishermen). However they acknowledge that the men and women who work in associated occupations such as fish trading and processing are also vulnerable in part because they are often within the fishermen’s sexual networks. This vulnerability stems from the nature and dynamics of the fish trade and fishing lifestyle in which a number of known or hypothesized ‘risk factors’ converge. (excerpt)

Cryptic invasion and dispersal of an American Daphnia in East Africa

We document the cryptic invasion of a North American genotype of Daphnia pulex into Kenya. During a survey of zooplankton samples and dormant egg banks of 41 natural lakes, ponds, and man-made reservoirs throughout central and southern Kenya, D. pulex was found at seven localities in the Rift Valley region. We used DNA sequencing (12S rDNA and cytochrome c oxidase subunit 1 gene [COI]) and microsatellite analyses (10 loci) to characterize each population genetically. A single haplotype was found for both 12S and COI sequences. Comparison with DNA sequences of the D. pulex complex from Europe and America reveals that the Kenyan D. pulex is not closely related to European D. pulex but clusters tightly with the American-Panarctic clade of D. pulex sensu stricto. Microsatellite data further reveal that all seven known Kenyan populations are genetically nearly identical and are dominated by a single clone. All populations except that in Lake Naivasha contained only one multilocus genotype, a fixed heterozygote for 3 of the 10 studied loci. Our data suggest that an obligately parthenogenetic clone of American D. pulex recently immigrated into Kenya and has subsequently dispersed over distances of several hundreds of kilometers. Most likely it was co-introduced accidentally during one of numerous stockings of North American fish or crayfish in Kenya—s Rift Valley lakes since the mid-1920s.

No association between Angiotensin Converting Enzyme (ACE) gene variation and endurance athlete status in Kenyans

East African runners are continually successful in international distance running. The extent to which genetic factors influence this phenomenon is unknown. The insertion (I) rather than deletion (D) of a 287 bp fragment in the human angiotensin converting enzyme ( ACE) gene is associated with lower circulating and tissue ACE activity and with endurance performance amongst Caucasians. To assess the association between ACE gene variation and elite endurance athlete status in an African population successful in distance running, DNA samples were obtained from 221 national Kenyan athletes (N), 70 international Kenyan athletes (I), and 85 members of the general Kenyan population (C). Blood samples were obtained from C and assayed for circulating ACE activity. ACE I/D (rs????—from NCBI SNPdb first time poly mentioned) genotype was determined, as was genotype at A22982GD (rs????—from NCBI SNPdb first time poly mentioned) which has been shown to associate more closely with ACE levels in African subjects than the I/D polymorphism. ACE I/D and A22982G genotypes explained 13 and 24% of variation in circulating ACE activity levels ( P = 0.034 and < 0.001 respectively). I/D genotype was not associated with elite endurance athlete status ( df = 4, χ 2 = 4.1, P = 0.39). In addition, genotype at 22982 was not associated with elite endurance athlete status ( df = 4, χ 2 = 5.7, P = 0.23). Nor was the A allele at 22982, which is associated with lower ACE activity, more prevalent in N (0.52) or I (0.41) relative to C (0.53). We conclude that ACE I/D and A22982G polymorphisms are not strongly associated with elite endurance athlete status amongst Kenyans.

Coronary artery disease and symptoms of depression in a Kenyan population

Depression and heart disease are replacing the traditional enemies of Africa such as infectious diseases and malnutrition as the increasing causes of disability and premature death. Little is known about the co-morbidity of heart disease and depression in Africa. To describe the prevalence of depression in Black Africans with and without Coronary Artery Disease as documented on coronary angiography at the Nairobi Hospital. Prospective comparative study. A private not for Profit 210 bed hospital, catering for fee paying middles class clintele. Of the eighteen patients with an abnormal angiogram, the highest score on the BDI was 9 while the average was 2.11. Of the seven with normal angiograms, the highest BDI was 5, and the average was 1.71. There was no statistical significance in these differences. While African scientists must continue to concentrate on the urgent medical priorities of today (AIDS, malaria, measles, etc), cognisance has to be made of the other emerging epidemic, of the co-morbidity of coronary artery disease and depression. That no significant difference in depression score between the two groups was found could be due to a number of reasons including the small sample size achieved in this first study of its kind in Kenya.

High‐resolution sequence‐based DPA1 typing identified two novel DPA1 alleles, DPA1*010303 and DPA1*0303, from a Kenyan population

We report here two novel DPA1 alleles, DPA1*010303 and DPA1*0303, identified from a Kenyan population during sequence-based HLA-DPA1 typing. Molecular cloning and sequencing of multiple clones confirmed that one of the new DPA1 alleles is identical to DPA1*010301 at exon 2, except for a single nucleotide substitution (ACG ACC) at codon 15. The new allele has been named by the WHO Nomenclature Committee as DPA1*010303. The second novel DPA1 allele is identical to DPA1*0301, except for a single nucleotide difference (GAA GAC) at codon 28 that changed the amino acid from Glu to Asp. The new allele has been named by the WHO Nomenclature Committee as DPA1*0303. Identification of the two novel DPA1 alleles reflects the genetic diversity of this East African population.

In-Migrants and Exclusion in East African Rangelands: Access, Tenure and Conflict

AbstractEast African rangelands have a long history of population mobility linked to competition over key resources, negotiated access, and outright conflict. Both in the literature and in local discourse, in‐migration is presented as leading to increased competition, driving poverty and social exclusion on the one hand, and conflict and violence on the other. Current analyses in developing countries identify economic differences, ethnic fault lines, ecological stresses and a breakdown in state provision of human and constitutional rights as factors in driving conflict. The present paper explores this interaction of in‐migration and conflict with respect to Kenyan and Tanzanian pastoralist areas and populations. Using quantitative and qualitative methods, patterns of resource access and control in Kenya and Tanzania Maasailand are explored in terms of the ways land and livestock are associated with migration status, ethnicity and wealth or political class. Contrasts and similarities between the two national contexts are used to develop a better understanding of the ways these factors operate under different systems of tenure and access. The conclusion briefly considers implications of these patterns, their potential for exacerbating poverty, and policies for minimising social exclusion and conflict in East African rangelands.

The dominance of Kenyans in distance running

AbstractKenyan runners, and especially those originating from the Kalenjin tribe, have dominated international middle- and long-distance running for over 40 years, prompting significant interest in the factors contributing to their success. Proposed explanations have included environmental factors, psychological advantage and favourable physiological characteristics, which may be genetically conferred or environmentally determined. Running is inherent within local Kenyan tradition and culture, and the Kenyan way of life, which involves many outdoor activities and pastimes in addition to mostly unfavourable living conditions, is conducive to enhanced distance running performance. Despite economic deprivation, Kenya has produced world and international running champions repeatedly over the past few decades; these champions have become role models for the younger generations, who take up running in the hope of a better future for themselves. Favourable environmental conditions such as altitude, diet and anthropometry, in addition to the motivational and socio-economic factors mentioned above, have all been proposed as possible reasons for the unsurpassed achievements of Kenyan distance runners. However, the fact that the majority of internationally successful runners originate from a small tribe that accounts for approximately 3% of the total Kenyan population also points to a possible genetic component. Whether this is subject to influence from other co-factors, such as altitude or training effects acquired during childhood, remains as yet unresolved.

Novel interferon regulatory factor-1 polymorphisms in a Kenyan population revealed by complete gene sequencing.

Variation in susceptibility to HIV-1 infection depends on numerous factors, and host genetic variation has been well-described as an important component. As a transcriptional regulator, interferon regulatory factor 1 (IRF-1) plays a key role in both innate and adaptive immunity against viral infection. IRF-1 has also been shown to directly interact with HIV-1 5' LTR and efficiently initiate or amplify HIV-1 replication. By complete gene sequencing, we investigated genetic polymorphism of the IRF-1 gene in an HIV-1-endemic Kenyan population. This population displayed extensive genetic diversity at the IRF-1 locus. Fifty-three single nucleotide polymorphisms (SNPs) were identified in this population, including 26 novel SNPs. Two insertion and one deletion polymorphisms in IRF-1 were also identified. Linkage disequilibrium (LD) among these genetic variations was shown to be common in IRF-1. The functional consequences of these mutations in the context of HIV-1/AIDS remain to be determined. We also identified 35 consistent discrepancies between IRF-1 GenBank sequences and our population based sequencing data, suggesting that the previously submitted GenBank data were not representative of the majority of human IRF-1 sequences.