Mitochondrial DNA diversity in two ethnic groups in Southeastern Kenya: Perspectives from the northeastern periphery of the bantu expansion

The Bantu languages are widely distributed throughout sub‐Saharan Africa. Genetic research supports linguists and historians who argue that migration played an important role in the spread of this language family, but the genetic data also indicates a more complex process involving substantial gene flow with resident populations. In order to understand the Bantu expansion process in east Africa, mtDNA hypervariable region I variation in 352 individuals from the Taita and Mijikenda ethnic groups was analyzed, and we evaluated the interactions that took place between the Bantu‐ and non‐Bantu‐speaking populations in east Africa. The Taita and Mijikenda are Bantu‐speaking agropastoralists from southeastern Kenya, at least some of whose ancestors probably migrated into the area as part of Bantu migrations that began around 3,000 BCE. Our analyses indicate that they show some distinctive differences that reflect their unique cultural histories. The Taita are genetically more diverse than the Mijikenda with larger estimates of genetic diversity. The Taita cluster with other east African groups, having high frequencies of haplogroups from that region, while the Mijikenda have high frequencies of central African haplogroups and cluster more closely with central African Bantu‐speaking groups. The non‐Bantu speakers who lived in southeastern Kenya before Bantu speaking groups arrived were at least partially incorporated into what are now Bantu‐speaking Taita groups. In contrast, gene flow from non‐Bantu speakers into the Mijikenda was more limited. These results suggest a more complex demographic history where the nature of Bantu and non‐Bantu interactions varied throughout the area. Am J Phys Anthropol 150:482–491, 2013. © 2013 Wiley Periodicals, Inc.     

Interethnic genetic differentiation in Africa: HLA class I antigens in The Gambia.

A total of 752 individuals from The Gambia, west Africa who are representative of the major ethnic groups in the capital, Banjul, were serologically typed for HLA-A, -B, and -C antigens. Although all were typically "African" in their antigenic profiles, some marked frequency differences were found between the ethnic groups. Genetic distance comparisons with several other African populations showed that, although these west African populations clustered closely together, the positions of the various ethnic groups in The Gambia were consistent with historical and linguistic evidence of their affinities with one another and with other African populations. Despite the potential confounding effects both of selection by infectious diseases and of genetic drift caused by local differences in population structure, HLA frequencies appear to be of value in measuring inter- and intraregional population affinities in sub-Saharan Africa.     

Genetic diversity,evolutionary history and implications for conservation of the lion (Panthera leo) in West and Central Africa

Aim In recent decades there has been a marked decline in the numbers of African lions (Panthera leo), especially in West Africa where the species is regionally endangered. Based on the climatological history of western Africa, we hypothesize that West and Central African lions have a unique evolutionary history, which is reflected by their genetic makeup. Location Sub‐Saharan Africa and India, with special focus on West and Central Africa. Method In this study 126 samples, throughout the lion’s complete geographic range, were subjected to phylogenetic analyses. DNA sequences of a mitochondrial region, containing cytochrome b, tRNAPro, tRNAThr and the left part of the control region, were analysed. Results Bayesian, maximum likelihood and maximum parsimony analyses consistently showed a distinction between lions from West and Central Africa and lions from southern and East Africa. West and Central African lions are more closely related to Asiatic lions than to the southern and East African lions. This can be explained by a Pleistocene extinction and subsequent recolonization of West Africa from refugia in the Middle East. This is further supported by the fact that the West and Central African clade shows relatively little genetic diversity and is therefore thought to be an evolutionarily young clade. Main conclusions The taxonomic division between an African and an Asian subspecies does not fully reflect the overall genetic diversity within lions. In order to conserve genetic diversity within the species, genetically distinct lineages should be prioritized. Understanding the geographic pattern of genetic diversity is key to developing conservation strategies, both for in situ management and for breeding of captive stocks.     

Paternal lineages in Libya inferred from Y‐chromosome haplogroups

Many studies based on genetic diversity of North African populations have contributed to elucidate the modelling of the genetic landscape in this region. North Africa is considered as a distinct spatial‐temporal entity on geographic, archaeological, and historical grounds, which has undergone the influence of different human migrations along its shaping. For instance, Libya, a North African country, was first inhabited by Berbers and then colonized by a variety of ethnic groups like Phoenicians, Greeks, Romans, Arabs and, in recent times, Italians. In this study, we contribute to clarify the genetic variation of Libya and consequently, of North African modern populations, by the study of Libyan male lineages. A total of 22 Y‐chromosome‐specific SNPs were genotyped in a sample of 175 Libyan males, allowing the characterization of 18 Y‐chromosomal haplogroups. The obtained data revealed a predominant Northwest African component represented by haplogroup E‐M81 (33.7%) followed by J(xJ1a,J2)‐M304 (27.4%), which is postulated to have a Middle Eastern origin. The comparative study with other populations (～5,400 individuals from North Africa, Middle East, Sub‐Saharan Africa, and Europe) revealed a general genetic homogeneity among North African populations (F_ST = 5.3 %; P‐value < 0.0001). Overall, the Y‐haplogroup diversity in Libya and in North Africa is characterized by two genetic components. The first signature is typical of Berber‐speaking people (E‐M81), the autochthonous inhabitants, whereas the second is (J(xJ1a,J2)‐M304), originating from Arabic populations. This is in agreement with the hypothesis of an Arabic expansion from the Middle East, shaping the North African genetic landscape. Am J Phys Anthropol 157:242–251, 2015. © 2015 Wiley Periodicals, Inc.     

Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers

Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Environmental drivers of freshwater macrophyte diversity and community composition in calcareous warm‐water rivers of America and Africa

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mtDNA sequence diversity in Africa.

mtDNA sequences were determined from 241 individuals from nine ethnic groups in Africa. When they were compared with published data from other groups, it was found that the !Kung, Mbuti, and Biaka show on the order of 10 times more sequence differences between the three groups, as well as between those and the other groups (the Fulbe, Hausa, Tuareg, Songhai, Kanuri, Yoruba, Mandenka, Somali, Tukana, and Kikuyu), than these other groups do between one other. Furthermore, the pairwise sequence distributions, patterns of coalescence events, and numbers of variable positions relative to the mean sequence difference indicate that the former three groups have been of constant size over time, whereas the latter have expanded in size. We suggest that this reflects subsistence patterns in that the populations that have expanded in size are food producers whereas those that have not are hunters and gatherers.     

Mitochondrial DNA genetic diversity among four ethnic groups in Sierra Leone

Although there are numerous ethnic groups in Sierra Leone, the Mende and Temne together account for approximately 60% of the total population. To see if genetic differences could be observed among ethnic groups in Sierra Leone, the nucleotide sequence of the hypervariable 1 (HV1) region of mitochondrial DNA (mtDNA) was determined from samples of the two major ethnic groups, the Mende (n=59) and Temne (n=121), and of two minor ethnic groups, the Loko (n=29) and Limba (n=67). Among these 276 HV1 sequences, 164 individual haplotypes were observed. An analysis of molecular variance indicated that the distribution of these haplotypes within the Limba sample was significantly different from that of the other ethnic groups. No significant genetic variation was seen between the Mende, Temne, and Loko. These results indicate that distinguishing genetic differences can be observed among ethnic groups residing in historically close proximity to one another. Furthermore, we observed some mitochondrial DNA haplotypes that are common among the Sierra Leone ethnic groups but that have not been observed in other published studies of West African ethnic groups. Therefore, we may have evidence for mtDNA lineages that are unique to this region of West Africa.     

The Relationship of Ethnicity,Socioeconomic Factors,and Overweight in U.S. Adolescents

Objective: To examine the extent to which race/ethnic differences in income and education account for sex‐specific disparities in overweight prevalence in white, African American, Hispanic, and Asian U.S. teens. Research Methods and Procedures: We used nationally representative data collected from 13,113 U.S. adolescents enrolled in the National Longitudinal Study of Adolescent Health. Logistic regression models were used to examine the relationship of family income and parental education to overweight prevalence (body mass index ≥ 85th percentile of age and sex‐specific cutoff points from the 2000 Centers for Disease Control and Prevention/National Center for Health Statistics growth charts). In addition, we used coefficients from our logistic regression models to project the effects on overweight prevalence of equalizing the socioeconomic status (SES) differences between race/ethnic groups. Results: Keeping adolescents in their same environments and changing only family income and parental education had a limited effect on the disparities in overweight prevalence. Ethnicity‐SES‐overweight differences were greater among females than males. Given that overweight prevalence decreased with increasing SES among white females and remained elevated and even increased among higher SES African‐American females, African‐American/white disparity in overweight prevalence increased at the highest SES. Conversely, disparity was lessened at the highest SES for white, Hispanic, and Asian females. Among males, disparity was lowest at the average SES level. Discussion: One cannot automatically assume that the benefits of increased SES found among white adults will transfer to other gender‐age‐ethnic groups. Our findings suggest that efforts to reduce overweight disparities between ethnic groups must look beyond income and education and focus on other factors, such as environmental, contextual, biological, and sociocultural factors.     

Ethnic differences in allelic distribution of IFN-g in South African women but no link with cervical cancer

BACKGROUND: The failure of specific types of human papillomaviruses (HPV) to raise effective immune responses may be important in the pathogenesis of cervical cancer, the second most common cancer in South African women. Polymorphisms of a number of cytokine genes have been implicated in inducing susceptibility or resistance to cancers caused by infectious agents owing to their role in determining host immune response. Polymorphisms of IL-10 and IFN-gamma genes are believed to influence the expression and/or secretion levels of their respective cytokines. METHODS AND RESULTS: In this study, women with histologically proven cancer of the cervix (n = 458) and hospital-based controls (n = 587) were investigated for bi-allelic -1082 (A/G) polymorphisms of IL-10 and the bi-allelic +874(A/T) polymorphisms of IFN-gamma. In addition, the distributions of the allelic frequencies were stratified in both the African and mixed race population groups of South Africa. We found striking differences in the allele distribution of IFN-gamma (X2 = 0.02) among the two ethnic groups. A significant increase in the allele distribution of the IFN-gamma AA genotype was found in the African group compared to the mixed population group (OR, 0.5; 95% CI, 0.2-1.0). For IL-10 there were no significant allelic differences between the two South African ethnic groups. Furthermore, when the ethnic groups were combined the IL-10 allelic frequencies in the combined South African data were similar to those observed in an Oriental population from Southern China and in an Italian population. However, the allele frequencies of the IFN-gamma genotype among the two South African ethnic groups were different when compared to an Italian Caucasoid group. While crude analysis of these data showed both statistically significantly increased and diminished risks of cervical cancer among high producers of INF-gamma and low producers of IL-10 respectively, these associations were no longer significant when the data were adjusted for confounding factors. CONCLUSION: These findings demonstrate a clear correlation between ethnicity and IFN-gamma polymorphism across different population groups. However, these differences in ethnicity and gene polymorphisms in the aforementioned cytokines are suggested not to influence the development of invasive cervical cancer but may represent an important susceptibility biomarker for other diseases and should be explored further.     

Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups

Technological and cultural innovations as well as climate changes are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ～ 10,000 years ago (ya). The expansion of Bantu languages (a family within the Niger-Congo phylum) ～ 5,000 ya represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sublineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu-speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1,195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, Democratic Republic of Congo, and Zambia). With the inclusion of published data, we analyzed 2,736 individuals from 26 groups representing all linguistic phyla and covering a large portion of sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using linear discriminant analysis on short tandem repeat (STR) haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggests that their expansion throughout sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found that linguistic affiliations played a notable role in shaping sub-Saharan African Y chromosomal diversity, although the impact of geography is clearly discernible.     

Commitment and paradox in sociological research: School integration in Israel*

Panethnicity ‐ the development of bridging organizations and the generalization of solidarity among ethnic subgroups ‐ is important theoretically because it focuses attention on ethnic change, and allows one to assess the relative importance of structural and cultural factors. In this article we present a framework for the study of panethnicity, generate research questions from this framework, and then test these questions by examining panethnicity within four broad racial/ethnic groupings: Asian Americans, Native Americans, Indo Americans and Latinos in the United States. A review of these four cases demonstrates that those groups with the greatest cross‐subgroup structural similarity (Asian Americans and Indo Americans) also display the greatest panethnic development and potential, despite their considerable cultural diversity. This suggests that structural factors are more important for understanding the development of panethnicity and, by extension, for understanding ethnic change generally.     

Differences in woody vegetation are unrelated to use by African elephants (Loxodonta africana) in Mkhuze Game Reserve, South Africa

The reintroduction of African elephants into fenced game reserves throughout South Africa has presented managers with several challenges. Although elephants are a natural part of southern African ecosystems, their confinement to fenced protected areas in South Africa has exacerbated their potential to impact their habitats negatively. However, many studies investigating the impact of elephants have failed to control for the effects of other browsers on the vegetative community. In this study, we used location data on an elephant herd to delineate high-use and low-use areas. This paired design allowed us to minimize confounding factors that could explain differences in the structure, diversity and utilization of woody species. We found little evidence to suggest elephant-mediated change in, or selection for, the structure or diversity of woody species; however, our results suggest that elephants may be altering the composition of species by preferentially using areas with higher canopy diversity and by enhancing sapling recruitment. Although stripping of bark was higher in high-use areas, there was no evidence of differential mortality of tree species. Therefore, in our study area, and over the current time scale, elephants are having a negligible impact on the vegetative community.     

Africa goes Europe: The complete phylogeography of the marbled white butterfly species complex Melanargia galathea/M. lachesis (Lepidoptera: Satyridae)

Climatic oscillations influence the distribution of species in time. Thermophilic species survived the ice ages in refugia around the Mediterranean. Northern Africa is one of the possibly important refugia. In this study we test the genetic differentiation between northern African and European populations, using the marbled white butterfly species complex, Melanargia galathea/M. lachesis, as a model. We studied 18 allozyme loci in 876 individuals from 23 populations representing a major part of Europe (northern Spain to Romania) and the western part of northern Africa (Atlas Mountains). The African populations resemble the European ones in allelic richness; their genetic diversity is higher than in Europe. Cluster analysis discriminated five European genetic groups: M. lachesis, a western European lineage, and three eastern European lineages. However, the African samples did not form a separate cluster within this phenogram, but clustered randomly within the Balkan/southeastern European groups. The genetic differentiation among the African populations (F_ST 8.8%) was higher than that within any of the European lineages (F_ST 2.6–5.5%). The high genetic diversity and the relatively strong differentiation of the four African populations sampled in a comparatively limited area of the Atlas Mountains indicate that the most probable origin of M. galathea is northern Africa, with its sibling species, M. lachesis, evolving in parallel in Iberia. Most probably, M. galathea colonised Europe first during the Eem interglacial, some 130 ky ago. Since M. lachesis must have existed on the Iberian peninsula during that period already, M. galathea should have reached Europe via Italy. The genetic differentiation to distinct groups in Europe most probably evolved during the following Würm glacial period.     

Leopard tortoises in southern Africa have greater genetic diversity in the north than in the south (Testudinidae)

In contrast to mammals, little is known about the phylogeographic structuring of widely distributed African reptile species. With the present study, we contribute data for the leopard tortoise (Stigmochelys pardalis). It ranges from the Horn of Africa southward to South Africa and westwards to southern Angola. However, its natural occurrence is disputed for some southern regions. To clarify the situation, we used mtDNA sequences and 14 microsatellite loci from 204 individuals mainly from southern Africa. Our results retrieved five mitochondrial clades; one in the south and two in the north‐west and north‐east of southern Africa, respectively, plus two distributed further north. Using microsatellites, the southern clade matched with a well‐defined southern nuclear cluster, whilst the two northern clades from southern Africa corresponded to another nuclear cluster with three subclusters. One subcluster had a western and central distribution, another occurred mostly in the north‐east, and the third in a small eastern region (Maputaland), which forms part of a biodiversity hotspot. Genetic diversity was low in the south and high in the north of our study region, particularly in the north‐east. Our results refuted that translocations influenced the genetic structure of leopard tortoises substantially. We propose that Pleistocene climatic fluctuations caused leopard tortoises to retract to distinct refugia in southern and northern regions and ascribe the high genetic diversity in the north of southern Africa to genetic structuring caused by the survival in three refuges and subsequent admixture, whereas tortoises in the south seem to have survived in only one continuous coastal refuge.     

Visceral fat, waist circumference, and BMI: impact of race/ethnicity

Objective: BMI and waist circumference are used to define risk from excess body fat. Limited data in women suggest that there may be racial/ethnic differences in visceral adipose tissue (VAT) at a given BMI or waist circumference. This study tested the hypothesis that racial/ethnic differences exist in both men and women in the relationship of anthropometric measures of body composition and computed tomography (CT)‐determined VAT or subcutaneous adipose tissue (SAT). Methods and Procedures: Subjects included 66 African American, 72 Hispanic, and 47 white men and women, aged ≥ 45. Waist circumference and BMI were measured using standard methods. Total abdominal and L4L5 VAT and SAT were measured using CT. Results: Among both men and women, groups did not differ in waist circumference or BMI. White men had greater L4L5 VAT than African‐American men, and both white and Hispanic men had greater total VAT than African‐American men. Among women, Hispanics and whites had greater L4L5 VAT than African Americans, and Hispanics had greater total VAT than African Americans. The slope of the linear relationship between BMI or waist circumference and VAT was lower in African Americans than in Hispanics and/or whites. Discussion: Middle‐aged and older African‐American men and women had lower VAT despite similar BMI and waist circumference measurements. Altered relationships between anthropometric measures and VAT may have implications for defining metabolic risk in different populations. Different waist circumference or BMI cutoff points may be necessary to adequately reflect risk in different racial/ethnic groups.     

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high‐resolution molecular analysis of nonrecombining Y‐chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el‐Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 ± 3,633 YBP. Similarly, theY‐chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

The African rainforest: odd man out or megafaunal landscape? African and Amazonian forests compared

Africa has been called the ‘odd man out’ because the hectare‐scale tree diversity of African equatorial forests is lower than that of forests in other parts of the tropics. Low diversity has been attributed to the smaller area of the African forest and a history of drought, fire and contraction. Several facts shed doubt on this interpretation. The current area of the central African forest is roughly 2 million km². Even during periods of Pleistocene contraction, numerous moist refugia remained, including 6 posited for Gabon, a country the size of the U. S. state of Colorado. The gamma‐diversity of Gabon is high, implying higher alpha diversities. Finally, tree diversities on small islands in the Solomons and Fiji archipelagos are twice those prevalent in Gabonese forests, suggesting that historical contractions may not have been sufficient to reduce diversity to its current level. To place the African situation in perspective, we compared tree stands in Gabon and the Peruvian Amazon. Peruvian forests contained a mean of 618 trees ≥ 10 cm dbh per ha vs 377 for Gabon, or 64% more. Peruvian forests contained relatively more small trees (≥ 10, <20 cm dbh) and many fewer large trees (≥ 20 cm dbh) than Gabonese forests. These structural differences were consistent across 10 Gabonese and 10 Peruvian sites and transcended local gradients in climate and geology, suggesting that they are intrinsic to the two continents. Tree species diversity in Perú is concentrated in the small tree class (≥ 10, <20 cm dbh), whereas it is highest in the larger tree classes in Gabon. Alpha diversity is apparently lower relative to gamma diversity in Africa than it is in Amazonian Perú , implying higher beta diversity. The densities of small plants (<1 m tall) are similar in Gabonese and Peruvian forests; the observed structural differences develop later at the sapling and small tree stages. Explaining the low hectare‐scale diversity of African forests thus reduces to understanding why the density and diversity of small trees is so anomalously low.     

STR Polymorphism in Indigenous Daghestan Populations

Genomic diversity of 21 STR loci has been studied in six ethnic populations of Daghestan (the Caucasus), namely, Avars, Dargins, Kubachians, Lezgins, Kumiks, and Nogais, and the results have been compared with these data for European, African, and East Asian ethnic groups. Daghestan is unique in its ethnic diversity, which is the greatest in the Caucasus: 26 out of approximately 50 autochthonous ethnic groups of the Caucasus live there. The genetic origin of this wide ethnic diversity of Daghestan and the Caucasus as a whole is still obscure. The genetic heterogeneity of Daghestan populations has been found to be lower than that of most other populations in the world. This is explained by a prolonged isolation and gene drift in their demographic history. Generalized genetic distances between ethnic groups calculated for the whole set of loci studied allow differentiating Asian populations from African ones, with European populations occupying intermediate positions. All Daghestan ethnic populations form a distinct common group together with some European populations (Finnish, Polish, and French). Nogais are genetically close to Southeast Asian populations. The genetic closeness and the apparently equal genetic diversity of Daghestan and European populations suggest that the ethnic differentiation of the ancestral populations of Daghestan and European ethnic groups occurred in the earliest populations of modern humans.