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Sample records for african hunter-gatherer populations

  1. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans

    PubMed Central

    Henn, Brenna M.; Gignoux, Christopher R.; Jobin, Matthew; Granka, Julie M.; Macpherson, J. M.; Kidd, Jeffrey M.; Rodríguez-Botigué, Laura; Ramachandran, Sohini; Hon, Lawrence; Brisbin, Abra; Lin, Alice A.; Underhill, Peter A.; Comas, David; Kidd, Kenneth K.; Norman, Paul J.; Parham, Peter; Bustamante, Carlos D.; Mountain, Joanna L.; Feldman, Marcus W.

    2011-01-01

    Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by FST, in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world. PMID:21383195

  2. Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers.

    PubMed

    Perry, George H; Foll, Matthieu; Grenier, Jean-Christophe; Patin, Etienne; Nédélec, Yohann; Pacis, Alain; Barakatt, Maxime; Gravel, Simon; Zhou, Xiang; Nsobya, Sam L; Excoffier, Laurent; Quintana-Murci, Lluis; Dominy, Nathaniel J; Barreiro, Luis B

    2014-09-02

    The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including enrichments for SNPs previously associated with stature variation in Europeans and for genes with growth hormone receptor and regulation functions. To test adaptive evolutionary hypotheses, we computed the haplotype-based integrated haplotype score (iHS) statistic and the level of population differentiation (FST) between the Batwa and their agricultural neighbors, the Bakiga, for each genomic SNP. Both |iHS| and FST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. In contrast, when we expanded our analysis to include Baka rainforest hunter-gatherers from Cameroon and Gabon (west central Africa) and Nzebi and Nzime neighboring agriculturalists, we did not observe elevated |iHS| or FST values in these genomic regions. Together, these results suggest adaptive and at least partially convergent origins of the pygmy phenotype even within Africa, supporting the hypothesis that small body size confers a selective advantage for tropical rainforest hunter-gatherers but raising questions about the antiquity of this behavior.

  3. Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

    PubMed Central

    Perry, George H.; Foll, Matthieu; Grenier, Jean-Christophe; Patin, Etienne; Nédélec, Yohann; Pacis, Alain; Barakatt, Maxime; Gravel, Simon; Zhou, Xiang; Nsobya, Sam L.; Excoffier, Laurent; Quintana-Murci, Lluis; Dominy, Nathaniel J.; Barreiro, Luis B.

    2014-01-01

    The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including enrichments for SNPs previously associated with stature variation in Europeans and for genes with growth hormone receptor and regulation functions. To test adaptive evolutionary hypotheses, we computed the haplotype-based integrated haplotype score (iHS) statistic and the level of population differentiation (FST) between the Batwa and their agricultural neighbors, the Bakiga, for each genomic SNP. Both |iHS| and FST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. In contrast, when we expanded our analysis to include Baka rainforest hunter-gatherers from Cameroon and Gabon (west central Africa) and Nzebi and Nzime neighboring agriculturalists, we did not observe elevated |iHS| or FST values in these genomic regions. Together, these results suggest adaptive and at least partially convergent origins of the pygmy phenotype even within Africa, supporting the hypothesis that small body size confers a selective advantage for tropical rainforest hunter-gatherers but raising questions about the antiquity of this behavior. PMID:25136101

  4. The epigenomic landscape of African rainforest hunter-gatherers and farmers

    PubMed Central

    Fagny, Maud; Patin, Etienne; MacIsaac, Julia L.; Rotival, Maxime; Flutre, Timothée; Jones, Meaghan J.; Siddle, Katherine J.; Quach, Hélène; Harmant, Christine; McEwen, Lisa M.; Froment, Alain; Heyer, Evelyne; Gessain, Antoine; Betsem, Edouard; Mouguiama-Daouda, Patrick; Hombert, Jean-Marie; Perry, George H.; Barreiro, Luis B.; Kobor, Michael S.; Quintana-Murci, Lluis

    2015-01-01

    The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation—particularly that correlated with historical lifestyle—shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time. PMID:26616214

  5. The epigenomic landscape of African rainforest hunter-gatherers and farmers.

    PubMed

    Fagny, Maud; Patin, Etienne; MacIsaac, Julia L; Rotival, Maxime; Flutre, Timothée; Jones, Meaghan J; Siddle, Katherine J; Quach, Hélène; Harmant, Christine; McEwen, Lisa M; Froment, Alain; Heyer, Evelyne; Gessain, Antoine; Betsem, Edouard; Mouguiama-Daouda, Patrick; Hombert, Jean-Marie; Perry, George H; Barreiro, Luis B; Kobor, Michael S; Quintana-Murci, Lluis

    2015-11-30

    The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation--particularly that correlated with historical lifestyle--shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time.

  6. Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set.

    PubMed

    Patin, Etienne; Laval, Guillaume; Barreiro, Luis B; Salas, Antonio; Semino, Ornella; Santachiara-Benerecetti, Silvana; Kidd, Kenneth K; Kidd, Judith R; Van der Veen, Lolke; Hombert, Jean-Marie; Gessain, Antoine; Froment, Alain; Bahuchet, Serge; Heyer, Evelyne; Quintana-Murci, Lluís

    2009-04-01

    The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter-gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter-gatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic events-size changes, population splits, and gene flow--ultimately giving rise to contemporary Pygmy (Western and Eastern) groups and neighboring agricultural populations. We studied the branching history of Pygmy hunter-gatherers and agricultural populations from Africa and estimated separation times and gene flow between these populations. We resequenced 24 independent noncoding regions across the genome, corresponding to a total of approximately 33 kb per individual, in 236 samples from seven Pygmy and five agricultural populations dispersed over the African continent. We used simulation-based inference to identify the historical model best fitting our data. The model identified included the early divergence of the ancestors of Pygmy hunter-gatherers and farming populations approximately 60,000 years ago, followed by a split of the Pygmies' ancestors into the Western and Eastern Pygmy groups approximately 20,000 years ago. Our findings increase knowledge of the history of the peopling of the African continent in a region lacking archaeological data. An appreciation of the demographic and adaptive history of African populations with different modes of subsistence should improve our understanding of the influence of human lifestyles on genome diversity.

  7. First molar size and wear within and among modern hunter-gatherers and agricultural populations.

    PubMed

    Górka, Katarzyna; Romero, Alejandro; Pérez-Pérez, Alejandro

    2015-08-01

    Apart from reflecting modern human dental variation, differences in dental size among populations provide a means for studying continuous evolutionary processes and their mechanisms. Dental wear, on the other hand, has been widely used to infer dietary adaptations and variability among or within diverse ancient human populations. Few such studies have focused on modern foragers and farmers, however, and diverse methods have been used. This research aimed to apply a single, standardized, and systematic quantitative procedure to measure dental size and dentin exposure in order to analyze differences among several hunter-gatherer and agricultural populations from various environments and geographic origins. In particular, we focused on sexual dimorphism and intergroup differences in the upper and lower first molars. Results indicated no sexual dimorphism in molar size and wear within the studied populations. Despite the great ethnographic variation in subsistence strategies among these populations, our findings suggest that differences in sexual division of labor do not affect dietary wear patterns.

  8. The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists.

    PubMed

    Patin, Etienne; Siddle, Katherine J; Laval, Guillaume; Quach, Hélène; Harmant, Christine; Becker, Noémie; Froment, Alain; Régnault, Béatrice; Lemée, Laure; Gravel, Simon; Hombert, Jean-Marie; Van der Veen, Lolke; Dominy, Nathaniel J; Perry, George H; Barreiro, Luis B; Verdu, Paul; Heyer, Evelyne; Quintana-Murci, Lluís

    2014-01-01

    The emergence of agriculture in West-Central Africa approximately 5,000 years ago, profoundly modified the cultural landscape and mode of subsistence of most sub-Saharan populations. How this major innovation has had an impact on the genetic history of rainforest hunter-gatherers-historically referred to as 'pygmies'-and agriculturalists, however, remains poorly understood. Here we report genome-wide SNP data from these populations located west-to-east of the equatorial rainforest. We find that hunter-gathering populations present up to 50% of farmer genomic ancestry, and that substantial admixture began only within the last 1,000 years. Furthermore, we show that the historical population sizes characterizing these communities already differed before the introduction of agriculture. Our results suggest that the first socio-economic interactions between rainforest hunter-gatherers and farmers introduced by the spread of farming were not accompanied by immediate, extensive genetic exchanges and occurred on a backdrop of two groups already differentiated by their specialization in two ecotopes with differing carrying capacities.

  9. Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

    PubMed Central

    Kim, Hie Lim; Ratan, Aakrosh; Perry, George H.; Montenegro, Alvaro; Miller, Webb; Schuster, Stephan C.

    2014-01-01

    The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/’hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100–150 kyr ago. In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80–100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations. PMID:25471224

  10. Biological diversity and population history of Middle Holocene hunter-gatherers from the Cis-Baikal region of Siberia.

    PubMed

    Movsesian, Alla A; Bakholdina, Varvara Yu; Pezhemsky, Denis V

    2014-12-01

    In the past decades, prehistoric hunter-gatherers of the Cis-Baikal region has been a subject of multidisciplinary research. In this study, we used nonmetric cranial traits to assess the genetic relationships between various spatial and temporal groups of Cis-Baikal Middle Holocene hunter-gatherers and to reveal genetic continuity between the Cis-Baikal Neolithic-Bronze Age population and modern native Siberians. Cranial series belonging to the bearers of the Early Neolithic Kitoi (n = 72), Late Neolithic Serovo (n = 54), and Early Bronze Glazkovo (n = 98) cultures were examined. Phenotypic differentiation was analyzed by the mean measure of divergence and Nei's genetic distances. Our results revealed several patterns of spatiotemporal biodiversity among the Cis-Baikal Middle Holocene populations, including biological similarity between the Early and Late Neolithic-Bronze Age groups, which suggests that the temporal hiatus between the Early and Late Neolithic does not necessarily imply genetic discontinuity in the region. The following possible scenarios of population history in the Cis-Baikal region are proposed: 1) continuous occupation with outside invasion of new migrant groups in the Late Neolithic and Bronze Age and 2) migration of the Early Neolithic groups to the nearby regions and subsequent return of their descendants to the ancestral territory. A comparison of Cis-Baikal Neolithic populations with modern Siberian natives suggests that the Сis-Baikal region could have been a source area for population expansions into different parts of Siberia in the Neolithic and Bronze Age times.

  11. Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

    PubMed Central

    Hsieh, PingHsun; Veeramah, Krishna R.; Lachance, Joseph; Tishkoff, Sarah A.; Wall, Jeffrey D.; Hammer, Michael F.; Gutenkunst, Ryan N.

    2016-01-01

    African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors. PMID:26888263

  12. The Ecological basis of hunter-gatherer subsistence in African Rain Forests: the Mbuti of eastern Zaire

    SciTech Connect

    Hart, T.B.; Hart, J.A.

    1986-03-01

    The Mbuti pygmies, hunter-gathers of the Ituri Forest of Zaire, trade forest products and labor for agricultural foods. It has been assumed that the Mbuti lived independently in the equatorial forest prior to its penetration by shifting cultivators. We assessed forest food resources (plant and animal) to determine their adequacy to support a hunting and gathering economy. For five months of the year, essentially none of the calorically important forest fruits and seeds are available. Honey is not abundant during this season of scarcity. Wild game meat is available year round, but the main animals caught have low fat content. This makes them a poor substitute for starch-dense agricultural foods, now staples in Mbuti diet. In general, in the closed evergreen forest zone, edible wild plant species are more abundant in agriculturally derived secondary forest than in primary forest. Similarly, they are more common at the savanna ecotone and in gallery forests. We suggest that it is unlikely that hunter-gatherers would have lived independently in the forest interior with its precarious resource base, when many of the food species they exploit are more abundant toward the savanna border.

  13. Recent origin and cultural reversion of a hunter-gatherer group.

    PubMed

    Oota, Hiroki; Pakendorf, Brigitte; Weiss, Gunter; von Haeseler, Arndt; Pookajorn, Surin; Settheetham-Ishida, Wannapa; Tiwawech, Danai; Ishida, Takafumi; Stoneking, Mark

    2005-03-01

    Contemporary hunter-gatherer groups are often thought to serve as models of an ancient lifestyle that was typical of human populations prior to the development of agriculture. Patterns of genetic variation in hunter-gatherer groups such as the Kung and African Pygmies are consistent with this view, as they exhibit low genetic diversity coupled with high frequencies of divergent mtDNA types not found in surrounding agricultural groups, suggesting long-term isolation and small population sizes. We report here genetic evidence concerning the origins of the Mlabri, an enigmatic hunter-gatherer group from northern Thailand. The Mlabri have no mtDNA diversity, and the genetic diversity at Y-chromosome and autosomal loci are also extraordinarily reduced in the Mlabri. Genetic, linguistic, and cultural data all suggest that the Mlabri were recently founded, 500-800 y ago, from a very small number of individuals. Moreover, the Mlabri appear to have originated from an agricultural group and then adopted a hunting-gathering subsistence mode. This example of cultural reversion from agriculture to a hunting-gathering lifestyle indicates that contemporary hunter-gatherer groups do not necessarily reflect a pre-agricultural lifestyle.

  14. Wealth Transmission and Inequality Among Hunter-Gatherers

    PubMed Central

    Hill, Kim; Marlowe, Frank; Nolin, David; Wiessner, Polly; Gurven, Michael; Bowles, Samuel; Mulder, Monique Borgerhoff; Hertz, Tom; Bell, Adrian

    2010-01-01

    We report quantitative estimates of intergenerational transmission and population-wide inequality for wealth measures in a set of hunter-gatherer populations. Wealth is defined broadly as factors that contribute to individual or household well-being, ranging from embodied forms such as weight and hunting success to material forms such household goods, as well as relational wealth in exchange partners. Intergenerational wealth transmission is low to moderate in these populations, but is still expected to have measurable influence on an individual’s life chances. Wealth inequality (measured with Gini coefficients) is moderate for most wealth types, matching what qualitative ethnographic research has generally indicated (if not the stereotype of hunter-gatherers as extreme egalitarians). We discuss some plausible mechanisms for these patterns, and suggest ways in which future research could resolve questions about the role of wealth in hunter-gatherer social and economic life. PMID:21151711

  15. Camp stability predicts patterns of hunter-gatherer cooperation.

    PubMed

    Smith, Daniel; Dyble, Mark; Thompson, James; Major, Katie; Page, Abigail E; Chaudhary, Nikhil; Salali, Gul Deniz; Vinicius, Lucio; Migliano, Andrea Bamberg; Mace, Ruth

    2016-07-01

    Humans regularly cooperate with non-kin, which has been theorized to require reciprocity between repeatedly interacting and trusting individuals. However, the role of repeated interactions has not previously been demonstrated in explaining real-world patterns of hunter-gatherer cooperation. Here we explore cooperation among the Agta, a population of Filipino hunter-gatherers, using data from both actual resource transfers and two experimental games across multiple camps. Patterns of cooperation vary greatly between camps and depend on socio-ecological context. Stable camps (with fewer changes in membership over time) were associated with greater reciprocal sharing, indicating that an increased likelihood of future interactions facilitates reciprocity. This is the first study reporting an association between reciprocal cooperation and hunter-gatherer band stability. Under conditions of low camp stability individuals still acquire resources from others, but do so via demand sharing (taking from others), rather than based on reciprocal considerations. Hunter-gatherer cooperation may either be characterized as reciprocity or demand sharing depending on socio-ecological conditions.

  16. Plant-animal subsistence ratios and macronutrient energy estimations in worldwide hunter-gatherer diets.

    PubMed

    Cordain, L; Miller, J B; Eaton, S B; Mann, N; Holt, S H; Speth, J D

    2000-03-01

    Both anthropologists and nutritionists have long recognized that the diets of modern-day hunter-gatherers may represent a reference standard for modern human nutrition and a model for defense against certain diseases of affluence. Because the hunter-gatherer way of life is now probably extinct in its purely un-Westernized form, nutritionists and anthropologists must rely on indirect procedures to reconstruct the traditional diet of preagricultural humans. In this analysis, we incorporate the most recent ethnographic compilation of plant-to-animal economic subsistence patterns of hunter-gatherers to estimate likely dietary macronutrient intakes (% of energy) for environmentally diverse hunter-gatherer populations. Furthermore, we show how differences in the percentage of body fat in prey animals would alter protein intakes in hunter-gatherers and how a maximal protein ceiling influences the selection of other macronutrients. Our analysis showed that whenever and wherever it was ecologically possible, hunter-gatherers consumed high amounts (45-65% of energy) of animal food. Most (73%) of the worldwide hunter-gatherer societies derived >50% (> or =56-65% of energy) of their subsistence from animal foods, whereas only 14% of these societies derived >50% (> or =56-65% of energy) of their subsistence from gathered plant foods. This high reliance on animal-based foods coupled with the relatively low carbohydrate content of wild plant foods produces universally characteristic macronutrient consumption ratios in which protein is elevated (19-35% of energy) at the expense of carbohydrates (22-40% of energy).

  17. Genetic discontinuity between local hunter-gatherers and central Europe's first farmers.

    PubMed

    Bramanti, B; Thomas, M G; Haak, W; Unterlaender, M; Jores, P; Tambets, K; Antanaitis-Jacobs, I; Haidle, M N; Jankauskas, R; Kind, C-J; Lueth, F; Terberger, T; Hiller, J; Matsumura, S; Forster, P; Burger, J

    2009-10-02

    After the domestication of animals and crops in the Near East some 11,000 years ago, farming had reached much of central Europe by 7500 years before the present. The extent to which these early European farmers were immigrants or descendants of resident hunter-gatherers who had adopted farming has been widely debated. We compared new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers and from modern Europeans. We find large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers share mtDNA types that are relatively rare in central Europeans today. Together, these analyses provide persuasive evidence that the first farmers were not the descendants of local hunter-gatherers but immigrated into central Europe at the onset of the Neolithic.

  18. Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota.

    PubMed

    Rampelli, Simone; Schnorr, Stephanie L; Consolandi, Clarissa; Turroni, Silvia; Severgnini, Marco; Peano, Clelia; Brigidi, Patrizia; Crittenden, Alyssa N; Henry, Amanda G; Candela, Marco

    2015-06-29

    Through human microbiome sequencing, we can better understand how host evolutionary and ontogenetic history is reflected in the microbial function. However, there has been no information on the gut metagenome configuration in hunter-gatherer populations, posing a gap in our knowledge of gut microbiota (GM)-host mutualism arising from a lifestyle that describes over 90% of human evolutionary history. Here, we present the first metagenomic analysis of GM from Hadza hunter-gatherers of Tanzania, showing a unique enrichment in metabolic pathways that aligns with the dietary and environmental factors characteristic of their foraging lifestyle. We found that the Hadza GM is adapted for broad-spectrum carbohydrate metabolism, reflecting the complex polysaccharides in their diet. Furthermore, the Hadza GM is equipped for branched-chain amino acid degradation and aromatic amino acid biosynthesis. Resistome functionality demonstrates the existence of antibiotic resistance genes in a population with little antibiotic exposure, indicating the ubiquitous presence of environmentally derived resistances. Our results demonstrate how the functional specificity of the GM correlates with certain environment and lifestyle factors and how complexity from the exogenous environment can be balanced by endogenous homeostasis. The Hadza gut metagenome structure allows us to appreciate the co-adaptive functional role of the GM in complementing the human physiology, providing a better understanding of the versatility of human life and subsistence.

  19. Gut microbiome of the Hadza hunter-gatherers

    PubMed Central

    Schnorr, Stephanie L.; Candela, Marco; Rampelli, Simone; Centanni, Manuela; Consolandi, Clarissa; Basaglia, Giulia; Turroni, Silvia; Biagi, Elena; Peano, Clelia; Severgnini, Marco; Fiori, Jessica; Gotti, Roberto; De Bellis, Gianluca; Luiselli, Donata; Brigidi, Patrizia; Mabulla, Audax; Marlowe, Frank; Henry, Amanda G.; Crittenden, Alyssa N.

    2014-01-01

    Human gut microbiota directly influences health and provides an extra means of adaptive potential to different lifestyles. To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls. Further comparisons with two rural farming African groups illustrate other features unique to Hadza that can be linked to a foraging lifestyle. These include absence of Bifidobacterium and differences in microbial composition between the sexes that probably reflect sexual division of labour. Furthermore, enrichment in Prevotella, Treponema and unclassified Bacteroidetes, as well as a peculiar arrangement of Clostridiales taxa, may enhance the Hadza’s ability to digest and extract valuable nutrition from fibrous plant foods. PMID:24736369

  20. Gut microbiome of the Hadza hunter-gatherers.

    PubMed

    Schnorr, Stephanie L; Candela, Marco; Rampelli, Simone; Centanni, Manuela; Consolandi, Clarissa; Basaglia, Giulia; Turroni, Silvia; Biagi, Elena; Peano, Clelia; Severgnini, Marco; Fiori, Jessica; Gotti, Roberto; De Bellis, Gianluca; Luiselli, Donata; Brigidi, Patrizia; Mabulla, Audax; Marlowe, Frank; Henry, Amanda G; Crittenden, Alyssa N

    2014-04-15

    Human gut microbiota directly influences health and provides an extra means of adaptive potential to different lifestyles. To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls. Further comparisons with two rural farming African groups illustrate other features unique to Hadza that can be linked to a foraging lifestyle. These include absence of Bifidobacterium and differences in microbial composition between the sexes that probably reflect sexual division of labour. Furthermore, enrichment in Prevotella, Treponema and unclassified Bacteroidetes, as well as a peculiar arrangement of Clostridiales taxa, may enhance the Hadza's ability to digest and extract valuable nutrition from fibrous plant foods.

  1. Play as a Foundation for Hunter-Gatherer Social Existence

    ERIC Educational Resources Information Center

    Gray, Peter

    2009-01-01

    The author offers the thesis that hunter-gatherers promoted, through cultural means, the playful side of their human nature and this made possible their egalitarian, nonautocratic, intensely cooperative ways of living. Hunter-gatherer bands, with their fluid membership, are likened to social-play groups, which people could freely join or leave.…

  2. Hunter-gatherer residential mobility and the marginal value of rainforest patches.

    PubMed

    Venkataraman, Vivek V; Kraft, Thomas S; Dominy, Nathaniel J; Endicott, Kirk M

    2017-03-21

    The residential mobility patterns of modern hunter-gatherers broadly reflect local resource availability, but the proximate ecological and social forces that determine the timing of camp movements are poorly known. We tested the hypothesis that the timing of such moves maximizes foraging efficiency as hunter-gatherers move across the landscape. The marginal value theorem predicts when a group should depart a camp and its associated foraging area and move to another based on declining marginal return rates. This influential model has yet to be directly applied in a population of hunter-gatherers, primarily because the shape of gain curves (cumulative resource acquisition through time) and travel times between patches have been difficult to estimate in ethnographic settings. We tested the predictions of the marginal value theorem in the context of hunter-gatherer residential mobility using historical foraging data from nomadic, socially egalitarian Batek hunter-gatherers (n = 93 d across 11 residential camps) living in the tropical rainforests of Peninsular Malaysia. We characterized the gain functions for all resources acquired by the Batek at daily timescales and examined how patterns of individual foraging related to the emergent property of residential movements. Patterns of camp residence times conformed well with the predictions of the marginal value theorem, indicating that communal perceptions of resource depletion are closely linked to collective movement decisions. Despite (and perhaps because of) a protracted process of deliberation and argument about when to depart camps, Batek residential mobility seems to maximize group-level foraging efficiency.

  3. Future Discounting in Congo Basin Hunter-Gatherers Declines with Socio-Economic Transitions.

    PubMed

    Salali, Gul Deniz; Migliano, Andrea Bamberg

    2015-01-01

    Humans have a tendency to discount the future; that is we value small, short-term rewards over larger, long-term rewards. The degree of future discounting, however, changes in response to socio-ecological factors. Here, we study Mbendjele BaYaka hunter-gatherers of northern Congo and their farmer neighbours to investigate adaptations in inter-temporal preferences in humans. We argue that in immediate-return systems, where food storage is absent and egalitarianism is enforced through levelling mechanisms, future discounting is an adaptive strategy to prevent wealth accumulation and the emergence of hierarchies. This ensures food sharing and allows for survival in unpredictable environments where there is risk of an energy shortfall. On the other hand, when food storage is made possible by the emergence of agriculture or as seen in some delayed-return hunter-gatherer populations, wealth accumulation, hierarchies and lower discount rates become the adaptive strategy. Therefore, individuals in immediate-return, egalitarian societies will discount the future more than those in non-egalitarian, delayed-return societies. Consistent with the predictions we found that market integration and socio-economic transitions decrease the future discounting in Mbendjele hunter-gatherers. Our measures of socio-economic differences marked this transition in hunter-gatherers living in a logging town. The degree of future-discounting was the same between more market-integrated hunter-gatherers and their farmer neighbours.

  4. Future Discounting in Congo Basin Hunter-Gatherers Declines with Socio-Economic Transitions

    PubMed Central

    Salali, Gul Deniz; Migliano, Andrea Bamberg

    2015-01-01

    Humans have a tendency to discount the future; that is we value small, short-term rewards over larger, long-term rewards. The degree of future discounting, however, changes in response to socio-ecological factors. Here, we study Mbendjele BaYaka hunter-gatherers of northern Congo and their farmer neighbours to investigate adaptations in inter-temporal preferences in humans. We argue that in immediate-return systems, where food storage is absent and egalitarianism is enforced through levelling mechanisms, future discounting is an adaptive strategy to prevent wealth accumulation and the emergence of hierarchies. This ensures food sharing and allows for survival in unpredictable environments where there is risk of an energy shortfall. On the other hand, when food storage is made possible by the emergence of agriculture or as seen in some delayed-return hunter-gatherer populations, wealth accumulation, hierarchies and lower discount rates become the adaptive strategy. Therefore, individuals in immediate-return, egalitarian societies will discount the future more than those in non-egalitarian, delayed-return societies. Consistent with the predictions we found that market integration and socio-economic transitions decrease the future discounting in Mbendjele hunter-gatherers. Our measures of socio-economic differences marked this transition in hunter-gatherers living in a logging town. The degree of future-discounting was the same between more market-integrated hunter-gatherers and their farmer neighbours. PMID:26381883

  5. Genome-wide evidence of Austronesian–Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar

    PubMed Central

    Pierron, Denis; Razafindrazaka, Harilanto; Pagani, Luca; Ricaut, François-Xavier; Antao, Tiago; Capredon, Mélanie; Sambo, Clément; Radimilahy, Chantal; Rakotoarisoa, Jean-Aimé; Blench, Roger M.; Letellier, Thierry; Kivisild, Toomas

    2014-01-01

    Linguistic and cultural evidence suggest that Madagascar was the final point of two major dispersals of Austronesian- and Bantu-speaking populations. Today, the Mikea are described as the last-known Malagasy population reported to be still practicing a hunter-gatherer lifestyle. It is unclear, however, whether the Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their lifestyle that separates them from the other contemporary populations of South Madagascar. To address these questions we have performed a genome-wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo, and 24 Temoro individuals, together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family, we observe that only one-third of their genetic ancestry is related to the populations of the Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life through cultural reversion, and selection signals suggest a genetic adaptation to their new lifestyle. PMID:24395773

  6. Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar.

    PubMed

    Pierron, Denis; Razafindrazaka, Harilanto; Pagani, Luca; Ricaut, François-Xavier; Antao, Tiago; Capredon, Mélanie; Sambo, Clément; Radimilahy, Chantal; Rakotoarisoa, Jean-Aimé; Blench, Roger M; Letellier, Thierry; Kivisild, Toomas

    2014-01-21

    Linguistic and cultural evidence suggest that Madagascar was the final point of two major dispersals of Austronesian- and Bantu-speaking populations. Today, the Mikea are described as the last-known Malagasy population reported to be still practicing a hunter-gatherer lifestyle. It is unclear, however, whether the Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their lifestyle that separates them from the other contemporary populations of South Madagascar. To address these questions we have performed a genome-wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo, and 24 Temoro individuals, together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family, we observe that only one-third of their genetic ancestry is related to the populations of the Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life through cultural reversion, and selection signals suggest a genetic adaptation to their new lifestyle.

  7. Gradients of occlusal wear in hunter-gatherers and agriculturalists.

    PubMed

    Deter, Christina A

    2009-03-01

    Occlusal wear was recorded in maxillary teeth from three North American late Archaic (3385 +/- 365 cal BC) hunter-gatherer sites (n = 306) and late Anasazi-early Zuni agricultural sites ( approximately 1300 AD) (n = 87). Comparisons were undertaken using descriptive and inferential statistics to determine differences between these groups, and along the maxillary tooth row. The hunter-gatherers had a significantly greater percentage of occlusal wear than the agriculturalists. For both hunter-gatherers and agriculturalists, occlusal wear was greatest on the central incisors and first molars. The third molars had the least amount of wear. It was inferred from these results that the hunter-gatherers had a more abrasive diet, and different daily task activities compared to the agriculturalists. One further finding was that wear patterns on anterior and posterior teeth are influenced by the order that teeth erupt into the jaw, as well as diet and behavior.

  8. Hunter-gatherers have less famine than agriculturalists.

    PubMed

    Berbesque, J Colette; Marlowe, Frank W; Shaw, Peter; Thompson, Peter

    2014-01-01

    The idea that hunter-gatherer societies experience more frequent famine than societies with other modes of subsistence is pervasive in the literature on human evolution. This idea underpins, for example, the 'thrifty genotype hypothesis'. This hypothesis proposes that our hunter-gatherer ancestors were adapted to frequent famines, and that these once adaptive 'thrifty genotypes' are now responsible for the current obesity epidemic. The suggestion that hunter-gatherers are more prone to famine also underlies the widespread assumption that these societies live in marginal habitats. Despite the ubiquity of references to 'feast and famine' in the literature describing our hunter-gatherer ancestors, it has rarely been tested whether hunter-gatherers suffer from more famine than other societies. Here, we analyse famine frequency and severity in a large cross-cultural database, in order to explore relationships between subsistence and famine risk. This is the first study to report that, if we control for habitat quality, hunter-gatherers actually had significantly less--not more--famine than other subsistence modes. This finding challenges some of the assumptions underlying for models of the evolution of the human diet, as well as our understanding of the recent epidemic of obesity and type 2 diabetes mellitus.

  9. Phenotypic plasticity of climbing-related traits in the ankle joint of great apes and rainforest hunter-gatherers.

    PubMed

    Venkataraman, Vivek V; Kraft, Thomas S; Desilva, Jeremy M; Dominy, Nathaniel J

    2013-01-01

    The "negrito" and African "pygmy" phenotypes are predominately exhibited by hunter-gatherers living in rainforest habitats. Foraging within such habitats is associated with a unique set of locomotor behaviors, most notably habitual vertical climbing during the pursuit of honey, fruit, and game. When performed frequently, this behavior is expected to correlate with developmentally plastic skeletal morphologies that respond to mechanical loading. Using six measurements in the distal tibia and talus that discriminate nonhuman primates by vertical climbing frequency, we tested the prediction that intraspecific variation in this behavior is reflected in the morphology of the ankle joint of habitually climbing human populations. First, to explore the plasticity of climbing-linked morphologies, we made comparisons between chimpanzees, gorillas, and orangutans from wild and captive settings. The analysis revealed significant differences in two climbing-linked traits (anterior expansion of the articular surface of the distal tibia and increased degree of talar wedging), indicating that these traits are sensitive to climbing behavior. However, our analyses did not reveal any signatures of climbing behavior in the ankles of habitually climbing hunter-gatherers. These results suggest that the detection of fine-grained differences in human locomotor behaviors at the ankle joint, particularly those associated with arboreality, may be obscured by the functional demands of terrestrial bipedalism. Accordingly, it may be difficult to use population-level characteristics of ankle morphology to make inferences about the climbing behavior of hominins in the fossil record, even when facultative arborealism is associated with key fitness benefits.

  10. Hunter-gatherers in southeast Asia: from prehistory to the present.

    PubMed

    Higham, Charles

    2013-01-01

    Anatomically modern hunter-gatherers expanded from Africa into Southeast Asia at least 50,000 years ago, where they probably encountered and interacted with populations of Homo erectus and Homo floresiensis and the recently discovered Denisovans. Simulation studies suggest that these hunter-gatherers may well have followed a coastal route that ultimately led to the settlement of Sahul, while archaeology confirms that they also crossed significant seas and explored well into the interior. They also adapted to marked environmental changes that alternated between relatively cool and dry conditions and warmer, wetter interludes. During the former, the sea fell by up to 120 m below its present level, which opened up a vast low-lying area known as Sundaland. Three principal alignments can be identified: the first involved the occupation of rock shelters in upland regions, the second has identified settlement on broad riverine floodplains, and the last concentrated on the raised beaches formed from about five millennia ago when the sea level was elevated above its present position. This cultural sequence was dislocated about 4 kya when rice and millet farmers infiltrated the lowlands of Southeast Asia ultimately from the Yangtze River valley. It is suggested that this led to two forms of interaction. In the first, the indigenous hunter-gatherers integrated with intrusive Neolithic communities and, while losing their cultural identity, contributed their genes to the present population of Southeast Asia. In the second, hunter-gatherers withdrew to rainforest refugia and, through selective pressures inherent in such an environment, survived as the small-bodied, dark-skinned humans found to this day in the Philippines, Peninsular Malaysia and Thailand, and the Andaman Islands. Beyond the impact of expansive rice farmers in Melanesia and Australia, hunter-gatherers continued to dominate until they encountered European settlement.

  11. The skeletal phenotype of "negritos" from the Andaman Islands and Philippines relative to global variation among hunter-gatherers.

    PubMed

    Stock, Jay T

    2013-01-01

    The "negrito hypothesis" suggests that populations of small-bodied foragers in South and Southeast Asia who share common phenotypic characteristics may also share a common, ancient origin. The key defining characteristics of the "negrito" phenotype, small body size, dark skin, and tightly curled hair, have been interpreted as linking these populations to sub-Saharan Africans. The underlying assumption of this interpretation is that the observed phenotypic similarities likely reflect shared ancestry rather than phenotypic convergence. Current genetic evidence is inconclusive, as it both demonstrates that negrito populations have genetic affinities with neighboring populations but also rare and ancient variation that suggests considerable isolation. This study investigates the skeletal phenotype of Andaman Islanders and Aeta foragers from the Philippines in the context of the phenotypic variation among other hunter-gatherers globally, to test whether they show a common, unique physique apart from small body size. Particular emphasis is placed on the comparison of negrito phenotypes to African, Asian, and Australian hunter-gatherer diversity to investigate phenotypic similarities to other populations globally. The results demonstrate that despite sharing small adult stature, the Andaman Islanders and Aeta show variation in body dimensions. In particular, the Andaman Islanders share a pattern of narrow bi-iliac breadth and short upper limbs with the Khoisan (Later Stone Age Southern Africans), whereas the Aeta and Efé show broader bi-iliac breadths relative to lower limb lengths. Although general similarities in size and proportions remain between the Andamanese and Aeta, differences in humero-femoral indices and arm length between these groups and the Efé demonstrate that there is not a generic "pygmy" phenotype. Our interpretations of negrito origins and adaptation must account for this phenotypic variation.

  12. Social networks and cooperation in hunter-gatherers.

    PubMed

    Apicella, Coren L; Marlowe, Frank W; Fowler, James H; Christakis, Nicholas A

    2012-01-25

    Social networks show striking structural regularities, and both theory and evidence suggest that networks may have facilitated the development of large-scale cooperation in humans. Here, we characterize the social networks of the Hadza, a population of hunter-gatherers in Tanzania. We show that Hadza networks have important properties also seen in modernized social networks, including a skewed degree distribution, degree assortativity, transitivity, reciprocity, geographic decay and homophily. We demonstrate that Hadza camps exhibit high between-group and low within-group variation in public goods game donations. Network ties are also more likely between people who give the same amount, and the similarity in cooperative behaviour extends up to two degrees of separation. Social distance appears to be as important as genetic relatedness and physical proximity in explaining assortativity in cooperation. Our results suggest that certain elements of social network structure may have been present at an early point in human history. Also, early humans may have formed ties with both kin and non-kin, based in part on their tendency to cooperate. Social networks may thus have contributed to the emergence of cooperation.

  13. Librarians as Hunter-Gatherers: Lessons Learned from an Excursion

    ERIC Educational Resources Information Center

    Cooper, Mindy M.

    2013-01-01

    Fueled by the pressing need for electronic resource usage statistics, librarians are finding themselves being thrust into the role of hunter-gatherer. This article discusses the work done at University Library at Indiana University-Purdue University Indianapolis to provide usage statistics for all its paid subscriptions for a 3-year period. The…

  14. Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians.

    PubMed

    Malmström, Helena; Gilbert, M Thomas P; Thomas, Mark G; Brandström, Mikael; Storå, Jan; Molnar, Petra; Andersen, Pernille K; Bendixen, Christian; Holmlund, Gunilla; Götherström, Anders; Willerslev, Eske

    2009-11-03

    The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.

  15. High mobility explains demand sharing and enforced cooperation in egalitarian hunter-gatherers

    PubMed Central

    Lewis, Hannah M.; Vinicius, Lucio; Strods, Janis; Mace, Ruth; Migliano, Andrea Bamberg

    2014-01-01

    ‘Simple’ hunter-gatherer populations adopt the social norm of ‘demand sharing’, an example of human hyper-cooperation whereby food brought into camps is claimed and divided by group members. Explaining how demand sharing evolved without punishment to free riders, who rarely hunt but receive resources from active hunters, has been a long-standing problem. Here we show through a simulation model that demand-sharing families that continuously move between camps in response to their energy income are able to survive in unpredictable environments typical of hunter-gatherers, while non-sharing families and sedentary families perish. Our model also predicts that non-producers (free riders, pre-adults and post-productive adults) can be sustained in relatively high numbers. As most of hominin pre-history evolved in hunter-gatherer settings, demand sharing may be an ancestral manifestation of hyper-cooperation and inequality aversion, allowing exploration of high-quality, hard-to-acquire resources, the evolution of fluid co-residence patterns and egalitarian resource distribution in the absence of punishment or warfare. PMID:25511874

  16. High mobility explains demand sharing and enforced cooperation in egalitarian hunter-gatherers.

    PubMed

    Lewis, Hannah M; Vinicius, Lucio; Strods, Janis; Mace, Ruth; Migliano, Andrea Bamberg

    2014-12-16

    'Simple' hunter-gatherer populations adopt the social norm of 'demand sharing', an example of human hyper-cooperation whereby food brought into camps is claimed and divided by group members. Explaining how demand sharing evolved without punishment to free riders, who rarely hunt but receive resources from active hunters, has been a long-standing problem. Here we show through a simulation model that demand-sharing families that continuously move between camps in response to their energy income are able to survive in unpredictable environments typical of hunter-gatherers, while non-sharing families and sedentary families perish. Our model also predicts that non-producers (free riders, pre-adults and post-productive adults) can be sustained in relatively high numbers. As most of hominin pre-history evolved in hunter-gatherer settings, demand sharing may be an ancestral manifestation of hyper-cooperation and inequality aversion, allowing exploration of high-quality, hard-to-acquire resources, the evolution of fluid co-residence patterns and egalitarian resource distribution in the absence of punishment or warfare.

  17. Modelling mechanisms of social network maintenance in hunter-gatherers

    PubMed Central

    Pearce, Eiluned

    2014-01-01

    Due to decreasing resource densities, higher latitude hunter-gatherers need to maintain their social networks over greater geographic distances than their equatorial counterparts. This suggests that as latitude increases, the frequency of face-to-face interaction decreases for ‘weak tie’ relationships in the outer mating pool (~500-strong) and tribal (~1500-strong) layers of a hunter-gatherer social network. A key question, then, is how a hunter-gatherer tribe sustains coherence as a single identifiable unit given that members are distributed across a large geographic area. The first step in answering this question is to establish whether the expectation that network maintenance raises a challenge for hunter-gatherers is correct, or whether sustaining inter-group contact is in fact trivial. Here I present a null model that represents mobile groups as randomly and independently moving gas particles. The aim of this model is to examine whether face-to-face contact can be maintained with every member of an individual’s tribe at all latitudes even under the baseline assumption of random movement. Contrary to baseline expectations, the number of encounters between groups predicted by the gas model cannot support tribal cohesion and is significantly negatively associated with absolute latitude. In addition, above ~40 degrees latitude random mobility no longer produces a sufficient number of encounters between groups to maintain contact across the 500-strong mating pool. These model predictions suggest that the outermost layers of hunter-gatherers’ social networks may require additional mechanisms of support in the form of strategies that either enhance encounter rates, such as coordinated mobility patterns, or lessen the need for face-to-face interaction, such as the use of symbolic artefacts to represent social affiliations. Given the predicted decline in encounters away from the equator, such additional supports might be most strongly expressed at high

  18. Hunter-Gatherers and the Origins of Religion.

    PubMed

    Peoples, Hervey C; Duda, Pavel; Marlowe, Frank W

    2016-09-01

    Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs. We reconstruct ancestral character states using a time-calibrated supertree based on published phylogenetic trees and linguistic classification and then test for correlated evolution between the characters and for the direction of cultural change. Results indicate that the oldest trait of religion, present in the most recent common ancestor of present-day hunter-gatherers, was animism, in agreement with long-standing beliefs about the fundamental role of this trait. Belief in an afterlife emerged, followed by shamanism and ancestor worship. Ancestor spirits or high gods who are active in human affairs were absent in early humans, suggesting a deep history for the egalitarian nature of hunter-gatherer societies. There is a significant positive relationship between most characters investigated, but the trait "high gods" stands apart, suggesting that belief in a single creator deity can emerge in a society regardless of other aspects of its religion.

  19. Using obsidian transfer distances to explore social network maintenance in late Pleistocene hunter-gatherers

    PubMed Central

    Pearce, Eiluned; Moutsiou, Theodora

    2014-01-01

    Social behaviour is notoriously difficult to study archaeologically and it is unclear how large the networks of prehistoric humans were, or how they remained connected. Maintaining social cohesion was crucial for early humans because social networks facilitate cooperation and are imperative for survival and reproduction. Recent hunter-gatherer social organisation typically comprises a number of nested layers, ranging from the nuclear family through to the ~1500-strong ethnolinguistic tribe. Here we compare maximum obsidian transfer distances from the late Pleistocene with ethnographic data on the size of the geographic areas associated with each of these social grouping layers in recent hunter-gatherers. The closest match between the two is taken to indicate the maximum social layer within which contact could be sustained by Pleistocene hominins. Within both the (sub)tropical African and Subarctic biomes, the maximum obsidian transfer distances for Pleistocene modern humans (~200km and ~400km respectively) correspond to the geographic ranges of the outermost tribal layer in recent hunter-gatherers. This suggests that modern humans could potentially sustain the cohesion of their entire tribe at all latitudes, even though networks are more dispersed nearer the poles. Neanderthal obsidian transfer distances (300km) indicate that although Neanderthal home ranges are larger than those of low latitude hominins, Neanderthals travelled shorter distances than modern humans living at the same high latitudes. We argue that, like modern humans, Neanderthals could have maintained tribal cohesion, but that their tribes were substantially smaller than those of contemporary modern humans living in similar environments. The greater time taken to traverse the larger modern human tribal ranges may have limited the frequency of their face-to-face interactions and thus necessitated additional mechanisms to ensure network connectivity, such as the exchange of symbolic artefacts

  20. Using obsidian transfer distances to explore social network maintenance in late Pleistocene hunter-gatherers.

    PubMed

    Pearce, Eiluned; Moutsiou, Theodora

    2014-12-01

    Social behaviour is notoriously difficult to study archaeologically and it is unclear how large the networks of prehistoric humans were, or how they remained connected. Maintaining social cohesion was crucial for early humans because social networks facilitate cooperation and are imperative for survival and reproduction. Recent hunter-gatherer social organisation typically comprises a number of nested layers, ranging from the nuclear family through to the ~1500-strong ethnolinguistic tribe. Here we compare maximum obsidian transfer distances from the late Pleistocene with ethnographic data on the size of the geographic areas associated with each of these social grouping layers in recent hunter-gatherers. The closest match between the two is taken to indicate the maximum social layer within which contact could be sustained by Pleistocene hominins. Within both the (sub)tropical African and Subarctic biomes, the maximum obsidian transfer distances for Pleistocene modern humans (~200km and ~400km respectively) correspond to the geographic ranges of the outermost tribal layer in recent hunter-gatherers. This suggests that modern humans could potentially sustain the cohesion of their entire tribe at all latitudes, even though networks are more dispersed nearer the poles. Neanderthal obsidian transfer distances (300km) indicate that although Neanderthal home ranges are larger than those of low latitude hominins, Neanderthals travelled shorter distances than modern humans living at the same high latitudes. We argue that, like modern humans, Neanderthals could have maintained tribal cohesion, but that their tribes were substantially smaller than those of contemporary modern humans living in similar environments. The greater time taken to traverse the larger modern human tribal ranges may have limited the frequency of their face-to-face interactions and thus necessitated additional mechanisms to ensure network connectivity, such as the exchange of symbolic artefacts

  1. Settlement-Size Scaling among Prehistoric Hunter-Gatherer Settlement Systems in the New World

    PubMed Central

    Haas, W. Randall; Klink, Cynthia J.; Maggard, Greg J.; Aldenderfer, Mark S.

    2015-01-01

    Settlement size predicts extreme variation in the rates and magnitudes of many social and ecological processes in human societies. Yet, the factors that drive human settlement-size variation remain poorly understood. Size variation among economically integrated settlements tends to be heavy tailed such that the smallest settlements are extremely common and the largest settlements extremely large and rare. The upper tail of this size distribution is often formalized mathematically as a power-law function. Explanations for this scaling structure in human settlement systems tend to emphasize complex socioeconomic processes including agriculture, manufacturing, and warfare—behaviors that tend to differentially nucleate and disperse populations hierarchically among settlements. But, the degree to which heavy-tailed settlement-size variation requires such complex behaviors remains unclear. By examining the settlement patterns of eight prehistoric New World hunter-gatherer settlement systems spanning three distinct environmental contexts, this analysis explores the degree to which heavy-tailed settlement-size scaling depends on the aforementioned socioeconomic complexities. Surprisingly, the analysis finds that power-law models offer plausible and parsimonious statistical descriptions of prehistoric hunter-gatherer settlement-size variation. This finding reveals that incipient forms of hierarchical settlement structure may have preceded socioeconomic complexity in human societies and points to a need for additional research to explicate how mobile foragers came to exhibit settlement patterns that are more commonly associated with hierarchical organization. We propose that hunter-gatherer mobility with preferential attachment to previously occupied locations may account for the observed structure in site-size variation. PMID:26536241

  2. Settlement-Size Scaling among Prehistoric Hunter-Gatherer Settlement Systems in the New World.

    PubMed

    Haas, W Randall; Klink, Cynthia J; Maggard, Greg J; Aldenderfer, Mark S

    2015-01-01

    Settlement size predicts extreme variation in the rates and magnitudes of many social and ecological processes in human societies. Yet, the factors that drive human settlement-size variation remain poorly understood. Size variation among economically integrated settlements tends to be heavy tailed such that the smallest settlements are extremely common and the largest settlements extremely large and rare. The upper tail of this size distribution is often formalized mathematically as a power-law function. Explanations for this scaling structure in human settlement systems tend to emphasize complex socioeconomic processes including agriculture, manufacturing, and warfare-behaviors that tend to differentially nucleate and disperse populations hierarchically among settlements. But, the degree to which heavy-tailed settlement-size variation requires such complex behaviors remains unclear. By examining the settlement patterns of eight prehistoric New World hunter-gatherer settlement systems spanning three distinct environmental contexts, this analysis explores the degree to which heavy-tailed settlement-size scaling depends on the aforementioned socioeconomic complexities. Surprisingly, the analysis finds that power-law models offer plausible and parsimonious statistical descriptions of prehistoric hunter-gatherer settlement-size variation. This finding reveals that incipient forms of hierarchical settlement structure may have preceded socioeconomic complexity in human societies and points to a need for additional research to explicate how mobile foragers came to exhibit settlement patterns that are more commonly associated with hierarchical organization. We propose that hunter-gatherer mobility with preferential attachment to previously occupied locations may account for the observed structure in site-size variation.

  3. Global human mandibular variation reflects differences in agricultural and hunter-gatherer subsistence strategies.

    PubMed

    von Cramon-Taubadel, Noreen

    2011-12-06

    Variation in the masticatory behavior of hunter-gatherer and agricultural populations is hypothesized to be one of the major forces affecting the form of the human mandible. However, this has yet to be analyzed at a global level. Here, the relationship between global mandibular shape variation and subsistence economy is tested, while controlling for the potentially confounding effects of shared population history, geography, and climate. The results demonstrate that the mandible, in contrast to the cranium, significantly reflects subsistence strategy rather than neutral genetic patterns, with hunter-gatherers having consistently longer and narrower mandibles than agriculturalists. These results support notions that a decrease in masticatory stress among agriculturalists causes the mandible to grow and develop differently. This developmental argument also explains why there is often a mismatch between the size of the lower face and the dentition, which, in turn, leads to increased prevalence of dental crowding and malocclusions in modern postindustrial populations. Therefore, these results have important implications for our understanding of human masticatory adaptation.

  4. Food Sharing among Hadza Hunter-Gatherer Children.

    PubMed

    Crittenden, Alyssa N; Zes, David A

    2015-01-01

    Human prosociality is one of the defining characteristics of our species, yet the ontogeny of altruistic behavior remains poorly understood. The evolution of widespread food sharing in humans helped shape cooperation, family formation, life history, language, and the development of economies of scale. While the behavioral and ecological correlates of food sharing among adults are widely studied, very little is known about food sharing among children. Here, in the first study to analyze the food sharing patterns of hunter-gatherer children, we show that while sharing may be biased towards kin, reciprocity characterizes the majority of all sharing dyads, both related and unrelated. These data lend support to the recent claim that discrimination among kin might be linked with reciprocal altruism theory. Furthermore, we show that age positively correlates with an increase in sharing, both in frequency and amount, supporting recent suggestions that prosocial behaviors and egalitarianism develop strongly in middle childhood when children acquire the normative rules of their society.

  5. Costs and benefits in hunter-gatherer punishment.

    PubMed

    Boehm, Christopher

    2012-02-01

    Hunter-gatherer punishment involves costs and benefits to individuals and groups, but the costs do not necessarily fit with the assumptions made in models that consider punishment to be altruistic--which brings in the free-rider problem and the problem of second-order free-riders. In this commentary, I present foragers' capital punishment patterns ethnographically, in the interest of establishing whether such punishment is likely to be costly; and I suggest that in many cases abstentions from punishment that might be taken as defections by free-riders are actually caused by social-structural considerations rather than being an effect of free-rider genes. This presentation of data supplements the ethnographic analysis provided by Guala.

  6. Food Sharing among Hadza Hunter-Gatherer Children

    PubMed Central

    Crittenden, Alyssa N.; Zes, David A.

    2015-01-01

    Human prosociality is one of the defining characteristics of our species, yet the ontogeny of altruistic behavior remains poorly understood. The evolution of widespread food sharing in humans helped shape cooperation, family formation, life history, language, and the development of economies of scale. While the behavioral and ecological correlates of food sharing among adults are widely studied, very little is known about food sharing among children. Here, in the first study to analyze the food sharing patterns of hunter-gatherer children, we show that while sharing may be biased towards kin, reciprocity characterizes the majority of all sharing dyads, both related and unrelated. These data lend support to the recent claim that discrimination among kin might be linked with reciprocal altruism theory. Furthermore, we show that age positively correlates with an increase in sharing, both in frequency and amount, supporting recent suggestions that prosocial behaviors and egalitarianism develop strongly in middle childhood when children acquire the normative rules of their society. PMID:26151637

  7. Enterocyte-Associated Microbiome of the Hadza Hunter-Gatherers

    PubMed Central

    Turroni, Silvia; Rampelli, Simone; Centanni, Manuela; Schnorr, Stephanie L.; Consolandi, Clarissa; Severgnini, Marco; Peano, Clelia; Soverini, Matteo; Falconi, Mirella; Crittenden, Alyssa N.; Henry, Amanda G.; Brigidi, Patrizia; Candela, Marco

    2016-01-01

    By means of a recently developed non-invasive ex vivo minimal model based on the interaction of the human enterocyte-like HT29 cell line and fecal slurries, we explored the enterocyte-associated microbiome of 21 Hadza hunter-gatherers and nine urban living Italians. Though reductionist, this model allows inferring the microbiota structural and functional arrangement as it interacts with enterocytes. Microbial suspensions obtained from Hadza or Italian stools were first evaluated for structural integrity by high resolution-scanning electron microscopy and co-incubated with HT29 cell monolayers. The enterocyte adherent microbiota fraction was then characterized by 16S rRNA gene sequencing and predictive functional profiling using PICRUSt. Compared to Italians, the Hadza enterocyte-associated microbiome was characterized by a greater amount of adhesive microorganisms with pathogenic potential, such as Proteobacteria, Erysipelotrichaceae, Enterococcus, Clostridium and Sarcina. These compositional characteristics were reflected in a functional enrichment in membrane transport, signal transduction, signaling molecules and interaction. Our results depict a new interesting mutualistic configuration of the enterocyte-associated microbiome in Hadza, stressing the importance of microbe-host interaction at the mucosal surface along the course of human evolution. PMID:27375586

  8. Adaptive memory: fitness relevance and the hunter-gatherer mind.

    PubMed

    Nairne, James S; Pandeirada, Josefa N S; Gregory, Karie J; Van Arsdall, Joshua E

    2009-06-01

    Recent studies suggest that human memory systems are "tuned" to remember information that is processed in terms of its fitness value. When people are asked to rate the relevance of words to a survival scenario, performance on subsequent surprise memory tests exceeds that obtained after most other known encoding techniques. The present experiments explored this effect using survival scenarios designed to mimic the division of labor thought to characterize early hunter-gatherer societies. It has been suggested that males and females have different cognitive specializations due to the unique survival tasks (hunting and gathering, respectively) they typically performed during periods of human evolution; the present experiments tested whether such specializations might be apparent in memory for words rated for relevance to these activities. Males and females were asked to rate the relevance of random words to prototypical hunting and gathering scenarios or to matched, non-fitness-relevant control scenarios (gathering food on a scavenger hunt or in a hunting contest). Surprise retention tests revealed superior memory for the words when they were rated for relevance to hunting and gathering scenarios, compared with when they were rated for relevance to the control scenarios, but no sex differences were found in memory performance.

  9. The ecological and evolutionary energetics of hunter-gatherer residential mobility.

    PubMed

    Hamilton, Marcus J; Lobo, José; Rupley, Eric; Youn, Hyejin; West, Geoffrey B

    2016-05-06

    Residential mobility is a key aspect of hunter-gatherer foraging economies and therefore is an issue of central importance in hunter-gatherer studies. Hunter-gatherers vary widely in annual rates of residential mobility. Understanding the sources of this variation has long been of interest to anthropologists and archeologists. The vast majority of hunter-gatherers who are dependent on terrestrial plants and animals move camp multiple times a year because local foraging patches become depleted and food, material, and social resources are heterogeneously distributed through time and space. In some environments, particularly along coasts, where resources are abundant and predictable, hunter-gatherers often become effectively sedentary. But even in these special cases, a central question is how these societies have maintained viable foraging economies while reducing residential mobility to near zero.

  10. Emergence of social complexity among coastal hunter-gatherers in the Atacama Desert of northern Chile

    PubMed Central

    Marquet, Pablo A.; Santoro, Calogero M.; Latorre, Claudio; Standen, Vivien G.; Abades, Sebastián R.; Rivadeneira, Marcelo M.; Arriaza, Bernardo; Hochberg, Michael E.

    2012-01-01

    The emergence of complex cultural practices in simple hunter-gatherer groups poses interesting questions on what drives social complexity and what causes the emergence and disappearance of cultural innovations. Here we analyze the conditions that underlie the emergence of artificial mummification in the Chinchorro culture in the coastal Atacama Desert in northern Chile and southern Peru. We provide empirical and theoretical evidence that artificial mummification appeared during a period of increased coastal freshwater availability and marine productivity, which caused an increase in human population size and accelerated the emergence of cultural innovations, as predicted by recent models of cultural and technological evolution. Under a scenario of increasing population size and extreme aridity (with little or no decomposition of corpses) a simple demographic model shows that dead individuals may have become a significant part of the landscape, creating the conditions for the manipulation of the dead that led to the emergence of complex mortuary practices. PMID:22891345

  11. Reevaluating a model of gender-biased gene flow among Sub-Saharan Hunter-gatherers and farmers.

    PubMed

    Anagnostou, Paolo; Battaggia, Cinzia; Capocasa, Marco; Boschi, Ilaria; Brisighelli, Francesca; Batini, Chiara; Spedini, Gabriella; Destro-Bisol, Giovanni

    2013-08-01

    In a previous study, we proposed a model for genetic admixture between African hunter-gatherers and food producers, in which we integrated demographic and genetic aspects together with ethnographic knowledge (Destro-Bisol et al. 2004b). In that study it was possible to test the model only using genetic information from widely dispersed and genetically heterogeneous populations. Here we reevaluate the congruence between the model and patterns of genetic variation using an anthropologically and geographically more homogeneous data set that includes Pygmies and farmers from Cameroon, Congo, and the Central African Republic. As implied by the model, the ratios of mtDNA to Y chromosome Nm estimates (effective population size, N, times the migration rate, m; 0.154 in Pygmies and 6.759 in farmers), support an asymmetric gene flow, with a higher Bantu-to-Pygmy gene flow for paternal than for maternal lineages, and vice versa for farmers. Analyses of intra- and interpopulation genetic variation further support the above observation, showing a prevailing effect of genetic drift on maternal lineages and gene flow on paternal lineages among Pygmies, and an opposite pattern among farmers. We also detected differences between patterns for classical and molecular measures of Y chromosome intrapopulation variation, which likely represent signatures of the introgression of Bantu lineages into the gene pool of Pygmy populations. On the whole, our results seem to reflect differences in the demographic history and the degree of patrilocality and polygyny between the two population groups, thus providing further support to our microevolutionary model in an anthropologically coherent framework.

  12. Origin and Diet of the Prehistoric Hunter-Gatherers on the Mediterranean Island of Favignana (Ègadi Islands, Sicily)

    PubMed Central

    Mannino, Marcello A.; Catalano, Giulio; Talamo, Sahra; Mannino, Giovanni; Di Salvo, Rosaria; Schimmenti, Vittoria; Lalueza-Fox, Carles; Messina, Andrea; Petruso, Daria; Caramelli, David; Richards, Michael P.; Sineo, Luca

    2012-01-01

    Hunter-gatherers living in Europe during the transition from the late Pleistocene to the Holocene intensified food acquisition by broadening the range of resources exploited to include marine taxa. However, little is known on the nature of this dietary change in the Mediterranean Basin. A key area to investigate this issue is the archipelago of the Ègadi Islands, most of which were connected to Sicily until the early Holocene. The site of Grotta d’Oriente, on the present-day island of Favignana, was occupied by hunter-gatherers when Postglacial environmental changes were taking place (14,000-7,500 cal BP). Here we present the results of AMS radiocarbon dating, palaeogenetic and isotopic analyses undertaken on skeletal remains of the humans buried at Grotta d’Oriente. Analyses of the mitochondrial hypervariable first region of individual Oriente B, which belongs to the HV-1 haplogroup, suggest for the first time on genetic grounds that humans living in Sicily during the early Holocene could have originated from groups that migrated from the Italian Peninsula around the Last Glacial Maximum. Carbon and nitrogen isotope analyses show that the Upper Palaeolithic and Mesolithic hunter-gatherers of Favignana consumed almost exclusively protein from terrestrial game and that there was only a slight increase in marine food consumption from the late Pleistocene to the early Holocene. This dietary change was similar in scale to that at sites on mainland Sicily and in the rest of the Mediterranean, suggesting that the hunter-gatherers of Grotta d’Oriente did not modify their subsistence strategies specifically to adapt to the progressive isolation of Favignana. The limited development of technologies for intensively exploiting marine resources was probably a consequence both of Mediterranean oligotrophy and of the small effective population size of these increasingly isolated human groups, which made innovation less likely and prevented transmission of fitness

  13. Did warfare among ancestral hunter-gatherers affect the evolution of human social behaviors?

    PubMed

    Bowles, Samuel

    2009-06-05

    Since Darwin, intergroup hostilities have figured prominently in explanations of the evolution of human social behavior. Yet whether ancestral humans were largely "peaceful" or "warlike" remains controversial. I ask a more precise question: If more cooperative groups were more likely to prevail in conflicts with other groups, was the level of intergroup violence sufficient to influence the evolution of human social behavior? Using a model of the evolutionary impact of between-group competition and a new data set that combines archaeological evidence on causes of death during the Late Pleistocene and early Holocene with ethnographic and historical reports on hunter-gatherer populations, I find that the estimated level of mortality in intergroup conflicts would have had substantial effects, allowing the proliferation of group-beneficial behaviors that were quite costly to the individual altruist.

  14. Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers.

    PubMed

    Quintana-Murci, Lluís; Quach, Hélène; Harmant, Christine; Luca, Francesca; Massonnet, Blandine; Patin, Etienne; Sica, Lucas; Mouguiama-Daouda, Patrick; Comas, David; Tzur, Shay; Balanovsky, Oleg; Kidd, Kenneth K; Kidd, Judith R; van der Veen, Lolke; Hombert, Jean-Marie; Gessain, Antoine; Verdu, Paul; Froment, Alain; Bahuchet, Serge; Heyer, Evelyne; Dausset, Jean; Salas, Antonio; Behar, Doron M

    2008-02-05

    Two groups of populations with completely different lifestyles-the Pygmy hunter-gatherers and the Bantu-speaking farmers-coexist in Central Africa. We investigated the origins of these two groups and the interactions between them, by analyzing mtDNA variation in 1,404 individuals from 20 farming populations and 9 Pygmy populations from Central Africa, with the aim of shedding light on one of the most fascinating cultural transitions in human evolution (the transition from hunting and gathering to agriculture). Our data indicate that this region was colonized gradually, with an initial L1c-rich ancestral population ultimately giving rise to current-day farmers, who display various L1c clades, and to Pygmies, in whom L1c1a is the only surviving clade. Detailed phylogenetic analysis of complete mtDNA sequences for L1c1a showed this clade to be autochthonous to Central Africa, with its most recent branches shared between farmers and Pygmies. Coalescence analyses revealed that these two groups arose through a complex evolutionary process characterized by (i) initial divergence of the ancestors of contemporary Pygmies from an ancestral Central African population no more than approximately 70,000 years ago, (ii) a period of isolation between the two groups, accounting for their phenotypic differences, (iii) long-standing asymmetric maternal gene flow from Pygmies to the ancestors of the farming populations, beginning no more than approximately 40,000 years ago and persisting until a few thousand years ago, and (iv) enrichment of the maternal gene pool of the ancestors of the farming populations by the arrival and/or subsequent demographic expansion of L0a, L2, and L3 carriers.

  15. Musculoskeletal stress markers in Natufian hunter-gatherers and Neolithic farmers in the Levant: the upper limb.

    PubMed

    Eshed, Vered; Gopher, Avi; Galili, Ehud; Hershkovitz, Israel

    2004-04-01

    This paper attempts to quantify the changes in activity patterns of early farming populations in the Levant through the musculoskeletal stress markers (MSM) of the upper limb as seen in skeletal remains. The transition to an agricultural way of life resulted in higher loads on the upper limb in Neolithic populations compared to the Natufian hunter-gatherer populations that preceded them. The MSM pattern for males and females indicates a gender-based division of labor both in the Natufian and the Neolithic. It may also suggest that people in the Neolithic period were engaged in different (new) activities and occupations compared to the Natufian.

  16. Mount Pinatubo, inflammatory cytokines, and the immunological ecology of Aeta hunter-gatherers.

    PubMed

    Bernstein, Robin M; Dominy, Nathaniel J

    2013-01-01

    Early growth cessation and reproduction are predicted to maximize fitness under conditions of high adult mortality, factors that could explain the pygmy phenotype of many rainforest hunter-gatherers. This life-history hypothesis is elegant but contentious in part because it lacks a clear biological mechanism. One mechanism stems from the field of human immunological ecology and the concept of inflammation "memory" across the life cycle and into subsequent generations. Maternal exposures to disease can influence immunological cues present in breast milk; because maternal provisioning via lactation occurs during critical periods of development, it is plausible that these cues can also mediate early growth cessation and small body size. Such epigenetic hypotheses are difficult to test, but the concept of developmental programming is attractive because it could explain how the stature of a population can change over time, in terms of both secular increases and rapid intergenerational decreases. Here we explore this concept by focusing on the Aeta, a population of former hunter-gatherers, and the Ilocano, a population of rice farmers. We predicted that Aeta mothers would produce breast milk with higher concentrations of four bioactive factors due to high infectious burdens. Further, we predicted that the concentrations of these factors would be highest in the cohort of women born in the early 1990s, when exposure to infectious disease was acute following the eruption of Mount Pinatubo in June 1991. We analyzed levels of adiponectin, C-reactive protein, and epidermal growth factor in the milk of 24 Aeta and 31 Ilocano women and found no detectable differences, whereas levels of transforming growth factor-?2 were elevated among the Aeta, particularly as a function of maternal age. We found no difference between cohorts divided by the volcanic eruption (n = 43 born before, n = 12 born after). We discuss the implications of our findings for the terminal investment

  17. A review: dietary restrictions on hunter-gatherer women and the implications for fertility and infant mortality.

    PubMed

    Spielmann, K A

    1989-09-01

    In many hunter gatherer societies, food taboos dictate the diets of females. These taboos often happen during their most critical reproductive times in their life, e.g., pregnancy. Among some subarctic Athapaskan societies, females at menarche cannot eat fresh meat. They, like other hunter gatherer societies, also restrict fresh meat consumption for menstruating women. Young women of the Aranda society in Australia cannot eat protein rich foods, e.g., lizards, until they have a child. Australian aboriginal societies restrict protein and fat foods for pregnant and lactating women. Even though the literature shows that the undernourished are inclined to reach menarche at a later age than those who eat a well balanced diet, it does not clearly establish whether differences in age at menarche significantly affect overall fertility. Research done on many different under or marginally nourished populations indicates that maternal nutritional health influences birth spacing significantly. Specifically, undernutrition causes longer postpartum amenorrhea. Therefore, lower fertility rates follow longer birth intervals. Research shows that poor maternal nutritional health does not prevent the fetus from surviving and growing. Yet mothers who do not consume many calories often have low birth weight infants. These infants are at high risk of dying because they have little to no fat reserves and they consume inadequate amounts of nutrition since the mothers cannot make insufficient amounts of milk. Since contemporary research shows that maternal nutritional health does effect fertility and infant mortality, food taboos do have the ability to influence population size. More research is needed to understand the factors that influenced the reproductive rates of past hunter-gatherer societies, so anthropologists can identify the demographically significant changes which sedentism and agriculture caused 10,000 years ago.

  18. Macrophysical climate models and Holocene hunter-gatherer subsistence shifts in Central Texas, USA

    NASA Astrophysics Data System (ADS)

    Mauldin, R. P.; Munoz, C.

    2013-12-01

    We use stable carbon isotopic values from bone collagen, as well as carbon values from carbonate extracted from bone apatite from 69 prehistoric human skeletal samples to investigate past resource use and climate relationships over the Middle and Late Holocene in Central Texas. Bone samples come from seven archaeological sites and samples date from 6,900 BP to the close of the prehistoric sequence at about 350 BP. Carbon isotopes from these samples suggest four broad dietary trends. From 6,900 through about 3,800 BP, carbon isotopes suggest a gradual increase in the consumption of resources that ultimately use a C3 photosynthetic pathway. A decline in δ13C in both collagen and carbonate values follows, suggesting a decrease in C3 resource use through roughly 2,900 BP. A variable, but once again increasing pattern on C3 resource use by prehistoric hunter-gatherers is indicated in bone isotopes through about 1,000 BP. After that date, a decrease in C3 resource dependence, with hints at greater subsistence diversity, is suggested through the close of the sequence at 350 BP. To assess the impact of climate shifts on this isotopic pattern, we developed a series of macrophysical climate models (MCM) for several locations in Central Texas focusing on fall, winter, and early spring precipitation. This fall-spring rainfall should closely determine C3 production. If subsistence shifts are responding to climate-induced changes in resource availability, then the measured hunter-gatherer carbon isotope trends summarized above should pattern with C3 production as monitored by the modeled fall-spring precipitation values. For the Middle Holocene portion of the sequence, the precipitation models suggest increasing C3 production, consistent with increasing C3 dependence shown in the isotopic data. A decline in C3 production between 3,900 and 3,000 BP in the models is also consistent with the isotopic decline at that point. After 3,000 BP, however, the coupling between fall

  19. Proving communal warfare among hunter-gatherers: The Quasi-Rousseauan error.

    PubMed

    Gat, Azar

    2015-01-01

    Was human fighting always there, as old as our species? Or is it a late cultural invention, emerging after the transition to agriculture and the rise of the state, which began, respectively, only around ten thousand and five thousand years ago? Viewed against the life span of our species, Homo sapiens, stretching back 150,000-200,000 years, let alone the roughly two million years of our genus Homo, this is the tip of the iceberg. We now have a temporal frame and plenty of empirical evidence for the "state of nature" that Thomas Hobbes and Jean-Jacque Rousseau discussed in the abstract and described in diametrically opposed terms. All human populations during the Pleistocene, until about 12,000 years ago, were hunter-gatherers, or foragers, of the simple, mobile sort that lacked accumulated resources. Studying such human populations that survived until recently or still survive in remote corners of the world, anthropology should have been uniquely positioned to answer the question of aboriginal human fighting or lack thereof. Yet access to, and the interpretation of, that information has been intrinsically problematic. The main problem has been the "contact paradox." Prestate societies have no written records of their own. Therefore, documenting them requires contact with literate state societies that necessarily affects the former and potentially changes their behavior, including fighting.

  20. Inter-group violence among early Holocene hunter-gatherers of West Turkana, Kenya.

    PubMed

    Mirazón Lahr, M; Rivera, F; Power, R K; Mounier, A; Copsey, B; Crivellaro, F; Edung, J E; Maillo Fernandez, J M; Kiarie, C; Lawrence, J; Leakey, A; Mbua, E; Miller, H; Muigai, A; Mukhongo, D M; Van Baelen, A; Wood, R; Schwenninger, J-L; Grün, R; Achyuthan, H; Wilshaw, A; Foley, R A

    2016-01-21

    The nature of inter-group relations among prehistoric hunter-gatherers remains disputed, with arguments in favour and against the existence of warfare before the development of sedentary societies. Here we report on a case of inter-group violence towards a group of hunter-gatherers from Nataruk, west of Lake Turkana, which during the late Pleistocene/early Holocene period extended about 30 km beyond its present-day shore. Ten of the twelve articulated skeletons found at Nataruk show evidence of having died violently at the edge of a lagoon, into which some of the bodies fell. The remains from Nataruk are unique, preserved by the particular conditions of the lagoon with no evidence of deliberate burial. They offer a rare glimpse into the life and death of past foraging people, and evidence that warfare was part of the repertoire of inter-group relations among prehistoric hunter-gatherers.

  1. The roles and impacts of human hunter-gatherers in North Pacific marine food webs

    NASA Astrophysics Data System (ADS)

    Dunne, Jennifer A.; Maschner, Herbert; Betts, Matthew W.; Huntly, Nancy; Russell, Roly; Williams, Richard J.; Wood, Spencer A.

    2016-02-01

    There is a nearly 10,000-year history of human presence in the western Gulf of Alaska, but little understanding of how human foragers integrated into and impacted ecosystems through their roles as hunter-gatherers. We present two highly resolved intertidal and nearshore food webs for the Sanak Archipelago in the eastern Aleutian Islands and use them to compare trophic roles of prehistoric humans to other species. We find that the native Aleut people played distinctive roles as super-generalist and highly-omnivorous consumers closely connected to other species. Although the human population was positioned to have strong effects, arrival and presence of Aleut people in the Sanak Archipelago does not appear associated with long-term extinctions. We simulated food web dynamics to explore to what degree introducing a species with trophic roles like those of an Aleut forager, and allowing for variable strong feeding to reflect use of hunting technology, is likely to trigger extinctions. Potential extinctions decreased when an invading omnivorous super-generalist consumer focused strong feeding on decreasing fractions of its possible resources. This study presents the first assessment of the structural roles of humans as consumers within complex ecological networks, and potential impacts of those roles and feeding behavior on associated extinctions.

  2. Reproductive trade-offs in extant hunter-gatherers suggest adaptive mechanism for the Neolithic expansion.

    PubMed

    Page, Abigail E; Viguier, Sylvain; Dyble, Mark; Smith, Daniel; Chaudhary, Nikhil; Salali, Gul Deniz; Thompson, James; Vinicius, Lucio; Mace, Ruth; Migliano, Andrea Bamberg

    2016-04-26

    The Neolithic demographic transition remains a paradox, because it is associated with both higher rates of population growth and increased morbidity and mortality rates. Here we reconcile the conflicting evidence by proposing that the spread of agriculture involved a life history quality-quantity trade-off whereby mothers traded offspring survival for increased fertility, achieving greater reproductive success despite deteriorating health. We test this hypothesis by investigating fertility, mortality, health, and overall reproductive success in Agta hunter-gatherers whose camps exhibit variable levels of sedentarization, mobility, and involvement in agricultural activities. We conducted blood composition tests in 345 Agta and found that viral and helminthic infections as well as child mortality rates were significantly increased with sedentarization. Nonetheless, both age-controlled fertility and overall reproductive success were positively affected by sedentarization and participation in cultivation. Thus, we provide the first empirical evidence, to our knowledge, of an adaptive mechanism in foragers that reconciles the decline in health and child survival with the observed demographic expansion during the Neolithic.

  3. The roles and impacts of human hunter-gatherers in North Pacific marine food webs

    PubMed Central

    Dunne, Jennifer A.; Maschner, Herbert; Betts, Matthew W.; Huntly, Nancy; Russell, Roly; Williams, Richard J.; Wood, Spencer A.

    2016-01-01

    There is a nearly 10,000-year history of human presence in the western Gulf of Alaska, but little understanding of how human foragers integrated into and impacted ecosystems through their roles as hunter-gatherers. We present two highly resolved intertidal and nearshore food webs for the Sanak Archipelago in the eastern Aleutian Islands and use them to compare trophic roles of prehistoric humans to other species. We find that the native Aleut people played distinctive roles as super-generalist and highly-omnivorous consumers closely connected to other species. Although the human population was positioned to have strong effects, arrival and presence of Aleut people in the Sanak Archipelago does not appear associated with long-term extinctions. We simulated food web dynamics to explore to what degree introducing a species with trophic roles like those of an Aleut forager, and allowing for variable strong feeding to reflect use of hunting technology, is likely to trigger extinctions. Potential extinctions decreased when an invading omnivorous super-generalist consumer focused strong feeding on decreasing fractions of its possible resources. This study presents the first assessment of the structural roles of humans as consumers within complex ecological networks, and potential impacts of those roles and feeding behavior on associated extinctions. PMID:26884149

  4. Reproductive trade-offs in extant hunter-gatherers suggest adaptive mechanism for the Neolithic expansion

    PubMed Central

    Viguier, Sylvain; Dyble, Mark; Smith, Daniel; Salali, Gul Deniz; Thompson, James; Vinicius, Lucio; Migliano, Andrea Bamberg

    2016-01-01

    The Neolithic demographic transition remains a paradox, because it is associated with both higher rates of population growth and increased morbidity and mortality rates. Here we reconcile the conflicting evidence by proposing that the spread of agriculture involved a life history quality–quantity trade-off whereby mothers traded offspring survival for increased fertility, achieving greater reproductive success despite deteriorating health. We test this hypothesis by investigating fertility, mortality, health, and overall reproductive success in Agta hunter-gatherers whose camps exhibit variable levels of sedentarization, mobility, and involvement in agricultural activities. We conducted blood composition tests in 345 Agta and found that viral and helminthic infections as well as child mortality rates were significantly increased with sedentarization. Nonetheless, both age-controlled fertility and overall reproductive success were positively affected by sedentarization and participation in cultivation. Thus, we provide the first empirical evidence, to our knowledge, of an adaptive mechanism in foragers that reconciles the decline in health and child survival with the observed demographic expansion during the Neolithic. PMID:27071109

  5. Use of domesticated pigs by Mesolithic hunter-gatherers in northwestern Europe.

    PubMed

    Krause-Kyora, Ben; Makarewicz, Cheryl; Evin, Allowen; Flink, Linus Girdland; Dobney, Keith; Larson, Greger; Hartz, Sönke; Schreiber, Stefan; von Carnap-Bornheim, Claus; von Wurmb-Schwark, Nicole; Nebel, Almut

    2013-01-01

    Mesolithic populations throughout Europe used diverse resource exploitation strategies that focused heavily on collecting and hunting wild prey. Between 5500 and 4200 cal BC, agriculturalists migrated into northwestern Europe bringing a suite of Neolithic technologies including domesticated animals. Here we investigate to what extent Mesolithic Ertebølle communities in northern Germany had access to domestic pigs, possibly through contact with neighbouring Neolithic agricultural groups. We employ a multidisciplinary approach, applying sequencing of ancient mitochondrial and nuclear DNA (coat colour-coding gene MC1R) as well as traditional and geometric morphometric (molar size and shape) analyses in Sus specimens from 17 Neolithic and Ertebølle sites. Our data from 63 ancient pig specimens show that Ertebølle hunter-gatherers acquired domestic pigs of varying size and coat colour that had both Near Eastern and European mitochondrial DNA ancestry. Our results also reveal that domestic pigs were present in the region ~500 years earlier than previously demonstrated.

  6. Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes.

    PubMed

    Hammer, Michael F; Karafet, Tatiana M; Park, Hwayong; Omoto, Keiichi; Harihara, Shinji; Stoneking, Mark; Horai, Satoshi

    2006-01-01

    Historic Japanese culture evolved from at least two distinct migrations that originated on the Asian continent. Hunter-gatherers arrived before land bridges were submerged after the last glacial maximum (>12,000 years ago) and gave rise to the Jomon culture, and the Yayoi migration brought wet rice agriculture from Korea beginning approximately 2,300 years ago. A set of 81 Y chromosome single nucleotide polymorphisms (SNPs) was used to trace the origins of Paleolithic and Neolithic components of the Japanese paternal gene pool, and to determine the relative contribution of Jomon and Yayoi Y chromosome lineages to modern Japanese. Our global sample consisted of >2,500 males from 39 Asian populations, including six populations sampled from across the Japanese archipelago. Japanese populations were characterized by the presence of two major (D and O) and two minor (C and N) clades of Y chromosomes, each with several sub-lineages. Haplogroup D chromosomes were present at 34.7% and were distributed in a U-shaped pattern with the highest frequency in the northern Ainu and southern Ryukyuans. In contrast, haplogroup O lineages (51.8%) were distributed in an inverted U-shaped pattern with a maximum frequency on Kyushu. Coalescent analyses of Y chromosome short tandem repeat diversity indicated that haplogroups D and C began their expansions in Japan approximately 20,000 and approximately 12,000 years ago, respectively, while haplogroup O-47z began its expansion only approximately 4,000 years ago. We infer that these patterns result from separate and distinct genetic contributions from both the Jomon and the Yayoi cultures to modern Japanese, with varying levels of admixture between these two populations across the archipelago. The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence.

  7. Altruistic punishment as an explanation of hunter-gatherer cooperation: how much has experimental economics achieved?

    PubMed

    Sugden, Robert

    2012-02-01

    The discovery of the altruistic punishment mechanism as a replicable experimental result is a genuine achievement of behavioural economics. The hypothesis that cooperation in hunter-gatherer societies is sustained by altruistic punishment is a scientifically legitimate conjecture, but it must be tested against real-world observations. Guala's doubts about the evidential support for this hypothesis are well founded.

  8. Last hunter-gatherers and first farmers of Europe.

    PubMed

    Tresset, Anne; Vigne, Jean-Denis

    2011-03-01

    The Neolithisation of Europe has seen the transformation of hunting-gathering societies into farming communities. At least partly exogenous in its origins, this process led to major transformations in many aspects of life-styles, such as social structures, land use or diet. It involved the arrival of new human populations and gave way to the importation, intentional or unwanted of many non-European animal and plant species. It also provoked important changes in interactions between humans and natural environments. In many respects, it set the foundations of long-term European peasantry developments and prefigured later agropastoral colonizations. As such, it must be seen as a major turning point in the history of European populations.

  9. A phytochemical-rich diet may explain the absence of age-related decline in visual acuity of Amazonian hunter-gatherers in Ecuador.

    PubMed

    London, Douglas S; Beezhold, Bonnie

    2015-02-01

    Myopia is absent in undisturbed hunter-gatherers but ubiquitous in modern populations. The link between dietary phytochemicals and eye health is well established, although transition away from a wild diet has reduced phytochemical variety. We hypothesized that when larger quantities and greater variety of wild, seasonal phytochemicals are consumed in a food system, there will be a reduced prevalence of degenerative-based eye disease as measured by visual acuity. We compared food systems and visual acuity across isolated Amazonian Kawymeno Waorani hunter-gatherers and neighboring Kichwa subsistence agrarians, using dietary surveys, dietary pattern observation, and Snellen Illiterate E visual acuity examinations. Hunter-gatherers consumed more food species (130 vs. 63) and more wild plants (80 vs. 4) including 76 wild fruits, thereby obtaining larger variety and quantity of phytochemicals than agrarians. Visual acuity was inversely related to age only in agrarians (r = -.846, P < .001). As hypothesized, when stratified by age (<40 and ≥ 40 years), Mann-Whitney U tests revealed that hunter-gatherers maintained high visual acuity throughout life, whereas agrarian visual acuity declined (P values < .001); visual acuity of younger participants was high across the board, however, did not differ between groups (P > .05). This unusual absence of juvenile-onset vision problems may be related to local, organic, whole food diets of subsistence food systems isolated from modern food production. Our results suggest that intake of a wider variety of plant foods supplying necessary phytochemicals for eye health may help maintain visual acuity and prevent degenerative eye conditions as humans age.

  10. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe.

    PubMed

    Skoglund, Pontus; Malmström, Helena; Raghavan, Maanasa; Storå, Jan; Hall, Per; Willerslev, Eske; Gilbert, M Thomas P; Götherström, Anders; Jakobsson, Mattias

    2012-04-27

    The farming way of life originated in the Near East some 11,000 years ago and had reached most of the European continent 5000 years later. However, the impact of the agricultural revolution on demography and patterns of genomic variation in Europe remains unknown. We obtained 249 million base pairs of genomic DNA from ~5000-year-old remains of three hunter-gatherers and one farmer excavated in Scandinavia and find that the farmer is genetically most similar to extant southern Europeans, contrasting sharply to the hunter-gatherers, whose distinct genetic signature is most similar to that of extant northern Europeans. Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe.

  11. The behavioral ecology of modern hunter-gatherers, and human evolution.

    PubMed

    Hawkes, K; O'Connell, J F; Rogers, L

    1997-01-01

    Modern day hunter-gatherers are an obvious source of information about human life in the past. But can modern people really tell us anything about other hominids, those represented only in the fossil record? In a world of state governments and a global economy, can present-day foragers even tell us much about life before agriculture? Some behavioral ecologists think so. Their findings show (1) that foraging practices are closely related to the character and distribution of local resources, (2) that men, women and children react to foraging opportunities quite differently, and (3) that sex and age difference in these reactions have important social causes and consequences. Some results directly challenge long-held views about hunter-gatherer economics and social organization, and the scenarios of human evolution based on them.

  12. Human behavior. Sex equality can explain the unique social structure of hunter-gatherer bands.

    PubMed

    Dyble, M; Salali, G D; Chaudhary, N; Page, A; Smith, D; Thompson, J; Vinicius, L; Mace, R; Migliano, A B

    2015-05-15

    The social organization of mobile hunter-gatherers has several derived features, including low within-camp relatedness and fluid meta-groups. Although these features have been proposed to have provided the selective context for the evolution of human hypercooperation and cumulative culture, how such a distinctive social system may have emerged remains unclear. We present an agent-based model suggesting that, even if all individuals in a community seek to live with as many kin as possible, within-camp relatedness is reduced if men and women have equal influence in selecting camp members. Our model closely approximates observed patterns of co-residence among Agta and Mbendjele BaYaka hunter-gatherers. Our results suggest that pair-bonding and increased sex egalitarianism in human evolutionary history may have had a transformative effect on human social organization.

  13. Looking at the Camp: Paleolithic Depiction of a Hunter-Gatherer Campsite

    PubMed Central

    García-Diez, Marcos; Vaquero, Manuel

    2015-01-01

    Landscapes and features of the everyday world were scarcely represented in Paleolithic art, especially those features associated with the human landscape (huts and campsites). On the contrary, other figurative motifs (especially animals) and signs, traditionally linked to the magic or religious conceptions of these hunter-gatherer societies, are the predominant themes of Upper Paleolithic art. This paper seeks to present an engraved schist slab recently found in the Molí del Salt site (North-eastern Iberia) and dated at the end of the Upper Paleolithic, ca. 13,800 years ago. This slab displays seven semicircular motifs that may be interpreted as the representation of dome-shaped huts. The analysis of individual motifs and the composition, as well as the ethnographic and archeological contextualization, suggests that this engraving is a naturalistic depiction of a hunter-gatherer campsite. Campsites can be considered the first human landscape, the first area of land whose visible features were entirely constructed by humans. Given the social meaning of campsites in hunter-gatherer life-styles, this engraving may be considered one of the first representations of the domestic and social space of a human group. PMID:26629824

  14. Looking at the Camp: Paleolithic Depiction of a Hunter-Gatherer Campsite.

    PubMed

    García-Diez, Marcos; Vaquero, Manuel

    2015-01-01

    Landscapes and features of the everyday world were scarcely represented in Paleolithic art, especially those features associated with the human landscape (huts and campsites). On the contrary, other figurative motifs (especially animals) and signs, traditionally linked to the magic or religious conceptions of these hunter-gatherer societies, are the predominant themes of Upper Paleolithic art. This paper seeks to present an engraved schist slab recently found in the Molí del Salt site (North-eastern Iberia) and dated at the end of the Upper Paleolithic, ca. 13,800 years ago. This slab displays seven semicircular motifs that may be interpreted as the representation of dome-shaped huts. The analysis of individual motifs and the composition, as well as the ethnographic and archeological contextualization, suggests that this engraving is a naturalistic depiction of a hunter-gatherer campsite. Campsites can be considered the first human landscape, the first area of land whose visible features were entirely constructed by humans. Given the social meaning of campsites in hunter-gatherer life-styles, this engraving may be considered one of the first representations of the domestic and social space of a human group.

  15. Early and middle holocene hunter-gatherer occupations in western Amazonia: the hidden shell middens.

    PubMed

    Lombardo, Umberto; Szabo, Katherine; Capriles, José M; May, Jan-Hendrik; Amelung, Wulf; Hutterer, Rainer; Lehndorff, Eva; Plotzki, Anna; Veit, Heinz

    2013-01-01

    We report on previously unknown early archaeological sites in the Bolivian lowlands, demonstrating for the first time early and middle Holocene human presence in western Amazonia. Multidisciplinary research in forest islands situated in seasonally-inundated savannahs has revealed stratified shell middens produced by human foragers as early as 10,000 years ago, making them the oldest archaeological sites in the region. The absence of stone resources and partial burial by recent alluvial sediments has meant that these kinds of deposits have, until now, remained unidentified. We conducted core sampling, archaeological excavations and an interdisciplinary study of the stratigraphy and recovered materials from three shell midden mounds. Based on multiple lines of evidence, including radiocarbon dating, sedimentary proxies (elements, steroids and black carbon), micromorphology and faunal analysis, we demonstrate the anthropogenic origin and antiquity of these sites. In a tropical and geomorphologically active landscape often considered challenging both for early human occupation and for the preservation of hunter-gatherer sites, the newly discovered shell middens provide evidence for early to middle Holocene occupation and illustrate the potential for identifying and interpreting early open-air archaeological sites in western Amazonia. The existence of early hunter-gatherer sites in the Bolivian lowlands sheds new light on the region's past and offers a new context within which the late Holocene "Earthmovers" of the Llanos de Moxos could have emerged.

  16. Twenty Thousand-Year-Old Huts at a Hunter-Gatherer Settlement in Eastern Jordan

    PubMed Central

    Maher, Lisa A.; Richter, Tobias; Macdonald, Danielle; Jones, Matthew D.; Martin, Louise; Stock, Jay T.

    2012-01-01

    Ten thousand years before Neolithic farmers settled in permanent villages, hunter-gatherer groups of the Epipalaeolithic period (c. 22–11,600 cal BP) inhabited much of southwest Asia. The latest Epipalaeolithic phase (Natufian) is well-known for the appearance of stone-built houses, complex site organization, a sedentary lifestyle and social complexity—precursors for a Neolithic way of life. In contrast, pre-Natufian sites are much less well known and generally considered as campsites for small groups of seasonally-mobile hunter-gatherers. Work at the Early and Middle Epipalaeolithic aggregation site of Kharaneh IV in eastern Jordan highlights that some of these earlier sites were large aggregation base camps not unlike those of the Natufian and contributes to ongoing debates on their duration of occupation. Here we discuss the excavation of two 20,000-year-old hut structures at Kharaneh IV that pre-date the renowned stone houses of the Natufian. Exceptionally dense and extensive occupational deposits exhibit repeated habitation over prolonged periods, and contain structural remains associated with exotic and potentially symbolic caches of objects (shell, red ochre, and burnt horn cores) that indicate substantial settlement of the site pre-dating the Natufian and outside of the Natufian homeland as currently understood. PMID:22355366

  17. Early and Middle Holocene Hunter-Gatherer Occupations in Western Amazonia: The Hidden Shell Middens

    PubMed Central

    Lombardo, Umberto; Szabo, Katherine; Capriles, José M.; May, Jan-Hendrik; Amelung, Wulf; Hutterer, Rainer; Lehndorff, Eva; Plotzki, Anna; Veit, Heinz

    2013-01-01

    We report on previously unknown early archaeological sites in the Bolivian lowlands, demonstrating for the first time early and middle Holocene human presence in western Amazonia. Multidisciplinary research in forest islands situated in seasonally-inundated savannahs has revealed stratified shell middens produced by human foragers as early as 10,000 years ago, making them the oldest archaeological sites in the region. The absence of stone resources and partial burial by recent alluvial sediments has meant that these kinds of deposits have, until now, remained unidentified. We conducted core sampling, archaeological excavations and an interdisciplinary study of the stratigraphy and recovered materials from three shell midden mounds. Based on multiple lines of evidence, including radiocarbon dating, sedimentary proxies (elements, steroids and black carbon), micromorphology and faunal analysis, we demonstrate the anthropogenic origin and antiquity of these sites. In a tropical and geomorphologically active landscape often considered challenging both for early human occupation and for the preservation of hunter-gatherer sites, the newly discovered shell middens provide evidence for early to middle Holocene occupation and illustrate the potential for identifying and interpreting early open-air archaeological sites in western Amazonia. The existence of early hunter-gatherer sites in the Bolivian lowlands sheds new light on the region’s past and offers a new context within which the late Holocene “Earthmovers” of the Llanos de Moxos could have emerged. PMID:24013964

  18. A Radiocarbon Chronology of Hunter-Gatherer Occupation from Bodega Bay, California, USA

    SciTech Connect

    Kennedy, M A; Russell, A D; Guilderson, T P

    2005-04-27

    The evolution of hunter-gatherer maritime adaptations in western North America has been a prominent topic of discussion among archaeologists in recent years (e.g. Arnold 1992; Erlandson and Colten 1991; Erlandson and Glassow 1997; Lightfoot 1993). Although vast coastal regions of the northeastern Pacific (for example, southern California) have been investigated in detail, our understanding of hunter-gatherer developments along the coast of northern California is limited. Previous research indicates that humans have exploited marine mammals, fish and shellfish along the northern California shoreline since the early Holocene (Schwaderer 1992). By the end of the late Holocene, some groups remained year-round on the coast subsisting primarily on marine resources (e.g. Gould 1975; Hildebrandt and Levulett 2002). However, a paucity of well-dated cultural deposits has hindered our understanding of these developments, particularly during the early and middle Holocene. The lack of a long and reliable chronological sequence has restricted our interpretations of behavioral change, including the adaptive strategies (such as foraging, mobility and settlement) used by human foragers to colonize and inhabit the coastal areas of this region. These shortcomings have also hindered comparative interpretations with other coastal and inland regions in western North America. Here we present a Holocene radiocarbon chronology of hunter-gatherer occupation based on contemporaneous samples of charcoal and Mytilus californianus (California sea mussel) shell recovered from seven archaeological sites near Bodega Bay, California. A series of 127 {sup 14}C ages reveal a chronological sequence that spans from ca. 8940-110 cal BP (1{sigma}) (7890-160 {sup 14}C yr BP = charcoal; 8934-101 {sup 14}C yr BP = shell). As part of this sequence, we report new {sup 14}C dates from the stratified cave and open-air midden deposits at Duncan's Landing (CA-SON-348/H). In addition, we present {sup 14}C ages

  19. HUNTER-GATHERER: Three search techniques integrated for natural language semantics

    SciTech Connect

    Beale, S.; Nirenburg, S.; Mahesh, K.

    1996-12-31

    This work integrates three related Al search techniques - constraint satisfaction, branch-and-bound and solution synthesis - and applies the result to semantic processing in natural language (NL). We summarize the approach as {open_quote}Hunter-Gatherer:{close_quotes} (1) branch-and-bound and constraint satisfaction allow us to {open_quote}hunt down{close_quotes} non-optimal and impossible solutions and prune them from the search space. (2) solution synthesis methods then {open_quote}gather{close_quotes} all optimal solutions avoiding exponential complexity. Each of the three techniques is briefly described, as well as their extensions and combinations used in our system. We focus on the combination of solution synthesis and branch-and-bound methods which has enabled near-linear-time processing in our applications. Finally, we illustrate how the use of our technique in a large-scale MT project allowed a drastic reduction in search space.

  20. Firewood, food and human niche construction: the potential role of Mesolithic hunter-gatherers in actively structuring Scotland's woodlands

    NASA Astrophysics Data System (ADS)

    Bishop, Rosie R.; Church, Mike J.; Rowley-Conwy, Peter A.

    2015-01-01

    Over the past few decades the potential role of Mesolithic hunter-gatherers in actively constructing their own niches, through the management of wild plants, has frequently been discussed. It is probable that Mesolithic hunter-gatherers systematically exploited specific woodland resources for food and fuel and influenced the 'natural' abundance or distribution of particular species within Mesolithic environments. Though there has been considerable discussion of the pollen evidence for potential small-scale human-woodland manipulation in Mesolithic Scotland, the archaeobotanical evidence for anthropogenic firewood and food selection has not been discussed in this context. This paper assesses the evidence for the active role of Mesolithic hunter-gatherer communities in systematically exploiting and managing woodlands for food and fuel in Scotland. While taphonomic factors may have impacted on the frequency of specific species in archaeobotanical assemblages, it is suggested that hunter-gatherers in Mesolithic Scotland were systematically using woodland plants, and in particular hazel and oak, for food and fuel. It is argued that the pollen evidence for woodland management is equivocal, but hints at the role of hunter-gatherers in shaping the structure of their environments, through the maintenance or creation of woodland clearings for settlement or as part of vegetation management strategies. It is proposed that Mesolithic hunter-gatherers may have actively contributed to niche construction and that the systematic use of hazel and oak as a fuel may reflect the deliberate pruning of hazel trees to increase nut-yields and the inadvertent - or perhaps deliberate - coppicing of hazel and oak during greenwood collection.

  1. Earliest evidence for caries and exploitation of starchy plant foods in Pleistocene hunter-gatherers from Morocco

    PubMed Central

    Humphrey, Louise T.; De Groote, Isabelle; Morales, Jacob; Barton, Nick; Collcutt, Simon; Bronk Ramsey, Christopher; Bouzouggar, Abdeljalil

    2014-01-01

    Dental caries is an infectious disease that causes tooth decay. The high prevalence of dental caries in recent humans is attributed to more frequent consumption of plant foods rich in fermentable carbohydrates in food-producing societies. The transition from hunting and gathering to food production is associated with a change in the composition of the oral microbiota and broadly coincides with the estimated timing of a demographic expansion in Streptococcus mutans, a causative agent of human dental caries. Here we present evidence linking a high prevalence of caries to reliance on highly cariogenic wild plant foods in Pleistocene hunter-gatherers from North Africa, predating other high caries populations and the first signs of food production by several thousand years. Archaeological deposits at Grotte des Pigeons in Morocco document extensive evidence for human occupation during the Middle Stone Age and Later Stone Age (Iberomaurusian), and incorporate numerous human burials representing the earliest known cemetery in the Maghreb. Macrobotanical remains from occupational deposits dated between 15,000 and 13,700 cal B.P. provide evidence for systematic harvesting and processing of edible wild plants, including acorns and pine nuts. Analysis of oral pathology reveals an exceptionally high prevalence of caries (51.2% of teeth in adult dentitions), comparable to modern industrialized populations with a diet high in refined sugars and processed cereals. We infer that increased reliance on wild plants rich in fermentable carbohydrates and changes in food processing caused an early shift toward a disease-associated oral microbiota in this population. PMID:24395774

  2. Schooling, Local Knowledge and Working Memory: A Study among Three Contemporary Hunter-Gatherer Societies.

    PubMed

    Reyes-García, Victoria; Pyhälä, Aili; Díaz-Reviriego, Isabel; Duda, Romain; Fernández-Llamazares, Álvaro; Gallois, Sandrine; Guèze, Maximilien; Napitupulu, Lucentezza

    2016-01-01

    Researchers have analysed whether school and local knowledge complement or substitute each other, but have paid less attention to whether those two learning models use different cognitive strategies. In this study, we use data collected among three contemporary hunter-gatherer societies with relatively low levels of exposure to schooling yet with high levels of local ecological knowledge to test the association between i) schooling and ii) local ecological knowledge and verbal working memory. Participants include 94 people (24 Baka, 25 Punan, and 45 Tsimane') from whom we collected information on 1) schooling and school related skills (i.e., literacy and numeracy), 2) local knowledge and skills related to hunting and medicinal plants, and 3) working memory. To assess working memory, we applied a multi-trial free recall using words relevant to each cultural setting. People with and without schooling have similar levels of accurate and inaccurate recall, although they differ in their strategies to organize recall: people with schooling have higher results for serial clustering, suggesting better learning with repetition, whereas people without schooling have higher results for semantic clustering, suggesting they organize recall around semantically meaningful categories. Individual levels of local ecological knowledge are not related to accurate recall or organization recall, arguably due to overall high levels of local ecological knowledge. While schooling seems to favour some organization strategies this might come at the expense of some other organization strategies.

  3. Traditional diet and food preferences of Australian aboriginal hunter-gatherers.

    PubMed

    O'Dea, K

    1991-11-29

    Until European settlement of Australia 200 years ago, Aborigines lived as nomadic hunter-gatherers all over the continent under widely varying geographic and climatic conditions. Successful survival depended on a comprehensive knowledge of the flora and fauna of their territory. Available data suggest that they were physically fit and lean, and consumed a varied diet in which animal foods were a major component. Despite this, the diet was not high in fat, as wild animal carcasses have very low fat contents through most of the year, and the meat is extremely lean. Everything on an animal carcass was eaten, including the small fat depots and organ meats (which were highly prized), bone marrow, some stomach contents, peritoneal fluid and blood. A wide variety of uncultivated plant foods was eaten in the traditional diet: roots, starchy tubers, seeds, fruits and nuts. The plant foods were generally high in fibre and contained carbohydrates, which was slowly digested and absorbed. Traditional methods of food preparation (usually baked whole or eaten raw) ensured maximum retention of nutrients. In general, traditional foods had a low energy density but high density of some nutrients. The low energy density of the diet and the labour intensity of food procurement provided a natural constraint on energy intake.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. Schooling, Local Knowledge and Working Memory: A Study among Three Contemporary Hunter-Gatherer Societies

    PubMed Central

    Reyes-García, Victoria; Pyhälä, Aili; Díaz-Reviriego, Isabel; Duda, Romain; Fernández-Llamazares, Álvaro; Gallois, Sandrine; Guèze, Maximilien; Napitupulu, Lucentezza

    2016-01-01

    Researchers have analysed whether school and local knowledge complement or substitute each other, but have paid less attention to whether those two learning models use different cognitive strategies. In this study, we use data collected among three contemporary hunter-gatherer societies with relatively low levels of exposure to schooling yet with high levels of local ecological knowledge to test the association between i) schooling and ii) local ecological knowledge and verbal working memory. Participants include 94 people (24 Baka, 25 Punan, and 45 Tsimane’) from whom we collected information on 1) schooling and school related skills (i.e., literacy and numeracy), 2) local knowledge and skills related to hunting and medicinal plants, and 3) working memory. To assess working memory, we applied a multi-trial free recall using words relevant to each cultural setting. People with and without schooling have similar levels of accurate and inaccurate recall, although they differ in their strategies to organize recall: people with schooling have higher results for serial clustering, suggesting better learning with repetition, whereas people without schooling have higher results for semantic clustering, suggesting they organize recall around semantically meaningful categories. Individual levels of local ecological knowledge are not related to accurate recall or organization recall, arguably due to overall high levels of local ecological knowledge. While schooling seems to favour some organization strategies this might come at the expense of some other organization strategies. PMID:26735297

  5. Competition for Cooperation: variability, benefits and heritability of relational wealth in hunter-gatherers

    PubMed Central

    Chaudhary, Nikhil; Salali, Gul Deniz; Thompson, James; Rey, Aude; Gerbault, Pascale; Stevenson, Edward Geoffrey Jedediah; Dyble, Mark; E. Page, Abigail; Smith, Daniel; Mace, Ruth; Vinicius, Lucio; Migliano, Andrea Bamberg

    2016-01-01

    Many defining human characteristics including theory of mind, culture and language relate to our sociality, and facilitate the formation and maintenance of cooperative relationships. Therefore, deciphering the context in which our sociality evolved is invaluable in understanding what makes us unique as a species. Much work has emphasised group-level competition, such as warfare, in moulding human cooperation and sociality. However, competition and cooperation also occur within groups; and inter-individual differences in sociality have reported fitness implications in numerous non-human taxa. Here we investigate whether differential access to cooperation (relational wealth) is likely to lead to variation in fitness at the individual level among BaYaka hunter-gatherers. Using economic gift games we find that relational wealth: a) displays individual-level variation; b) provides advantages in buffering food risk, and is positively associated with body mass index (BMI) and female fertility; c) is partially heritable. These results highlight that individual-level processes may have been fundamental in the extension of human cooperation beyond small units of related individuals, and in shaping our sociality. Additionally, the findings offer insight in to trends related to human sociality found from research in other fields such as psychology and epidemiology. PMID:27404514

  6. Competition for Cooperation: variability, benefits and heritability of relational wealth in hunter-gatherers.

    PubMed

    Chaudhary, Nikhil; Salali, Gul Deniz; Thompson, James; Rey, Aude; Gerbault, Pascale; Stevenson, Edward Geoffrey Jedediah; Dyble, Mark; E Page, Abigail; Smith, Daniel; Mace, Ruth; Vinicius, Lucio; Migliano, Andrea Bamberg

    2016-07-12

    Many defining human characteristics including theory of mind, culture and language relate to our sociality, and facilitate the formation and maintenance of cooperative relationships. Therefore, deciphering the context in which our sociality evolved is invaluable in understanding what makes us unique as a species. Much work has emphasised group-level competition, such as warfare, in moulding human cooperation and sociality. However, competition and cooperation also occur within groups; and inter-individual differences in sociality have reported fitness implications in numerous non-human taxa. Here we investigate whether differential access to cooperation (relational wealth) is likely to lead to variation in fitness at the individual level among BaYaka hunter-gatherers. Using economic gift games we find that relational wealth: a) displays individual-level variation; b) provides advantages in buffering food risk, and is positively associated with body mass index (BMI) and female fertility; c) is partially heritable. These results highlight that individual-level processes may have been fundamental in the extension of human cooperation beyond small units of related individuals, and in shaping our sociality. Additionally, the findings offer insight in to trends related to human sociality found from research in other fields such as psychology and epidemiology.

  7. Hunter-Gatherer Color Naming Provides New Insight into the Evolution of Color Terms.

    PubMed

    Lindsey, Delwin T; Brown, Angela M; Brainard, David H; Apicella, Coren L

    2015-09-21

    Most people name the myriad colors in the environment using between two and about a dozen color terms, with great variation within and between languages. Investigators generally agree that color lexicons evolve from fewer terms to more terms, as technology advances and color communication becomes increasingly important. However, little is understood about the color naming systems at the least technologically advanced end of the continuum. The Hadza people of Tanzania are nomadic hunter-gatherers who live a subsistence lifestyle that was common before the advent of agriculture (see Supplemental Experimental Procedures, section I;), suggesting that the Hadzane language should be at an early stage of color lexicon evolution. When Hadza, Somali, and US informants named 23 color samples, Hadza informants named only the black, white, and red samples with perfect consensus. Otherwise, they used low-consensus terms or responded "don't know." However, even low-consensus color terms grouped test colors into lexical categories that aligned with those found in other world languages. Furthermore, information-theoretic analysis showed that color communication efficiency within the Hadza, Somali, and US language communities falls on the same continuum as other world languages. Thus, the structure of color categories is in place in Hadzane, even though words for many of the categories are not in general use. These results suggest that even very simple color lexicons include precursors of many color categories but that these categories are initially represented in a diverse and distributed fashion.

  8. Ancient human genomes suggest three ancestral populations for present-day Europeans.

    PubMed

    Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H; Schraiber, Joshua G; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M; Brisighelli, Francesca; Busby, George B J; Cali, Francesco; Churnosov, Mikhail; Cole, David E C; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A; Gallego Romero, Irene; Gubina, Marina; Hammer, Michael; Henn, Brenna M; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl A; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G; Ruiz-Linares, Andres; Tishkoff, Sarah A; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

    2014-09-18

    We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.

  9. Macronutrient contributions of insects to the diets of hunter-gatherers: a geometric analysis.

    PubMed

    Raubenheimer, David; Rothman, Jessica M; Pontzer, Herman; Simpson, Stephen J

    2014-06-01

    We present a geometric model for examining the macronutrient contributions of insects in the diets of pre-agricultural humans, and relate the findings to some contemporary societies that regularly eat insects. The model integrates published data on the macronutrient composition of insects and other foods in the diets of humans, recommended human macronutrient intakes, and estimated macronutrient intakes to examine the assumption that insects provided to pre-agricultural humans an invertebrate equivalent of vertebrate-derived meats, serving primarily as a source of protein. Our analysis suggests that insects vary more widely in their macronutrient content than is likely to be the case for most wild vertebrate meats, spanning a broad range of protein, fat and carbohydrate concentrations. Potentially, therefore, in terms of their proportional macronutrient composition, insects could serve as equivalents not only of wild meat, but of a range of other foods including some shellfish, nuts, pulses, vegetables and even fruits. Furthermore, humans might systematically manipulate the composition of edible insects to meet specific needs through pre-ingestive processing, such as cooking and selective removal of body parts. We present data suggesting that in modern societies for which protein is the more limiting macronutrient, pre-ingestive processing of edible insects might serve to concentrate protein. It is likely, however, that the dietary significance of insects was different for Paleolithic hunter-gatherers who were more limited in non-protein energy. Our conclusions are constrained by available data, but highlight the need for further studies, and suggest that our model provides an integrative framework for conceiving these studies.

  10. Hunter-gatherer color naming provides new insight into the evolution of color terms

    PubMed Central

    Lindsey, Delwin T.; Brown, Angela M.; Brainard, David H.; Apicella, Coren L.

    2015-01-01

    SUMMARY Most people name the myriad colors in the environment using between two and about a dozen color terms [1], with great variation within and between languages [2]. Investigators generally agree that color lexicons evolve from fewer terms to more terms, as technology advances and color communication becomes increasingly important [3]. However, little is understood about the color naming systems at the least technologically-advanced end of the continuum. The Hadza people of Tanzania are nomadic hunter-gatherers who live a subsistence lifestyle that was common before the advent of agriculture (see SM-I, [4]), suggesting that the Hadzane language should be at an early stage of color lexicon evolution. When Hadza, Somali, and U.S. informants named 23 color samples, Hadza informants named only the black, white and red samples with perfect consensus. Otherwise, they used low-consensus terms, or responded “don’t know”. However, even low-consensus color terms grouped test colors into lexical categories that aligned with those found in other world languages [5]. Furthermore, information-theoretic analysis showed that color communication efficiency within the Hadza, Somali, and U.S. language communities falls on the same continuum as other world languages. Thus, the structure of color categories is in place in Hadzane, even though words for many of the categories are not in general use. These results suggest that even very simple color lexicons include precursors of many color categories, but that these categories are initially represented in a diverse and distributed fashion. PMID:26365254

  11. Ancient DNA from Hunter-Gatherer and Farmer Groups from Northern Spain Supports a Random Dispersion Model for the Neolithic Expansion into Europe

    PubMed Central

    Hervella, Montserrat; Izagirre, Neskuts; Alonso, Santos; Fregel, Rosa; Alonso, Antonio; Cabrera, Vicente M.; de la Rúa, Concepción

    2012-01-01

    Background/Principal Findings The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe. Methodology/Significance Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe. Conclusion The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various

  12. Lactase persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists.

    PubMed

    Breton, Gwenna; Schlebusch, Carina M; Lombard, Marlize; Sjödin, Per; Soodyall, Himla; Jakobsson, Mattias

    2014-04-14

    The ability to digest milk into adulthood, lactase persistence (LP), as well as specific genetic variants associated with LP, is heterogeneously distributed in global populations. These variants were most likely targets of selection when some populations converted from hunter-gatherer to pastoralist or farming lifestyles. Specific LP polymorphisms are associated with particular geographic regions and populations; however, they have not been extensively studied in southern Africa. We investigate the LP-regulatory region in 267 individuals from 13 southern African populations (including descendants of hunter-gatherers, pastoralists, and agropastoralists), providing the first comprehensive study of the LP-regulatory region in a large group of southern Africans. The "East African" LP single-nucleotide polymorphism (SNP) (14010G>C) was found at high frequency (>20%) in a strict pastoralist Khoe population, the Nama of Namibia, suggesting a connection to East Africa, whereas the "European" LP SNP (13910C>T) was found in populations of mixed ancestry. Using genome-wide data from various African populations, we identify admixture (13%) in the Nama, from an Afro-Asiatic group dating to >1,300 years ago, with the remaining fraction of their genomes being from San hunter-gatherers. We also find evidence of selection around the LCT gene among Khoe-speaking groups, and the substantial frequency of the 14010C variant among the Nama is best explained by adaptation to digesting milk. These genome-local and genome-wide results support a model in which an East African group brought pastoralist practices to southern Africa and admixed with local hunter-gatherers to form the ancestors of Khoe people.

  13. Re-evaluating the resource potential of lomas fog oasis environments for Preceramic hunter-gatherers under past ENSO modes on the south coast of Peru

    NASA Astrophysics Data System (ADS)

    Beresford-Jones, David; Pullen, Alexander G.; Whaley, Oliver Q.; Moat, Justin; Chauca, George; Cadwallader, Lauren; Arce, Susana; Orellana, Alfonso; Alarcón, Carmela; Gorriti, Manuel; Maita, Patricia K.; Sturt, Fraser; Dupeyron, Agathe; Huaman, Oliver; Lane, Kevin J.; French, Charles

    2015-12-01

    Lomas - ephemeral seasonal oases sustained by ocean fogs - were critical to ancient human ecology on the desert Pacific coast of Peru: one of humanity's few independent hearths of agriculture and "pristine" civilisation. The role of climate change since the Late Pleistocene in determining productivity and extent of past lomas ecosystems has been much debated. Here we reassess the resource potential of the poorly studied lomas of the south coast of Peru during the long Middle Pre-ceramic period (c. 8000-4500 BP): a period critical in the transition to agriculture, the onset of modern El Niño Southern Oscillation ('ENSO') conditions, and eustatic sea-level rise and stabilisation and beach progradation. Our method combines vegetation survey and herbarium collection with archaeological survey and excavation to make inferences about both Preceramic hunter-gatherer ecology and the changed palaeoenvironments in which it took place. Our analysis of newly discovered archaeological sites - and their resource context - show how lomas formations defined human ecology until the end of the Middle Preceramic Period, thereby corroborating recent reconstructions of ENSO history based on other data. Together, these suggest that a five millennia period of significantly colder seas on the south coast induced conditions of abundance and seasonal predictability in lomas and maritime ecosystems, that enabled Middle Preceramic hunter-gatherers to reduce mobility by settling in strategic locations at the confluence of multiple eco-zones at the river estuaries. Here the foundations of agriculture lay in a Broad Spectrum Revolution that unfolded, not through population pressure in deteriorating environments, but rather as an outcome of resource abundance.

  14. The genetic structure and history of Africans and African Americans.

    PubMed

    Tishkoff, Sarah A; Reed, Floyd A; Friedlaender, Françoise R; Ehret, Christopher; Ranciaro, Alessia; Froment, Alain; Hirbo, Jibril B; Awomoyi, Agnes A; Bodo, Jean-Marie; Doumbo, Ogobara; Ibrahim, Muntaser; Juma, Abdalla T; Kotze, Maritha J; Lema, Godfrey; Moore, Jason H; Mortensen, Holly; Nyambo, Thomas B; Omar, Sabah A; Powell, Kweli; Pretorius, Gideon S; Smith, Michael W; Thera, Mahamadou A; Wambebe, Charles; Weber, James L; Williams, Scott M

    2009-05-22

    Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observed high levels of mixed ancestry in most populations, reflecting historical migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (approximately 71%), European (approximately 13%), and other African (approximately 8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.

  15. The African diaspora: history, adaptation and health.

    PubMed

    Rotimi, Charles N; Tekola-Ayele, Fasil; Baker, Jennifer L; Shriner, Daniel

    2016-12-01

    The trans-Atlantic slave trade brought millions of Africans to the New World. Advances in genomics are providing novel insights into the history and health of Africans and the diasporan populations. Recent examples reviewed here include the unraveling of substantial hunter-gatherer and 'Eurasian' admixtures across sub-Saharan Africa, expanding our understanding of ancestral African genetics; the global ubiquity of mixed ancestry; the revealing of African ancestry in Latin Americans that likely derived from the slave trade; and understanding of the ancestral backgrounds of APOL1 and LPL found to influence kidney disease and lipid levels, respectively, providing specific insights into disease etiology and health disparities.

  16. Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders.

    PubMed

    Karafet, Tatiana M; Lansing, J S; Redd, Alan J; Reznikova, Svetlana; Watkins, Joseph C; Surata, S P K; Arthawiguna, W A; Mayer, Laura; Bamshad, Michael; Jorde, Lynn B; Hammer, Michael F

    2005-02-01

    The island of Bali lies near the center of the southern chain of islands in the Indonesian archipelago, which served as a stepping-stone for early migrations of hunter-gatherers to Melanesia and Australia and for more recent migrations of Austronesian farmers from mainland Southeast Asia to the Pacific. Bali is the only Indonesian island with a population that currently practices the Hindu religion and preserves various other Indian cultural, linguistic, and artistic traditions (Lansing 1983). Here, we examine genetic variation on the Y chromosomes of 551 Balinese men to investigate the relative contributions of Austronesian farmers and pre-Neolithic hunter-gatherers to the contemporary Balinese paternal gene pool and to test the hypothesis of recent paternal gene flow from the Indian subcontinent. Seventy-one Y-chromosome binary polymorphisms (single nucleotide polymorphisms, SNPs) and 10 Y-chromosome-linked short tandem repeats (STRs) were genotyped on a sample of 1,989 Y chromosomes from 20 populations representing Indonesia (including Bali), southern China, Southeast Asia, South Asia, the Near East, and Oceania. SNP genotyping revealed 22 Balinese lineages, 3 of which (O-M95, O-M119, and O-M122) account for nearly 83.7% of Balinese Y chromosomes. Phylogeographic analyses suggest that all three major Y-chromosome haplogroups migrated to Bali with the arrival of Austronesian speakers; however, STR diversity patterns associated with these haplogroups are complex and may be explained by multiple waves of Austronesian expansion to Indonesia by different routes. Approximately 2.2% of contemporary Balinese Y chromosomes (i.e., K-M9*, K-M230, and M lineages) may represent the pre-Neolithic component of the Indonesian paternal gene pool. In contrast, eight other haplogroups (e.g., within H, J, L, and R), making up approximately 12% of the Balinese paternal gene pool, appear to have migrated to Bali from India. These results indicate that the Austronesian expansion had a

  17. Evidence for aging theories from the study of a hunter-gatherer people (Ache of Paraguay).

    PubMed

    Libertini, G

    2013-09-01

    In the late seventies, a small tribal population of Paraguay, the Ache, living under natural conditions, was studied. Data from this population turn out to be useful for considerations about evolutionary hypotheses on the aging phenomenon. 1) Ache show an age-related increasing mortality, which strongly limits the mean duration of life, as observed in other studies on mammal and bird species. 2) According to current theories on aging, in the wild very few or no individual reach old age and, so, aging cannot be directly influenced by natural selection. However, data from our population show that a significant proportion of the population reaches in the wild 60 and 70 years of age. 3) Data from Ache are also in agreement with the observation about an inverse correlation between extrinsic mortality and deaths due to the age-related increasing mortality. 4) For many gerontologists, the age-related decline of vital functions is a consequence of the gradual decline of cell turnover, genetically determined and regulated by the declining duplication capacities of stem cells. The current interpretation is that these restrictions are a general defense against the proliferation of any tumoral mass. However, among wild Ache cancer is virtually unknown in non-elderly subjects, and only among older individuals are there deaths attributable to oncological diseases. Moreover, fitness decline begins long before oncological diseases have fatal effects in significant numbers. This completely disproves the current hypothesis, because a supposed defense against a deadly disease cannot exterminate a population before the disease begins to kill. These data are consistent with similar data from other species studied under natural conditions, and they bring new arguments against the non-adaptive interpretation of aging and in support of the adaptive interpretation.

  18. Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view

    PubMed Central

    Turroni, Silvia; Fiori, Jessica; Rampelli, Simone; Schnorr, Stephanie L.; Consolandi, Clarissa; Barone, Monica; Biagi, Elena; Fanelli, Flaminia; Mezzullo, Marco; Crittenden, Alyssa N.; Henry, Amanda G.; Brigidi, Patrizia; Candela, Marco

    2016-01-01

    The recent characterization of the gut microbiome of traditional rural and foraging societies allowed us to appreciate the essential co-adaptive role of the microbiome in complementing our physiology, opening up significant questions on how the microbiota changes that have occurred in industrialized urban populations may have altered the microbiota-host co-metabolic network, contributing to the growing list of Western diseases. Here, we applied a targeted metabolomics approach to profile the fecal metabolome of the Hadza of Tanzania, one of the world’s few remaining foraging populations, and compared them to the profiles of urban living Italians, as representative of people in the post-industrialized West. Data analysis shows that during the rainy season, when the diet is primarily plant-based, Hadza are characterized by a distinctive enrichment in hexoses, glycerophospholipids, sphingolipids, and acylcarnitines, while deplete in the most common natural amino acids and derivatives. Complementary to the documented unique metagenomic features of their gut microbiome, our findings on the Hadza metabolome lend support to the notion of an alternate microbiome configuration befitting of a nomadic forager lifestyle, which helps maintain metabolic homeostasis through an overall scarcity of inflammatory factors, which are instead highly represented in the Italian metabolome. PMID:27624970

  19. Access to Electric Light Is Associated with Shorter Sleep Duration in a Traditionally Hunter-Gatherer Community.

    PubMed

    de la Iglesia, Horacio O; Fernández-Duque, Eduardo; Golombek, Diego A; Lanza, Norberto; Duffy, Jeanne F; Czeisler, Charles A; Valeggia, Claudia R

    2015-08-01

    Access to electric light might have shifted the ancestral timing and duration of human sleep. To test this hypothesis, we studied two communities of the historically hunter-gatherer indigenous Toba/Qom in the Argentinean Chaco. These communities share the same ethnic and sociocultural background, but one has free access to electricity while the other relies exclusively on natural light. We fitted participants in each community with wrist activity data loggers to assess their sleep-wake cycles during one week in the summer and one week in the winter. During the summer, participants with access to electricity had a tendency to a shorter daily sleep bout (43 ± 21 min) than those living under natural light conditions. This difference was due to a later daily bedtime and sleep onset in the community with electricity, but a similar sleep offset and rise time in both communities. In the winter, participants without access to electricity slept longer (56 ± 17 min) than those with access to electricity, and this was also related to earlier bedtimes and sleep onsets than participants in the community with electricity. In both communities, daily sleep duration was longer during the winter than during the summer. Our field study supports the notion that access to inexpensive sources of artificial light and the ability to create artificially lit environments must have been key factors in reducing sleep in industrialized human societies.

  20. Access to Electric Light Is Associated with Shorter Sleep Duration in a Traditionally Hunter-Gatherer Community

    PubMed Central

    de la Iglesia, Horacio O.; Fernández-Duque, Eduardo; Golombek, Diego A.; Lanza, Norberto; Duffy, Jeanne F.; Czeisler, Charles A.; Valeggia, Claudia R.

    2017-01-01

    Access to electric light might have shifted the ancestral timing and duration of human sleep. To test this hypothesis, we studied two communities of the historically hunter-gatherer indigenous Toba/Qom in the Argentinean Chaco. These communities share the same ethnic and sociocultural background, but one has free access to electricity while the other relies exclusively on natural light. We fitted participants in each community with wrist activity data loggers to assess their sleep-wake cycles during one week in the summer and one week in the winter. During the summer, participants with access to electricity had a tendency to a shorter daily sleep bout (43 ± 21 min) than those living under natural light conditions. This difference was due to a later daily bedtime and sleep onset in the community with electricity, but a similar sleep offset and rise time in both communities. In the winter, participants without access to electricity slept longer (56 ± 17 min) than those with access to electricity, and this was also related to earlier bedtimes and sleep onsets than participants in the community with electricity. In both communities, daily sleep duration was longer during the winter than during the summer. Our field study supports the notion that access to inexpensive sources of artificial light and the ability to create artificially lit environments must have been key factors in reducing sleep in industrialized human societies. PMID:26092820

  1. Site Formation Processes and Hunter-Gatherers Use of Space in a Tropical Environment: A Geo-Ethnoarchaeological Approach from South India

    PubMed Central

    Friesem, David E.; Lavi, Noa; Madella, Marco; Ajithprasad, P.; French, Charles

    2016-01-01

    Hunter-gatherer societies have distinct social perceptions and practices which are expressed in unique use of space and material deposition patterns. However, the identification of archaeological evidence associated with hunter-gatherer activity is often challenging, especially in tropical environments such as rainforests. We present an integrated study combining ethnoarchaeology and geoarchaeology in order to study archaeological site formation processes related to hunter-gatherers’ ways of living in tropical forests. Ethnographic data was collected from an habitation site of contemporary hunter-gatherers in the forests of South India, aimed at studying how everyday activities and way of living dictate patterns of material deposition. Ethnoarchaeological excavations of abandoned open-air sites and a rock-shelter of the same group located deep in the forests, involved field observations and sampling of sediments from the abandoned sites and the contemporary site. Laboratory analyses included geochemical analysis (i.e., FTIR, ICP-AES), phytolith concentration analysis and soil micromorphology. The results present a dynamic spatial deposition pattern of macroscopic, microscopic and chemical materials, which stem from the distinctive ways of living and use of space by hunter-gatherers. This study shows that post-depositional processes in tropical forests result in poor preservation of archaeological materials due to acidic conditions and intensive biological activity within the sediments. Yet, the multiple laboratory-based analyses were able to trace evidence for activity surfaces and their maintenance practices as well as localized concentrations of activity remains such as the use of plants, metals, hearths and construction materials. PMID:27783683

  2. Role of wild plant foods among late Holocene hunter-gatherers from Central and North Patagonia (South America): an approach from dental evidence.

    PubMed

    Bernal, Valeria; Novellino, Paula; Gonzalez, Paula N; Perez, S Ivan

    2007-08-01

    This study evaluates the role of plant foods in the subsistence of hunter-gatherers that inhabited the Central East, Northwest, and Northeast Patagonia (Argentina) during the late Holocene (ca. 3,000-500 years BP). The goal of the present study is to assess the temporal variation of dental caries ratio and wear rate in skeletal samples to ascertain if the biological information supports the dietary shift toward greater consumption of wild plant foods around 1,500 years BP, suggested by other types of evidence. The authors registered caries, antemortem and postmortem tooth loss, and tooth wear from eight samples belonging to hunter-gatherers from Patagonia for which chronological sequences from early late Holocene (ca. 3,000-1,500 years BP) up to final late Holocene (ca. 1,500-500 years BP) are available. The results indicate that caries percentages in Patagonian samples fall within the range established for hunter-gatherers but there are significant geographical differences. In addition, caries ratio does not change significantly through time, so the amount of carbohydrates consumed seems to have remained fairly constant since 3,000 years BP. In contrast, there is a marked temporal trend toward the reduction of wear rates in the three areas, suggesting a faster rate in early late Holocene than in final late Holocene. These results would reflect a change to less hard and/or abrasive diets in the final late Holocene, probably owing to differences in food processing methods employed.

  3. Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence

    PubMed Central

    Morton, Elise R.; Lynch, Joshua; Froment, Alain; Lafosse, Sophie; Heyer, Evelyne; Przeworski, Molly; Blekhman, Ran; Ségurel, Laure

    2015-01-01

    The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon. PMID:26619199

  4. An examination of gender bias on the eighth-grade MEAP science test as it relates to the Hunter Gatherer Theory of Spatial Sex Differences

    NASA Astrophysics Data System (ADS)

    Armstrong-Hall, Judy Gail

    The purpose of this study was to apply the Hunter-Gatherer Theory of sex spatial skills to responses to individual questions by eighth grade students on the Science component of the Michigan Educational Assessment Program (MEAP) to determine if sex bias was inherent in the test. The Hunter-Gatherer Theory on Spatial Sex Differences, an original theory, that suggested a spatial dimorphism concept with female spatial skill of pattern recall of unconnected items and male spatial skills requiring mental movement. This is the first attempt to apply the Hunter-Gatherer Theory on Spatial Sex Differences to a standardized test. An overall hypothesis suggested that the Hunter-Gatherer Theory of Spatial Sex Differences could predict that males would perform better on problems involving mental movement and females would do better on problems involving the pattern recall of unconnected items. Responses to questions on the 1994-95 MEAP requiring the use of male spatial skills and female spatial skills were analyzed for 5,155 eighth grade students. A panel composed of five educators and a theory developer determined which test items involved the use of male and female spatial skills. A MANOVA, using a random sample of 20% of the 5,155 students to compare male and female correct scores, was statistically significant, with males having higher scores on male spatial skills items and females having higher scores on female spatial skills items. Pearson product moment correlation analyses produced a positive correlation for both male and female performance on both types of spatial skills. The Hunter-Gatherer Theory of Spatial Sex Differences appears to be able to predict that males could perform better on the problems involving mental movement and females could perform better on problems involving the pattern recall of unconnected items. Recommendations for further research included: examination of male/female spatial skill differences at early elementary and high school levels to

  5. Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel.

    PubMed

    Bučková, Jana; Cerný, Viktor; Novelletto, Andrea

    2013-05-01

    The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. Moreover, the R1b-M343 is represented in our dataset exclusively in the Fulani group and our analyses infer a north-to-south African migration route during a recent past.

  6. Genome-Wide SNP Analysis of Southern African Populations Provides New Insights into the Dispersal of Bantu-Speaking Groups

    PubMed Central

    González-Santos, Miguel; Montinaro, Francesco; Oosthuizen, Ockie; Oosthuizen, Erica; Busby, George B.J.; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo; Capelli, Cristian

    2015-01-01

    The expansion of Bantu-speaking agropastoralist populations had a great impact on the genetic, linguistic, and cultural variation of sub-Saharan Africa. It is generally accepted that Bantu languages originated in an area around the present border between Cameroon and Nigeria approximately 5,000 years ago, from where they spread South and East becoming the largest African linguistic branch. The demic consequences of this event are reflected in the relatively high genetic homogeneity observed across most of sub-Saharan Africa populations. In this work, we explored genome-wide single nucleotide polymorphism data from 28 populations to characterize the genetic components present in sub-Saharan African populations. Combining novel data from four Southern African populations with previously published results, we reject the hypothesis that the “non-Bantu” genetic component reported in South-Eastern Africa (Mozambique) reflects extensive gene flow between incoming agriculturalist and resident hunter-gatherer communities. We alternatively suggest that this novel component is the result of demographic dynamics associated with the Bantu dispersal. PMID:26363465

  7. [African population in history].

    PubMed

    Yang, S

    1984-11-29

    The growth rate of the African population has been fluctuating throughout history, affected by political, social, and economic events. 6000 years ago, the majority of the population was based in North Africa, because farming had been developed there. However, between the 11th and the 16th centuries, there was a constant decline in the population of that region, due to invasions from Europe and the black plague. During the same period, the population in the area south of the Sahara grew rapidly, as people there had gone into the iron tool period and farming had been developed. From the 16th to the mid-17th Century, population growth was considerable in Africa; more people had learned the technology of irrigation, corn and potatoes had been introduced from South America, and colonialism was not yet an issue. From the mid-17th to the mid-19th Century, there was no growth, due to the slave trade and wars between tribes. One estimate sets the direct and indirect loss during this period, as a result of the slave trade, at 100 million people. From the 1850s to the end of World War I, population growth started up again, chiefly influenced by the fact that the slave trade had essentially come to a half and modern medical care had become available on the continent. However, in central Africa, the region which suffered the worst blow from the slave trade, growth was very slow, while in East Africa the population was declining because of wars between colonists and natives, as well as natural disasters. Increases in population during this period were a result of immigration from Europe and India. From the end of World War I to the present, growth has been rapid, given improvements in medical services and standards of living, while most of the former colonies became independent after the 1950s. Consequently, almost all African countries are under great pressure now with regard to their populations.

  8. Static and moving frontiers: the genetic landscape of Southern African Bantu-speaking populations.

    PubMed

    Marks, Sarah J; Montinaro, Francesco; Levy, Hila; Brisighelli, Francesca; Ferri, Gianmarco; Bertoncini, Stefania; Batini, Chiara; Busby, George B J; Arthur, Charles; Mitchell, Peter; Stewart, Brian A; Oosthuizen, Ockie; Oosthuizen, Erica; D'Amato, Maria Eugenia; Davison, Sean; Pascali, Vincenzo; Capelli, Cristian

    2015-01-01

    A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.

  9. Ancient human genomes suggest three ancestral populations for present-day Europeans

    PubMed Central

    Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H.; Schraiber, Joshua G.; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I.; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A.; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M.; Brisighelli, Francesca; Busby, George B. J.; Cali, Francesco; Churnosov, Mikhail; Cole, David E. C.; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A.; Romero, Irene Gallego; Gubina, Marina; Hammer, Michael; Henn, Brenna M.; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R.; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W.; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B.; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G.; Ruiz-Linares, Andres; Tishkoff, Sarah A.; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E.; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

    2014-01-01

    We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages. PMID:25230663

  10. Preferences for symmetry in human faces in two cultures: data from the UK and the Hadza, an isolated group of hunter-gatherers.

    PubMed

    Little, Anthony C; Apicella, Coren L; Marlowe, Frank W

    2007-12-22

    Many studies show agreement within and between cultures for general judgements of facial attractiveness. Few studies, however, have examined the attractiveness of specific traits and few have examined preferences in hunter-gatherers. The current study examined preferences for symmetry in both the UK and the Hadza, a hunter-gatherer society of Tanzania. We found that symmetry was more attractive than asymmetry across both the cultures and was more strongly preferred by the Hadza than in the UK. The different ecological conditions may play a role in generating this difference. Such variation in preference may be adaptive if it reflects adaptation to local conditions. Symmetry is thought to indicate genetic quality, which may be more important among the Hadza with much higher mortality rates from birth onwards. Hadza men who were more often named as good hunters placed a greater value on symmetry in female faces. These results suggest that high quality Hadza men are more discriminating in their choice of faces. Hadza women had increased preferences for symmetry in men's faces when they were pregnant or nursing, perhaps due to their increased discrimination and sensitivity to foods and disease harmful to a foetus or nursing infant. These results imply that symmetry is an evolutionarily relevant trait and that variation in symmetry preference appears strategic both between cultures and within individuals of a single culture.

  11. Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia.

    PubMed

    Aimé, Carla; Verdu, Paul; Ségurel, Laure; Martinez-Cruz, Begoña; Hegay, Tatyana; Heyer, Evelyne; Austerlitz, Frédéric

    2014-10-01

    The transition from hunting and gathering to plant and animal domestication was one of the most important cultural and technological revolutions in human history. According to archeologists and paleoanthropologists, this transition triggered major demographic expansions. However, few genetic studies have found traces of Neolithic expansions in the current repartition of genetic polymorphism, pointing rather toward Paleolithic expansions. Here, we used microsatellite autosomal data to investigate the past demographic history of 87 African and Eurasian human populations with contrasted lifestyles (nomadic hunter-gatherers, semi-nomadic herders and sedentary farmers). Likely due to the combination of a higher mutation rate and the possibility to analyze several loci as independent replicates of the coalescent process, the analysis of microsatellite data allowed us to infer more recent expansions than previous genetic studies, potentially resulting from the Neolithic transition. Despite the variability in their location and environment, we found consistent expansions for all sedentary farmers, while we inferred constant population sizes for all hunter-gatherers and most herders that could result from constraints linked to a nomadic or semi-nomadic lifestyle and/or competition for land between herders and farmers. As an exception, we inferred expansions for Central Asian herders. This might be linked with the arid environment of this area that may have been more favorable to nomadic herders than to sedentary farmers. Alternatively, current Central Asian herders may descent from populations who have first experienced a transition from hunter-gathering to sedentary agropastoralism, and then a second transition to nomadic herding.

  12. Barley (Hordeum vulgare) in the Okhotsk culture (5th-10th century AD) of northern Japan and the role of cultivated plants in hunter-gatherer economies.

    PubMed

    Leipe, Christian; Sergusheva, Elena A; Müller, Stefanie; Spengler, Robert N; Goslar, Tomasz; Kato, Hirofumi; Wagner, Mayke; Weber, Andrzej W; Tarasov, Pavel E

    2017-01-01

    This paper discusses archaeobotanical remains of naked barley recovered from the Okhotsk cultural layers of the Hamanaka 2 archaeological site on Rebun Island, northern Japan. Calibrated ages (68% confidence interval) of the directly dated barley remains suggest that the crop was used at the site ca. 440-890 cal yr AD. Together with the finds from the Oumu site (north-eastern Hokkaido Island), the recovered seed assemblage marks the oldest well-documented evidence for the use of barley in the Hokkaido Region. The archaeobotanical data together with the results of a detailed pollen analysis of contemporaneous sediment layers from the bottom of nearby Lake Kushu point to low-level food production, including cultivation of barley and possible management of wild plants that complemented a wide range of foods derived from hunting, fishing, and gathering. This qualifies the people of the Okhotsk culture as one element of the long-term and spatially broader Holocene hunter-gatherer cultural complex (including also Jomon, Epi-Jomon, Satsumon, and Ainu cultures) of the Japanese archipelago, which may be placed somewhere between the traditionally accepted boundaries between foraging and agriculture. To our knowledge, the archaeobotanical assemblages from the Hokkaido Okhotsk culture sites highlight the north-eastern limit of prehistoric barley dispersal. Seed morphological characteristics identify two different barley phenotypes in the Hokkaido Region. One compact type (naked barley) associated with the Okhotsk culture and a less compact type (hulled barley) associated with Early-Middle Satsumon culture sites. This supports earlier suggestions that the "Satsumon type" barley was likely propagated by the expansion of the Yayoi culture via south-western Japan, while the "Okhotsk type" spread from the continental Russian Far East region, across the Sea of Japan. After the two phenotypes were independently introduced to Hokkaido, the boundary between both barley domains possibly

  13. Agent-based modeling for the landuse change of hunter-gather societies and the impacts on biodiversity in Guyana

    NASA Astrophysics Data System (ADS)

    Iwamura, T.; Fragoso, J.; Lambin, E.

    2012-12-01

    The interactions with animals are vital to the Amerindian, indigenous people, of Rupunini savannah-forest in Guyana. Their connections extend from basic energy and protein resource to spiritual bonding through "paring" to a certain animal in the forest. We collected extensive dataset of 23 indigenous communities for 3.5 years, consisting 9900 individuals from 1307 households, as well as animal observation data in 8 transects per communities (47,000 data entries). In this presentation, our research interest is to model the driver of land use change of the indigenous communities and its impacts on the ecosystem in the Rupunini area under global change. Overarching question we would like to answer with this program is to find how and why "tipping-point" from hunting gathering society to the agricultural society occurs in the future. Secondary question is what is the implication of the change to agricultural society in terms of biodiversity and carbon stock in the area, and eventually the well-being of Rupunini people. To answer the questions regarding the society shift in agriculture activities, we built as simulation with Agent-Based Modeling (Multi Agents Simulation). We developed this simulation by using Netlogo, the programming environment specialized for spatially explicit agent-based modeling (ABM). This simulation consists of four different process in the Rupunini landscape; forest succession, animal population growth, hunting of animals, and land clearing for agriculture. All of these processes are carried out by a set of computational unit, called "agents". In this program, there are four types of agents - patches, villages, households, and animals. Here, we describe the impacts of hunting on the biodiversity based on actual demographic data from one village named Crush Water. Animal population within the hunting territory of the village stabilized but Agouti/Paca dominates the landscape with little population of armadillos and peccaries. White-tailed deers

  14. Climate-driven environmental changes around 8,200 years ago favoured increases in cetacean strandings and Mediterranean hunter-gatherers exploited them

    PubMed Central

    Mannino, Marcello A.; Talamo, Sahra; Tagliacozzo, Antonio; Fiore, Ivana; Nehlich, Olaf; Piperno, Marcello; Tusa, Sebastiano; Collina, Carmine; Di Salvo, Rosaria; Schimmenti, Vittoria; Richards, Michael P.

    2015-01-01

    Cetacean mass strandings occur regularly worldwide, yet the compounded effects of natural and anthropogenic factors often complicate our understanding of these phenomena. Evidence of past stranding episodes may, thus, be essential to establish the potential influence of climate change. Investigations on bones from the site of Grotta dell’Uzzo in North West Sicily (Italy) show that the rapid climate change around 8,200 years ago coincided with increased strandings in the Mediterranean Sea. Stable isotope analyses on collagen from a large sample of remains recovered at this cave indicate that Mesolithic hunter-gatherers relied little on marine resources. A human and a red fox dating to the 8.2-kyr-BP climatic event, however, acquired at least one third of their protein from cetaceans. Numerous carcasses should have been available annually, for at least a decade, to obtain these proportions of meat. Our findings imply that climate-driven environmental changes, caused by global warming, may represent a serious threat to cetaceans in the near future. PMID:26573384

  15. Climate-driven environmental changes around 8,200 years ago favoured increases in cetacean strandings and Mediterranean hunter-gatherers exploited them

    NASA Astrophysics Data System (ADS)

    Mannino, Marcello A.; Talamo, Sahra; Tagliacozzo, Antonio; Fiore, Ivana; Nehlich, Olaf; Piperno, Marcello; Tusa, Sebastiano; Collina, Carmine; di Salvo, Rosaria; Schimmenti, Vittoria; Richards, Michael P.

    2015-11-01

    Cetacean mass strandings occur regularly worldwide, yet the compounded effects of natural and anthropogenic factors often complicate our understanding of these phenomena. Evidence of past stranding episodes may, thus, be essential to establish the potential influence of climate change. Investigations on bones from the site of Grotta dell’Uzzo in North West Sicily (Italy) show that the rapid climate change around 8,200 years ago coincided with increased strandings in the Mediterranean Sea. Stable isotope analyses on collagen from a large sample of remains recovered at this cave indicate that Mesolithic hunter-gatherers relied little on marine resources. A human and a red fox dating to the 8.2-kyr-BP climatic event, however, acquired at least one third of their protein from cetaceans. Numerous carcasses should have been available annually, for at least a decade, to obtain these proportions of meat. Our findings imply that climate-driven environmental changes, caused by global warming, may represent a serious threat to cetaceans in the near future.

  16. Climate-driven environmental changes around 8,200 years ago favoured increases in cetacean strandings and Mediterranean hunter-gatherers exploited them.

    PubMed

    Mannino, Marcello A; Talamo, Sahra; Tagliacozzo, Antonio; Fiore, Ivana; Nehlich, Olaf; Piperno, Marcello; Tusa, Sebastiano; Collina, Carmine; Di Salvo, Rosaria; Schimmenti, Vittoria; Richards, Michael P

    2015-11-17

    Cetacean mass strandings occur regularly worldwide, yet the compounded effects of natural and anthropogenic factors often complicate our understanding of these phenomena. Evidence of past stranding episodes may, thus, be essential to establish the potential influence of climate change. Investigations on bones from the site of Grotta dell'Uzzo in North West Sicily (Italy) show that the rapid climate change around 8,200 years ago coincided with increased strandings in the Mediterranean Sea. Stable isotope analyses on collagen from a large sample of remains recovered at this cave indicate that Mesolithic hunter-gatherers relied little on marine resources. A human and a red fox dating to the 8.2-kyr-BP climatic event, however, acquired at least one third of their protein from cetaceans. Numerous carcasses should have been available annually, for at least a decade, to obtain these proportions of meat. Our findings imply that climate-driven environmental changes, caused by global warming, may represent a serious threat to cetaceans in the near future.

  17. Ancient lipids document continuity in the use of early hunter-gatherer pottery through 9,000 years of Japanese prehistory.

    PubMed

    Lucquin, Alexandre; Gibbs, Kevin; Uchiyama, Junzo; Saul, Hayley; Ajimoto, Mayumi; Eley, Yvette; Radini, Anita; Heron, Carl P; Shoda, Shinya; Nishida, Yastami; Lundy, Jasmine; Jordan, Peter; Isaksson, Sven; Craig, Oliver E

    2016-04-12

    The earliest pots in the world are from East Asia and date to the Late Pleistocene. However, ceramic vessels were only produced in large numbers during the warmer and more stable climatic conditions of the Holocene. It has long been assumed that the expansion of pottery was linked with increased sedentism and exploitation of new resources that became available with the ameliorated climate, but this hypothesis has never been tested. Through chemical analysis of their contents, we herein investigate the use of pottery across an exceptionally long 9,000-y sequence from the Jōmon site of Torihama in western Japan, intermittently occupied from the Late Pleistocene to the mid-Holocene. Molecular and isotopic analyses of lipids from 143 vessels provides clear evidence that pottery across this sequence was predominantly used for cooking marine and freshwater resources, with evidence for diversification in the range of aquatic products processed during the Holocene. Conversely, there is little indication that ruminant animals or plants were processed in pottery, although it is evident from the faunal and macrobotanical remains that these foods were heavily exploited. Supported by other residue analysis data from Japan, our results show that the link between pottery and fishing was established in the Late Paleolithic and lasted well into the Holocene, despite environmental and socio-economic change. Cooking aquatic products in pottery represents an enduring social aspect of East Asian hunter-gatherers, a tradition based on a dependable technology for exploiting a sustainable resource in an uncertain and changing world.

  18. Provisioning offspring and others: risk-energy trade-offs and gender differences in hunter-gatherer foraging strategies.

    PubMed

    Codding, Brian F; Bird, Rebecca Bliege; Bird, Douglas W

    2011-08-22

    Offspring provisioning is commonly referenced as the most important influence on men's and women's foraging decisions. However, the provisioning of other adults may be equally important in determining gender differences in resource choice, particularly when the goals of provisioning offspring versus others cannot be met with the acquisition of the same resources. Here, we examine how resources vary in their expected daily energetic returns and in the variance or risk around those returns. We predict that when available resources impose no trade-off between risk and energy, the targets of men's and women's foraging will converge on high-energy, low-risk resources that allow for the simultaneous provisioning of offspring and others. However, when minimizing risk and maximizing energy trade-off with one another, we expect men's foraging to focus on provisioning others through the unreliable acquisition of large harvests, while women focus on reliably acquiring smaller harvests to feed offspring. We test these predictions with foraging data from three populations (Aché, Martu and Meriam). The results uphold the predictions, suggesting that men's and women's foraging interests converge when high-energy resources can be reliably acquired, but diverge when higher-energy resources are associated with higher levels of risk. Social factors, particularly the availability of alloparental support, may also play a major role.

  19. Dietary reconstruction of the El Sidrón Neandertal familial group (Spain) in the context of other Neandertal and modern hunter-gatherer groups. A molar microwear texture analysis.

    PubMed

    Estalrrich, Almudena; El Zaatari, Sireen; Rosas, Antonio

    2017-03-01

    Here, we present the analysis of occlusal molar microwear textures of eight individuals from the El Sidrón Neandertal group (Spain). The aims of the study were: 1) to document potential age-, sex-, and maternal lineage-related differences in diet within a Neandertal familial group, and 2) to place the diet of El Sidrón individuals in the context of those of other Neandertal groups. This study also offers an interpretation of the diet of the El Sidrón Neandertals by comparing their microwear signatures to those of recent hunter-gatherer populations with diverse but known diets. The intra-group examination of the microwear signatures are consistent with the females of the El Sidrón group having had more abrasive diets or having used their teeth in more para-masticatory activities than did the males. Aside from the potential sex-related differences in diet, no additional intra-group dietary separation, such as by age group or maternal lineage, was observed. In comparison to other Neandertals, El Sidrón individuals, as a group, have microwear signatures most similar to those of other Neandertals from wooded habitats and different from those that lived in more open habitats. This result is expected based on the available paleoenvironmental reconstructions from El Sidrón Cave. The diet of the El Sidrón Neandertals, just like their Neandertal counterparts from similar wooded habitats, is interpreted as having been mixed, consisting of both meat and vegetable foods.

  20. Genetics and southern African prehistory: an archaeological view.

    PubMed

    Mitchell, Peter

    2010-01-01

    Southern African populations speaking languages that are often - but inaccurately - grouped together under the label 'Khoisan' are an important focus of molecular genetic research, not least in tracking the early stages of human genetic diversification. This paper reviews these studies from an archaeological standpoint, concentrating on modern human origins, the introduction of pastoralism to southern Africa and admixture between the region's indigenous foragers and incoming Bantu-speaking farmers. To minimise confusion and facilitate correlation with anthropological, linguistic and archaeological data it emphasises the need to use ethnolinguistic labels accurately and with due regard for the particular histories of individual groups. It also stresses the geographically and culturally biased nature of the genetic studies undertaken to date, which employ data from only a few 'Khoisan' groups. Specific topics for which the combined deployment of genetic and archaeological methods would be particularly useful include the early history of Ju-Hoan- and Tuu-speaking hunter-gatherers, the expansion of Khoe-speaking populations, the chronology of genetic exchange between hunter-gatherers and farmers, and the origins of the Sotho/Tswana- and Nguni-speaking populations that dominate much of southern Africa today.

  1. Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming.

    PubMed

    Aimé, Carla; Laval, Guillaume; Patin, Etienne; Verdu, Paul; Ségurel, Laure; Chaix, Raphaëlle; Hegay, Tatyana; Quintana-Murci, Lluis; Heyer, Evelyne; Austerlitz, Frédéric

    2013-12-01

    Demographic changes are known to leave footprints on genetic polymorphism. Together with the increased availability of large polymorphism data sets, coalescent-based methods allow inferring the past demography of populations from their present-day patterns of genetic diversity. Here, we analyzed both nuclear (20 noncoding regions) and mitochondrial (HVS-I) resequencing data to infer the demographic history of 66 African and Eurasian human populations presenting contrasting lifestyles (nomadic hunter-gatherers, nomadic herders, and sedentary farmers). This allowed us to investigate the relationship between lifestyle and demography and to address the long-standing debate about the chronology of demographic expansions and the Neolithic transition. In Africa, we inferred expansion events for farmers, but constant population sizes or contraction events for hunter-gatherers. In Eurasia, we inferred higher expansion rates for farmers than herders with HVS-I data, except in Central Asia and Korea. Although isolation and admixture processes could have impacted our demographic inferences, these processes alone seem unlikely to explain the contrasted demographic histories inferred in populations with different lifestyles. The small expansion rates or constant population sizes inferred for herders and hunter-gatherers may thus result from constraints linked to nomadism. However, autosomal data revealed contraction events for two sedentary populations in Eurasia, which may be caused by founder effects. Finally, the inferred expansions likely predated the emergence of agriculture and herding. This suggests that human populations could have started to expand in Paleolithic times, and that strong Paleolithic expansions in some populations may have ultimately favored their shift toward agriculture during the Neolithic.

  2. What the Wind Won't Take Away: The Oral History of an African Foraging Woman.

    ERIC Educational Resources Information Center

    Shostak, Marjorie

    1987-01-01

    Describes the author's research with an African hunter-gatherer society and the collection of oral life histories of its members. Discusses five questions about the uses of personal narrative such as "Can personal narrative be used as ethnography?" Concludes that no better tool exists to describe the human condition than the personal…

  3. Human adaptation and population differentiation in the light of ancient genomes

    PubMed Central

    Key, Felix M.; Fu, Qiaomei; Romagné, Frédéric; Lachmann, Michael; Andrés, Aida M.

    2016-01-01

    The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. PMID:26988143

  4. The African Genome Variation Project shapes medical genetics in Africa.

    PubMed

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O; Choudhury, Ananyo; Ritchie, Graham R S; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N; Young, Elizabeth H; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S

    2015-01-15

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  5. The African Genome Variation Project shapes medical genetics in Africa

    NASA Astrophysics Data System (ADS)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2015-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  6. Genome-wide patterns of population structure and admixture in West Africans and African Americans.

    PubMed

    Bryc, Katarzyna; Auton, Adam; Nelson, Matthew R; Oksenberg, Jorge R; Hauser, Stephen L; Williams, Scott; Froment, Alain; Bodo, Jean-Marie; Wambebe, Charles; Tishkoff, Sarah A; Bustamante, Carlos D

    2010-01-12

    Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th-75th percentiles: 11.6-27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

  7. Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture.

    PubMed

    Pool, John E; Corbett-Detig, Russell B; Sugino, Ryuichi P; Stevens, Kristian A; Cardeno, Charis M; Crepeau, Marc W; Duchen, Pablo; Emerson, J J; Saelao, Perot; Begun, David J; Langley, Charles H

    2012-01-01

    Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa F(ST) were found to be enriched in genomic regions of locally elevated

  8. Apparent variation in Neanderthal admixture among African populations is consistent with gene flow from Non-African populations.

    PubMed

    Wang, Shuoguo; Lachance, Joseph; Tishkoff, Sarah A; Hey, Jody; Xing, Jinchuan

    2013-01-01

    Recent studies have found evidence of introgression from Neanderthals into modern humans outside of sub-Saharan Africa. Given the geographic range of Neanderthals, the findings have been interpreted as evidence of gene exchange between Neanderthals and modern humans descended from the Out-of-Africa (OOA) migration. Here, we examine an alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African modern humans who were the ancestors of those involved in the OOA migration. Under the alternative model, if the population structure among present-day Africans predates the OOA migration, we might find some African populations show a signal of Neanderthal introgression whereas others do not. To test this alternative model, we compiled a whole-genome data set including 38 sub-Saharan Africans from eight populations and 25 non-African individuals from five populations. We assessed differences in the amount of Neanderthal-like single-nucleotide polymorphism alleles among these populations and observed up to 1.5% difference in the number of Neanderthal-like alleles among African populations. Further analyses suggest that these differences are likely due to recent non-African admixture in these populations. After accounting for recent non-African admixture, our results do not support the alternative model of older (e.g., >100 kya) admixture between modern humans and Neanderthal-like hominids within Africa.

  9. Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries.

    PubMed

    Uren, Caitlin; Kim, Minju; Martin, Alicia R; Bobo, Dean; Gignoux, Christopher R; van Helden, Paul D; Möller, Marlo; Hoal, Eileen G; Henn, Brenna M

    2016-09-01

    Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.

  10. Genetic diversity and conservation of South African indigenous chicken populations.

    PubMed

    Mtileni, B J; Muchadeyi, F C; Maiwashe, A; Groeneveld, E; Groeneveld, L F; Dzama, K; Weigend, S

    2011-06-01

    In this study, we compare the level and distribution of genetic variation between South African conserved and village chicken populations using microsatellite markers. In addition, diversity in South African chickens was compared to that of a reference data set consisting of other African and purebred commercial lines. Three chicken populations Venda, Ovambo and Eastern Cape and four conserved flocks of the Venda, Ovambo, Naked Neck and Potchefstroom Koekoek from the Poultry Breeding Resource Unit of the Agricultural Research Council were genotyped at 29 autosomal microsatellite loci. All markers were polymorphic. Village chicken populations were more diverse than conservation flocks. structure software was used to cluster individuals to a predefined number of 2 ≤ K ≤ 6 clusters. The most probable clustering was found at K = 5 (95% identical runs). At this level of differentiation, the four conservation flocks separated as four independent clusters, while the three village chicken populations together formed another cluster. Thus, cluster analysis indicated a clear subdivision of each of the conservation flocks that were different from the three village chicken populations. The contribution of each South African chicken populations to the total diversity of the chickens studied was determined by calculating the optimal core set contributions based on Marker estimated kinship. Safe set analysis was carried out using bootstrapped kinship values calculated to relate the added genetic diversity of seven South African chicken populations to a set of reference populations consisting of other African and purebred commercial broiler and layer chickens. In both core set and the safe set analyses, village chicken populations scored slightly higher to the reference set compared to conservation flocks. Overall, the present study demonstrated that the conservation flocks of South African chickens displayed considerable genetic variability that is different from that of the

  11. Modeling Human Population Separation History Using Physically Phased Genomes

    PubMed Central

    Song, Shiya; Sliwerska, Elzbieta; Emery, Sarah; Kidd, Jeffrey M.

    2017-01-01

    Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Maasai, and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati, and Centre de’Etude du Polymorphism Humain European populations and analyzed population size and separation history using the pairwise sequentially Markovian coalescent and multiple sequentially Markovian coalescent models. We find that statistically phased haplotypes yield a more recent split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard isolation-with-migration model. We inferred that the separation between hunter-gatherer populations and other populations happened ∼120–140 KYA, with gene flow continuing until 30–40 KYA; separation between west-African and out-of-African populations happened ∼70–80 KYA; while the separation between Maasai and out-of-African populations happened ∼50 KYA. PMID:28049708

  12. East African cheetahs: evidence for two population bottlenecks?

    PubMed

    O'Brien, S J; Wildt, D E; Bush, M; Caro, T M; FitzGibbon, C; Aggundey, I; Leakey, R E

    1987-01-01

    A combined population genetic and reproductive analysis was undertaken to compare free-ranging cheetahs from east Africa (Acinonyx jubatus raineyi) with the genetically impoverished and reproductively impaired south African subspecies (Acinonyx jubatus jubatus). Like that of their south African counterparts, the quality of semen specimens from east African cheetahs was poor, with a low concentration of spermatozoa (25.3 X 10(6) per ejaculate) and a high incidence of morphological abnormalities (79%). From an electrophoretic survey of the products of 49 genetic loci in A. jubatus raineyi, two allozyme polymorphisms were detected; one of these, for a nonspecific esterase, shows an allele that is rare (less than 1% incidence) in south African specimens. Estimates of polymorphism (2-4%) and average heterozygosity (0.0004-0.014) affirm the cheetah as the least genetically variable felid species. The genetic distance between south and east African cheetahs was low (0.004), suggesting that the development of genetic uniformity preceded the recent geographic isolation of the subspecies. We propose that at least two population bottlenecks followed by inbreeding produced the modern cheetah species. The first and most extreme was ancient, possibly late Pleistocene (circa 10,000 years ago); the second was more recent (within the last century) and led to the south African populations.

  13. East African cheetahs: evidence for two population bottlenecks?

    PubMed Central

    O'Brien, S J; Wildt, D E; Bush, M; Caro, T M; FitzGibbon, C; Aggundey, I; Leakey, R E

    1987-01-01

    A combined population genetic and reproductive analysis was undertaken to compare free-ranging cheetahs from east Africa (Acinonyx jubatus raineyi) with the genetically impoverished and reproductively impaired south African subspecies (Acinonyx jubatus jubatus). Like that of their south African counterparts, the quality of semen specimens from east African cheetahs was poor, with a low concentration of spermatozoa (25.3 X 10(6) per ejaculate) and a high incidence of morphological abnormalities (79%). From an electrophoretic survey of the products of 49 genetic loci in A. jubatus raineyi, two allozyme polymorphisms were detected; one of these, for a nonspecific esterase, shows an allele that is rare (less than 1% incidence) in south African specimens. Estimates of polymorphism (2-4%) and average heterozygosity (0.0004-0.014) affirm the cheetah as the least genetically variable felid species. The genetic distance between south and east African cheetahs was low (0.004), suggesting that the development of genetic uniformity preceded the recent geographic isolation of the subspecies. We propose that at least two population bottlenecks followed by inbreeding produced the modern cheetah species. The first and most extreme was ancient, possibly late Pleistocene (circa 10,000 years ago); the second was more recent (within the last century) and led to the south African populations. PMID:3467370

  14. Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.

    PubMed

    Hsieh, PingHsun; Woerner, August E; Wall, Jeffrey D; Lachance, Joseph; Tishkoff, Sarah A; Gutenkunst, Ryan N; Hammer, Michael F

    2016-03-01

    Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.

  15. Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

    PubMed Central

    Hsieh, PingHsun; Woerner, August E.; Wall, Jeffrey D.; Lachance, Joseph; Tishkoff, Sarah A.; Gutenkunst, Ryan N.; Hammer, Michael F.

    2016-01-01

    Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr. PMID:26888264

  16. Polymorphic Alu insertions in six Brazilian African-derived populations.

    PubMed

    Cotrim, Nelson Henderson; Auricchio, Maria Teresa B M; Vicente, João Pedro; Otto, Paulo A; Mingroni-Netto, Regina Célia

    2004-01-01

    At least 25 African-derived populations (quilombo remnants) are believed to exist in the Ribeira River Valley, located in the southern part of São Paulo State, Brazil. We studied four Alu polymorphic loci (APO, ACE, TPA25, and FXIIIB) in individuals belonging to six quilombo remnants in addition to individuals sampled from the city of São Paulo. The allelic frequencies observed in the quilombo remnants were similar to those previously observed in African-derived populations from Central and North America. Genetic variability indexes (Fst and Gst values) in our quilombos were higher than the reported values for the majority of other populations analyzed for the same kind of markers, but lower than the variability usually observed in Amerindian groups. The observed high degree of genetic differentiation may be due to genetic drift, especially the founder effect. Our results suggest that these populations behave genetically as semi-isolates. The degree of genetic variability within populations was larger than among them, a finding described in other studies. In the neighbor-joining tree, some of the Brazilian quilombos clustered with the African and African-derived populations (São Pedro and Galvão), others with the Europeans (Pilões, Maria Rosa, and Abobral). Pedro Cubas was placed in an isolated branch. Principal component analysis was also performed and confirmed the trends observed in the neighbor-joining tree. Overall, the quilombos showed a higher degree of gene flow than average when compared to other worldwide populations, but similar to other African-derived populations.

  17. Chitotriosidase deficiency: a mutation update in an african population.

    PubMed

    Arndt, Silke; Hobbs, Angela; Sinclaire, Iain; Lane, Anthony B

    2013-01-01

    Human plasma chitotriosidase activity is a commonly used diagnostic and therapeutic biomarker for non-neuronopathic Gaucher disease. Chitotriosidase deficiency is common in non-African populations and is primarily caused by a 24 bp duplication in the encoding gene (CHIT1). Allele frequencies for the 24 bp duplication range from 20-50 % outside Africa. The present study found chitotriosidase deficiency to be rare in the South African Black population (1.6 %) and the otherwise common 24 bp duplication is absent in this African population. Instead, chitotriosidase deficiency is caused by a 4 bp deletion across the exon/intron 10 boundary (E/I-10_delGAgt) of the CHIT1 gene. The exact position of this mutation was found to differ from the previously reported location. Allele frequencies for six coding variants of CHIT1 (p.G102S, p.G354R, 24 bp duplication, E/I-10_delGAgt, p.A442V/G) were determined and the 4 bp deletion was found to be in complete linkage disequilibrium (LD) with two of the coding variants (p.G354R and p.A442V). The in silico assessments of the two missense mutations in LD predict a protein-damaging nature and functional studies are needed to clarify if one or both abolish the enzyme's activity. Overall, the low frequency of chitotriosidase deficiency in South African Blacks makes chitotriosidase activity an excellent biomarker of choice in this population.

  18. Intellectual Disability in the Context of a South African Population

    ERIC Educational Resources Information Center

    Kromberg, Jennifer; Zwane, Esther; Manga, Prashiela; Venter, Andre; Rosen, Eric; Christianson, Arnold

    2008-01-01

    Childhood disabilities, including intellectual disabilities (ID), are thought to occur in 5-17% of children in developing countries around the world. In order to identify and describe the childhood disabilities occurring in a rural South African population, as well as the context in which they occur, a study was carried out in the Bushbuckridge…

  19. Fostering Healthy Lifestyles in the African American Population

    ERIC Educational Resources Information Center

    Murimi, Mary; Chrisman, Matthew S.; McAllister, Tiffany; McDonald, Olevia D.

    2015-01-01

    Approximately 8.3% of the U.S. population (25.8 million people) is affected by type 2 diabetes. The burden of diabetes is disproportionately greater in the African American community. Compared with non-Hispanic Caucasian adults, the risk of diagnosed type 2 diabetes was 77% higher among non-Hispanic Blacks, who are 27% more likely to die of…

  20. Third African Population Conference. Dakar / Ngor Declaration on Population, Family and Sustainable Development.

    PubMed

    1994-01-01

    The Third African Population Conference was held in Dakar over the period December 7-12, 1992, on the theme of population, family, and sustainable development. The conference examined the implementation of the Kilimanjaro Program of Action for African Population and Self-Reliant Development, the African family in the context of socioeconomic development, strategies for sustainable development, emerging population problems and new orientations and strategies, and population policies and programs in Africa. The Dakar/Ngor Declaration on Population, Family, and Sustainable Development was adopted and is presented in the following sections: preamble; principles and objectives; recommendations for population, sustained economic growth, sustainable development, family, fertility and family planning, mortality, morbidity, AIDS, urbanization, migration, physical planning, refugees and displaced persons, women in development, children, youth, data collection and analysis, information dissemination, training and research, and information, education and communication; resource mobilization; and follow-up and implementation.

  1. Human African trypanosomiasis in endemic populations and travellers.

    PubMed

    Blum, J A; Neumayr, A L; Hatz, C F

    2012-06-01

    Human African trypanosomiasis (HAT) or sleeping sickness is caused by the protozoan parasites Trypanosoma brucei (T.b.) gambiense (West African form) and T.b. rhodesiense (East African form) that are transmitted by the bite of the tsetse fly, Glossina spp.. Whereas most patients in endemic populations are infected with T.b. gambiense, most tourists are infected with T.b. rhodesiense. In endemic populations, T.b. gambiense HAT is characterized by chronic and intermittent fever, headache, pruritus, and lymphadenopathy in the first stage and by sleep disturbances and neuro-psychiatric disorders in the second stage. Recent descriptions of the clinical presentation of T.b. rhodesiense in endemic populations show a high variability in different foci. The symptomatology of travellers is markedly different from the usual textbook descriptions of African HAT patients. The onset of both infections is almost invariably an acute and febrile disease. Diagnosis and treatment are difficult and rely mostly on old methods and drugs. However, new molecular diagnostic technologies are under development. A promising new drug combination is currently evaluated in a phase 3 b study and further new drugs are under evaluation.

  2. Asymmetric introgression of African genes in honeybee populations (Apis mellifera L.) in Central Mexico.

    PubMed

    Kraus, F B; Franck, P; Vandame, R

    2007-08-01

    The Africanization of the honeybee (Apis mellifera) in South America is one of the most spectacular examples of biological invasions. In this study, we analyzed the Africanization process in Central Mexico along an altitudinal transect from 72 to 2800 m, using both mitochondrial and nuclear DNA markers. The mitochondrial analysis revealed that the two high-altitude populations had a significantly greater percentage of African mitotypes (95%) than the three lowland populations (67%), indicating successful spreading of Africanized swarms to these altitudes. All populations (highland and lowland) had a similar overall proportion of African alleles at nuclear loci (58%). Thus, all populations showed an asymmetric introgression of African nuclear and mtDNA. Colonies with African mitotypes had, on average, significantly more African nuclear alleles (60%) than those with European mitotypes (51%). Furthermore, the three lowland populations showed clear signs of linkage disequilibrium, while the two high-altitude populations did not, indicating recent genetic introgression events into the lowland populations.

  3. Population affinities of African Colombians to Sub-Saharan Africans based on dental morphology.

    PubMed

    Delgado-Burbano, M E

    2007-01-01

    The Atlantic slave trade moved more than 13 million Africans to American lands between the 15th and 19th centuries. Previous historical, linguistic, and social-cultural studies suggested a Western-Central Bantu African origin for the Colombian slaves; however, their precise provenance remains unclear. The present study investigates the variation of the epigenetic dental traits in the deciduous and permanent dentition and phenotypic affinities of a contemporary Afro-Colombian community (n=178) in an attempt to identify their possible African ancestors. The results of a multivariate analysis of principal components show that Afro-descendents from Guapi have strong phenotypic relationships with several Bantu-speakers groups of Western and Western-Central Africa (Sub-Saharan region), specifically from Gabon, Congo, Pygmies, Nigeria, Cameroon, Togo and Benin. In concordance with recent mtDNA studies, this research suggests a distant but important relationship between Afro-Colombians and Eastern and South-Eastern African populations. This analysis also shows a marked dental divergence with North African samples. The dental information is not very different from the cultural, linguistic and historic data; however, it is more in agreement with studies based on molecular variation. In addition, this study reveals that African-Americans from North America, Central America-Caribbean and South America have high biological variation essentially identical to their several Sub-Saharan sources. Although a microevolutionary model, based on differential rates of gene flow with Native American and European-American groups and little selective pressures influence, better explains the phenotypic variation observed, more African-American dental samples must be analyzed from a regional perspective.

  4. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

    PubMed Central

    Dobon, Begoña; Hassan, Hisham Y.; Laayouni, Hafid; Luisi, Pierre; Ricaño-Ponce, Isis; Zhernakova, Alexandra; Wijmenga, Cisca; Tahir, Hanan; Comas, David; Netea, Mihai G.; Bertranpetit, Jaume

    2015-01-01

    East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations. PMID:26017457

  5. Cancer patterns in three African populations compared with the United States black population.

    PubMed

    Walker, A R; Walker, B F; Segal, I

    1993-07-01

    Cancer incidence rates and patterns in three African populations in the Gambia, Mali and South Africa, have been compared with corresponding data on the Black population in Connecticut, USA. In the African populations, total rates for cancer are much lower than that of US Blacks, even allowing for under-reporting. Chief cancers are those of the oesophagus, liver and cervix. In Mali, stomach cancer is very common. As to trends, among South African Blacks, a population in transition, rates are rising, albeit slowly, of cancers of prosperity--prostate, lung, breast and colon-rectum. Salient questions are: can the number of cancers of underprivilege be lessened, and can cancers linked with rising socioeconomic states be restrained? Discussions of common risk factors, including diet, reproduction, smoking and drinking practices, indicate that for Africans as a whole, continuing poverty will prevent major changes in cancer pattern and rises in occurrence of the disease. However, should prosperity increase for Africans in big cities, rates are ultimately likely to attain those prevailing in the US Black population. Significant avoiding action seems almost impossible.

  6. An essay on agriculture and population pressure.

    PubMed

    Macdonald, Andrew S

    2012-01-01

    This is an essay highlighting the fundamental importance of agriculture (historical and present) in the agro-socioeconomic evolution of human societies, from the times of the hunter/gatherers to the modern day. Attention is drawn in the text to the importance of deforestation in relation to micro and macro climate changes, and the vital role of carbon dioxide to plant and animal life. The essay also relates the world's natural resources to the present unsustainable population pressures.

  7. Demography of the Hadza, an increasing and high density population of Savanna foragers.

    PubMed

    Blurton Jones, N G; Smith, L C; O'Connell, J F; Hawkes, K; Kamuzora, C L

    1992-10-01

    This is a report on the demography of the Hadza, a population of East African hunter-gatherers. In it, we describe the results of a census, and our estimation of age structure, survivorship, mean age of women at childbearing, number of live children, total population size and density, and rate of change since 1967. We show that relevant measures fit closely the stable population model North 6 chosen by Dyson to represent Hadza demography in the 1960s. We compare aspects of Hadza demography with surrounding non-Hadza and with the !Kung. Among other things, we find that the Hadza have a higher population density, higher fertility, and a faster population growth rate than do the !Kung. These demographic differences are consistent with our expectations, which were based on differences in the costs and benefits of foraging in the two regions. We also show that Hadza demographic parameters display remarkable consistency over the past 20 years. Since neighboring populations have been encroaching on the area used by the Hadza, and Hadza foragers have been subject to interludes of externally imposed settlement, this consistency is surprising. We discuss some of the implications.

  8. Lactase deficiency in the South African black population.

    PubMed

    Segal, I; Gagjee, P P; Essop, A R; Noormohamed, A M

    1983-12-01

    H2 breath analysis was carried out to determine the prevalence of lactase deficiency in different tribes of the South African Black population. Lactase deficiency was common (78%), despite the fact that two of the largest tribes (Zulu and Xhosa) are cattle herders and milk drinkers. This apparent anomaly is due to the consumption of a traditional fermented buttermilk, ("amasi" which has a low lactose content) instead of fresh milk. The most important reason for lactase deficiency, however, is that the South African Blacks originated in the West and Central African zone of nonmilking and took up dairying and milk use fairly recently. Thus they have not had enough time for genetic selection for lactase deficiency through life. The implications inherent in this study are that it would be more prudent to supply milk to developing countries in the form of a fermented milk product such as buttermilk. This is readily accepted by the Black population and would not be counter to accepted cultural practice.

  9. APOL1 and nephropathy progression in populations of African ancestry.

    PubMed

    Freedman, Barry I

    2013-09-01

    Marked familial aggregation of chronic kidney disease suggests that inherited factors play a major role in nephropathy susceptibility. Molecular genetics analyses have identified a number of genes reproducibly associated with a broad range of renal phenotypes. Most associations show polygenic inheritance patterns with limited effect size. In contrast, genetic association between the apolipoprotein L1 (APOL1) gene and several severe nondiabetic forms of kidney disease in African Americans approach Mendelian inheritance patterns and account for a large proportion of glomerulosclerosis in populations of African ancestry. Emerging data support an important role for APOL1 in the progression of diverse etiologies of kidney disease, in concert with requisite environmental (gene*environment) and inherited (gene*gene) interactions. This article reviews the current status of APOL1-associated nephropathy and discusses research questions under active investigation in the search for a cure for these severe and often progressive kidney diseases.

  10. Freezing African Elephant Semen as a New Population Management Tool

    PubMed Central

    Hermes, Robert; Saragusty, Joseph; Göritz, Frank; Bartels, Paul; Potier, Romain; Baker, Barbara; Streich, W. Jürgen; Hildebrandt, Thomas B.

    2013-01-01

    Background The captive elephant population is not self-sustaining and with a limited number of breeding bulls, its genetic diversity is in decline. One way to overcome this is to import young and healthy animals from the wild. We introduce here a more sustainable alternative method - importation of semen from wild bulls without removing them from their natural habitat. Due to the logistics involved, the only practical option would be to transport cryopreserved sperm. Despite some early reports on African elephant semen cryopreservation, the utility of this new population management tool has not been evaluated. Methodology/Principal Findings Semen was collected by electroejaculation from 14 wild African savanna elephant (Loxodonta africana) bulls and cryopreserved using the directional freezing technique. Sperm treatments evaluated included the need for centrifugation, the use of hen or quail yolk, the concentration of glycerol (3%, 5% or 7%) in the extender, and maintenance of motility over time after thawing. Our results suggest that dilution in an extender containing hen yolk and 7% glycerol after centrifugation best preserved post-thaw sperm motility when compared to all other treatments (P≤0.012 for all). Using this approach we were able to achieve after thawing (mean ± SD) 54.6±3.9% motility, 85.3±2.4% acrosome integrity, and 86.8±4.6% normal morphology with no decrease in motility over 1 h incubation at 37°C. Sperm cryopreserved during this study has already lead to a pregnancy of a captive female elephant following artificial insemination. Conclusions/Significance With working techniques for artificial insemination and sperm cryopreservation of both African and Asian elephants in hand, population managers can now enrich captive or isolated wild elephant populations without removing valuable individuals from their natural habitat. PMID:23483917

  11. African Ancestry is a Risk Factor for Asthma and High Total IgE Levels in African Admixed Populations

    PubMed Central

    Vergara, Candelaria; Murray, Tanda; Rafaels, Nicholas; Lewis, Rachel; Campbell, Monica; Foster, Cassandra; Gao, Li; Faruque, Mezbah; Oliveira, Ricardo Riccio; Carvalho, Edgar; Araujo, Maria Ilma; Cruz, Alvaro A.; Watson, Harold; Mercado, Dilia; Knight-Madden, Jennifer; Ruczinski, Ingo; Dunston, Georgia; Ford, Jean; Caraballo, Luis; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.

    2014-01-01

    Characterization of genetic admixture of populations in the Americas and the Caribbean is of interest for anthropological, epidemiological, and historical reasons. Asthma has a higher prevalence and is more severe in populations with a high African component. Association of African ancestry with asthma has been demonstrated. We estimated admixture proportions of samples from six trihybrid populations of African descent and determined the relationship between African ancestry and asthma and total serum IgE levels (tIgE). We genotyped 237 ancestry informative markers in asthmatics and nonasthmatic controls from Barbados (190/277), Jamaica (177/529), Brazil (40/220), Colombia (508/625), African Americans from New York (207/171), and African Americans from Baltimore/Washington, D.C. (625/757). We estimated individual ancestries and evaluated genetic stratification using Structure and principal component analysis. Association of African ancestry and asthma and tIgE was evaluated by regression analysis. Mean SD African ancestry ranged from 0.76 ± 0.10 among Barbadians to 0.33 ± 0.13 in Colombians. The European component varied from 0.14 ± 0.05 among Jamaicans and Barbadians to 0.26 ± 0.08 among Colombians. African ancestry was associated with risk for asthma in Colombians (odds ratio (OR) = 4.5, P = 0.001) Brazilians (OR = 136.5, P = 0.003), and African Americans of New York (OR: 4.7; P = 0.040). African ancestry was also associated with higher tIgE levels among Colombians (β = 1.3, P = 0.04), Barbadians (β = 3.8, P = 0.03), and Brazilians (β = 1.6, P = 0.03). Our findings indicate that African ancestry can account for, at least in part, the association between asthma and its associated trait, tIgE levels. PMID:23554133

  12. The oral susceptibility of South African field populations of Culicoides to African horse sickness virus.

    PubMed

    Venter, G J; Wright, I M; Van Der Linde, T C; Paweska, J T

    2009-12-01

    Twenty-two isolates of African horse sickness virus (AHSV), representing its distinct serotypes, geographical and historical origins, were fed to three populations of South African livestock-associated Culicoides spp. (Diptera, Ceratopogonidae). Infective blood meals included 12 recent isolates, nine historical reference strains and one live attenuated vaccine strain serotype 7 (AHSV-7) of the virus. Field-collected midges were fed through a chicken-skin membrane on sheep blood spiked with one of the viruses, which concentrations ranged from 5.4 to 8.8 log(10)TCID(50)/mL of blood. After 10 days incubation at 23.5 degrees C, AHSV was isolated from 11 Culicoides species. Standard in vitro passaging of AHSV-7, used for the preparation of live attenuated vaccine, did not reduce its ability to infect Culicoides species. Virus recovery rates in orally infected Culicoides midges differed significantly between species and populations, serotypes, isolates and seasons. Significant variations in oral susceptibility recorded in this study emphasize a complex inter-relationship between virus and vector, which is further influenced by multiple intrinsic and extrinsic factors. As it is not possible to standardize all these factors under laboratory conditions, conclusive assessment of the role of field-collected Culicoides midges in the transmission of orbiviruses remains problematic. Nevertheless, results of this study suggest the potential for multi-vector transmission of AHSV virus in South Africa.

  13. FastStats: Health of Black or African American non-Hispanic Population

    MedlinePlus

    ... Health of Black or African American non-Hispanic Population Recommend on Facebook Tweet Share Compartir Data are ... Source: Summary Health Statistics Tables for the U.S. Population: National Health Interview Survey, 2015, Table P-1c [ ...

  14. Morphometric and genetic changes in a population of Apis mellifera after 34 years of Africanization.

    PubMed

    Francoy, T M; Wittmann, D; Steinhage, V; Drauschke, M; Müller, S; Cunha, D R; Nascimento, A M; Figueiredo, V L C; Simões, Z L P; De Jong, D; Arias, M C; Gonçalves, L S

    2009-01-01

    Though the replacement of European bees by Africanized honey bees in tropical America has attracted considerable attention, little is known about the temporal changes in morphological and genetic characteristics in these bee populations. We examined the changes in the morphometric and genetic profiles of an Africanized honey bee population collected near where the original African swarms escaped, after 34 years of Africanization. Workers from colonies sampled in 1968 and in 2002 were morphometrically analyzed using relative warps analysis and an Automatic Bee Identification System (ABIS). All the colonies had their mitochondrial DNA identified. The subspecies that mixed to form the Africanized honey bees were used as a comparison for the morphometric analysis. The two morphometric approaches showed great similarity of Africanized bees with the African subspecies, Apis mellifera scutellata, corroborating with other markers. We also found the population of 1968 to have the pattern of wing venation to be more similar to A. m. scutellata than the current population. The mitochondrial DNA of European origin, which was very common in the 1968 population, was not found in the current population, indicating selective pressure replacing the European with the African genome in this tropical region. Both morphometric methodologies were very effective in discriminating the A. mellifera groups; the non-linear analysis of ABIS was the most successful in identifying the bees, with more than 94% correct classifications.

  15. North African Jewish and non-Jewish populations form distinctive, orthogonal clusters

    PubMed Central

    Campbell, Christopher L.; Palamara, Pier F.; Dubrovsky, Maya; Botigué, Laura R.; Fellous, Marc; Atzmon, Gil; Oddoux, Carole; Pearlman, Alexander; Hao, Li; Henn, Brenna M.; Burns, Edward; Bustamante, Carlos D.; Comas, David; Friedman, Eitan; Pe'er, Itsik; Ostrer, Harry

    2012-01-01

    North African Jews constitute the second largest Jewish Diaspora group. However, their relatedness to each other; to European, Middle Eastern, and other Jewish Diaspora groups; and to their former North African non-Jewish neighbors has not been well defined. Here, genome-wide analysis of five North African Jewish groups (Moroccan, Algerian, Tunisian, Djerban, and Libyan) and comparison with other Jewish and non-Jewish groups demonstrated distinctive North African Jewish population clusters with proximity to other Jewish populations and variable degrees of Middle Eastern, European, and North African admixture. Two major subgroups were identified by principal component, neighbor joining tree, and identity-by-descent analysis—Moroccan/Algerian and Djerban/Libyan—that varied in their degree of European admixture. These populations showed a high degree of endogamy and were part of a larger Ashkenazi and Sephardic Jewish group. By principal component analysis, these North African groups were orthogonal to contemporary populations from North and South Morocco, Western Sahara, Tunisia, Libya, and Egypt. Thus, this study is compatible with the history of North African Jews—founding during Classical Antiquity with proselytism of local populations, followed by genetic isolation with the rise of Christianity and then Islam, and admixture following the emigration of Sephardic Jews during the Inquisition. PMID:22869716

  16. Genetic evidence for larger African population size during recent human evolution.

    PubMed

    Relethford, J H; Jorde, L B

    1999-03-01

    Genetic evidence suggests that the long-term average effective size of sub-Saharan Africa is larger than other geographic regions. A method is described that allows estimation of relative long-term regional population sizes. This method is applied to 60 microsatellite DNA loci from a sample of 72 sub-Saharan Africans, 63 East Asians, and 120 Europeans. Average heterozygosity is significantly higher in the sub-Saharan African sample. Expected heterozygosity was computed for each region and locus using a population genetic model based on the null hypothesis of equal long-term population sizes. Average residual heterozygosity is significantly higher in the sub-Saharan African sample, indicating that African population size was larger than other regions during recent human evolution. The best fit of the model is with relative population weights of 0.73 for sub-Saharan Africa, 0.09 for East Asia, and 0.18 for Europe. These results are similar to those obtained using craniometric variation for these three geographic regions. These results, combined with inferences from other genetic studies, support a major role of Africa in the origin of modern humans. It is less clear, however, whether complete African replacement is the most appropriate model. An alternative is an African origin with non-African gene flow. While Africa is an important region in recent human evolution, it is not clear whether the gene pool of our species is completely out of Africa or predominately out of Africa.

  17. Skull and limb morphology differentially track population history and environmental factors in the transition to agriculture in Europe.

    PubMed

    von Cramon-Taubadel, Noreen; Stock, Jay T; Pinhasi, Ron

    2013-09-22

    The Neolithic transition in Europe was a complex mosaic spatio-temporal process, involving both demic diffusion from the Near East and the cultural adoption of farming practices by indigenous hunter-gatherers. Previous analyses of Mesolithic hunter-gatherers and Early Neolithic farmers suggest that cranial shape variation preserves the population history signature of the Neolithic transition. However, the extent to which these same demographic processes are discernible in the postcranium is poorly understood. Here, for the first time, crania and postcranial elements from the same 11 prehistoric populations are analysed together in an internally consistent theoretical and methodological framework. Results show that while cranial shape reflects the population history differences between Mesolithic and Neolithic lineages, relative limb dimensions exhibit significant congruence with environmental variables such as latitude and temperature, even after controlling for geography and time. Also, overall limb size is found to be consistently larger in hunter-gatherers than farmers, suggesting a reduction in size related to factors other than thermoregulatory adaptation. Therefore, our results suggest that relative limb dimensions are not tracking the same demographic population history as the cranium, and point to the strong influence of climatic, dietary and behavioural factors in determining limb morphology, irrespective of underlying neutral demographic processes.

  18. Skeletal biology and the history of Native Americans and African Americans.

    PubMed

    Kiple, K F; Tarver, H M

    1992-01-01

    The authors incorporate data from skeletal remains in an attempt to construct health profiles for the Amerindian population before Columbus's arrival and for the antebellum black slave populations of North America and the Caribbean. They examine the impact of poor nutrition among slaves, as evidenced in bone and tooth samples, on infant and childhood mortality, fertility, and adult mortality. They go on to suggest that the change from a hunter-gatherer life-style to a more sedentary agricultural one resulted in poorer health for the Amerindian population. However, agriculture made soft foods more available, allowing women to wean their children earlier, thus increasing overall fertility.

  19. A study on ten short tandem repeat systems: African immigrant and Spanish population data.

    PubMed

    Gamero, J J; Romero, J L; Gonzalez, J L; Arufe, M I; Cuesta, M I; Corte-Real, F; Carvalho, M; Anjos, M J; Vieira, D N; Vide, M C

    2000-06-05

    This work presents the results obtained from a genetic-population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy-Weinberg equilibrium were detected.

  20. A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations

    PubMed Central

    Chimusa, Emile R.; Meintjies, Ayton; Tchanga, Milaine; Mulder, Nicola; Seoighe, Cathal; Soodyall, Himla; Ramesar, Rajkumar

    2015-01-01

    We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region. PMID:25811879

  1. Frequency and origins of hemoglobin S mutation in African-derived Brazilian populations.

    PubMed

    De Mello Auricchio, Maria Teresa Balester; Vicente, João Pedro; Meyer, Diogo; Mingroni-Netto, Regina Célia

    2007-12-01

    Africans arrived in Brazil as slaves in great numbers, mainly after 1550. Before the abolition of slavery in Brazil in 1888, many communities, called quilombos, were formed by runaway or abandoned African slaves. These communities are presently referred to as remnants of quilombos, and many are still partially genetically isolated. These remnants can be regarded as relicts of the original African genetic contribution to the Brazilian population. In this study we assessed frequencies and probable geographic origins of hemoglobin S (HBB*S) mutations in remnants of quilombo populations in the Ribeira River valley, São Paulo, Brazil, to reconstruct the history of African-derived populations in the region. We screened for HBB*S mutations in 11 quilombo populations (1,058 samples) and found HBB*S carrier frequencies that ranged from 0% to 14%. We analyzed beta-globin gene cluster haplotypes linked to the HBB*S mutation in 86 chromosomes and found the four known African haplotypes: 70 (81.4%) Bantu (Central Africa Republic), 7 (8.1%) Benin, 7 (8.1%) Senegal, and 2 (2.3%) Cameroon haplotypes. One sickle cell homozygote was Bantu/Bantu and two homozygotes had Bantu/Benin combinations. The high frequency of the sickle cell trait and the diversity of HBB*S linked haplotypes indicate that Brazilian remnants of quilombos are interesting repositories of genetic diversity present in the ancestral African populations.

  2. Age at breast cancer diagnosis in populations of african and European ancestry.

    PubMed

    Kadhel, Philippe; Multigner, Luc

    2014-01-01

    Based on US national cancer registry data, age differences at breast cancer diagnosis have been reported between African-American women and European-American women. Such differences between populations of African and European ancestry have not been studied in other countries at a nationwide level. Here, we report and compare descriptive nationwide epidemiological indicators of invasive breast cancer for the populations of European ancestry living in the US and in mainland France and for women of African ancestry living in the US and in the French West Indies (Martinique and Guadeloupe). Based on the available data, we determined age frequency distributions, world age-standardized incidence, and the distribution of expected cases of breast cancer in a standard population of women by age. The age frequency distributions revealed that women of African ancestry were younger at diagnosis than women of European ancestry. By contrast, compared with the US regardless of ancestry and mainland France, the standardized incidences appeared lower, and the largest numbers of expected cases younger, in the French West Indies. The populations with African ancestry were not homogeneous in terms of epidemiologic indicators of age-related breast cancer. These descriptive findings suggest that populations of African ancestry cannot be considered uniform when determining whether it would be appropriate to decrease the age of entry into screening programs for breast cancer.

  3. Rapid morphological changes in populations of hybrids between Africanized and European honey bees.

    PubMed

    Francoy, T M; Gonçalves, L S; De Jong, D

    2012-09-17

    African honey bees, introduced to Brazil in 1956, rapidly dominated the previously introduced European subspecies. To better understand how hybridization between these different types of bees proceeded, we made geometric morphometric analyses of the wing venation patterns of specimens resulting from crosses made between Africanized honey bees (predominantly Apis mellifera scutellata) and Italian honey bees (A. mellifera ligustica) from 1965 to 1967, at the beginning of the Africanization process, in an apiary about 150 km from the original introduction site. Two virgin queens reared from an Italian parental were instrumentally inseminated with semen from drones from an Africanized parental. Six F(1) queens from one of these colonies were open mated with Africanized drones. Resultant F(1) drones were backcrossed to 50 Italian and 50 Africanized parental queens. Five backcross workers were collected from each of eight randomly selected colonies of each type of backcross (N = 5 bees x 8 colonies x 2 types of backcrosses). The F1 progeny (40 workers and 30 drones) was found to be morphologically closer to the Africanized than to the European parental (N = 20 drones and 40 workers, each); Mahalanobis square distances = 21.6 versus 25.8, respectively, for the workers, and 39.9 versus 46.4, respectively, for the drones. The worker progenies of the backcrosses (N = 40, each) were placed between the respective parental and the F(1) progeny, although closer to the Africanized than to the Italian parentals (Mahalanobis square distance = 6.2 versus 12.1, respectively). Consequently, the most common crosses at the beginning of the Africanization process would have generated individuals more similar to Africanized than to Italian bees. This adds a genetic explanation for the rapid changes in the populational morphometric profile in recently colonized areas. Africanized alleles of wing venation pattern genes are apparently dominant and epistatic.

  4. Genetic structure of the gentle Africanized honey bee population (gAHB) in Puerto Rico

    PubMed Central

    2013-01-01

    Background The Africanized honey bee is one of the most spectacular invasions in the Americas. African bees escaped from apiaries in Brazil in 1956, spread over Americas and by 1994 they were reported in Puerto Rico. In contrast to other places, the oceanic island conditions in Puerto Rico may mean a single introduction and different dynamics of the resident European and new-coming Africanized bees. To examine the genetic variation of honey bee feral populations and colonies from different locations in Puerto Rico, we used eight known polymorphic microsatellite loci. Results In Puerto Rico, gAHB population does not show any genetic structure (Fst = 0.0783), and is best described as one honey bee population, product of hybridization of AHB and EHB. The genetic variability in this Africanized population was similar to that reported in studies from Texas. We observed that European private allele frequencies are high in all but one locus. This contrasts with mainland Africanized populations, where European allele frequencies are diminished. Two loci with European private alleles, one on Linkage Group 7, known to carry two known defensiveness Quantitative Trait Loci (QTLs), and the other on Linkage Group 1, known to carry three functionally studied genes and 11 candidate genes associated with Varroa resistance mechanisms were respectively, significantly greater or lower in European allele frequency than the other loci with European private alleles. Conclusions Genetic structure of Puerto Rico gAHB differs from mainland AHB populations, probably representing evolutionary processes on the island. PMID:23915100

  5. Substance Abuse in Rural African-American Populations.

    ERIC Educational Resources Information Center

    Dawkins, Marvin P.; Williams, Mary M.

    More research into illicit substance abuse in rural African-American communities is needed. The existing literature indicates that patterns of use for licit substances (alcohol and cigarettes) are either similar for rural Blacks and Whites or lower for Blacks. However, the negative health and social consequences of smoking and abusive drinking are…

  6. Religiosity and Risky Sexual Behaviors among an African American Church-based Population

    PubMed Central

    Hawes, Starlyn M.; Berkley-Patton, Jannette Y.

    2014-01-01

    African Americans are disproportionately burdened by STDs and HIV in the US. This study examined the relationships between demographics, religiosity, and sexual risk behaviors among 255 adult African American church-based participants. Although participants were highly religious, they reported an average of seven lifetime sex partners and most inconsistently used condoms. Several demographic variables and religiosity significantly predicted lifetime HIV-related risk factors. Taken together, findings indicated that this population is at risk for HIV. Future research should continue to identify correlates of risky sexual behavior among African American parishioners to facilitate the development of HIV risk reduction interventions in their church settings. PMID:23054481

  7. Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

    PubMed

    Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

    2017-01-01

    The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.

  8. The Third African Population Conference adopts the draft Dakar / Ngor Declaration on Population, Family and Sustainable Development.

    PubMed

    1993-01-01

    The 3rd African Population Conference, held in Dakar, Senegal, December 7-12, 1992, adopted the draft Dakar/Ngor Declaration on Population, Family and Sustainable Development in preparation for the 1994 Cairo International Conference on Population and Development. The meeting was attended by 50 member states and many observers from various United Nations Organizations and nongovernmental organizations (NGOs). The Conference reviewed the lessons learned from the implementation of the Kilimanjaro Program of Action on Population (KAP), which had been adopted in 1984. The draft Declaration focused on the following areas: a) population, sustained economic growth, and sustainable development; family; fertility and family planning; mortality, morbidity and AIDS; urbanization and migration; refugees and displaced persons; women in development; children; data collection and analysis, information dissemination, training and research; information, education and communication; b) the role of: private and nongovernmental organizations; the subregional and regional groupings; the World Bank and relevant organizations of the United Nations System; and the international community; c) resource mobilization; and d) implementation of the Declaration. African countries should integrate population policies so as to reduce population growth from the present rate of 3.0% per annum to 2.5% by the year 2000 and to 2% by the year 2010. Environmental issues and food security were given special attention. The targets set on the contraceptive prevalence rate for Africa were to reach 20% by the year 2000 and 40% by the year 2010. The following targets were to be attained by the year 2000: life expectancy in Africa at least 55 years; an infant mortality rate of less than 50 per 1000 live births; childhood mortality rate of 70 or less. Programs to prevent AIDS were also stressed. The Declaration called on UN organizations, the World Bank, the Organization of African Unity, and the African

  9. Breakfast habits of adolescents in for South African populations.

    PubMed

    Walker, A R; Walker, B F; Jones, J; Ncongwane, J

    1982-10-01

    Breakfast habits by using questionnaires, were established in a total of 4717 South African pupils of 16 to 18 yr. In the groups of rural and urban Black, Indian, European-African-Malay, and white pupils studied, respective proportions who had no solid breakfast (both sexes combined) were approximately 21, 19, 13, 13, and 14%. Proportions who had only porridge or bread (or toast) plus drink were 77, 73, 61, 71, and 56%. Such breakfast provided ranges of means of 223 to 345 kcal, 9 to 14 g protein, 7 to 18 g fat, 51 to 185 mg calcium, and 3.2 to 5.1 mg iron. Proportions who had a cooked breakfast (including egg, meat, fish), eaten with or without a cereal food, were 1, 4, 17, 8, and 29%. Such meals contributed means of 495 to 704 kcal, 11 to 26 g protein, 24 to 39 g fat, 110 to 225 mg calcium, and 3.9 to 5.5 mg iron. In the South African groups studied, the issue of breakfast or no breakfast had no clear-cut bearing on weight, height, class position, or frequency of absence from school. The degree by which, in a given community, nutrition in general and breakfast in particular, regulates health and/or academic performance, needs proper research in prospective studies.

  10. Complex population structure in African village dogs and its implications for inferring dog domestication history.

    PubMed

    Boyko, Adam R; Boyko, Ryan H; Boyko, Corin M; Parker, Heidi G; Castelhano, Marta; Corey, Liz; Degenhardt, Jeremiah D; Auton, Adam; Hedimbi, Marius; Kityo, Robert; Ostrander, Elaine A; Schoenebeck, Jeffrey; Todhunter, Rory J; Jones, Paul; Bustamante, Carlos D

    2009-08-18

    High genetic diversity of East Asian village dogs has recently been used to argue for an East Asian origin of the domestic dog. However, global village dog genetic diversity and the extent to which semiferal village dogs represent distinct, indigenous populations instead of admixtures of various dog breeds has not been quantified. Understanding these issues is critical to properly reconstructing the timing, number, and locations of dog domestication. To address these questions, we sampled 318 village dogs from 7 regions in Egypt, Uganda, and Namibia, measuring genetic diversity >680 bp of the mitochondrial D-loop, 300 SNPs, and 89 microsatellite markers. We also analyzed breed dogs, including putatively African breeds (Afghan hounds, Basenjis, Pharaoh hounds, Rhodesian ridgebacks, and Salukis), Puerto Rican street dogs, and mixed breed dogs from the United States. Village dogs from most African regions appear genetically distinct from non-native breed and mixed-breed dogs, although some individuals cluster genetically with Puerto Rican dogs or United States breed mixes instead of with neighboring village dogs. Thus, African village dogs are a mosaic of indigenous dogs descended from early migrants to Africa, and non-native, breed-admixed individuals. Among putatively African breeds, Pharaoh hounds, and Rhodesian ridgebacks clustered with non-native rather than indigenous African dogs, suggesting they have predominantly non-African origins. Surprisingly, we find similar mtDNA haplotype diversity in African and East Asian village dogs, potentially calling into question the hypothesis of an East Asian origin for dog domestication.

  11. Complex population structure in African village dogs and its implications for inferring dog domestication history

    PubMed Central

    Boyko, Adam R.; Boyko, Ryan H.; Boyko, Corin M.; Parker, Heidi G.; Castelhano, Marta; Corey, Liz; Degenhardt, Jeremiah D.; Auton, Adam; Hedimbi, Marius; Kityo, Robert; Ostrander, Elaine A.; Schoenebeck, Jeffrey; Todhunter, Rory J.; Jones, Paul; Bustamante, Carlos D.

    2009-01-01

    High genetic diversity of East Asian village dogs has recently been used to argue for an East Asian origin of the domestic dog. However, global village dog genetic diversity and the extent to which semiferal village dogs represent distinct, indigenous populations instead of admixtures of various dog breeds has not been quantified. Understanding these issues is critical to properly reconstructing the timing, number, and locations of dog domestication. To address these questions, we sampled 318 village dogs from 7 regions in Egypt, Uganda, and Namibia, measuring genetic diversity >680 bp of the mitochondrial D-loop, 300 SNPs, and 89 microsatellite markers. We also analyzed breed dogs, including putatively African breeds (Afghan hounds, Basenjis, Pharaoh hounds, Rhodesian ridgebacks, and Salukis), Puerto Rican street dogs, and mixed breed dogs from the United States. Village dogs from most African regions appear genetically distinct from non-native breed and mixed-breed dogs, although some individuals cluster genetically with Puerto Rican dogs or United States breed mixes instead of with neighboring village dogs. Thus, African village dogs are a mosaic of indigenous dogs descended from early migrants to Africa, and non-native, breed-admixed individuals. Among putatively African breeds, Pharaoh hounds, and Rhodesian ridgebacks clustered with non-native rather than indigenous African dogs, suggesting they have predominantly non-African origins. Surprisingly, we find similar mtDNA haplotype diversity in African and East Asian village dogs, potentially calling into question the hypothesis of an East Asian origin for dog domestication. PMID:19666600

  12. Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-02

    Gene conversion results in the nonreciprocal transfer of genetic information between two recombining sequences, and there is evidence that this process is biased toward G and C alleles. However, the strength of GC-biased gene conversion (gBGC) in human populations and its effects on hereditary disease have yet to be assessed on a genomic scale. Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data sets. We find that genetic distances (FST and population branch statistics) are modified by gBGC. In addition, the site frequency spectrum is left-shifted when ancestral alleles are favored by gBGC and right-shifted when derived alleles are favored by gBGC. Allele frequency shifts due to gBGC mimic the effects of natural selection. As expected, these effects are strongest in high-recombination regions of the human genome. By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb ≈ 0.05 to 0.09. We also find that derived alleles favored by gBGC are much more likely to be homozygous than derived alleles at unbiased SNPs (+42.2% to 62.8%). This results in a curse of the converted, whereby gBGC causes substantial increases in hereditary disease risks. Taken together, our findings reveal that GC-biased gene conversion has important population genetic and public health implications.

  13. Working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history

    PubMed Central

    Scheinfeldt, Laura B.; Soi, Sameer; Tishkoff, Sarah A.

    2010-01-01

    Although Africa is the origin of modern humans, the pattern and distribution of genetic variation and correlations with cultural and linguistic diversity in Africa have been understudied. Recent advances in genomic technology, however, have led to genomewide studies of African samples. In this article, we discuss genetic variation in African populations contextualized with what is known about archaeological and linguistic variation. What emerges from this review is the importance of using independent lines of evidence in the interpretation of genetic and genomic data in the reconstruction of past population histories. PMID:20445100

  14. Genetic structure of a unique admixed population: implications for medical research.

    PubMed

    Patterson, Nick; Petersen, Desiree C; van der Ross, Richard E; Sudoyo, Herawati; Glashoff, Richard H; Marzuki, Sangkot; Reich, David; Hayes, Vanessa M

    2010-02-01

    STATEMENT: In naming population groups, we think a chief aim is to use terms that the group members use themselves, or find familiar and comfortable. The terms used in this manuscript to describe populations are as historically correct as possible and are chosen so as not to offend any population group. Two of the authors (DCP and REvdR) belong to the Coloured population, with one of the authors (REvdR) having contributed extensively to current literature on the history of the Coloured people of South Africa and served as Vice-President of the South African Institute of Race Relations. According to the 2001 South African census (http://www.statssa.gov.za/census01/HTML/CInBrief/CIB2001.pdf), "Statistics South Africa continues to classify people by population group, in order to monitor progress in moving away from the apartheid-based discrimination of the past. However, membership of a population group is now based on self-perception and self-classification, not on a legal definition. Five options were provided on the questionnaire, Black African, Coloured, Indian or Asian, White and Other. Responses in the category 'Other' were very few and were therefore imputed". We have elected to use the term Bushmen rather than San to refer to the hunter-gatherer people of Southern Africa. Although they have no collective name for themselves, this decision was based on the term Bushmen (or Bossiesman) being the more familiar to the communities themselves, while the term San is the more accepted academic classification. Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study, we describe the complex genetic substructure of a unique and recently admixed population arising approximately 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900 000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected

  15. Estimation of the ancestral effective population sizes of African great apes under different selection regimes.

    PubMed

    Schrago, Carlos G

    2014-08-01

    Reliable estimates of ancestral effective population sizes are necessary to unveil the population-level phenomena that shaped the phylogeny and molecular evolution of the African great apes. Although several methods have previously been applied to infer ancestral effective population sizes, an analysis of the influence of the selective regime on the estimates of ancestral demography has not been thoroughly conducted. In this study, three independent data sets under different selective regimes were used were composed to tackle this issue. The results showed that selection had a significant impact on the estimates of ancestral effective population sizes of the African great apes. The inference of the ancestral demography of African great apes was affected by the selection regime. The effects, however, were not homogeneous along the ancestral populations of great apes. The effective population size of the ancestor of humans and chimpanzees was more impacted by the selection regime when compared to the same parameter in the ancestor of humans, chimpanzees and gorillas. Because the selection regime influenced the estimates of ancestral effective population size, it is reasonable to assume that a portion of the discrepancy found in previous studies that inferred the ancestral effective population size may be attributable to the differential action of selection on the genes sampled.

  16. Modifiable determinants of healthcare utilization within the African-American population.

    PubMed Central

    Rust, George; Fryer, George E.; Phillips, Robert L.; Daniels, Elvan; Strothers, Harry; Satcher, David

    2004-01-01

    BACKGROUND: Significant health disparities directly affect the African-American population. Most previous studies of disparities in access to and utilization of healthcare have focused on black-white differences rather than focusing on "within-group" analysis of African Americans. OBJECTIVE: To tease out the differential effects of modifiable risk factors (such as health insurance, usual source of care, and poverty) from personal characteristics (age, gender, rural residence) on healthcare utilization within the African-American population. METHODS: Secondary data analysis of 3462 records from African-American respondents to the 1999 Medical Expenditure Panel Survey (MEPS) Household File, a nationally representative survey of the civilian, noninstitutionalized U.S. population in 1999. RESULTS: We found significant variation in the number of office visits, outpatient clinic visits, hospital discharges, days hospitalized, and fills of prescribed medication among 3462 African-American respondents who represent a U.S. population of 36,538,639 persons. Personal nonmodifiable characteristics such as age and gender were significantly related to healthcare utilization. Poverty and rural residence were also significantly correlated, but the strongest modifiable predictors of healthcare utilization for Afrcan-American persons in 1999 were whether or not individuals had health insurance and/or a usual source of care. Emergency department visits were the only form of care that showed remarkably little variation based on these modifiable risk factors. CONCLUSIONS: The three modifiable factors of poverty, uninsurance, and having a primary care medical home have a dramatic effect on patterns of care for African-American patients and could be independently targeted for intervention. PMID:15481745

  17. Sex estimation using diagonal diameter measurements of molar teeth in African American populations.

    PubMed

    Peckmann, Tanya R; Meek, Susan; Dilkie, Natasha; Mussett, Michelle

    2015-11-01

    Teeth are often recovered in forensic cases due to their postmortem longevity. The goal of the present research was to investigate the degree of sexual dimorphism in the permanent molars of African Americans using crown and cervical diagonal diameters. Discriminant functions developed from a modern Greek population were tested for accuracy of sex estimation in an African American population. One hundred and three (53 males and 50 females) individuals ranging in age from 16 years to 66 years old were used from the Robert J. Terry Anatomical Skeletal Collection. Four diagonal diameter measurements were taken for each of the left mandibular and maxillary molars: mesiobuccal-distolingual crown diameter, mesiolingual-distobuccal crown diameter, mesiobuccal-distolingual cervical diameter, and mesiolingual-distobuccal cervical diameter. The overall percentage of accuracy of the modern Greek discriminant functions when applied to the African American sample was between 53.8% and 63.6%. Males were more accurately classified (93.6%-100%) than females (0%-18.2%). The African American population specific direct discriminant functions showed accuracy rates from 72.6% to 100% for the original data and 40%-72.3% for the cross-validated data. The African American stepwise discriminant functions showed accuracy rates from 63.9% to 77.6% for the original and cross-validated data. Comparisons to other populations were made. The results suggest that, in teeth, there is variation in the degree of sexual dimorphism between populations and discriminant functions for sex estimation in dentition are population specific.

  18. Gene-centric meta-analysis of lipid traits in African, East Asian and Hispanic populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Meta-analyses of European populations has successfully identified genetic variants in over 100 loci associated with lipid levels, but our knowledge in other ethnicities remains limited. To address this, we performed dense genotyping of circa 2,000 candidate genes in 7,657 African Americans, 1,315 Hi...

  19. Temporal pattern of africanization in a feral honeybee population from Texas inferred from mitochondrial DNA.

    PubMed

    Pinto, M Alice; Rubink, William L; Coulson, Robert N; Patton, John C; Johnston, J Spencer

    2004-05-01

    The invasion of Africanized honeybees (Apis mellifera L.) in the Americas provides a window of opportunity to study the dynamics of secondary contact of subspecies of bees that evolved in allopatry in ecologically distinctive habitats of the Old World. We report here the results of an 11-year mitochondrial DNA survey of a feral honeybee population from southern United States (Texas). The mitochondrial haplotype (mitotype) frequencies changed radically during the 11-year study period. Prior to immigration of Africanized honeybees, the resident population was essentially of eastern and western European maternal ancestry. Three years after detection of the first Africanized swarm there was a mitotype turnover in the population from predominantly eastern European to predominantly A. m. scutellata (ancestor of Africanized honeybees). This remarkable change in the mitotype composition coincided with arrival of the parasitic mite Varroa destructor, which was likely responsible for severe losses experienced by colonies of European ancestry. From 1997 onward the population stabilized with most colonies of A. m. scutellata maternal origin.

  20. Breast cancer incidence and mortality in a Caribbean population: comparisons with African-Americans.

    PubMed

    Hennis, Anselm J; Hambleton, Ian R; Wu, Suh-Yuh; Leske, Maria Cristina; Nemesure, Barbara

    2009-01-15

    We describe breast cancer incidence and mortality in the predominantly African-origin population of Barbados, which shares an ancestral origin with African-Americans. Age-standardized incidence rates were calculated from histologically confirmed breast cancer cases identified during a 45-month period (July 2002-March 2006). Mortality rates were estimated from death registrations over 10-years starting January 1995. There were 396 incident cases of breast cancer for an incidence rate of 78.1 (95% confidence interval (CI) 70.5-86.3), standardized to the US population. Breast cancer incidence in African-Americans between 2000 and 2004 was 143.7 (142.0-145.5) per 100,000. Incidence peaked at 226.6 (174.5-289.4) per 100,000 among Barbadian women aged 50-54 years, and declined thereafter, a pattern in marked contrast to trends in African-American women, whose rates continued to increase to a peak of 483.5 per 100,000 in those aged 75-79 years. Incidence rate ratios comparing Barbadian and African-American women showed no statistically significant differences among women aged>or=55 years (pAfrican-American women may suggest a greater contribution from genetic factors in younger women, and from environmental factors in older women. Studies in intermediate risk populations, such as Barbados, may assist the understanding of racial disparities in breast cancer.

  1. Identification of a novel locus associated with skin colour in African-admixed populations

    PubMed Central

    Hernandez-Pacheco, Natalia; Flores, Carlos; Alonso, Santos; Eng, Celeste; Mak, Angel C. Y.; Hunstman, Scott; Hu, Donglei; White, Marquitta J.; Oh, Sam S.; Meade, Kelley; Farber, Harold J.; Avila, Pedro C.; Serebrisky, Denise; Thyne, Shannon M.; Brigino-Buenaventura, Emerita; Rodriguez-Cintron, William; Sen, Saunak; Kumar, Rajesh; Lenoir, Michael; Rodriguez-Santana, Jose R.; Burchard, Esteban G.; Pino-Yanes, Maria

    2017-01-01

    Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10−5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10−14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10−10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10−9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation. PMID:28300201

  2. African genetic ancestry is associated with a protective effect on Dengue severity in colombian populations.

    PubMed

    Chacón-Duque, Juan Camilo; Adhikari, Kaustubh; Avendaño, Efren; Campo, Omer; Ramirez, Ruth; Rojas, Winston; Ruiz-Linares, Andrés; Restrepo, Berta Nelly; Bedoya, Gabriel

    2014-10-01

    The wide variation in severity displayed during Dengue Virus (DENV) infection may be influenced by host susceptibility. In several epidemiological approaches, differences in disease outcomes have been found between some ethnic groups, suggesting that human genetic background has an important role in disease severity. In the Caribbean, It has been reported that populations of African descent present considerable less frequency of severe forms compared with Mestizo and White self-reported groups. Admixed populations offer advantages for genetic epidemiology studies due to variation and distribution of alleles, such as those involved in disease susceptibility, as well to provide explanations of individual variability in clinical outcomes. The current study analysed three Colombian populations, which like most of Latin American populations, are made up of the product of complex admixture processes between European, Native American and African ancestors; having as a main goal to assess the effect of genetic ancestry, estimated with 30 Ancestry Informative Markers (AIMs), on DENV infection severity. We found that African ancestry has a protective effect against severe outcomes under several systems of clinical classification: Severe Dengue (OR: 0.963 for every 1% increase in African ancestry, 95% confidence interval (0.934-0.993), p-value: 0.016), Dengue Haemorrhagic Fever (OR: 0.969, 95% CI (0.947-0.991), p-value: 0.006), and occurrence of haemorrhages (OR: 0.971, 95% CI (0.952-0.989), p-value: 0.002). Conversely, decrease from 100% to 0% African ancestry significantly increases the chance of severe outcomes: OR is 44-fold for Severe Dengue, 24-fold for Dengue Haemorrhagic Fever, and 20-fold for occurrence of haemorrhages. Furthermore, several warning signs also showed statistically significant association given more evidences in specific stages of DENV infection. These results provide consistent evidence in order to infer statistical models providing a framework for

  3. Strategies for successful conduct of research with low-income African American populations.

    PubMed

    Adderley-Kelly, Beatrice; Green, Pauline M

    2005-01-01

    Health disparities among racial and ethnic minorities are associated with poor health outcomes. African Americans bear a disproportionate amount of the burden of health disparities. The elimination of health disparities among the nation's racial and ethnic groups requires immediate action that the health care community cannot accomplish in isolation. Eliminating health disparities calls for new and non-traditional partnerships across diverse sectors of the community that include research initiatives using culturally competent and participatory action methodologies. While there is much evidence documenting health disparities in racial and ethnic groups, there is little evidence of successful interventions that address health disparities in African Americans. Furthermore, there is little direction for successful strategies for recruiting African Americans for participation in health disparities research. This article addresses important factors to consider when conducting research with low income African Americans based on the authors' research experience in health promotion and cancer detection and prevention. Strategies for successful conduct of research with low income African American populations are offered.

  4. Role of MYH9 and APOL1 in African and non-African populations with Lupus Nephritis

    PubMed Central

    Lin, Chee Paul; Adrianto, Indra; Lessard, Christopher J.; Kelly, Jennifer A.; Kaufman, Kenneth M.; Guthridge, Joel M.; Freedman, Barry I.; Anaya, Juan-Manuel; Alarcón-Riquelme, Marta E.; Pons-Estel, Bernardo A.; Martin, Javier; Glenn, Stuart; Adler, Adam; Bae, Sang-Cheol; Park, So-Yeon; Bang, So-Young; Song, Yeong-Wook; Boackle, Susan A.; Brown, Elizabeth E.; Edberg, Jeffrey C.; Alarcón, Graciela S.; Petri, Michelle A.; Criswell, Lindsey A.; Ramsey-Goldman, Rosalind; Reveille, John D.; Vila, Luis M.; Gilkeson, Gary S.; Kamen, Diane L.; Ziegler, Julie; Jacob, Chaim O.; Rasmussen, Astrid; James, Judith A.; Kimberly, Robert P.; Merrill, Joan T.; Niewold, Timothy B.; Scofield, R. Hal; Stevens, Anne M.; Tsao, Betty P.; Vyse, Timothy J.; Langefeld, Carl D.; Moser, Kathy L.; Harley, John B.; Gaffney, Patrick M.; Montgomery, Courtney G.

    2012-01-01

    Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by autoantibody production and organ damage. Lupus nephritis (LN) is one of the most severe manifestations of SLE. Multiple studies reported associations between renal diseases and variants in the non-muscle myosin heavy chain 9 (MYH9) and the neighboring apolipoprotein L 1 (APOL1) genes. We evaluated 167 variants spanning MYH9 for association with LN in a multiethnic sample. The two previously identified risk variants in APOL1 were also tested for association with LN in European-Americans (EAs) (N = 579) and African-Americans (AAs) (N = 407). Multiple peaks of association exceeding a Bonferroni corrected p-value of p < 2.03 × 10−3 were observed between LN and MYH9 in EAs (N=4620), with the most pronounced association at rs2157257 (p = 4.7 × 10−4; odds ratio [OR]=1.205). A modest effect with MYH9 was also detected in Gullah (rs8136069, p = 0.0019, OR = 2.304). No association between LN and MYH9 was found in AAs, Asians, Amerindians or Hispanics. This study provides the first investigation of MYH9 in LN in non-Africans and of APOL1 in LN in any population and presents novel insight into the potential role of MYH9 in LN in EAs. PMID:22189356

  5. Extensive Copy Number Variations in Admixed Indian Population of African Ancestry: Potential Involvement in Adaptation

    PubMed Central

    Dash, Debasis; Mukerji, Mitali

    2014-01-01

    Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation. PMID:25398783

  6. Molecular Diagnosis of Inherited Retinal Diseases in Indigenous African Populations by Whole-Exome Sequencing

    PubMed Central

    Roberts, Lisa; Ratnapriya, Rinki; du Plessis, Morné; Chaitankar, Vijender; Ramesar, Raj S.; Swaroop, Anand

    2016-01-01

    Purpose A majority of genes associated with inherited retinal diseases (IRDs) have been identified in patients of European origin. Indigenous African populations exhibit rich genomic diversity, and evaluation of reported genetic mutations has yielded low returns so far. Our goal was to perform whole-exome sequencing (WES) to examine variants in known IRD genes in underrepresented African cohorts. Methods Whole-exome sequencing was performed on 56 samples from 16 families with diverse IRD phenotypes that had remained undiagnosed after screening for known mutations using genotyping-based microarrays (Asper Ophthalmics). Variants in reported IRD genes were identified using WES and validated by Sanger sequencing. Custom TaqMan assays were used to screen for identified mutations in 193 unrelated indigenous Africans with IRDs. Results A total of 3494 variants were identified in 217 known IRD genes, leading to the identification of seven different mutations (including six novel) in six genes (RHO, PRPF3, PRPF31, ABCA4, CERKL, and PDE6B) in six distinct families. TaqMan screening in additional probands revealed identical homozygous CERKL and PDE6B variants in four more patients. Conclusions This is the first report of WES of patients with IRDs in indigenous African populations. Our study identified genetic defects in almost 40% of the families analyzed, significantly enhancing the molecular diagnosis of IRD in South Africa. Thus, WES of understudied cohorts seems to present an effective strategy for determining novel mutations in heterogeneous retinal diseases. PMID:27898983

  7. Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations

    PubMed Central

    Montinaro, Francesco; Busby, George B. J.; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L.; Capelli, Cristian

    2017-01-01

    The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries. PMID:27838627

  8. The role of ancestry in TB susceptibility of an admixed South African population.

    PubMed

    Daya, Michelle; van der Merwe, Lize; van Helden, Paul D; Möller, Marlo; Hoal, Eileen G

    2014-07-01

    Genetic susceptibility to tuberculosis (TB) has been well established and this, taken together with variation in susceptibility observed between different geographic and ethnic populations, implies that susceptibility to TB may in part be affected by ethnicity. In a previous genome-wide TB case-control study (642 cases and 91 controls) of the admixed South African Coloured (SAC) population, we found a positive correlation between African San ancestry and TB susceptibility, and negative correlations with European and Asian ancestries. Since genome-wide data was available for only a small number of controls in the previous study, we endeavored to validate this finding by genotyping a panel of ancestry informative markers (AIMs) in additional individuals, yielding a data set of 918 cases and 507 controls. Ancestry proportions were estimated using the AIMs for each of the source populations of the SAC (African San, African non-San, European, South Asian and East Asian). Using logistic regression models to test for association between TB and ancestry, we confirmed the substantial effect of ancestry on TB susceptibility. We also investigated the effect of adjusting for ancestry in candidate gene TB association studies of the SAC. We report a polymorphism that is no longer significantly associated with TB after adjustment for ancestry, a polymorphism that is significantly associated with TB only after adjustment for ancestry, and a polymorphism where the association significance remains unchanged. By comparing the allele frequencies of these polymorphisms in the source populations of the SAC, we demonstrate that association results are likely to be affected by adjustment for ancestry if allele frequencies differ markedly in the source populations of the SAC.

  9. Estimating African American admixture proportions by use of population-specific alleles.

    PubMed Central

    Parra, E J; Marcini, A; Akey, J; Martinson, J; Batzer, M A; Cooper, R; Forrester, T; Allison, D B; Deka, R; Ferrell, R E; Shriver, M D

    1998-01-01

    We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philadelphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine autosomal DNA markers. These markers either are population-specific or show frequency differences >45% between the parental populations and are thus especially informative for admixture. European genetic ancestry ranged from 6.8% (Jamaica) to 22.5% (New Orleans). The unique utility of these markers is reflected in the low variance associated with these admixture estimates (SEM 1.3%-2.7%). We also estimated the male and female European contribution to African Americans, on the basis of informative mtDNA (haplogroups H and L) and Y Alu polymorphic markers. Results indicate a sex-biased gene flow from Europeans, the male contribution being substantially greater than the female contribution. mtDNA haplogroups analysis shows no evidence of a significant maternal Amerindian contribution to any of the 10 populations. We detected significant nonrandom association between two markers located 22 cM apart (FY-null and AT3), most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations. The strength of this association and the substantial genetic distance between FY and AT3 emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental populations. PMID:9837836

  10. Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans

    PubMed Central

    Taravella, Angela M.; Bustamante, Carlos D.; Sikora, Martin

    2017-01-01

    The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of positive selection in humans. Despite this, details of the timing and mode of selection at DARC remain poorly understood. Here, we use sequencing data from over 1,000 individuals in twenty-one human populations, as well as ancient human genomes, to perform a fine-scale investigation of the evolutionary history of DARC. We estimate the time to most recent common ancestor (TMRCA) of the most common FY*O haplotype to be 42 kya (95% CI: 34–49 kya). We infer the FY*O null mutation swept to fixation in Africa from standing variation with very low initial frequency (0.1%) and a selection coefficient of 0.043 (95% CI:0.011–0.18), which is among the strongest estimated in the human genome. We estimate the TMRCA of the FY*A mutation in non-Africans to be 57 kya (95% CI: 48–65 kya) and infer that, prior to the sweep of FY*O, all three alleles were segregating in Africa, as highly diverged populations from Asia and ≠Khomani San hunter-gatherers share the same FY*A haplotypes. We test multiple models of admixture that may account for this observation and reject recent Asian or European admixture as the cause. PMID:28282382

  11. No evidence for a large difference in ALS frequency in populations of African and European origin: a population based study in inner city London.

    PubMed

    Rojas-Garcia, Ricardo; Scott, Kirsten M; Roche, Jose Carlos; Scotton, William; Martin, Naomi; Janssen, Anna; Goldstein, Laura H; Leigh, P Nigel; Ellis, Cathy M; Shaw, Christopher E; Al-Chalabi, Ammar

    2012-01-01

    Abstract Previous studies have suggested a lower incidence of ALS in people of African origin. We used a population based register in an urban setting from inner city London postcodes where there is a large population of people of African ancestry to compare the frequency of ALS in people of European and African origin. Population statistics stratified by age, gender and ethnicity were obtained from the 2001 census. Incidence and prevalence were calculated in each ethnic group. Results showed that in a population of 683,194, of which 22% were of African ancestry, 88 individuals with ALS were identified over a seven-year period, including 14 people with African ancestry. The adjusted incidence in people of African ancestry was 1.35 per 100,000 person-years (95% CI 0.72-2.3) and in those of European ancestry 1.97 per 100,000 person-years (95% CI 1.55-2.48). In conclusion, in this small population based study we could not detect a difference in rates of ALS between people of African ancestry and those of European ancestry.

  12. Development and Validation of the Body Size Scale for Assessing Body Weight Perception in African Populations

    PubMed Central

    Cohen, Emmanuel; Bernard, Jonathan Y.; Ponty, Amandine; Ndao, Amadou; Amougou, Norbert; Saïd-Mohamed, Rihlat; Pasquet, Patrick

    2015-01-01

    Background The social valorisation of overweight in African populations could promote high-risk eating behaviours and therefore become a risk factor of obesity. However, existing scales to assess body image are usually not accurate enough to allow comparative studies of body weight perception in different African populations. This study aimed to develop and validate the Body Size Scale (BSS) to estimate African body weight perception. Methods Anthropometric measures of 80 Cameroonians and 81 Senegalese were used to evaluate three criteria of adiposity: body mass index (BMI), overall percentage of fat, and endomorphy (fat component of the somatotype). To develop the BSS, the participants were photographed in full face and profile positions. Models were selected for their representativeness of the wide variability in adiposity with a progressive increase along the scale. Then, for the validation protocol, participants self-administered the BSS to assess self-perceived current body size (CBS), desired body size (DBS) and provide a “body self-satisfaction index.” This protocol included construct validity, test-retest reliability and convergent validity and was carried out with three independent samples of respectively 201, 103 and 1115 Cameroonians. Results The BSS comprises two sex-specific scales of photos of 9 models each, and ordered by increasing adiposity. Most participants were able to correctly order the BSS by increasing adiposity, using three different words to define body size. Test-retest reliability was consistent in estimating CBS, DBS and the “body self-satisfaction index.” The CBS was highly correlated to the objective BMI, and two different indexes assessed with the BSS were consistent with declarations obtained in interviews. Conclusion The BSS is the first scale with photos of real African models taken in both full face and profile and representing a wide and representative variability in adiposity. The validation protocol proved its

  13. Review of studies on metabolic genes and cancer in populations of African descent

    PubMed Central

    Ragin, Camille C.; Langevin, Scott; Rubin, Scott; Taioli, Emanuela

    2010-01-01

    Genetic polymorphisms described for a number of enzymes involved in the metabolism of tobacco carcinogens and alcohol have been linked to increase cancer risk. Racial disparities in cancer between Whites and populations of African descent are well documented. In addition to differences in access to health care, both environment and genetic factors and their interaction may contribute to the increased cancer risk in minority populations. We reviewed the literature to identify case-control studies that included subjects of African descent. Meta analyses investigating the association of genetic polymorphisms in tobacco metabolic genes and cancer were performed. While several genes and cancers have been studied, only one or two studies per gene for each cancer site have been published, with the exception of breast (CYP1A1 and CYP1B1), lung (GSTM1, CYP1A1, and NQO1) and prostate (CYP3A4 A293G and CYP17). Marginal statistically significant associations were observed for CYP3A4 A293G and CYP17 5'UTR polymorphisms and prostate cancer. Our findings support the need for additional genetic association studies of breast, prostate and lung cancers that include a larger number of minority participants. Since incidence and mortality rates for these cancers rank highest among populations of African descent concentrated research in these areas are warranted. PMID:20027111

  14. A geometric morphometric approach to the quantification of population variation in sub-Saharan African crania.

    PubMed

    Franklin, Daniel; Cardini, Andrea; Oxnard, Charles E

    2010-01-01

    We report here on new data examining cranial variation in 18 modern human sub-Saharan African populations. Previously, we investigated variation within southern Africa; we now extend our analyses to include a series of Central, East, and West African crania, to further knowledge of the relationships between, and variation and regional morphological patterning in, those populations. The sample comprises 377 male individuals; the three-dimensional coordinates of 96 landmarks are analyzed using Procrustes-based methods. Interpopulation variation is examined by calculating shape distances between groups, which are compared using resampling statistics and parametric tests. Phenotypic variance, as a proxy for genetic variance, is measured and compared across populations. Principal components and cluster analyses are employed to explore relationships between the populations. Shape differences are visualized using three-dimensional rendered models. Observed disparity patterns imply a mix of differences and similarities across populations, with no apparent support for genetic bottlenecks, which is likely a consequence of migrations that may have influenced differences in cranial form; supporting data are found in recent molecular studies. The Pygmy sample had the most distinctive cranial morphology; characteristically small in size with marked prognathism. These features characterized, although less strongly, the neighboring Bateke, and are possibly related to similar selective pressures in conjunction with interbreeding. Small cranial size is also involved in the considerable distinctiveness of the San and Khoikhoi. The statistical procedures applied in this study afford a powerful and robust means of quantifying and visualizing the magnitude and pattern of cranial variation between sub-Saharan African populations.

  15. Child Abuse and the Eye in an African Population

    PubMed Central

    Adebayo, Modupe

    2017-01-01

    Purpose There is a paucity of data on child abuse and the eye in West Africa. Therefore, a need exists to determine the causes and circumstances surrounding these occurrences and their effects on the eye and vision in a pediatric population. Methods A 3-year study of consecutive cases of ocular features that presented to an eye clinic following a history suggestive of child abuse along with any associated eye injury was carried out. Socio-demographic characteristics were obtained, as were the presenting and posttreatment visual acuity, and a full clinical eye examination was also done. Results Fifty-six children with 56 affected eyes were examined. The male to female ratio was 1.8 : 1; the mean age was 8.25 ± 3.5 years; and the subjects were predominately primary school children 30 (53.6%). The most common ocular disorders were conjunctiva hyperemia (46.4%), corneal abrasion/ulcer (25.4%), hyphema/uveitis (42.9%), retinal detachment (7.1%), sclera rupture (7.1%), and globe perforation (21.4%). The intraocular pressure was raised in 17.9% of participants. Presenting versus posttreatment visual acuities showed normal vision in four (7.1%) vs. eighteen (32.1%), visual impairment in 12 (21.4%) vs. six (10.7%), severe visual impairment in 20 (35.7%) vs. 12 (21.4%), and blindness in 12 (21.4%) vs. 14 (25%), p < 0.001. The most common injurious agents were canes (25.0%) and sticks (17.9%). The people who inflicted the injuries were parents/relatives (uncles) in 35.7% of cases and the children themselves (accidents) in 21.4% of cases. Circumstances predisposing participants to eye injuries were child labor in 39.3% and beatings in 25.0%. Complications were cataracts (25.0%), corneal opacity (39.3%), and retinal detachment (7.1%). Conclusions Injuries commonly resulted from canes and sticks used during beatings, as well as from child labor, corporal punishment, accidents, and assaults. Legislation and laws need to be enacted to prevent negative psychosocial and economic

  16. Geometric morphometric study of population variation in indigenous southern African crania.

    PubMed

    Franklin, D; Freedman, L; Milne, N; Oxnard, C E

    2007-01-01

    Much of our understanding of population variation in southern Africa is derived from traditional morphometric research. In the search for new perspectives, this paper reports on new geometric morphometric data examining cranial variation in 12 modern human populations from southern Africa. In total, 298 male Bantu-speaking individuals were studied. In addition, a small Khoisan (Khoikhoi and San) series was also examined. The purpose of this study was to investigate Khoisan-Bantu morphological similarities and differences, and to examine variation within both the Bantu-speaking and Khoisan populations. The three-dimensional coordinates of 96 landmarks were analyzed, using the shape-analysis software morphologika. Interpopulation variation was examined by calculating Procrustes distances between groups; a cluster analysis was then used to summarize phenetic relationships. A principal components analysis explored the relationships between populations; shape differences were visualized and explored using three-dimensional rendered models, and further interpreted using thin-plate splines. Morphological differences are present within and between the crania of Bantu-speaking and Khoisan individuals. The Khoisan demonstrate features (e.g., a pentagonoid vault, more rounded forehead contour, and a small and less prognathic face) that clearly distinguish them from Bantu-speaking populations. Although southern African Bantu-speaking populations are clearly closely related, they show population-specific features (e.g., the crania of more southerly populations (Xhosa, Southern Sotho, and Zulu) are characteristically more brachycephalic and less prognathic). This study suggests that differential admixture with adjacent Khoisan peoples has contributed to diversity within southern African Bantu-speaking populations.

  17. Association studies in QTL regions linked to bovine trypanotolerance in a West African crossbred population.

    PubMed

    Dayo, G K; Gautier, M; Berthier, D; Poivey, J P; Sidibe, I; Bengaly, Z; Eggen, A; Boichard, D; Thevenon, S

    2012-04-01

    African animal trypanosomosis is a parasitic blood disease transmitted by tsetse flies and is widespread in sub-Saharan Africa. West African taurine breeds have the ability, known as trypanotolerance, to limit parasitaemia and anaemia and remain productive in enzootic areas. Several quantitative trait loci (QTL) underlying traits related to trypanotolerance have been identified in an experimentally infected F(2) population resulting from a cross between taurine and zebu cattle. Although this information is highly valuable, the QTL remain to be confirmed in populations subjected to natural conditions of infection, and the corresponding regions need to be refined. In our study, 360 West African cattle were phenotyped for the packed cell volume control under natural conditions of infection in south-western Burkina Faso. Phenotypes were assessed by analysing data from previous cattle monitored over 2 years in an area enzootic for trypanosomosis. We further genotyped for 64 microsatellite markers mapping within four previously reported QTL on BTA02, BTA04, BTA07 and BTA13. These data enabled us to estimate the heritability of the phenotype using the kinship matrix between individuals computed from genotyping data. Thus, depending on the estimators considered and the method used, the heritability of anaemia control ranged from 0.09 to 0.22. Finally, an analysis of association identified an allele of the MNB42 marker on BTA04 as being strongly associated with anaemia control, and a candidate gene, INHBA, as being close to that marker.

  18. Prevalence of sexual violence and posttraumatic stress disorder in an urban African-American population.

    PubMed

    Walsh, Kate; Koenen, Karestan C; Aiello, Allison E; Uddin, Monica; Galea, Sandro

    2014-12-01

    Sexual violence is prevalent nationally and contributes to psychopathology in the general population. Despite elevated traumatic event exposure among economically disadvantaged urban-dwelling African-Americans, there is insufficient information on lifetime sexual violence exposure and associated psychopathology in this population. In 2008-2009, 1,306 African-Americans from a Detroit household probability sample reported on lifetime rape and sexual assault and past-month and lifetime posttraumatic stress disorder (PTSD). Lifetime sexual violence prevalence was 26.3 % for women and 5.1 % for men. Relative to non-victims, sexual violence victims: reported more other traumatic events; had 4 times greater unadjusted odds of past-month and lifetime PTSD; had 1.6 times greater adjusted odds of lifetime PTSD only after controlling for other traumatic events. Sexual violence was associated with increased risk for lifetime PTSD and exposure to other traumas. Findings highlight a need to screen for sexual violence and PTSD among urban African-Americans.

  19. Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry

    PubMed Central

    Kessler, Michael D.; Yerges-Armstrong, Laura; Taub, Margaret A.; Shetty, Amol C.; Maloney, Kristin; Jeng, Linda Jo Bone; Ruczinski, Ingo; Levin, Albert M.; Williams, L. Keoki; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Boorgula, Meher Preethi; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Scott, Alan F.; Vergara, Candelaria; Gao, Jingjing; Hu, Yijuan; Johnston, Henry Richard; Qin, Zhaohui S.; Padhukasahasram, Badri; Dunston, Georgia M.; Faruque, Mezbah U.; Kenny, Eimear E.; Gietzen, Kimberly; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-YounA; Kumar, Rajesh; Schleimer, Robert; Bustamante, Carlos; De La Vega, Francisco M.; Gignoux, Chris R.; Shringarpure, Suyash S.; Musharoff, Shaila; Wojcik, Genevieve; Burchard, Esteban G.; Eng, Celeste; Gourraud, Pierre-Antoine; Hernandez, Ryan D.; Lizee, Antoine; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O.; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Abecasis, Goncalo; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Pissamai, Maul R. N.; Trevor, Maul R. N.; Watson, Harold; Araujo, Maria Ilma; Oliveira, Ricardo Riccio; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Herrera-Paz, Edwin Francisco; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Vasquez, Olga Marina; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria; O'Connor, Timothy D.

    2016-01-01

    To characterize the extent and impact of ancestry-related biases in precision genomic medicine, we use 642 whole-genome sequences from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) project to evaluate typical filters and databases. We find significant correlations between estimated African ancestry proportions and the number of variants per individual in all variant classification sets but one. The source of these correlations is highlighted in more detail by looking at the interaction between filtering criteria and the ClinVar and Human Gene Mutation databases. ClinVar's correlation, representing African ancestry-related bias, has changed over time amidst monthly updates, with the most extreme switch happening between March and April of 2014 (r=0.733 to r=−0.683). We identify 68 SNPs as the major drivers of this change in correlation. As long as ancestry-related bias when using these clinical databases is minimally recognized, the genetics community will face challenges with implementation, interpretation and cost-effectiveness when treating minority populations. PMID:27725664

  20. Inferences of demography and selection in an African population of Drosophila melanogaster.

    PubMed

    Singh, Nadia D; Jensen, Jeffrey D; Clark, Andrew G; Aquadro, Charles F

    2013-01-01

    It remains a central problem in population genetics to infer the past action of natural selection, and these inferences pose a challenge because demographic events will also substantially affect patterns of polymorphism and divergence. Thus it is imperative to explicitly model the underlying demographic history of the population whenever making inferences about natural selection. In light of the considerable interest in adaptation in African populations of Drosophila melanogaster, which are considered ancestral to the species, we generated a large polymorphism data set representing 2.1 Mb from each of 20 individuals from a Ugandan population of D. melanogaster. In contrast to previous inferences of a simple population expansion in eastern Africa, our demographic modeling of this ancestral population reveals a strong signature of a population bottleneck followed by population expansion, which has significant implications for future demographic modeling of derived populations of this species. Taking this more complex underlying demographic history into account, we also estimate a mean X-linked region-wide rate of adaptation of 6 × 10(-11)/site/generation and a mean selection coefficient of beneficial mutations of 0.0009. These inferences regarding the rate and strength of selection are largely consistent with most other estimates from D. melanogaster and indicate a relatively high rate of adaptation driven by weakly beneficial mutations.

  1. Large-Scale Selective Sweep among Segregation Distorter Chromosomes in African Populations of Drosophila melanogaster

    PubMed Central

    Presgraves, Daven C.; Gérard, Pierre R.; Cherukuri, Anjuli; Lyttle, Terrence W.

    2009-01-01

    Segregation Distorter (SD) is a selfish, coadapted gene complex on chromosome 2 of Drosophila melanogaster that strongly distorts Mendelian transmission; heterozygous SD/SD + males sire almost exclusively SD-bearing progeny. Fifty years of genetic, molecular, and theory work have made SD one of the best-characterized meiotic drive systems, but surprisingly the details of its evolutionary origins and population dynamics remain unclear. Earlier analyses suggested that the SD system arose recently in the Mediterranean basin and then spread to a low, stable equilibrium frequency (1–5%) in most natural populations worldwide. In this report, we show, first, that SD chromosomes occur in populations in sub-Saharan Africa, the ancestral range of D. melanogaster, at a similarly low frequency (∼2%), providing evidence for the robustness of its equilibrium frequency but raising doubts about the Mediterranean-origins hypothesis. Second, our genetic analyses reveal two kinds of SD chromosomes in Africa: inversion-free SD chromosomes with little or no transmission advantage; and an African-endemic inversion-bearing SD chromosome, SD-Mal, with a perfect transmission advantage. Third, our population genetic analyses show that SD-Mal chromosomes swept across the African continent very recently, causing linkage disequilibrium and an absence of variability over 39% of the length of the second chromosome. Thus, despite a seemingly stable equilibrium frequency, SD chromosomes continue to evolve, to compete with one another, or evade suppressors in the genome. PMID:19412335

  2. High genetic connectivity among estuarine populations of the riverbream Acanthopagrus vagus along the southern African coast

    NASA Astrophysics Data System (ADS)

    Oosthuizen, Carel J.; Cowley, Paul D.; Kyle, Scotty R.; Bloomer, Paulette

    2016-12-01

    Physical and/or physiological constraints are assumed to isolate fish populations confined to or dependent on estuarine habitats. Strong isolation by distance is thus expected to affect connectivity. Such structuring has important implications for sustainable utilisation and replenishment of estuarine stocks that are heavily exploited. Here we present a preliminary investigation of the phylogenetic relationships of the riverbream (Acanthopagrus species) along the southern African coast and the geographic genetic structure of what appears to be a locally endemic species or lineage. Mitochondrial DNA (mtDNA) cytochrome b sequences support the notion that the species occurring along the southern African coast is A. vagus and not A. berda as previously thought. Yet, the taxonomy of this widespread Indo-West Pacific species or species-complex requires more in-depth investigation. No genetic differentiation was detected among estuarine populations of A. vagus based on the analyses of mtDNA ND2 gene sequences and 10 polymorphic nuclear microsatellite markers. The star-like genealogy and statistical analyses are consistent with a recent population expansion event. Spatial analyses of microsatellite genotypes fail to reject the null hypothesis of panmixia, indicative of a recent population expansion or ongoing gene flow between different estuaries. The northern localities were identified as containing most of the observed variation. This study not only provides insight into the phylogenetic relationship of A. vagus relative to other Acanthopagrus species but also sheds light on the demographic history and contemporary gene flow of the species.

  3. Evaluation of microsatellite markers for populations studies and forensic identification of African lions (Panthera leo).

    PubMed

    Miller, Susan M; Harper, Cindy K; Bloomer, Paulette; Hofmeyr, Jennifer; Funston, Paul J

    2014-01-01

    The South African lion (Panthera leo) population is highly fragmented. One-third of its wild lions occur in small (<1000 km(2)) reserves. These lions were reintroduced from other areas of the species' historical range. Management practices on these reserves have not prioritized genetic provenance or heterozygosity. These trends potentially constrain the conservation value of these lions. To ensure the best management and long-term survival of these subpopulations as a viable collective population, the provenance and current genetic diversity must be described. Concurrently, poaching of lions to supply a growing market for lion bones in Asia may become a serious conservation challenge in the future. Having a standardized, validated method for matching confiscated lion parts with carcasses will be a key tool in investigating these crimes. We evaluated 28 microsatellites in the African lion using samples from 18 small reserves and 1 captive facility in South Africa, two conservancies in Zimbabwe, and Kruger National and Kgalagadi Transfrontier Parks to determine the loci most suited for population management and forensic genetic applications. Twelve microsatellite loci with a match probability of 1.1×10(-5) between siblings were identified for forensics. A further 10 could be added for population genetics studies.

  4. Sahara: Barrier or corridor? Nonmetric cranial traits and biological affinities of North African late Holocene populations.

    PubMed

    Nikita, Efthymia; Mattingly, David; Lahr, Marta Mirazón

    2012-02-01

    The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ~3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D(2) distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D(2) distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region.

  5. Inbreeding Avoidance Influences the Viability of Reintroduced Populations of African Wild Dogs (Lycaon pictus)

    PubMed Central

    Becker, Penny A.; Miller, Philip S.; Gunther, Micaela Szykman; Somers, Michael J.; Wildt, David E.; Maldonado, Jesús E.

    2012-01-01

    The conservation of many fragmented and small populations of endangered African wild dogs (Lycaon pictus) relies on understanding the natural processes affecting genetic diversity, demographics, and future viability. We used extensive behavioural, life-history, and genetic data from reintroduced African wild dogs in South Africa to (1) test for inbreeding avoidance via mate selection and (2) model the potential consequences of avoidance on population persistence. Results suggested that wild dogs avoided mating with kin. Inbreeding was rare in natal packs, after reproductive vacancies, and between sibling cohorts (observed on 0.8%, 12.5%, and 3.8% of occasions, respectively). Only one of the six (16.7%) breeding pairs confirmed as third-order (or closer) kin consisted of animals that were familiar with each other, while no other paired individuals had any prior association. Computer-simulated populations allowed to experience inbreeding had only a 1.6% probability of extinction within 100 years, whereas all populations avoiding incestuous matings became extinct due to the absence of unrelated mates. Populations that avoided mating with first-order relatives became extinct after 63 years compared with persistence of 37 and 19 years for those also prevented from second-order and third-order matings, respectively. Although stronger inbreeding avoidance maintains significantly more genetic variation, our results demonstrate the potentially severe demographic impacts of reduced numbers of suitable mates on the future viability of small, isolated wild dog populations. The rapid rate of population decline suggests that extinction may occur before inbreeding depression is observed. PMID:22615933

  6. Inbreeding avoidance influences the viability of reintroduced populations of African wild dogs (Lycaon pictus).

    PubMed

    Becker, Penny A; Miller, Philip S; Gunther, Micaela Szykman; Somers, Michael J; Wildt, David E; Maldonado, Jesús E

    2012-01-01

    The conservation of many fragmented and small populations of endangered African wild dogs (Lycaon pictus) relies on understanding the natural processes affecting genetic diversity, demographics, and future viability. We used extensive behavioural, life-history, and genetic data from reintroduced African wild dogs in South Africa to (1) test for inbreeding avoidance via mate selection and (2) model the potential consequences of avoidance on population persistence. Results suggested that wild dogs avoided mating with kin. Inbreeding was rare in natal packs, after reproductive vacancies, and between sibling cohorts (observed on 0.8%, 12.5%, and 3.8% of occasions, respectively). Only one of the six (16.7%) breeding pairs confirmed as third-order (or closer) kin consisted of animals that were familiar with each other, while no other paired individuals had any prior association. Computer-simulated populations allowed to experience inbreeding had only a 1.6% probability of extinction within 100 years, whereas all populations avoiding incestuous matings became extinct due to the absence of unrelated mates. Populations that avoided mating with first-order relatives became extinct after 63 years compared with persistence of 37 and 19 years for those also prevented from second-order and third-order matings, respectively. Although stronger inbreeding avoidance maintains significantly more genetic variation, our results demonstrate the potentially severe demographic impacts of reduced numbers of suitable mates on the future viability of small, isolated wild dog populations. The rapid rate of population decline suggests that extinction may occur before inbreeding depression is observed.

  7. Africanization of a feral honey bee (Apis mellifera) population in South Texas: does a decade make a difference?

    PubMed

    Rangel, Juliana; Giresi, Melissa; Pinto, Maria Alice; Baum, Kristen A; Rubink, William L; Coulson, Robert N; Johnston, John Spencer

    2016-04-01

    The arrival to the United States of the Africanized honey bee, a hybrid between European subspecies and the African subspecies Apis mellifera scutellata, is a remarkable model for the study of biological invasions. This immigration has created an opportunity to study the dynamics of secondary contact of honey bee subspecies from African and European lineages in a feral population in South Texas. An 11-year survey of this population (1991-2001) showed that mitochondrial haplotype frequencies changed drastically over time from a resident population of eastern and western European maternal ancestry, to a population dominated by the African haplotype. A subsequent study of the nuclear genome showed that the Africanization process included bidirectional gene flow between European and Africanized honey bees, giving rise to a new panmictic mixture of A. m. scutellata- and European-derived genes. In this study, we examined gene flow patterns in the same population 23 years after the first hybridization event occurred. We found 28 active colonies inhabiting 92 tree cavities surveyed in a 5.14 km(2) area, resulting in a colony density of 5.4 colonies/km(2). Of these 28 colonies, 25 were of A. m. scutellata maternal ancestry, and three were of western European maternal ancestry. No colonies of eastern European maternal ancestry were detected, although they were present in the earlier samples. Nuclear DNA revealed little change in the introgression of A. m. scutellata-derived genes into the population compared to previous surveys. Our results suggest this feral population remains an admixed swarm with continued low levels of European ancestry and a greater presence of African-derived mitochondrial genetic composition.

  8. Glossina fuscipes populations provide insights for Human African Trypanosomiasis transmission in Uganda

    PubMed Central

    Aksoy, Serap; Caccone, Adalgisa; Galvani, Alison P.; Okedi, Loyce M.

    2013-01-01

    Uganda has both forms of human African trypanosomiasis (HAT): the chronic gambiense disease in the northwest and the acute rhodesiense disease in the south. The recent spread of rhodesiense into central Uganda has raised concerns given the different control strategies the two diseases require. We present knowledge on the population genetics of the major vector species Glossina fuscipes fuscipes in Uganda with a focus on population structure, measures of gene flow between populations, and the occurrence of polyandry. The microbiome composition and diversity is discussed, focusing on their potential role on trypanosome infection outcomes. We discuss the implications of these findings for large-scale tsetse control programs, including suppression or eradication, being undertaken in Uganda and potential future genetic applications. PMID:23845311

  9. Glossina fuscipes populations provide insights for human African trypanosomiasis transmission in Uganda.

    PubMed

    Aksoy, Serap; Caccone, Adalgisa; Galvani, Alison P; Okedi, Loyce M

    2013-08-01

    Uganda has both forms of human African trypanosomiasis (HAT): the chronic gambiense disease in the northwest and the acute rhodesiense disease in the south. The recent spread of rhodesiense into central Uganda has raised concerns given the different control strategies the two diseases require. We present knowledge on the population genetics of the major vector species Glossina fuscipes fuscipes in Uganda with a focus on population structure, measures of gene flow between populations, and the occurrence of polyandry. The microbiome composition and diversity is discussed, focusing on their potential role on trypanosome infection outcomes. We discuss the implications of these findings for large-scale tsetse control programs, including suppression or eradication, being undertaken in Uganda, and potential future genetic applications.

  10. Pharmacogenomics Implications of Using Herbal Medicinal Plants on African Populations in Health Transition

    PubMed Central

    Thomford, Nicholas E.; Dzobo, Kevin; Chopera, Denis; Wonkam, Ambroise; Skelton, Michelle; Blackhurst, Dee; Chirikure, Shadreck; Dandara, Collet

    2015-01-01

    The most accessible points of call for most African populations with respect to primary health care are traditional health systems that include spiritual, religious, and herbal medicine. This review focusses only on the use of herbal medicines. Most African people accept herbal medicines as generally safe with no serious adverse effects. However, the overlap between conventional medicine and herbal medicine is a reality among countries in health systems transition. Patients often simultaneously seek treatment from both conventional and traditional health systems for the same condition. Commonly encountered conditions/diseases include malaria, HIV/AIDS, hypertension, tuberculosis, and bleeding disorders. It is therefore imperative to understand the modes of interaction between different drugs from conventional and traditional health care systems when used in treatment combinations. Both conventional and traditional drug entities are metabolized by the same enzyme systems in the human body, resulting in both pharmacokinetics and pharmacodynamics interactions, whose properties remain unknown/unquantified. Thus, it is important that profiles of interaction between different herbal and conventional medicines be evaluated. This review evaluates herbal and conventional drugs in a few African countries and their potential interaction at the pharmacogenomics level. PMID:26402689

  11. Additive genetic variation in schizophrenia risk is shared by populations of African and European descent.

    PubMed

    de Candia, Teresa R; Lee, S Hong; Yang, Jian; Browning, Brian L; Gejman, Pablo V; Levinson, Douglas F; Mowry, Bryan J; Hewitt, John K; Goddard, Michael E; O'Donovan, Michael C; Purcell, Shaun M; Posthuma, Danielle; Visscher, Peter M; Wray, Naomi R; Keller, Matthew C

    2013-09-05

    To investigate the extent to which the proportion of schizophrenia's additive genetic variation tagged by SNPs is shared by populations of European and African descent, we analyzed the largest combined African descent (AD [n = 2,142]) and European descent (ED [n = 4,990]) schizophrenia case-control genome-wide association study (GWAS) data set available, the Molecular Genetics of Schizophrenia (MGS) data set. We show how a method that uses genomic similarities at measured SNPs to estimate the additive genetic correlation (SNP correlation [SNP-rg]) between traits can be extended to estimate SNP-rg for the same trait between ethnicities. We estimated SNP-rg for schizophrenia between the MGS ED and MGS AD samples to be 0.66 (SE = 0.23), which is significantly different from 0 (p(SNP-rg = 0) = 0.0003), but not 1 (p(SNP-rg = 1) = 0.26). We re-estimated SNP-rg between an independent ED data set (n = 6,665) and the MGS AD sample to be 0.61 (SE = 0.21, p(SNP-rg = 0) = 0.0003, p(SNP-rg = 1) = 0.16). These results suggest that many schizophrenia risk alleles are shared across ethnic groups and predate African-European divergence.

  12. THE IMPACT OF HISPANIC POPULATION GROWTH ON THE OUTLOOK OF AFRICAN AMERICANS

    PubMed Central

    Taylor, Marylee C.; Schroeder, Matthew B.

    2014-01-01

    We know too little about the effects of immigration on black Americans. If prior research yields mixed evidence about immigration’s consequences for the objective well-being of African Americans, it is silent about effects of immigration on blacks’ subjective well-being. To fill that void, this paper assesses the impact of the expanding Hispanic population on black Americans from a social psychological perspective. We ask whether blacks’ self-reported distress, social distrust, or attitudes toward Hispanics and immigrants are affected by the size of the local Hispanic population or by the percentage growth in local Hispanic residents. Answers come from responses of non-Hispanic black participants in the 1998–2002 General Social Surveys, linked to 1990 and 2000 census data. Contrary to pessimistic claims, most social psychological outcomes, including measures of economic distress, manifest no impact of local Hispanic numbers. The four exceptions, significant effects of local Hispanic population share or percentage growth evenly split in valence, underscore the complexity of recent immigration’s effects on African Americans. PMID:25242830

  13. Genetic Relatedness of African and United States Populations of Cercospora zeae-maydis.

    PubMed

    Dunkle, L D; Levy, M

    2000-05-01

    Two taxonomically identical but genetically distinct sibling species, designated groups I and II, of Cercospora zeae-maydis cause gray leaf spot of maize in the United States. Isolates of the gray leaf spot pathogen from Africa were compared with isolates from the United States by amplified fragment length polymorphism (AFLP) analysis and restriction digests of internal transcribed spacer (ITS) regions and 5.8S ribosomal DNA (rDNA), as well as by morphological and cultural characteristics. The isolates from Africa were morphologically indistinguishable from the U.S. isolates in both groups, but like isolates of group II, they grew more slowly and failed to produce detectable amounts of cercosporin in culture. Analysis of restriction fragments from the ITS and rDNA regions digested with five endonucleases indicated that all of the African isolates shared the profile of the C. zeae-maydis group II population from the eastern United States and, thus, are distinct from the group I population, which is more prevalent in the United States and other parts of the world. Cluster analysis of 85 AFLP loci confirmed that the African and U.S. group II populations were conspecific (greater than 97% average similarity) with limited variability. Among all group II isolates, only 8 of 57 AFLP loci were polymorphic, and none was specific to either population. Thus, although gray leaf spot was reported in the United States several decades prior to the first record in Africa, the relative age of the two populations on their respective continents could not be ascertained with confidence. The absence of C. zeae-maydis group I in our samples from four countries in the major maize-producing region of Africa as well as the greater AFLP haplotype diversity found in the African group II population, however, suggest that Africa was the source of C. zeae-maydis group II in the United States. The overall paucity of AFLP variation in this sibling species further suggests that its origin is

  14. Protection from Cardiovascular Disease Due to Increased High-Density Lipoprotein Cholesterol in African Black Populations: Myth or Reality?

    PubMed

    Woudberg, Nicholas J; Goedecke, Julia H; Lecour, Sandrine

    2016-10-20

    The burden of cardiovascular disease (CVD) in sub-Saharan Africa has increased over the last decade. Despite this, African Black populations present with relatively low incidences of coronary heart disease and ischemic heart disease, which may be attributed to their lower total cholesterol, triglycerides and low-density lipoprotein cholesterol concentrations, compared with White populations. Commensurate with these lower lipid levels, it was believed that high-density lipoprotein cholesterol (HDL-C) concentrations would be higher in Black populations compared with their White counterparts. This is based on data from previous studies of African and African American populations; however, recent studies conducted in Africa found similar or lower HDL-C concentrations in Black compared with White individuals. Current research, therefore, suggests that HDL-C may not be a good indicator of cardiovascular risk and future research should focus on HDL quality (vs quantity), by measuring HDL functionality and subclass.

  15. Evolution of human longevity, population pressure and the origins of warfare.

    PubMed

    Holliday, Robin

    2005-01-01

    In a protected environment, humans have the longest lifespan of all primates. However, during the emergence of Homo sapiens from pre-hominids, the expectation of life at birth would have been quite low. On the basis of reasonable assumptions, an average expectation of life of less than 20 years is sufficient to maintain a population of hunter-gatherers. As individuals became better adapted to their environment, the mortality rate would gradually decrease, and this would result in the survival of more offspring to adulthood. Thus, the population will increase, and one of the consequences in human evolution is the migration of human communities to many new habitats. The development of agriculture provided a more reliable source of food, and stimulated further the increase in population size. Villages became towns, and then cities, states and empires arose which had very large populations, and competed for land and other resources. Armies were raised and were often at war. All this was due to population pressure, as Malthus had realised more than 200 years ago. However, neither he, nor any of the others who discussed warfare, understood that the demographic changes that produced large human populations was a steady increase in the expectation of life at birth. This inevitably occurred at the same time as man gradually gained more control over his environment, and achieved far more reproductive success than is seen in hunter-gatherers living in a harsh, stressful environment.

  16. Gene-centric analysis of serum cotinine levels in African and European American populations.

    PubMed

    Hamidovic, Ajna; Goodloe, Robert J; Bergen, Andrew W; Benowitz, Neal L; Styn, Mindi A; Kasberger, Jay L; Choquet, Helene; Young, Taylor R; Meng, Yan; Palmer, Cameron; Pletcher, Mark; Kertesz, Stefan; Hitsman, Brian; Spring, Bonnie; Jorgenson, Eric

    2012-03-01

    To date, most genetic association studies of tobacco use have been conducted in European American subjects using the phenotype of smoking quantity (cigarettes per day). However, smoking quantity is a very imprecise measure of exposure to tobacco smoke constituents. Analyses of alternate phenotypes and populations may improve our understanding of tobacco addiction genetics. Cotinine is the major metabolite of nicotine, and measuring serum cotinine levels in smokers provides a more objective measure of nicotine dose than smoking quantity. Previous genetic association studies of serum cotinine have focused on individual genes. We conducted a genetic association study of the biomarker in African American (N=365) and European American (N=315) subjects from the Coronary Artery Risk Development in Young Adults study using a chip containing densely-spaced tag SNPs in ∼2100 genes. We found that rs11187065, located in the non-coding region (intron 1) of insulin-degrading enzyme (IDE), was the most strongly associated SNP (p=8.91 × 10(-6)) in the African American cohort, whereas rs11763963, located on chromosome 7 outside of a gene transcript, was the most strongly associated SNP in European Americans (p=1.53 × 10(-6)). We then evaluated how the top variant association in each population performed in the other group. We found that the association of rs11187065 in IDE was also associated with the phenotype in European Americans (p=0.044). Our top SNP association in European Americans, rs11763963 was non-polymorphic in our African American sample. It has been previously shown that psychostimulant self-administration is reduced in animals with lower insulin because of interference with dopamine transmission in the brain reward centers. Our finding provides a platform for further investigation of this, or additional mechanisms, involving the relationship between insulin and self-administered nicotine dose.

  17. Legal ivory trade in a corrupt world and its impact on African elephant populations.

    PubMed

    Bennett, Elizabeth L

    2015-02-01

    Illegal hunting of African elephants (Loxodonta africana) for ivory is causing rapid declines in their populations. Since 2007, illegal ivory trade has more than doubled. African elephants are facing the most serious conservation crisis since 1989, when international trade was banned. One solution proposed is establishment of a controlled legal trade in ivory. High prices for ivory mean that the incentives to obtain large quantities are high, but the quantity of tusks available for trade are biologically constrained. Within that context, effective management of a legal ivory trade would require robust systems to be in place to ensure that ivory from illegally killed elephants cannot be laundered into a legal market. At present, that is not feasible due to corruption among government officials charged with implementing wildlife-related legislation. With organized criminal enterprises involved along the whole commodity chain, corruption enables the laundering of illegal ivory into legal or potentially legal markets. Poachers and traffickers can rapidly pay their way out of trouble, so the financial incentives to break the law heavily outweigh those of abiding by it. Maintaining reliable permitting systems and leak-proof chains of custody in this context is challenging, and effective management breaks down. Once illegal ivory has entered the legal trade, it is difficult or impossible for enforcement officers to know what is legal and illegal. Addressing corruption throughout a trade network that permeates countries across the globe will take decades, if it can ever be achieved. That will be too late for wild African elephants at current rates of loss. If we are to conserve remaining wild populations, we must close all markets because, under current levels of corruption, they cannot be controlled in a way that does not provide opportunities for illegal ivory being laundered into legal markets.

  18. Bayesian estimation of the phylogeography of African gorillas with genome-differentiated population trees.

    PubMed

    Kim, Joungyoun; Larget, Bret

    2014-09-01

    Phylogeography investigates the historical process that is responsible for the contemporary geographic distributions of populations in a species. The inference is made on the basis of molecular sequence data sampled from modern-day populations. The estimates, however, may fluctuate depending on the relevant genomic regions, because the evolution mechanism of each genome is unique, even within the same individual. In this article, we propose a genome-differentiated population tree model that allows the existence of separate population trees for each homologous genome. In each population tree, the unique evolutionary characteristics account for each genome, along with their homologous relationship; therefore, the approach can distinguish the evolutionary history of one genome from that of another. In addition to the separate divergence times, the new model can estimate separate effective population sizes, gene-genealogies and other mutation parameters. For Bayesian inference, we developed a Markov chain Monte Carlo (MCMC) methodology with a novel MCMC algorithm which can mix over a complicated state space. The stability of the new estimator is demonstrated through comparison with the Monte Carlo samples and other methods, as well as MCMC convergence diagnostics. The analysis of African gorilla data from two homologous loci reveals discordant divergence times between loci, and this discrepancy is explained by male-mediated gene flows until the end of the last ice age.

  19. Modeling the effects of trophy selection and environmental disturbance on a simulated population of African lions.

    PubMed

    Whitman, Karyl L; Starfield, Anthony M; Quadling, Henley; Packer, Craig

    2007-06-01

    Tanzania is a premier destination for trophy hunting of African lions (Panthera leo) and is home to the most extensive long-term study of unhunted lions. Thus, it provides a unique opportunity to apply data from a long-term field study to a conservation dilemma: How can a trophy-hunted species whose reproductive success is closely tied to social stability be harvested sustainably? We used an individually based, spatially explicit, stochastic model, parameterized with nearly 40 years of behavioral and demographic data on lions in the Serengeti, to examine the separate effects of trophy selection and environmental disturbance on the viability of a simulated lion population in response to annual harvesting. Female population size was sensitive to the harvesting of young males (> or = 3 years), whereas hunting represented a relatively trivial threat to population viability when the harvest was restricted to mature males (> or = 6 years). Overall model performance was robust to environmental disturbance and to errors in age assessment based on nose coloration as an index used to age potential trophies. Introducing an environmental disturbance did not eliminate the capacity to maintain a viable breeding population when harvesting only older males, and initially depleted populations recovered within 15-25 years after the disturbance to levels comparable to hunted populations that did not experience a catastrophic event. These results are consistent with empirical observations of lion resilience to environmental stochasticity.

  20. Male reproductive parasitism: a factor in the africanization of European honey-bee populations.

    PubMed

    Rinderer, T E; Hellmich, R L; Danka, R G; Collins, A M

    1985-05-31

    Africanized drone honey bees (Apis mellifera) migrate into European honey-bee colonies in large numbers, but Africanized colonies only rarely host drones from other colonies. This migration leads to a strong mating advantage for Africanized bees since it both inhibits European drone production and enhances Africanized drone production.

  1. Genetic relatedness and disrupted social structure in a poached population of African elephants.

    PubMed

    Gobush, Kathleen; Kerr, Ben; Wasser, Samuel

    2009-02-01

    We use genetic measures of relatedness and observations of female bonding to examine the demographic signature of historically heavy poaching of a population of free-ranging African elephants. We collected dung samples to obtain DNA and observed behaviour from 102 elephant families over a 25-month period in 2003-2005 in Mikumi National Park, Tanzania. Poaching reduced the population by 75% in the decade prior to the 1989 ivory trade ban; park records indicate that poaching dropped significantly in Mikumi following the ban. Using 10 microsatellite loci, DNA was genotyped in 203 elephants and pair-wise relatedness was calculated among adult females within and between groups. The Mikumi population is characterized by small group size, considerable variation in group relatedness, females with no first-order adult relatives and females that form only weak social bonds. We used gene-drop analysis and a model of a genetically intact pedigree to compare our observed Mikumi group relatedness to a simulated genetically intact unpoached expectation. The majority of groups in Mikumi contain 2 to 3 adults; of these, 45% were classified as genetically disrupted. Bonding, quantified with a pair-wise association index, was significantly correlated with relatedness; however only half of the females formed strong bonds with other females, and relatedness was substantially lower for a given bond strength as compared to an unpoached population. Female African elephants without kin demonstrated considerable behavioural plasticity in this disturbed environment, grouping with other females lacking kin, with established groups, or remaining alone, unable to form any stable adult female-bonds. We interpret these findings as the remaining effect of poaching disturbance in Mikumi, despite a drop in the level of poaching since the commercial trade in ivory was banned 15 years ago.

  2. Bight of Benin: a Maternal Perspective of Four Beninese Populations and their Genetic Implications on the American Populations of African Ancestry.

    PubMed

    Primativo, Giuseppina; Ottoni, Claudio; Biondi, Gianfranco; Serafino, Sara; Martínez-Labarga, Cristina; Larmuseau, Maarten H D; Scardi, Michele; Decorte, Ronny; Rickards, Olga

    2017-03-01

    The understanding of the first movements of the ancestral populations within the African continent is still unclear, particularly in West Africa, due to several factors that have shaped the African genetic pool across time. To improve the genetic representativeness of the Beninese population and to better understand the patterns of human settlement inside West Africa and the dynamics of peopling of the Democratic Republic of Benin, we analyzed the maternal genetic variation of 193 Beninese individuals belonging to Bariba, Berba, Dendi, and Fon populations. Results support the oral traditions indicating that the western neighbouring populations have been the ancestors of the first Beninese populations, and the extant genetic structure of the Beninese populations is most likely the result of admixture between populations from neighbouring countries and native people. The present findings highlight how the Beninese populations contributed to the gene pool of the extant populations of some American populations of African ancestry. This strengthens the hypothesis that the Bight of Benin was not only an assembly point for the slave trade during the Trans-Atlantic Slave Trade but also an important slave trapping area.

  3. Suppression of Pratylenchus penetrans Populations in Potato and Tomato using African Marigolds

    PubMed Central

    Alexander, Samuel A.; Waldenmaier, Christine M.

    2002-01-01

    Current strategies for management of Pratylenchus penetrans in both white potato and tomato consist of the use of fumigant or non-fumigant nematicides or crop rotation. The objective of this study was to determine if double-cropping African marigolds (Tagetes erecta) with potatoes or tomatoes could reduce P. penetrans populations. Plots were 10 m × 3 m arranged in a randomized complete block design with four replications. Treatments included marigolds, potatoes or tomatoes, and natural weedy fallow followed by either potatoes or tomatoes. Nematode populations were sampled before spring planting, between crops in August and after harvest in November. During the 3 years of the study, P. penetrans soil population density declined by an average of 93% from the pre-plant level when marigold was grown in rotation with potato and by 98% when marigold was grown.in rotation with tomato. Weedy fallow preceding potato resulted in an average decline in P. penetrans soil population density of 38%, and a similar decrease (37%) was seen when fallow preceded tomato. There was a significant reduction in the number of P. penetrans found in both potato and tomato roots when the crops followed marigolds. These results suggest that P. penetrans population density may be significantly reduced when marigolds are double-cropped with potatoes or tomatoes. PMID:19265920

  4. Novel variants of major drug-metabolising enzyme genes in diverse African populations and their predicted functional effects

    PubMed Central

    2009-01-01

    Pharmacogenetics enables personalised therapy based on genetic profiling and is increasingly applied in drug discovery. Medicines are developed and used together with pharmacodiagnostic tools to achieve desired drug efficacy and safety margins. Genetic polymorphism of drug-metabolising enzymes such as cytochrome P450s (CYPs) and N-acetyltransferases (NATs) has been widely studied in Caucasian and Asian populations, yet studies on African variants have been less extensive. The aim of the present study was to search for novel variants of CYP2C9, CYP2C19, CYP2D6 and NAT2 genes in Africans, with a particular focus on their prevalence in different populations, their relevance to enzyme functionality and their potential for personalised therapy. Blood samples from various ethnic groups were obtained from the AiBST Biobank of African Populations. The nine exons and exon-intron junctions of the CYP genes and exon 2 of NAT2 were analysed by direct DNA sequencing. Computational tools were used for the identification, haplotype analysis and prediction of functional effects of novel single nucleotide polymorphisms (SNPs). Novel SNPs were discovered in all four genes, grouped to existing haplotypes or assigned new allele names, if possible. The functional effects of non-synonymous SNPs were predicted and known African-specific variants were confirmed, but no significant differences were found in the frequencies of SNPs between African ethnicities. The low prevalence of our novel variants and most known functional alleles is consistent with the generally high level of diversity in gene loci of African populations. This indicates that profiles of rare variants reflecting interindividual variability might become the most relevant pharmacodiagnostic tools explaining Africans' diversity in drug response. PMID:19164093

  5. Associations between Common Variants in Iron-Related Genes with Haematological Traits in Populations of African Ancestry

    PubMed Central

    Tanaka, Toshiko; Towers, G. Wayne; Verhoef, Hans; Veenemans, Jacobien; Talsma, Elise F.; Harryvan, Jan; Boekschoten, Mark V.; Feskens, Edith J.; Melse-Boonstra, Alida

    2016-01-01

    Background Large genome-wide association (GWA) studies of European ancestry individuals have identified multiple genetic variants influencing iron status. Studies on the generalizability of these associations to African ancestry populations have been limited. These studies are important given interethnic differences in iron status and the disproportionate burden of iron deficiency among African ancestry populations. Methods We tested the associations of 20 previously identified iron status-associated single nucleotide polymorphisms (SNPs) in 628 Kenyans, 609 Tanzanians, 608 South Africans and 228 African Americans. In each study, we examined the associations present between 20 SNPs with ferritin and haemoglobin, adjusting for age, sex and CRP levels. Results In the meta analysis including all 4 African ancestry cohorts, we replicated previously reported associations with lowered haemoglobin concentrations for rs2413450 (β = -0.19, P = 0.02) and rs4820268 (β = -0.16, P = 0.04) in TMPRSS6. An association with increased ferritin concentrations was also confirmed for rs1867504 in TF (β = 1.04, P = <0.0001) in the meta analysis including the African cohorts only. Conclusions In all meta analyses, we only replicated 4 of the 20 single nucleotide polymorphisms reported to be associated with iron status in large GWA studies of European ancestry individuals. While there is now evidence for the associations of a number of genetic variants with iron status in both European and African ancestry populations, the considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of iron status in ethnically diverse populations. PMID:27332551

  6. Population differentiation of the African cyprinid Barbus neumayeri across dissolved oxygen regimes

    PubMed Central

    Harniman, Robert; Merritt, Thomas J S; Chapman, Lauren J; Lesbarrères, David; Martinez, Mery L

    2013-01-01

    Population level response to hypoxia has become an issue of global significance because of increased frequency and intensity of hypoxic events worldwide, and the potential for global warming to exacerbate hypoxic stress. In this study, we sequenced two nuclear intronic regions and a single mitochondrial region across seven populations of the African cyprinid, Barbus neumayeri from two river drainages in Uganda: the Rwembaita Swamp-Njuguta River System and the Dura River. We then examined two indices of population structure, GST and Jost's D, to detect links between oxygen availability and genetic variation and to determine if population genetic structure was associated with (i) dissolved oxygen regime (hypoxia or normoxia), (ii) geographical distance, or (iii) a combination of dissolved oxygen regime and geographical distance. Our results indicate that over a large scale (between drainages), geographical distance significantly affects the genetic structure of populations. However, within a single drainage, dissolved oxygen regime plays a key role in determining the genetic structure of populations. Within the Rwembaita-Njuguta system, gene flow was high between locations of similar oxygen regimes, but low between areas characterized by divergent oxygen regimes. Interestingly, GST analyses appear to yield less realistic measures of population structure than Jost's D, suggesting that caution must be taken when interpreting and comparing the results from different studies. These results support the idea that aquatic dissolved oxygen can act as a selective force limiting gene flow among populations of aquatic species and therefore should be considered when implementing conservation plans and assessing environmental impact of human activities. PMID:23789062

  7. The Uncertain Significance of Low Vitamin D levels in African Descent Populations: A Review of the Bone and Cardiometabolic Literature

    PubMed Central

    O'Connor, Michelle Y; Thoreson, Caroline K; Ramsey, Natalie L M; Ricks, Madia; Sumner, Anne E

    2014-01-01

    Vitamin D levels in people of African descent are often described as inadequate or deficient. Whether low vitamin D levels in people of African descent lead to compromised bone or cardiometabolic health is unknown. Clarity on this issue is essential because if clinically significant vitamin D deficiency is present, vitamin D supplementation is necessary. However, if vitamin D is metabolically sufficient, vitamin D supplementation could be wasteful of scarce resources and even harmful. In this review vitamin D physiology is described with a focus on issues specific to populations of African descent such as the influence of melanin on endogenous vitamin D production and lactose intolerance on the willingness of people to ingest vitamin D fortified foods. Then data on the relationship of vitamin D to bone and cardiometabolic health in people of African descent are evaluated. PMID:24267433

  8. Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south-eastern United States and Caribbean Islands.

    PubMed

    Kao, Joyce Y; Zubair, Asif; Salomon, Matthew P; Nuzhdin, Sergey V; Campo, Daniel

    2015-04-01

    Drosophila melanogaster is postulated to have colonized North America in the past several 100 years in two waves. Flies from Europe colonized the east coast United States while flies from Africa inhabited the Caribbean, which if true, make the south-east US and Caribbean Islands a secondary contact zone for African and European D. melanogaster. This scenario has been proposed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes of flies from populations in the south-east US and Caribbean Islands and examined these populations in conjunction with population sequences from the west coast US, Africa, and Europe. We find that west coast US populations are closely related to the European population, likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in south-east US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude. Our genomic analysis of D. melanogaster populations from the south-east US and Caribbean Islands provides more evidence for the Caribbean Islands as the source of previously reported novel African alleles found in other east coast US populations. We also find the border between the south-east US and the Caribbean island to be the admixture hot zone where distinctly African-like Caribbean flies become genomically more similar to European-like south-east US flies. Our findings have important implications for previous studies examining the generation of east coast US clines via selection.

  9. Colloquium paper: working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history.

    PubMed

    Scheinfeldt, Laura B; Soi, Sameer; Tishkoff, Sarah A

    2010-05-11

    Although Africa is the origin of modern humans, the pattern and distribution of genetic variation and correlations with cultural and linguistic diversity in Africa have been understudied. Recent advances in genomic technology, however, have led to genomewide studies of African samples. In this article, we discuss genetic variation in African populations contextualized with what is known about archaeological and linguistic variation. What emerges from this review is the importance of using independent lines of evidence in the interpretation of genetic and genomic data in the reconstruction of past population histories.

  10. Nasal septal and craniofacial form in European- and African-derived populations.

    PubMed

    Holton, Nathan E; Yokley, Todd R; Figueroa, Aaron

    2012-09-01

    As a component of the chondrocranium, the nasal septum influences the anteroposterior dimensions of the facial skeleton. The role of the septum as a facial growth center, however, has been studied primarily in long-snouted mammals, and its precise influence on human facial growth is not as well understood. Whereas the nasal septum may be important in the anterior growth of the human facial skeleton early in ontogeny, the high incidence of nasal septal deviation in humans suggests the septum's influence on human facial length is limited to the early phases of facial growth. Nevertheless, the nasal septum follows a growth trajectory similar to the facial skeleton and, as such, its prolonged period of growth may influence other aspects of facial development. Using computed tomography scans of living human subjects (n = 70), the goal of the present study is to assess the morphological relationship between the nasal septum and facial skeleton in European- and African-derived populations, which have been shown to exhibit early developmental differences in the nasal septal-premaxillary complex. First we assessed whether there is population variation in the size of the nasal septum in European- and African-derived samples. This included an evaluation of septal deviation and the spatial constraints that influence variation in this condition. Next, we assessed the relationship between nasal septal size and craniofacial shape using multivariate regression techniques. Our results indicate that there is significant population variation in septal size and magnitude of septal deviation, both of which are greater in the European-derived sample. While septal deviation suggests a disjunction between the nasal septum and other components of the facial skeleton, we nevertheless found a significant relationship between the size of the nasal septum and craniofacial shape, which appears to largely be a response to the need to accommodate variation in nasal septal size.

  11. Incremental impact of breast cancer SNP panel on risk classification in a screening population of white and African American women.

    PubMed

    McCarthy, Anne Marie; Armstrong, Katrina; Handorf, Elizabeth; Boghossian, Leigh; Jones, Marisa; Chen, Jinbo; Demeter, Mirar Bristol; McGuire, Erin; Conant, Emily F; Domchek, Susan M

    2013-04-01

    Breast cancer risk prediction remains imperfect, particularly among non-white populations. This study examines the impact of including single-nucleotide polymorphism (SNP) alleles in risk prediction for white and African American women undergoing screening mammogram. Using a prospective cohort study, standard risk information and buccal swabs were collected at the time of screening mammography. A 12 SNP panel was performed by deCODE genetics. Five-year and lifetime risks incorporating SNPs were calculated by multiplying estimated Breast Cancer Risk Assessment Tool (BCRAT) risk by the total genetic risk ratio. Concordance between the BCRAT and the combined model (BCRAT + SNPs) in identifying high-risk women was measured using the kappa statistic. SNP data were available for 810 women (39 % African American, 55 % white). The mean BCRAT 5-year risk was 1.71 % for whites and 1.18 % for African Americans. Mean genetic risk ratios were 1.09 in whites and 1.29 in African Americans. Among whites, three SNPs had higher frequencies, and among African Americans, seven SNPs had higher and four had lower high-risk allele frequencies than previously reported. Agreement between the BCRAT and the combined model was relatively low for identifying high-risk women (5-year κ = 0.54, lifetime κ = 0.36). Addition of SNPs had the greatest effect among African Americans, with 12.4 % identified as having high-5-year risk by BCRAT, but 33 % by the combined model. A greater proportion of African Americans were reclassified as having high-5-year risk than whites using the combined model (21 vs. 10 %). The addition of SNPs to the BCRAT reclassifies the high-risk status of some women undergoing screening mammography, particularly African Americans. Further research is needed to determine the clinical validity and utility of the SNP panel for use in breast cancer risk prediction, particularly among African Americans for whom these risk alleles have generally not been validated.

  12. Incorporating parasite data in population structure studies of South African sardine Sardinops sagax.

    PubMed

    Van Der Lingen, Carl David; Weston, Laura Frances; Ssempa, Nurudean Norman; Reed, Cecile Catharine

    2015-01-01

    A multidisciplinary approach has been applied to examine the population structure of sardine Sardinops sagax off South Africa, where this species supports significant fisheries and is also of ecological and eco-tourism importance. Observations of discontinuous sardine distribution patterns, discrete spawning grounds and significant spatial differences in a variety of phenotypic characteristics have suggested the existence of discrete western, southern and eastern sardine sub-populations or stocks. The use of parasites as biological tags to elucidate sardine population structure has recently been investigated, and strong spatial gradients around South Africa in the prevalence, mean infection intensity and mean abundance of a digenean 'tetracotyle' type metacercarial endoparasite considered to be of the genus Cardiocephaloides and found in the humours of fish eyes support and have proved particularly convincing evidence for the sardine multiple stock hypothesis. A discontinuous distribution in the occurrence of another parasite, the coccidean Eimeria sardinae found in fish testes, has provided additional but weaker evidence of discrete stocks. These results have contributed to a changed understanding of the population structure of South African sardine and have significant implications for management of the fisheries for this species.

  13. A survey of blood pressure distribution in Pygmy and Bantu populations in Cameroon.

    PubMed

    Kesteloot, H; Ndam, N; Sasaki, S; Kowo, M; Seghers, V

    1996-01-01

    A blood pressure survey was performed in isolated Pygmy communities and Bantu population samples living either in close relationship with the Pygmies or in separate areas within the same region. The Pygmies are still living as hunter-gatherers, whereas the Bantus rely on agriculture for food provision. Mean blood pressures in Pygmies were 130/85 mm Hg in males and 126/80 mm Hg in females and in Bantus were 137/87 mm Hg in males and 136/84 mm Hg in females. In spot urine the mean urinary sodium concentration was higher in Bantus than Pygmies (86 versus 37 mmol/L in males; 95 versus 56 mmol/L in females). In the total population urinary potassium concentration was very high (150 mmol/L), calcium concentration very low (0.4 mmol/L), and urea concentration low (6.9 g/L). After adjustment for age, height, weight, and sex, no racial differences in blood pressure were present. Blood pressure increased with age but body mass index did not. Diastolic pressure correlated significantly but negatively with urinary sodium in multiple regression analysis. Our study demonstrates that blood pressure increases with age in hunter-gatherer populations on a low to moderately high sodium diet in the presence of a low urinary excretion of calcium coupled with a low protein intake.

  14. Relative tibia long bone growth in the Libben and Bt-5 prehistoric skeletal populations.

    PubMed

    Mensforth, R P

    1985-10-01

    Patterns of tibia long bone growth were examined for the Libben Late Woodland and Bt-5 Late Archaic hunter-gatherer skeletal groups. Subadults included in the analyses ranged in age from birth to 10 years. The primary goals were to identify potential differences in relative tibia growth and evaluate the extent to which such differences were concordant with demographic and epidemiological characteristics of the two groups. Methods used were designed to minimize the shortcomings of unknown age and sex of the skeleton, small sample sizes, and population differences in adult size attained. Results showed that Bt-5 preadolescent growth performance and health status in general were superior to those of the Libben group. Modifications in the rate and timing of Libben tibia growth occurred early and were primarily restricted to the weaning period. It is suggested that high levels of infectious disease experienced in the first years of life at Libben played a substantial role in the etiology of early long bone growth retardation, a greater prevalence of iron deficiency anemia in the childhood years, and elevated levels of subadult morbidity and mortality compared to Bt-5. Paleodemographic, paleoepidemiological, and modern comparative population data that support these inferences are discussed. No evidence of chronic malnutrition owing to dietary inadequacy was observed for either group. Alternatively, higher population density and greater degree of sedentism alone may have been responsible for elevated disease loads at Libben compared to low levels that were observed for the seasonally mobile semisedentary Bt-5 hunter-gatherers.

  15. Internet and Mobile Technology Use Among Urban African American Parents: Survey Study of a Clinical Population

    PubMed Central

    Godoy, Leandra; Shabazz, Kanya

    2014-01-01

    Background There is considerable potential for mobile technologies to empower pediatric patients and families by improving their communication with health professionals. National surveys suggest minority parents frequently communicate via mobile technology, but it is uncertain how amenable they are to receiving health care information in this format. Although the low cost and far reach characteristics of mobile health (mHealth) technology makes it advantageous for communication with minority parents, data on acceptance are needed. Objective The objective of the study was to determine utilization of mobile and Internet technology by African American parents in an urban, underserved population, and to assess their interest in receiving health information via text messaging or other technologies (eg, social media and the Internet). Methods A survey was administered to parents of children aged 1-12 years covered by public insurance receiving care at 3 pediatric primary care centers in Washington, DC. Results The African American sample (N=302) was composed of primarily single (75.8%, 229/302) mothers. Almost half had more than a high school education (47.7%, 144/302) and incomes above US $25,000 per year (43.0%, 130/302). Most (97.0%, 293/302) reported owning a cell phone, of which 91.1% (275/302) used it to text and 78.5% (237/302) used it to access the Internet. Most had service plans with unlimited text and data, but 26.5% (80/302) experienced service interruptions in the previous year. Home Internet access was more prevalent among those with higher income (86.2%, 112/130), but it was still relatively pervasive among lower income families (66.9%, 83/124). In adjusted logistic regression models, African American mothers with income greater than US $25,000 annually were 4 times as likely to own a tablet computer than their lower income counterparts. Of the participants, 80.8% (244/302) used social networking, primarily Facebook, and 74.2% (224/302) were interested in

  16. STRATEGIES FOR EQUITABLE PHARMACOGENOMIC-GUIDED WARFARIN DOSING AMONG EUROPEAN AND AFRICAN AMERICAN INDIVIDUALS IN A CLINICAL POPULATION

    PubMed Central

    WILEY, LAURA K.; VANHOUTEN, JACOB P.; SAMUELS, DAVID C.; ALDRICH, MELINDA C.; RODEN, DAN M.; PETERSON, JOSH F.; DENNY, JOSHUA C.

    2017-01-01

    The blood thinner warfarin has a narrow therapeutic range and high inter- and intra-patient variability in therapeutic doses. Several studies have shown that pharmacogenomic variants help predict stable warfarin dosing. However, retrospective and randomized controlled trials that employ dosing algorithms incorporating pharmacogenomic variants under perform in African Americans. This study sought to determine if: 1) including additional variants associated with warfarin dose in African Americans, 2) predicting within single ancestry groups rather than a combined population, or 3) using percentage African ancestry rather than observed race, would improve warfarin dosing algorithms in African Americans. Using BioVU, the Vanderbilt University Medical Center biobank linked to electronic medical records, we compared 25 modeling strategies to existing algorithms using a cohort of 2,181 warfarin users (1,928 whites, 253 blacks). We found that approaches incorporating additional variants increased model accuracy, but not in clinically significant ways. Race stratification increased model fidelity for African Americans, but the improvement was small and not likely to be clinically significant. Use of percent African ancestry improved model fit in the context of race misclassification. PMID:27897005

  17. Epidemiological features of amyotrophic lateral sclerosis in a large clinic-based African American population.

    PubMed

    Kazamel, Mohamed; Cutter, Gary; Claussen, Gwendolyn; Alsharabati, Mohammad; Oh, Shin J; Lu, Liang; King, Peter H

    2013-09-01

    Our objective was to identify the main clinical and epidemiological features of ALS in a large cohort of African American (AA) patients and compare them to Caucasian (CA) patients in a clinic-based population. We retrospectively identified 207 patients who were diagnosed with ALS based on the revised El Escorial criteria (60 AA and 147 CA subjects). Patients were seen in the Neuromuscular Division at the University Medical Center. We compared epidemiological and clinical features of these two groups, focusing on age of onset and diagnosis, clinical presentation and survival. Results showed that AA patients had a significantly younger age of disease onset (55 years vs. 61 years for CA, p = 0.011) and were diagnosed at an earlier age (56 years vs. 62 years, p = 0.012). In younger ALS patients (< 45 years of age), there was a significant difference in gender frequency, with females predominating in the AA population and males in the CA population (p = 0.025). In a multivariable Cox proportional hazard model, survival rates were not different between the groups. In both groups, survival significantly increased with younger age. In conclusion, AA patients presented at an earlier age, but there was no difference in survival compared to CA patients. A gender reversal occurred in younger ALS patients, with AA patients more likely to be female and CA patients more likely to be male.

  18. Conservation and monitoring of a persecuted African lion population by Maasai warriors.

    PubMed

    Dolrenry, Stephanie; Hazzah, Leela; Frank, Laurence G

    2016-06-01

    Although Africa has many threatened species and biological hot spots, there are few citizen science schemes, particularly in rural communities, and there has been limited evaluation of existing programs. We engaged traditional Maasai warriors (pastoralist men aged 15 to 35) in community-based conservation and demographic monitoring of a persecuted African lion (Panthera leo) population. Through direct engagement, we investigated whether a citizen science approach employing local warriors, who had no formal education, could produce reliable data on the demographics, predation, and movements of a species with which their communities have been in conflict for generations. Warriors were given benefits such as literacy training and skill enhancement and engaged in the monitoring of the lions. The trained warriors reported on lion sign across an area nearly 4000 km(2) . Scientists worked together with the warriors to verify their reports and gather observations on the lion population. Using the verified reports and collected observations, we examined our scientific knowledge relative to the lion population preceding and during the citizen science program. Our observations showed that data quality and quantity improved with the involvement and training of the participants. Furthermore, because they engaged in conservation and gained personal benefits, the participants came to appreciate a species that was traditionally their foe. We believe engaging other local communities in biodiversity conservation and monitoring may be an effective conservation approach in rural Africa.

  19. Do microplastic loads reflect the population demographics along the southern African coastline?

    PubMed

    Nel, Holly Astrid; Hean, Jeffrey William; Noundou, Xavier Siwe; Froneman, Pierre William

    2017-02-15

    Plastic pollution is a major anthropogenic contaminant effecting the marine environment and is often associated with high human population densities and industrial activities. The microplastic (63 to 5000μm) burden of beach sediment and surf-zone water was investigated at selected sites along the entire length of the South African coastline. It was predicted that samples collected in areas of high population density, would contain a higher microplastic burden than those along coasts that demonstrate very low population densities. With the exception of water column microplastics within Richard's Bay Harbour (413.3±77.53particles·m(-3)) and Durban Harbour (1200±133.2particles·m(-3)), there were no significant spatial differences in microplastic loads. This supports the theory that harbours act as a source of microplastics for the surrounding marine environment. Additionally, the absence of any spatial variation highlights the possible long range distribution of microplastic pollutants by large scale ocean currents.

  20. Disparities in the Population Distribution of African American and Non-Hispanic White Smokers along the Quitting Continuum

    ERIC Educational Resources Information Center

    Trinidad, Dennis R.; Xie, Bin; Fagan, Pebbles; Pulvers, Kim; Romero, Devan R.; Blanco, Lyzette; Sakuma, Kari-Lyn K.

    2015-01-01

    Purpose: To examine disparities and changes over time in the population-level distribution of smokers along a cigarette quitting continuum among African American smokers compared with non-Hispanic Whites. Methods: Secondary data analyses of the 1999, 2002, 2005, and 2008 California Tobacco Surveys (CTS). The CTS are large, random-digit-dialed,…

  1. Polymorphisms of Estrogen Metabolism-Related Genes and Prostate Cancer Risk in Two Populations of African Ancestry

    PubMed Central

    Emeville, Elise; Ferdinand, Séverine; Punga, Augustin; Lufuma, Simon; Blanchet, Pascal; Romana, Marc; Multigner, Luc

    2016-01-01

    Background Estrogens are thought to play a critical role in prostate carcinogenesis. It has been suggested that polymorphisms of genes encoding enzymes involved in estrogen metabolism are risk factors for prostate cancer. However, few studies have been performed on populations of African ancestry, which are known to have a high risk of prostate cancer. Objective We investigated whether functional polymorphisms of CYP17, CYP19, CYP1B1, COMT and UGT1A1 affected the risk of prostate cancer in two different populations of African ancestry. Methods In Guadeloupe (French West Indies), we compared 498 prostate cancer patients and 565 control subjects. In Kinshasa (Democratic Republic of Congo), 162 prostate cancer patients were compared with 144 controls. Gene polymorphisms were determined by the SNaPshot technique or short tandem repeat PCR analysis. Logistic regression was used to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI). Results The AA genotype and the A allele of rs4680 (COMT) appeared to be inversely associated with the risk of prostate cancer in adjusted models for both Afro-Caribbean and native African men. For the A allele, a significant inverse association was observed among cases with low-grade Gleason scores and localized clinical stage, in both populations. Conclusions These preliminary results support the hypothesis that polymorphisms of genes encoding enzymes involved in estrogen metabolism may modulate the risk of prostate cancer in populations of African ancestry. PMID:27074016

  2. Tobago Prostate Survey: Prostate Cancer Risk in a Large Population-Based Study of Men of African Descent

    DTIC Science & Technology

    2001-06-01

    control studies suggest that sex hormone related polymorphisms and surrogate hormone measures are related to prostate cancer. This Tobago population...our hypothesis that, as observed in African American men, Afro-Caribbean men experience a high risk for prostate cancer. Results from the pilot case

  3. Adaptive divergence between lake and stream populations of an East African cichlid fish.

    PubMed

    Theis, Anya; Ronco, Fabrizia; Indermaur, Adrian; Salzburger, Walter; Egger, Bernd

    2014-11-01

    Divergent natural selection acting in different habitats may build up barriers to gene flow and initiate speciation. This speciation continuum can range from weak or no divergence to strong genetic differentiation between populations. Here, we focus on the early phases of adaptive divergence in the East African cichlid fish Astatotilapia burtoni, which occurs in both Lake Tanganyika (LT) and inflowing rivers. We first assessed the population structure and morphological differences in A. burtoni from southern LT. We then focused on four lake-stream systems and quantified body shape, ecologically relevant traits (gill raker and lower pharyngeal jaw) as well as stomach contents. Our study revealed the presence of several divergent lake-stream populations that rest at different stages of the speciation continuum, but show the same morphological and ecological trajectories along the lake-stream gradient. Lake fish have higher bodies, a more superior mouth position, longer gill rakers and more slender pharyngeal jaws, and they show a plant/algae and zooplankton-biased diet, whereas stream fish feed more on snails, insects and plant seeds. A test for reproductive isolation between closely related lake and stream populations did not detect population-assortative mating. Analyses of F1 offspring reared under common garden conditions indicate that the detected differences in body shape and gill raker length do not constitute pure plastic responses to different environmental conditions, but also have a genetic basis. Taken together, the A. burtoni lake-stream system constitutes a new model to study the factors that enhance and constrain progress towards speciation in cichlid fishes.

  4. Effects of Methyl Eugenol Feeding on Mating Compatibility of Asian Population of Bactrocera dorsalis (Diptera: Tephritidae) with African Population and with B. carambolae.

    PubMed

    Haq, Ihsan Ul; Vreysen, Marc J B; Schutze, Mark; Hendrichs, Jorge; Shelly, Todd

    2016-02-01

    Males of some species included in the Bactrocera dorsalis complex are strongly attracted to methyl eugenol (ME) (1,2-dimethoxy-4-(2-propenyl) benzene), a natural compound occurring in a variety of plant species. ME feeding of males of the B. dorsalis complex is known to enhance their mating competitiveness. Within B. dorsalis, recent studies show that Asian and African populations of B. dorsalis are sexually compatible, while populations of B. dorsalis and Bactrocera carambolae are relatively incompatible. The objectives of this study were to examine whether ME feeding by males affects mating compatibility between Asian and African populations of B. dorsalis and ME feeding reduces male mating incompatibility between B. dorsalis (Asian population) and B. carambolae. The data confirmed that Asian and African populations of B. dorsalis are sexually compatible for mating and showed that ME feeding only increased the number of matings. Though ME feeding also increased the number of matings of B. dorsalis (Asian population) and B. carambolae males but the sexual incompatibility between both species was not reduced by treatment with ME. These results conform to the efforts resolving the biological species limits among B. dorsalis complex and have implications for fruit fly control programs in fields and horticultural trade.

  5. Effects of Methyl Eugenol Feeding on Mating Compatibility of Asian Population of Bactrocera dorsalis (Diptera: Tephritidae) with African Population and with B. carambolae

    PubMed Central

    Haq, Ihsan ul; Vreysen, Marc J. B.; Schutze, Mark; Hendrichs, Jorge; Shelly, Todd

    2016-01-01

    Males of some species included in the Bactrocera dorsalis complex are strongly attracted to methyl eugenol (ME) (1,2-dimethoxy-4-(2-propenyl) benzene), a natural compound occurring in a variety of plant species. ME feeding of males of the B. dorsalis complex is known to enhance their mating competitiveness. Within B. dorsalis, recent studies show that Asian and African populations of B. dorsalis are sexually compatible, while populations of B. dorsalis and Bactrocera carambolae are relatively incompatible. The objectives of this study were to examine whether ME feeding by males affects mating compatibility between Asian and African populations of B. dorsalis and ME feeding reduces male mating incompatibility between B. dorsalis (Asian population) and B. carambolae. The data confirmed that Asian and African populations of B. dorsalis are sexually compatible for mating and showed that ME feeding only increased the number of matings. Though ME feeding also increased the number of matings of B. dorsalis (Asian population) and B. carambolae males but the sexual incompatibility between both species was not reduced by treatment with ME. These results conform to the efforts resolving the biological species limits among B. dorsalis complex and have implications for fruit fly control programs in fields and horticultural trade. PMID:26362991

  6. Principal component analysis under population genetic models of range expansion and admixture.

    PubMed

    François, Olivier; Currat, Mathias; Ray, Nicolas; Han, Eunjung; Excoffier, Laurent; Novembre, John

    2010-06-01

    In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agriculture, in which farmers expanded from the Near East approximately 10,000 years ago and replaced the resident hunter-gatherer populations with little or no interbreeding. These interpretations of the PC maps have been recently questioned as the original results can be reproduced under models of spatially covarying allele frequencies without any expansion. Here, we study PC maps for data simulated under models of range expansion and admixture. Our simulations include a spatially realistic model of Neolithic farmer expansion and assume various levels of interbreeding between farmer and resident hunter-gatherer populations. An important result is that under a broad range of conditions, the gradients in PC1 maps are oriented along a direction perpendicular to the axis of the expansion, rather than along the same axis as the expansion. We propose that this surprising pattern is an outcome of the "allele surfing" phenomenon, which creates sectors of high allele-frequency differentiation that align perpendicular to the direction of the expansion.

  7. Clinical outcome of skin yaws lesions after treatment with benzathinebenzylpenicillin in a pygmy population in Lobaye, Central African Republic

    PubMed Central

    2011-01-01

    Background Yaws is a bacterial skin and bone infectious disease caused by Treponema pallidum pertenue. It is endemic, particularly among pygmies in Central African Republic. To assess the clinical cure rate after treatment with benzathinepenicillin in this population, we conducted a cohort survey of 243 patients in the Lobaye region. Findings and conclusion The rate of healing of lesions after 5 months was 95.9%. This relatively satisfactory level of therapeutic response implies that yaws could be controlled in the Central African Republic. Thus, reinforcement of the management of new cases and of contacts is suggested. PMID:22171605

  8. Under-reporting of dietary energy intake in five populations of the African diaspora.

    PubMed

    Orcholski, Lindsay; Luke, Amy; Plange-Rhule, Jacob; Bovet, Pascal; Forrester, Terrence E; Lambert, Estelle V; Dugas, Lara R; Kettmann, Elizabeth; Durazo-Arvizu, Ramon A; Cooper, Richard S; Schoeller, Dale A

    2015-02-14

    Studies on the role of diet in the development of chronic diseases often rely on self-report surveys of dietary intake. Unfortunately, many validity studies have demonstrated that self-reported dietary intake is subject to systematic under-reporting, although the vast majority of such studies have been conducted in industrialised countries. The aim of the present study was to investigate whether or not systematic reporting error exists among the individuals of African ancestry (n 324) in five countries distributed across the Human Development Index (HDI) scale, a UN statistic devised to rank countries on non-income factors plus economic indicators. Using two 24 h dietary recalls to assess energy intake and the doubly labelled water method to assess total energy expenditure, we calculated the difference between these two values ((self-report - expenditure/expenditure) × 100) to identify under-reporting of habitual energy intake in selected communities in Ghana, South Africa, Seychelles, Jamaica and the USA. Under-reporting of habitual energy intake was observed in all the five countries. The South African cohort exhibited the highest mean under-reporting ( - 52·1% of energy) compared with the cohorts of Ghana ( - 22·5%), Jamaica ( - 17·9%), Seychelles ( - 25·0%) and the USA ( - 18·5%). BMI was the most consistent predictor of under-reporting compared with other predictors. In conclusion, there is substantial under-reporting of dietary energy intake in populations across the whole range of the HDI, and this systematic reporting error increases according to the BMI of an individual.

  9. Sex difference of autosomal alleles in populations of European and African descent

    PubMed Central

    Zuo, Lingjun; Wang, Tong; Lin, Xiandong; Wang, Jijun; Tan, Yunlong; Wang, Xiaoping; Yu, Xueqing; Luo, Xingguang

    2015-01-01

    In the present study, we aimed to report the individual sex-different genetic markers across autosomes in European- and African-origin populations. A total of 8,400 females and 8,081 males in 19 independent cohorts were genotyped across genomes using Illumina or Affymetrix arrays. The allele frequencies were compared between females and males in 9 non-clean cohorts (with some human disease traits) using genome-wide logistic regression and then the nominally significant associations were replicated across 10 clean cohorts (without disease traits). Meta-analysis was performed to derive the combined p values across all cohorts. We found 13 markers that were genome-wide significant (p≤5×10−8) between females and males in the meta-analysis of all cohorts of European descent, including rs7740449 at SYNE1, rs7531151 at PLD5, rs697455 at PPP1R12B, rs6745746 at LOC100128413, rs17000079 at PARM1, rs11948070 at PDE4D, rs7801825 at INSIG1, rs9551642 at MTUS2, rs2932174 at TPTE2, rs1961597 at SALL3, rs4117529 at METTL4, rs6021473 at SALL4 and rs6092466 at RAE1, and one marker, i.e., rs10145208 at PCNX, that was genome-wide significant in the meta-analysis of all cohorts of African descent. The most robust finding was rs7740449 at SYNE1, next to ESR1. We conclude that there are many sex-different markers on autosomes. These markers may be informative in differentiating females and males. PMID:26702338

  10. Genetic risk factors for nonsyndromic cleft lip with or without cleft palate in a Brazilian population with high African ancestry.

    PubMed

    do Rego Borges, Andrea; Sá, Jamile; Hoshi, Ryuichi; Viena, Camila Sane; Mariano, Lorena C; de Castro Veiga, Patricia; Medrado, Alena Peixoto; Machado, Renato Assis; de Aquino, Sibele Nascimento; Messetti, Ana Camila; Spritz, Richard A; Coletta, Ricardo D; Reis, Silvia R A

    2015-10-01

    Nonsyndromic cleft lip with or without cleft palate (NSCL ± P) is the most common orofacial birth defect, exhibiting variable prevalence around the world, often attributed to ethnic and environmental differences. Linkage analyses and genome-wide association studies have identified several genomic susceptibility regions for NSCL ± P, mostly in European-derived or Asian populations. Genetic predisposition to NSCL ± P is ethnicity-dependent, and the genetic basis of susceptibility to NSCL ± P likely varies among populations. The population of Brazil is highly admixed, with highly variable ancestry; thus, the genetic determinants of NSCL ± P susceptibility may be quite different. This study tested association of 8 single-nucleotide polymorphisms (SNPs), previously identified by genome-wide studies in other populations, with NSCL ± P in a Brazilian population with high African ancestry. SNPs rs560426, rs642961, rs1530300, rs987525, rs3758249, rs7078160, rs17085106, and rs13041247 were genotyped in 293 Brazilian patients with NSCL ± P and 352 unaffected Brazilian controls. Each sample was also genotyped for 40 biallelic short insertion/deletion polymorphic markers to characterize genetic ancestry. The average African ancestry background was 31.1% for the NSCL ± P group and 36.7% for the control group. After adjustment for ancestry and multiple testing, the minor alleles of rs3758249 (OR: 1.58, 95% CI: 1.25-2.01, P = 0.0001) and rs7078160 (OR: 1.59, 95% CI: 1.21-2.07, P = 0.0002) were significantly associated with risk of NSCL ± P. Polymorphisms located in IRF6 (rs642961) and 8q24 (rs1530300 and rs987525) showed marginal associations in this Brazilian population with high African ancestry. These results indicate that rs3758249 at 9q22 and rs7078160 at 10q25.3 represent risk loci for NSCL ± P in the Brazilian population with high African ancestry.

  11. Firearm and Nonfirearm Homicide in 5 South African Cities: A Retrospective Population-Based Study

    PubMed Central

    Thompson, Mary Lou; Myers, Jonathan E.

    2014-01-01

    Objective. We assessed the effectiveness of South Africa’s Firearm Control Act (FCA), passed in 2000, on firearm homicide rates compared with rates of nonfirearm homicide across 5 South African cities from 2001 to 2005. Methods. We conducted a retrospective population-based study of 37 067 firearm and nonfirearm homicide cases. Generalized linear models helped estimate and compare time trends of firearm and nonfirearm homicides, adjusting for age, sex, race, day of week, city, year of death, and population size. Results. There was a statistically significant decreasing trend regarding firearm homicides from 2001, with an adjusted year-on-year homicide rate ratio of 0.864 (95% confidence interval [CI] = 0.848, 0.880), representing a decrease of 13.6% per annum. The year-on-year decrease in nonfirearm homicide rates was also significant, but considerably lower at 0.976 (95% CI = 0.954, 0.997). Results suggest that 4585 (95% CI = 4427, 4723) lives were saved across 5 cities from 2001 to 2005 because of the FCA. Conclusions. Strength, timing and consistent decline suggest stricter gun control mediated by the FCA accounted for a significant decrease in homicide overall, and firearm homicide in particular, during the study period. PMID:24432917

  12. Context-dependent survival, fecundity and predicted population-level consequences of brucellosis in African buffalo.

    PubMed

    Gorsich, Erin E; Ezenwa, Vanessa O; Cross, Paul C; Bengis, Roy G; Jolles, Anna E

    2015-07-01

    Chronic infections may have negative impacts on wildlife populations, yet their effects are difficult to detect in the absence of long-term population monitoring. Brucella abortus, the bacteria responsible for bovine brucellosis, causes chronic infections and abortions in wild and domestic ungulates, but its impact on population dynamics is not well understood. We report infection patterns and fitness correlates of bovine brucellosis in African buffalo based on (1) 7 years of cross-sectional disease surveys and (2) a 4-year longitudinal study in Kruger National Park (KNP), South Africa. We then used a matrix population model to translate these observed patterns into predicted population-level effects. Annual brucellosis seroprevalence ranged from 8·7% (95% CI = 1·8-15·6) to 47·6% (95% CI = 35·1-60·1) increased with age until adulthood (>6) and varied by location within KNP. Animals were on average in worse condition after testing positive for brucellosis (F = -5·074, P < 0·0001), and infection was associated with a 2·0 (95% CI = 1·1-3·7) fold increase in mortality (χ(2)  = 2·039, P = 0·036). Buffalo in low body condition were associated with lower reproductive success (F = 2·683, P = 0·034), but there was no association between brucellosis and pregnancy or being observed with a calf. For the range of body condition scores observed in the population, the model-predicted growth rate was λ = 1·11 (95% CI = 1·02-1·21) in herds without brucellosis and λ = 1·00 (95% CI = 0·85-1·16) when brucellosis seroprevalence was 30%. Our results suggest that brucellosis infection can potentially result in reduced population growth rates, but because these effects varied with demographic and environmental conditions, they may remain unseen without intensive, longitudinal monitoring.

  13. [Partnership in population and development. First African Meeting on South-South Partnership in Reproductive Health and Population, Tunis, July 9-11, 1997].

    PubMed

    1997-09-01

    10 southern hemisphere countries (Bangladesh, Colombia, Egypt, Kenya, Indonesia, Morocco, Mexico, Thailand, Tunisia, and Zimbabwe) have created a new international initiative known as the "Partnership in Population and Development." The principal objective is to create a more effective mechanism for developing countries to share their experiences through technical assistance and south-south coordination. The 10 countries have developed population and family planning programs over the past 2 decades with the support of the Rockefeller Foundation, World Bank, and UN Population Fund. The Partnership in Population and Development is directed by an Administrative Council composed of representatives from each country, who are generally the highest officials in the area of reproductive health and family planning. The First African Meeting for South-South Cooperation in Reproductive Health/Family Planning and Population, held in Tunis in July 1997, was organized in collaboration with the Secretariat of the partnership and with the participation of representatives of 12 French-speaking African countries and of several international organizations. The meeting allowed the participants to express their opinions concerning the principles of the South-South Partnership and the practical mechanisms that would allow it to facilitate exchanges of information and experiences between African countries.

  14. Hunter-Gatherer Responses to the 8.2 Ka Cold Event in the Fennoscandian Arctic

    NASA Astrophysics Data System (ADS)

    Manninen, M. A.

    2014-12-01

    Because of a marked influence of warm Atlantic water to primary productivity in the Barents Sea, the marine ecosystem in northernmost Fennoscandia is sensitive to disturbances in the North Atlantic oceanographic system. The 8.2 ka climate event, according to current knowledge, was triggered by a disturbance in the North Atlantic Thermohaline circulation. This suggests concurrent and strong climatic and marine cooling in the area covering the northernmost parts of Finland, Norway, and Sweden during the climate event. In this area ecosystem response to the 8.2 ka event can therefore be expected to have been prominent, which in turn should be reflected in the contemporary human socio-economic systems. A study that employs lithic technological, statistical, and spatial analyses of Late Mesolithic (ca. 8450-6850 cal BP) lithic technology and settlement configuration in the area indicates that lithic technology and settlement patterns were reorganised following the climatic and marine cooling. The studied groups changed their lithic technology as a result of developments that led to increased use of terrestrial resources and an accompanying long-distance coast/inland residential mobility pattern. Besides lithic technological changes and long-distance mobility on land, decreased marine productivity probably also explains the disappearance of semi-subterranean houses from the coast at ca. 8200 cal BP, while their reappearance after ca. 7500 cal BP can be linked to a increased influx of warm salty water into the Barents Sea. The results suggest that in the past a long period of decreased influx of Atlantic water into the Barents Sea has had disastrous consequences for the marine ecosystem. At present the Barents Sea fisheries have notable economic importance and produce, for example, over 90% of the Norwegian Atlantic cod (Gadus morhua) catch.

  15. Sleep paralysis and trauma, psychiatric symptoms and disorders in an adult African American population attending primary medical care.

    PubMed

    Mellman, Thomas A; Aigbogun, Notalelomwan; Graves, Ruth Elaine; Lawson, William B; Alim, Tanya N

    2008-01-01

    The occurrence of sleep paralysis (SP) absent narcolepsy appears to not be uncommon in African Americans and probably other non-European groups. Prior research has linked SP to trauma and psychiatric disorders and suggested a specific relationship to panic disorder in African Americans. The objective of our study was to evaluate relationships of SP with trauma, concurrent psychiatric symptoms and lifetime psychiatric diagnoses in an adult African American population recruited from primary care. Cross sectional study with surveys and diagnostic interviews; Patients attending primary care clinics filled out a survey that determined the 6 month prevalence and associated features of SP, a panic disorder screen, the self-rated Hamilton Depression Scale, and an inventory of trauma exposure. A subset of trauma-exposed participants (N = 142) received comprehensive diagnostic interviews that incorporated the Structured Clinical Interview for DSM-IV and the Clinician Assessed PTSD Scale. Four hundred and forty-one adults participated (mean age-40.0 SD = 13.3, 68% female, 95% African American). Fourteen percent endorsed recent SP. In approximately 1/3 of those with SP, episodes also featured panic symptoms. SP was strongly associated with trauma history, and concurrent anxiety and mood symptoms. SP was not associated with specific psychiatric disorders other than lifetime (but not current) alcohol or substance use disorders. Our findings suggest that SP is not uncommon in adult African Americans and is associated with trauma and concurrent distress but not with a specific psychiatric diagnosis.

  16. Population pharmacokinetics of rifapentine and its primary desacetyl metabolite in South African tuberculosis patients.

    PubMed

    Langdon, Grant; Wilkins, Justin; McFadyen, Lynn; McIlleron, Helen; Smith, Peter; Simonsson, Ulrika S H

    2005-11-01

    This study was designed to describe the population pharmacokinetics of rifapentine (RFP) and 25-desacetyl RFP in a South African pulmonary tuberculosis patient population. Special reference was made to studying the influence of previous exposure to rifampin (RIF) and the variability in pharmacokinetic parameters between patients and between occasions and the influence of different covariates. Patients were included in the study if they had been receiving first-line antimycobacterial therapy (rifampin, isoniazid, pyrazinamide, and ethambutol) for not less than 4 weeks and not more than 6 weeks and were divided into three RFP dosage groups based on weight: 600 mg, <45 kg; 750 mg, 46 to 55 kg; and 900 mg, >55 kg. Participants received a single oral dose of RFP together with concomitant antimycobacterial agents, excluding RIF, on study days 1 and 5 after they ingested a soup-based meal. The RFP and 25-desacetyl RFP concentration-time data were analyzed by nonlinear mixed-effect modeling using NONMEM. The pharmacokinetics of the parent drug were modeled separately, and the individual pharmacokinetic parameters were used as inputs for the 25-desacetyl RFP pharmacokinetic model. A one-compartment disposition model was found to best describe the data for both the parent and the metabolite, and the metabolite was assumed to be formed only from the central compartment of the parent drug. Prior treatment with RIF did not alter the pharmacokinetics of RFP but appeared to increase the excretion of 25-desacetyl RFP in a nonlinear fashion. The RFP oral clearance and volume of distribution were found to increase by 0.049 liter/h and 0.691 liter, respectively, with a 1-kg increase from the median weight of 50 kg. The oral clearance of 25-desacetyl RFP was found to be 35% lower in female patients. The model developed here describes the population pharmacokinetics of RFP and its primary metabolite in tuberculosis patients and includes the effects of prior administration with RIF and

  17. Population Pharmacokinetics of Rifapentine and Its Primary Desacetyl Metabolite in South African Tuberculosis Patients

    PubMed Central

    Langdon, Grant; Wilkins, Justin; McFadyen, Lynn; McIlleron, Helen; Smith, Peter; Simonsson, Ulrika S. H.

    2005-01-01

    This study was designed to describe the population pharmacokinetics of rifapentine (RFP) and 25-desacetyl RFP in a South African pulmonary tuberculosis patient population. Special reference was made to studying the influence of previous exposure to rifampin (RIF) and the variability in pharmacokinetic parameters between patients and between occasions and the influence of different covariates. Patients were included in the study if they had been receiving first-line antimycobacterial therapy (rifampin, isoniazid, pyrazinamide, and ethambutol) for not less than 4 weeks and not more than 6 weeks and were divided into three RFP dosage groups based on weight: 600 mg, <45 kg; 750 mg, 46 to 55 kg; and 900 mg, >55 kg. Participants received a single oral dose of RFP together with concomitant antimycobacterial agents, excluding RIF, on study days 1 and 5 after they ingested a soup-based meal. The RFP and 25-desacetyl RFP concentration-time data were analyzed by nonlinear mixed-effect modeling using NONMEM. The pharmacokinetics of the parent drug were modeled separately, and the individual pharmacokinetic parameters were used as inputs for the 25-desacetyl RFP pharmacokinetic model. A one-compartment disposition model was found to best describe the data for both the parent and the metabolite, and the metabolite was assumed to be formed only from the central compartment of the parent drug. Prior treatment with RIF did not alter the pharmacokinetics of RFP but appeared to increase the excretion of 25-desacetyl RFP in a nonlinear fashion. The RFP oral clearance and volume of distribution were found to increase by 0.049 liter/h and 0.691 liter, respectively, with a 1-kg increase from the median weight of 50 kg. The oral clearance of 25-desacetyl RFP was found to be 35% lower in female patients. The model developed here describes the population pharmacokinetics of RFP and its primary metabolite in tuberculosis patients and includes the effects of prior administration with RIF and

  18. Common biological networks underlie genetic risk for alcoholism in African- and European-American populations

    PubMed Central

    Kos, Mark Z.; Yan, Jia; Dick, Danielle M.; Agrawal, Arpana; Bucholz, Kathleen K.; Rice, John P.; Johnson, Eric O.; Schuckit, Marc; Kuperman, Sam; Kramer, John; Goate, Alison M.; Tischfield, Jay A.; Foroud, Tatiana; Nurnberger, John; Hesselbrock, Victor; Porjesz, Bernice; Bierut, Laura J.; Edenberg, Howard J.; Almasy, Laura

    2013-01-01

    Alcohol dependence (AD) is a heritable substance addiction with adverse physical and psychological consequences, representing a major health and economic burden on societies worldwide. Genes thus far implicated via linkage, candidate gene and genome-wide association studies (GWAS) account for only a small fraction of its overall risk, with effects varying across ethnic groups. Here we investigate the genetic architecture of alcoholism and report on the extent to which common, genome-wide SNPs collectively account for risk of AD in two US populations, African-Americans (AAs) and European-Americans (EAs). Analyzing GWAS data for two independent case-control sample sets, we compute polymarker scores that are significantly associated with alcoholism (P=1.64 × 10−3 and 2.08 × 10−4 for EAs and AAs, respectively), reflecting the small individual effects of thousands of variants derived from patterns of allelic architecture that are population-specific. Simulations show that disease models based on rare and uncommon causal variants (MAF<0.05) best fit the observed distribution of polymarker signals. When scoring bins were annotated for gene location and examined for constituent biological networks, gene enrichment is observed for several cellular processes and functions in both EA and AA populations, transcending their underlying allelic differences. Our results reveal key insights into the complex etiology of AD, raising the possibility of an important role for rare and uncommon variants, and identify polygenic mechanisms that encompass a spectrum of disease liability, with some, such as chloride transporters and glycine metabolism genes, displaying subtle, modifying effects that are likely to escape detection in most GWAS designs. PMID:23607416

  19. Common biological networks underlie genetic risk for alcoholism in African- and European-American populations.

    PubMed

    Kos, M Z; Yan, J; Dick, D M; Agrawal, A; Bucholz, K K; Rice, J P; Johnson, E O; Schuckit, M; Kuperman, S; Kramer, J; Goate, A M; Tischfield, J A; Foroud, T; Nurnberger, J; Hesselbrock, V; Porjesz, B; Bierut, L J; Edenberg, H J; Almasy, L

    2013-07-01

    Alcohol dependence (AD) is a heritable substance addiction with adverse physical and psychological consequences, representing a major health and economic burden on societies worldwide. Genes thus far implicated via linkage, candidate gene and genome-wide association studies (GWAS) account for only a small fraction of its overall risk, with effects varying across ethnic groups. Here we investigate the genetic architecture of alcoholism and report on the extent to which common, genome-wide SNPs collectively account for risk of AD in two US populations, African-Americans (AAs) and European-Americans (EAs). Analyzing GWAS data for two independent case-control sample sets, we compute polymarker scores that are significantly associated with alcoholism (P = 1.64 × 10(-3) and 2.08 × 10(-4) for EAs and AAs, respectively), reflecting the small individual effects of thousands of variants derived from patterns of allelic architecture that are population specific. Simulations show that disease models based on rare and uncommon causal variants (MAF < 0.05) best fit the observed distribution of polymarker signals. When scoring bins were annotated for gene location and examined for constituent biological networks, gene enrichment is observed for several cellular processes and functions in both EA and AA populations, transcending their underlying allelic differences. Our results reveal key insights into the complex etiology of AD, raising the possibility of an important role for rare and uncommon variants, and identify polygenic mechanisms that encompass a spectrum of disease liability, with some, such as chloride transporters and glycine metabolism genes, displaying subtle, modifying effects that are likely to escape detection in most GWAS designs.

  20. Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection.

    PubMed

    Bhatia, Gaurav; Patterson, Nick; Pasaniuc, Bogdan; Zaitlen, Noah; Genovese, Giulio; Pollack, Samuela; Mallick, Swapan; Myers, Simon; Tandon, Arti; Spencer, Chris; Palmer, Cameron D; Adeyemo, Adebowale A; Akylbekova, Ermeg L; Cupples, L Adrienne; Divers, Jasmin; Fornage, Myriam; Kao, W H Linda; Lange, Leslie; Li, Mingyao; Musani, Solomon; Mychaleckyj, Josyf C; Ogunniyi, Adesola; Papanicolaou, George; Rotimi, Charles N; Rotter, Jerome I; Ruczinski, Ingo; Salako, Babatunde; Siscovick, David S; Tayo, Bamidele O; Yang, Qiong; McCarroll, Steve; Sabeti, Pardis; Lettre, Guillaume; De Jager, Phil; Hirschhorn, Joel; Zhu, Xiaofeng; Cooper, Richard; Reich, David; Wilson, James G; Price, Alkes L

    2011-09-09

    The study of recent natural selection in human populations has important applications to human history and medicine. Positive natural selection drives the increase in beneficial alleles and plays a role in explaining diversity across human populations. By discovering traits subject to positive selection, we can better understand the population level response to environmental pressures including infectious disease. Our study examines unusual population differentiation between three large data sets to detect natural selection. The populations examined, African Americans, Nigerians, and Gambians, are genetically close to one another (F(ST) < 0.01 for all pairs), allowing us to detect selection even with moderate changes in allele frequency. We also develop a tree-based method to pinpoint the population in which selection occurred, incorporating information across populations. Our genome-wide significant results corroborate loci previously reported to be under selection in Africans including HBB and CD36. At the HLA locus on chromosome 6, results suggest the existence of multiple, independent targets of population-specific selective pressure. In addition, we report a genome-wide significant (p = 1.36 × 10(-11)) signal of selection in the prostate stem cell antigen (PSCA) gene. The most significantly differentiated marker in our analysis, rs2920283, is highly differentiated in both Africa and East Asia and has prior genome-wide significant associations to bladder and gastric cancers.

  1. A cryptic mitochondrial DNA link between North European and West African dogs.

    PubMed

    Adeola, Adeniyi C; Ommeh, Sheila C; Song, Jiao-Jiao; Olaogun, S Charles; Sanke, Oscar J; Yin, Ting-Ting; Wang, Guo-Dong; Wu, Shi-Fang; Zhou, Zhong-Yin; Lichoti, Jacqueline K; Agwanda, Bernard R; Dawuda, Philip M; Murphy, Robert W; Peng, Min-Sheng; Zhang, Ya-Ping

    2016-11-24

    Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1 (but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.

  2. Genetic variation in IGFBP2 and IGFBP5 is associated with breast cancer in populations of African descent.

    PubMed

    Garner, Chad P; Ding, Yuan C; John, Esther M; Ingles, Sue A; Olopade, Olufunmilayo I; Huo, Dezheng; Adebamowo, Clement; Ogundiran, Temidayo; Neuhausen, Susan L

    2008-04-01

    The insulin-like growth factor (IGF) signaling pathway is thought to play a major role in the etiology of breast cancer. Although incidence rates of breast cancer overall are lower in African Americans than in Caucasians, African-American women have a higher incidence under age 40 years, are diagnosed with more advanced disease, and have poorer prognosis. We investigated the association of breast cancer and genetic variants in genes in the IGF signaling pathway in a population-based case-control study of African-American women. We found significant associations at a locus encompassing parts of the IGFBP2 and IGFBP5 genes on chromosome 2q35, which we then replicated in a case-control study of Nigerian women. Based on those initial findings, we genotyped a total of 34 single nucleotide polymorphisms (SNPs) across the region in both study populations. Statistically significant associations with breast cancer were observed across approximately 50 kb of DNA sequence encompassing three exons in the 3' end of IGFBP2 and three exons in the 3' end of IGFBP5. SNPs were associated with breast cancer risk with P values as low as P = 0.0038 and P = 0.01 in African-Americans and Nigerians, respectively. This study is the first to report associations between genetic variants in IGFBP2 and IGFBP5 and breast cancer risk.

  3. Analysis of betaS and betaA genes in a Mexican population with African roots.

    PubMed

    Magaña, María Teresa; Ongay, Zoyla; Tagle, Juan; Bentura, Gilberto; Cobián, José G; Perea, F Javier; Casas-Castañeda, Maricela; Sánchez-López, Yoaly J; Ibarra, Bertha

    2002-01-01

    To investigate the origin of the beta(A) and beta(S) genes in a Mexican population with African roots and a high frequency of hemoglobin S, we analyzed 467 individuals (288 unrelated) from different towns in the states of Guerrero and Oaxaca in the Costa Chica region. The frequency of the sickle-cell trait was 12.8%, which may represent a public health problem. The frequencies of the beta-haplotypes were determined from 350 nonrelated chromosomes (313 beta(A) and 37 beta(S)). We observed 15 different beta(A) haplotypes, the most common of which were haplotypes 1 (48.9%), 2 (13.4%), and 3 (13.4%). The calculation of pairwise distributions and Nei's genetic distance analysis using 32 worldwide populations showed that the beta(A) genes are more closely related to those of Mexican Mestizos and North Africans. Bantu and Benin haplotypes and haplotype 9 were related to the beta(S) genes, with frequencies of 78.8, 18.2, and 3.0%, respectively. Comparison of these haplotypes with 17 other populations revealed a high similitude with the population of the Central African Republic. These data suggest distinct origins for the beta(A) and beta(S) genes in Mexican individuals from the Costa Chica region.

  4. A Review of Dietary Surveys in the Adult South African Population from 2000 to 2015.

    PubMed

    Mchiza, Zandile J; Steyn, Nelia P; Hill, Jillian; Kruger, Annamarie; Schönfeldt, Hettie; Nel, Johanna; Wentzel-Viljoen, Edelweiss

    2015-09-23

    One serious concern of health policymakers in South Africa is the fact that there is no national data on the dietary intake of adult South Africans. The only national dietary study was done in children in 1999. Hence, it becomes difficult to plan intervention and strategies to combat malnutrition without national data on adults. The current review consequently assessed all dietary studies in adults from 2000 to June 2015 in an attempt to portray typical adult dietary intakes and to assess possible dietary deficiencies. Notable findings were that, in South Africa micronutrient deficiencies are still highly prevalent and energy intakes varied between very low intakes in informal settlements to very high intakes in urban centers. The most commonly deficient food groups observed are fruit and vegetables, and dairy. This has been attributed to high prices and lack of availability of these food groups in poorer urban areas and townships. In rural areas, access to healthy foods also remains a problem. A national nutrition monitoring system is recommended in order to identify dietary deficiencies in specific population groups.

  5. A Review of Dietary Surveys in the Adult South African Population from 2000 to 2015

    PubMed Central

    Mchiza, Zandile J.; Steyn, Nelia P.; Hill, Jillian; Kruger, Annamarie; Schönfeldt, Hettie; Nel, Johanna; Wentzel-Viljoen, Edelweiss

    2015-01-01

    One serious concern of health policymakers in South Africa is the fact that there is no national data on the dietary intake of adult South Africans. The only national dietary study was done in children in 1999. Hence, it becomes difficult to plan intervention and strategies to combat malnutrition without national data on adults. The current review consequently assessed all dietary studies in adults from 2000 to June 2015 in an attempt to portray typical adult dietary intakes and to assess possible dietary deficiencies. Notable findings were that, in South Africa micronutrient deficiencies are still highly prevalent and energy intakes varied between very low intakes in informal settlements to very high intakes in urban centers. The most commonly deficient food groups observed are fruit and vegetables, and dairy. This has been attributed to high prices and lack of availability of these food groups in poorer urban areas and townships. In rural areas, access to healthy foods also remains a problem. A national nutrition monitoring system is recommended in order to identify dietary deficiencies in specific population groups. PMID:26404371

  6. Culturally Competent Strategies for Recruitment and Retention of African-American Populations into Clinical Trials

    PubMed Central

    Otado, Jane; Kwagyan, John; Edwards, Diana; Ukaegbu, Alice; Rockcliffe, Faun; Osafo, Nana

    2015-01-01

    Purpose To identify successful recruitment strategies, challenges and best practices for researchers to engage African American communities in clinical studies taken into consideration target participants’ culture and context. Methods We reviewed 50 studies conducted from 2001-2012 at an inner-city research center to determine the type, duration, anticipated enrollments and actual enrollments. Survey was sent to study coordinators to obtain data on recruitment and retention strategies, challenges and dropout rates. We also interviewed 25 study coordinators on challenges and strategies. Results Of the 50 studies, 24 had completed recruitment at the time of this report. The completed studies achieved a median recruitment rate of 88% [range: 50-110]. Successful recruitment and retention strategies included: field-based strategy and snowballing. Major barriers were: distrust, compensation, education disadvantage, lack of interest and inability to have study partner. Strategies to reduce barriers included providing informational sessions, disseminating newsletters about study outcomes. Best practices include being culturally sensitive including demonstrating a caring attitude and being responsive to participants needs. Conclusions Cultural competence is critical in order to design and implement successful recruitment strategies in this population. Research teams should comprised of multi-ethnic staff, involve the community, demonstrate trust and deliver concise education of the research endeavor. PMID:25974328

  7. Subarachnoid hemorrhage in the African-American population: a cooperative study.

    PubMed Central

    Dennis, G. C.; Welch, B.; Cole, A. N.; Mendoza, R.; Morgan, J.; Epps, J.; Bernard, E.; St Louis, P.

    1997-01-01

    The clinical outcome of patients following subarachnoid hemorrhage is complicated by delayed cerebral ischemia and contributing factors such as hypertension. To observe the impact of hypertension and delayed cerebral ischemia on the outcome of a predominantly African-American cohort following subarachnoid hemorrhage, both retrospective (n = 42) and prospective (n = 21) studies were conducted. In the total pool (n = 63), the mean age was 49.7 years (range: 17 to 80) with a preponderance of female patients (70%). Aneurysm formation was significant in the region of the posterior communicating artery. Of the patients reviewed, 73.8% had preexisting hypertension and 45.9% developed delayed cerebral ischemia. Approximately 89% of the patients who suffered from delayed cerebral ischemia had hypertension. Results failed to display any significant beneficial association between the use of the calcium channel blocker nimodipine and delayed cerebral ischemia. Use of the antifibrinolytic drug aminocaproic acid demonstrated a worse patient outcome. It is not recommended that aminocaproic acid be used in this population. Subsequently, due to the proportional occurrence of delayed cerebral ischemia in hypertensive patients following subarachnoid hemorrhage, it is suggested that prophylactic surgical management of unruptured intracranial aneurysms be considered in hypertensive patients. Further study is needed to discern the association between hypertension, delayed cerebral ischemia, and stroke in patients following subarachnoid hemorrhage. PMID:9046763

  8. Genetic architecture of skin and eye color in an African-European admixed population.

    PubMed

    Beleza, Sandra; Johnson, Nicholas A; Candille, Sophie I; Absher, Devin M; Coram, Marc A; Lopes, Jailson; Campos, Joana; Araújo, Isabel Inês; Anderson, Tovi M; Vilhjálmsson, Bjarni J; Nordborg, Magnus; Correia E Silva, António; Shriver, Mark D; Rocha, Jorge; Barsh, Gregory S; Tang, Hua

    2013-03-01

    Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3 × 10(-62), SLC24A5 P = 9.6 × 10(-9)) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4 × 10(-27), TYR P = 1.1 × 10(-9), APBA2[OCA2] P = 1.5 × 10(-8), SLC45A2 P = 6 × 10(-9)) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.

  9. Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape.

    PubMed

    de Wit, Erika; Delport, Wayne; Rugamika, Chimusa E; Meintjes, Ayton; Möller, Marlo; van Helden, Paul D; Seoighe, Cathal; Hoal, Eileen G

    2010-08-01

    Admixed populations present unique opportunities to discover the genetic factors underlying many multifactorial diseases. The geographical position and complex history of South Africa has led to the establishment of the unique admixed population known as the South African Coloured. Not much is known about the genetic make-up of this population, and the historical record is patchy. We genotyped 959 individuals from the Western Cape area, self-identified as belonging to this population, using the Affymetrix 500k genotyping platform. This resulted in nearly 75,000 autosomal SNPs that could be compared with populations represented in the International HapMap Project and the Human Genome Diversity Project. Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan (32-43%), Bantu-speaking Africans (20-36%), European (21-28%) and a smaller Asian contribution (9-11%), depending on the model used. This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population.

  10. Genome-Wide Association of Body Fat Distribution in African Ancestry Populations Suggests New Loci

    PubMed Central

    Lange, Leslie; Demerath, Ellen W.; Palmas, Walter; Wojczynski, Mary K.; Ellis, Jaclyn C.; Vitolins, Mara Z.; Liu, Simin; Papanicolaou, George J.; Irvin, Marguerite R.; Xue, Luting; Griffin, Paula J.; Nalls, Michael A.; Adeyemo, Adebowale; Liu, Jiankang; Li, Guo; Ruiz-Narvaez, Edward A.; Chen, Wei-Min; Chen, Fang; Henderson, Brian E.; Millikan, Robert C.; Ambrosone, Christine B.; Strom, Sara S.; Guo, Xiuqing; Andrews, Jeanette S.; Sun, Yan V.; Mosley, Thomas H.; Yanek, Lisa R.; Shriner, Daniel; Haritunians, Talin; Rotter, Jerome I.; Speliotes, Elizabeth K.; Smith, Megan; Rosenberg, Lynn; Mychaleckyj, Josyf; Nayak, Uma; Spruill, Ida; Garvey, W. Timothy; Pettaway, Curtis; Nyante, Sarah; Bandera, Elisa V.; Britton, Angela F.; Zonderman, Alan B.; Rasmussen-Torvik, Laura J.; Chen, Yii-Der Ida; Ding, Jingzhong; Lohman, Kurt; Kritchevsky, Stephen B.; Zhao, Wei; Peyser, Patricia A.; Kardia, Sharon L. R.; Kabagambe, Edmond; Broeckel, Ulrich; Chen, Guanjie; Zhou, Jie; Wassertheil-Smoller, Sylvia; Neuhouser, Marian L.; Rampersaud, Evadnie; Psaty, Bruce; Kooperberg, Charles; Manson, JoAnn E.; Kuller, Lewis H.; Ochs-Balcom, Heather M.; Johnson, Karen C.; Sucheston, Lara; Ordovas, Jose M.; Palmer, Julie R.; Haiman, Christopher A.; McKnight, Barbara; Howard, Barbara V.; Becker, Diane M.; Bielak, Lawrence F.; Liu, Yongmei; Allison, Matthew A.; Grant, Struan F. A.; Burke, Gregory L.; Patel, Sanjay R.; Schreiner, Pamela J.; Borecki, Ingrid B.; Evans, Michele K.; Taylor, Herman; Sale, Michele M.; Howard, Virginia; Carlson, Christopher S.; Rotimi, Charles N.; Cushman, Mary; Harris, Tamara B.; Reiner, Alexander P.; Cupples, L. Adrienne; North, Kari E.; Fox, Caroline S.

    2013-01-01

    Central obesity, measured by waist circumference (WC) or waist-hip ratio (WHR), is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS) of fat distribution among those of predominantly African ancestry (AA). We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1). Overall, 25 SNPs with single genomic control (GC)-corrected p-values<5.0×10−6 were followed-up (stage 2) in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA) WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10−8 for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10−8 for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5×10−8; RREB1: p = 5.7×10−8). Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region) in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN). Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02). In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce

  11. Ethical and legal implications of whole genome and whole exome sequencing in African populations

    PubMed Central

    2013-01-01

    limited settings. Summary We conclude that, in order to meet the unique requirements of performing next generation sequencing-related research in African populations, novel approaches to the informed consent process are required. This will help to avoid infringement of privacy of individual subjects as well as to ensure that informed consent adheres to acceptable data protection levels with regard to use and transfer of such information. PMID:23714101

  12. Population pharmacokinetic modeling of glibenclamide in poorly controlled South African type 2 diabetic subjects

    PubMed Central

    Rambiritch, Virendra; Naidoo, Poobalan; Maharaj, Breminand; Pillai, Goonaseelan

    2016-01-01

    Aim The aim of this study was to describe the pharmacokinetics (PK) of glibenclamide in poorly controlled South African type 2 diabetic subjects using noncompartmental and model-based methods. Methods A total of 24 subjects with type 2 diabetes were administered increasing doses (0 mg/d, 2.5 mg/d, 5 mg/d, 10 mg/d, and 20 mg/d) of glibenclamide daily at 2-week intervals. Plasma glibenclamide, glucose, and insulin determinations were performed. Blood sampling times were 0 minute, 30 minutes, 60 minutes, 90 minutes, and 120 minutes (post breakfast sampling) and 240 minutes, 270 minutes, 300 minutes, 330 minutes, 360 minutes, and 420 minutes (post lunch sampling) on days 14, 28, 42, 56, and 70 for doses of 0 mg, 2.5 mg, 5.0 mg, 10 mg, and 20 mg, respectively. Blood sampling was performed after the steady state was reached. A total of 24 individuals in the data set contributed to a total of 841 observation records. The PK was analyzed using noncompartmental analysis methods, which were implemented in WinNonLin®, and population PK analysis using NONMEM®. Glibenclamide concentration data were log transformed prior to fitting. Results A two-compartmental disposition model was selected after evaluating one-, two-, and three-compartmental models to describe the time course of glibenclamide plasma concentration data. The one-compartment model adequately described the data; however, the two-compartment model provided a better fit. The three-compartment model failed to achieve successful convergence. A more complex model, to account for enterohepatic recirculation that was observed in the data, was unsuccessful. Conclusion In South African diabetic subjects, glibenclamide demonstrates linear PK and was best described by a two-compartmental model. Except for the absorption rate constant, the other PK parameters reported in this study are comparable to those reported in the scientific literature. The study is limited by the small study sample size and inclusion of poorly

  13. Enhanced Statistical Tests for GWAS in Admixed Populations: Assessment using African Americans from CARe and a Breast Cancer Consortium

    PubMed Central

    Pasaniuc, Bogdan; Zaitlen, Noah; Lettre, Guillaume; Chen, Gary K.; Tandon, Arti; Kao, W. H. Linda; Ruczinski, Ingo; Fornage, Myriam; Siscovick, David S.; Zhu, Xiaofeng; Larkin, Emma; Lange, Leslie A.; Cupples, L. Adrienne; Yang, Qiong; Akylbekova, Ermeg L.; Musani, Solomon K.; Divers, Jasmin; Mychaleckyj, Joe; Li, Mingyao; Papanicolaou, George J.; Millikan, Robert C.; Ambrosone, Christine B.; John, Esther M.; Bernstein, Leslie; Zheng, Wei; Hu, Jennifer J.; Ziegler, Regina G.; Nyante, Sarah J.; Bandera, Elisa V.; Ingles, Sue A.; Press, Michael F.; Chanock, Stephen J.; Deming, Sandra L.; Rodriguez-Gil, Jorge L.; Palmer, Cameron D.; Buxbaum, Sarah; Ekunwe, Lynette; Hirschhorn, Joel N.; Henderson, Brian E.; Myers, Simon; Haiman, Christopher A.; Reich, David; Patterson, Nick; Wilson, James G.; Price, Alkes L.

    2011-01-01

    While genome-wide association studies (GWAS) have primarily examined populations of European ancestry, more recent studies often involve additional populations, including admixed populations such as African Americans and Latinos. In admixed populations, linkage disequilibrium (LD) exists both at a fine scale in ancestral populations and at a coarse scale (admixture-LD) due to chromosomal segments of distinct ancestry. Disease association statistics in admixed populations have previously considered SNP association (LD mapping) or admixture association (mapping by admixture-LD), but not both. Here, we introduce a new statistical framework for combining SNP and admixture association in case-control studies, as well as methods for local ancestry-aware imputation. We illustrate the gain in statistical power achieved by these methods by analyzing data of 6,209 unrelated African Americans from the CARe project genotyped on the Affymetrix 6.0 chip, in conjunction with both simulated and real phenotypes, as well as by analyzing the FGFR2 locus using breast cancer GWAS data from 5,761 African-American women. We show that, at typed SNPs, our method yields an 8% increase in statistical power for finding disease risk loci compared to the power achieved by standard methods in case-control studies. At imputed SNPs, we observe an 11% increase in statistical power for mapping disease loci when our local ancestry-aware imputation framework and the new scoring statistic are jointly employed. Finally, we show that our method increases statistical power in regions harboring the causal SNP in the case when the causal SNP is untyped and cannot be imputed. Our methods and our publicly available software are broadly applicable to GWAS in admixed populations. PMID:21541012

  14. Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations.

    PubMed

    Labuschagne, Christiaan; Nupen, Lisa; Kotzé, Antoinette; Grobler, Paul J; Dalton, Desiré L

    2015-10-01

    Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half-siblings or cousins) is strongly suggested.

  15. Karyotypical characteristics of two allopatric African populations of anhydrobiotic Polypedilum Kieffer, 1912 (Diptera, Chironomidae) originating from Nigeria and Malawi

    PubMed Central

    Petrova, Ninel A.; Cornette, Richard; Shimura, Sachiko; Gusev, Oleg A.; Pemba, Dylo; Kikawada, Takahiro; Zhirov, Sergey V.; Okuda, Takashi

    2015-01-01

    Abstract The African chironomid Polypedilum vanderplanki Hinton, 1951 is the only chironomid able to withstand almost complete desiccation in an ametabolic state known as anhydrobiosis. The karyotypes of two allopatric populations of this anhydrobiotic chironomid, one from Nigeria and another from Malawi, were described according to the polytene giant chromosomes. The karyotype from the Nigerian population was presented as the reference chromosome map for Polypedilum vanderplanki. Both populations, Nigerian and Malawian, showed the same number of chromosomes (2n=8), but important differences were found in the band sequences of polytene chromosomes, and in the number and the arrangement of active regions between the two populations. Such important differences raise the possibility that the Malawian population could constitute a distinct new species of anhydrobiotic chironomid. PMID:26140160

  16. Secretarybird Sagittarius serpentarius population trends and ecology: insights from South African citizen science data.

    PubMed

    Hofmeyr, Sally D; Symes, Craig T; Underhill, Leslie G

    2014-01-01

    Data from two long-term citizen science projects were used to examine the status and ecology of a Red List species, the Secretarybird Sagittarius serpentarius (Vulnerable), in South Africa. The first phase of the Southern African Bird Atlas Project operated from 1987 until 1992, and the second phase began in 2007. The Coordinated Avifaunal Roadcounts (CAR) project began in 1993 and by 1998 had expanded to cover much of the south-eastern half of the country. Data submitted up until April 2013 were used. A new method of comparing reporting rates between atlas projects was developed. Changing reporting rates are likely to reflect changes in abundance; in this instance the data suggest that the Secretarybird population decreased across much of South Africa between the two atlas projects, with a widespread important decrease in the Kruger National Park. Habitat data from the CAR project were analysed to gain insight into the ecology of the species. Secretarybirds tended to avoid transformed habitats across much of the area covered by the CAR project. In the winter rainfall region of the Western Cape, which is characterised by heavily transformed fynbos vegetation, at least 50% of Secretarybirds recorded were in transformed environments. This implies that in the Fynbos biome, at least, Secretarybirds have adapted to transformed environments to some degree. However, in the rest of the country it is likely that habitat loss, largely through widespread bush encroachment but also through agriculture, afforestation, and urbanisation, is a major threat to the species. The methods developed here represent a new approach to analysing data from long-term citizen science projects, which can provide important insights into a species' conservation status and ecology.

  17. ECG is an inefficient screening-tool for left ventricular hypertrophy in normotensive African children population

    PubMed Central

    Creta, Antonio; Campanale, Cosimo Marco; Fittipaldi, Mario; Giorgino, Riccardo; Quintarelli, Fabio; Satriano, Umberto; Cruciani, Alessandro; Antinolfi, Vincenzo; Di Berardino, Stefano; Costanzo, Davide; Bettini, Ranieri; Mangiameli, Giuseppe; Caricato, Marco; Mottini, Giovanni

    2016-01-01

    Background Left ventricular hypertrophy (LVH) is a marker of pediatric hypertension and predicts development of cardiovascular events. Electrocardiography (ECG) screening is used in pediatrics to detect LVH thanks to major accessibility, reproducibility and easy to use compared to transthoracic echocardiography (TTE), that remains the standard technique. Several diseases were previously investigated, but no data exists regarding our study population. The aim of our study was to evaluate the relationship between electrocardiographic and echocardiographic criteria of LVH in normotensive African children. Methods We studied 313 children (mean age 7,8 ± 3 yo), in north-Madagascar. They underwent ECG and TTE. Sokolow-Lyon index was calculated to identify ECG-LVH (>35 mm). Left ventricle mass (LVM) with TTE was calculated and indexed by height2.7 (LVMI2.7) and weight (LVMIw). We report the prevalence of TTE-LVH using three methods: (1) calculating percentiles age- and sex- specific with values >95th percentile identifying LVH; (2) LVMI2.7 >51 g/m2.7; (3) LVMIw >3.4 g/weight. Results 40 (13%) children showed LVMI values >95th percentile, 24 children (8%) an LVMI2.7 >51 g/m2.7 while 19 children (6%) an LVMIw >3.4 g/kg. LVH-ECG by Sokolow-Lyon index was present in five, three and three children respectively, with poor values of sensitivity (ranging from 13 to 16%), positive predictive value (from 11 to 18%) and high values of specificity (up to 92%). The effects of anthropometrics parameters on Sokolow-Lyon were analyzed and showed poor correlation. Conclusion ECG is a poor screening test for detecting LVH in children. In clinical practice, TTE remains the only tool to be used to exclude LVH. PMID:27651998

  18. The Episode of Genetic Drift Defining the Migration of Humans out of Africa Is Derived from a Large East African Population Size

    PubMed Central

    Elnour, Mohamed Ali; Isabirye, Dan; Okello, John; Hussien, Ayman; Kwiatksowski, Dominic; Hirbo, Jibril; Tishkoff, Sara; Ibrahim, Muntaser E.

    2014-01-01

    Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount. PMID:24845801

  19. The episode of genetic drift defining the migration of humans out of Africa is derived from a large east African population size.

    PubMed

    Elhassan, Nuha; Gebremeskel, Eyoab Iyasu; Elnour, Mohamed Ali; Isabirye, Dan; Okello, John; Hussien, Ayman; Kwiatksowski, Dominic; Hirbo, Jibril; Tishkoff, Sara; Ibrahim, Muntaser E

    2014-01-01

    Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.

  20. Genetic Associations of PPARGC1A with Type 2 Diabetes: Differences among Populations with African Origins.

    PubMed

    Cheema, Amanpreet K; Li, Tan; Liuzzi, Juan P; Zarini, Gustavo G; Dorak, Mehmet T; Huffman, Fatma G

    2015-01-01

    The aim of this study was to assess the differences in correlation of PPARGC1A polymorphisms with type 2 diabetes (T2D) risk in adults of African origins: African Americans and Haitian Americans. The case-control study consisted of >30 years old, self-identified Haitian Americans (n = 110 cases and n = 116 controls) and African Americans (n = 124 cases and n = 122 controls) living in South Florida with and without T2D. Adjusted logistic regression indicated that both SNP rs7656250 (OR = 0.22, P = 0.005) and rs4235308 (OR = 0.42, P = 0.026) showed protective association with T2D in Haitian Americans. In African Americans, however, rs4235308 showed significant risk association with T2D (OR = 2.53, P = 0.028). After stratification with sex, in Haitian Americans, both rs4235308 (OR = 0.38, P = 0.026) and rs7656250 (OR = 0.23, P = 0.006) showed protective association with T2D in females whereas in African American males rs7656250 had statistically significant protective effect on T2D (OR = 0.37, P = 0.043). The trends observed for genetic association of PPARGC1A SNPs, rs4235308, and rs7656250 for T2D between Haitian Americans and African Americans point out differences in Black race and warrant replicative study with larger sample size.

  1. Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populations.

    PubMed

    Berg, Ingrid L; Neumann, Rita; Sarbajna, Shriparna; Odenthal-Hesse, Linda; Butler, Nicola J; Jeffreys, Alec J

    2011-07-26

    PRDM9 is a major specifier of human meiotic recombination hotspots, probably via binding of its zinc-finger repeat array to a DNA sequence motif associated with hotspots. However, our view of PRDM9 regulation, in terms of motifs defined and hotspots studied, has a strong bias toward the PRDM9 A variant particularly common in Europeans. We show that population diversity can reveal a second class of hotspots specifically activated by PRDM9 variants common in Africans but rare in Europeans. These African-enhanced hotspots nevertheless share very similar properties with their counterparts activated by the A variant. The specificity of hotspot activation is such that individuals with differing PRDM9 genotypes, even within the same population, can use substantially if not completely different sets of hotspots. Each African-enhanced hotspot is activated by a distinct spectrum of PRDM9 variants, despite the fact that all are predicted to bind the same sequence motif. This differential activation points to complex interactions between the zinc-finger array and hotspots and identifies features of the array that might be important in controlling hotspot activity.

  2. Population Structure of Clinical Pseudomonas aeruginosa from West and Central African Countries

    PubMed Central

    Cholley, Pascal; Ka, Roughyatou; Guyeux, Christophe; Thouverez, Michelle; Guessennd, Nathalie; Ghebremedhin, Beniam; Frank, Thierry; Bertrand, Xavier; Hocquet, Didier

    2014-01-01

    Background Pseudomonas aeruginosa (PA) has a non-clonal, epidemic population with a few widely distributed and frequently encountered sequence types (STs) called ‘high-risk clusters’. Clinical P. aeruginosa (clinPA) has been studied in all inhabited continents excepted in Africa, where a very few isolates have been analyzed. Here, we characterized a collection of clinPA isolates from four countries of West and Central Africa. Methodology 184 non-redundant isolates of clinPA from hospitals of Senegal, Ivory Coast, Nigeria, and Central African Republic were genotyped by MLST. We assessed their resistance level to antibiotics by agar diffusion and identified the extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs) by sequencing. The population structure of the species was determined by a nucleotide-based analysis of the entire PA MLST database and further localized on the phylogenetic tree (i) the sequence types (STs) of the present collection, (ii) the STs by continents, (iii) ESBL- and MBL-producing STs from the MLST database. Principal Findings We found 80 distinct STs, of which 24 had no relationship with any known STs. ‘High-risk’ international clonal complexes (CC155, CC244, CC235) were frequently found in West and Central Africa. The five VIM-2-producing isolates belonged to CC233 and CC244. GES-1 and GES-9 enzymes were produced by one CC235 and one ST1469 isolate, respectively. We showed the spread of ‘high-risk’ international clonal complexes, often described as multidrug-resistant on other continents, with a fully susceptible phenotype. The MBL- and ESBL-producing STs were scattered throughout the phylogenetic tree and our data suggest a poor association between a continent and a specific phylogroup. Conclusions ESBL- and MBL-encoding genes are borne by both successful international clonal complexes and distinct local STs in clinPA of West and Central Africa. Furthermore, our data suggest that the spread of a ST could be

  3. The Y Alu polymorphism in southern African populations and its relationship to other Y-specific polymorphisms

    SciTech Connect

    Spurdle, A.B.; Jenkins, T. ); Hammer, M.F. )

    1994-02-01

    Y-linked polymorphisms were studied in a number of African populations. The frequency of the alleles of a Y-specific Alu insertion polymorphism, termed the [open quotes]Y Alu polymorphism,[close quotes] was determined in 889 individuals from 23 different African population groups. A trend in frequency was observed, with the insert largely absent in Caucasoid populations, at intermediate frequency in the Khoisan, and at high frequency in Negroids. The insert predates diversification of Homo sapiens, since it occurs in all groups. The Alu insertion is believed to result from a unique mutation event, and comparisons between this and several other Y-linked polymorphisms were carried out in an attempt to validate their usefulness in population and evolutionary studies. The p21A1/Taql and pDP31/EcoRI polymorphisms and 49a/TaqI alleles were all shown to have arisen on more than one occasion, and evidence exists for a preraciation crossover event between the Y-linked pseudoautosomal XY275 locus and the Y chromosome pseudoautosomal boundary. 33 refs., 4 figs., 5 tabs.

  4. Phenol sulphotransferase SULT1A1 polymorphism: molecular diagnosis and allele frequencies in Caucasian and African populations.

    PubMed Central

    Coughtrie, M W; Gilissen, R A; Shek, B; Strange, R C; Fryer, A A; Jones, P W; Bamber, D E

    1999-01-01

    Sulphation, catalysed by members of the sulphotransferase (SULT) enzyme family, is an important component of the body's chemical defence mechanism, but also acts to bioactivate mutagens such as hydroxylated aryl and heterocyclic amines. A major human sulphotransferase, SULT1A1 (P-PST), metabolizes and/or bioactivates many drugs, iodothyronines and hydroxylated aromatic amines. The enzyme activity varies widely within the population and is under genetic control. We have developed an assay detecting a G-->A transition in SULT1A1 that causes an Arg213-->His substitution associated with low SULT activity and altered enzyme properties, and have used it to assess the SULT1A1 genotype in Caucasian (n=293) and African (Nigerian, n=52) populations. We show that the mutant SULT1A1*2 allele is present at frequencies of 0.321 and 0.269 in the Caucasian and African populations respectively. We also demonstrate a significant age-related difference in SULT1A1 genotype within our Caucasian population, with increasing incidence of SULT1A1*1 homozygosity and decreasing incidence of SULT1A1*2 homozygosity with increasing age, indicating a potential association of SULT1A1*1 allozyme(s) with protection against cell and/or tissue damage during aging. PMID:9854023

  5. Geographic information systems: a useful tool to approach African swine fever surveillance management of wild pig populations.

    PubMed

    Rolesu, Sandro; Aloi, Daniela; Ghironi, Annalisa; Oggiano, Nicolino; Oggiano, Annalisa; Puggioni, Giantonella; Patta, Cristiana; Farina, Salvatore; Montinaro, Salvatore

    2007-01-01

    The epidemiological surveillance of African swine fever in wild pig populations requires the previous collection of numerous samples of biological materials for virological and serological testing from each animal that has been killed during the hunting season. The number of samples needs to demonstrate the absence of the disease at a prevalence level of 5% (and confidence level of 95%) in the area subject observed. Since the typology of the territory suitable for maintaining wild pig populations and the precise location can be identified, it is possible to pinpoint specific areas within Sardinia where organised sampling is undertaken. The results from tests are used to estimate the prevalence of the disease in the wild pig population in the place of origin. Areas were identified using the geographic information system technology with support from maps in the field. The correct localisation of seropositivity has led to the redefinition of high-risk areas for African swine fever. Results from the outbreaks and the surveillance of the wild pig population has confirmed the decreasing role of the wild boar in maintaining the disease.

  6. FACTORS RELATED TO HIV TESTING AMONG AN AFRICAN AMERICAN CHURCH-AFFILIATED POPULATION

    PubMed Central

    Berkley-Patton, Jannette; Moore, Erin W.; Hawes, Starlyn M.; Thompson, Carole Bowe; Bohn, Alexandria

    2014-01-01

    HIV continues to disproportionately impact communities of color, and more calls are being extended to African American churches to assist in HIV education and screening efforts. However, no studies have reported on the HIV testing practices of African American church-affiliated persons. This study examines demographic, social, and behavioral factors associated with ever receiving an HIV test and last 12-month HIV testing. Findings indicated not having insurance and condom use were predictors of ever receiving an HIV test. Predictors of HIV testing in the last 12 months included marital status (i.e., single, divorced, separated, or widowed) and intentions to get tested for HIV in the near future. These predictors should be considered when designing HIV education and screening interventions for African American church settings. PMID:22468975

  7. The species flocks of East African cichlid fishes: recent advances in molecular phylogenetics and population genetics

    NASA Astrophysics Data System (ADS)

    Salzburger, Walter; Meyer, Axel

    With more than 3,000 species, the fish family Cichlidae is one of the most species-rich families of vertebrates. Cichlids occur in southern and central America, Africa, Madagascar, and India. The hotspot of their biodiversity is East Africa, where they form adaptive radiations composed of hundreds of endemic species in several lakes of various sizes and ages. The unparalleled species richness of East African cichlids has been something of a conundrum for evolutionary biologists and ecologists, since it has been in doubt whether these hundreds of species arose by allopatric speciation or whether it is necessary to invoke somewhat less traditional models of speciation, such as micro-allopatric, peripatric, or even sympatric speciation or evolution through sexual selection mediated by female choice. Ernst Mayr's analyses of these evolutionary uniquely diverse species assemblages have contributed to a more direct approach to this problem and have led to a deeper understanding of the patterns and processes that caused the formation of these huge groups of species. We review here recent molecular data on population differentiation and phylogenetics, which have helped to unravel, to some extent, the patterns and processes that led to the formation and ecological maintenance of cichlid species flocks. It is becoming apparent that sexually selected traits do play an important role in speciation in micro-allopatric or even sympatric settings. Species richness seems to be roughly correlated with the surface area, but not the age, of the lakes. We observe that the oldest lineages of a species flock of cichlids are often less species-rich and live in the open water or deepwater habitats. While the species flocks of the Lake Malawai and the Lake Victoria areas were shown to be monophyletic, the cichlid assemblage of Lake Tanganyika seems to consist of several independent species flocks. Cichlids emerge as an evolutionary model system in which many fundamental questions in

  8. Neotropical Africanized honey bees have African mitochondrial DNA.

    PubMed

    Smith, D R; Taylor, O R; Brown, W M

    1989-05-18

    Non-indigenous African honey bees have invaded most of South and Central America in just over 30 years. The genetic composition of this population and the means by which it rapidly colonizes new territory remain controversial. In particular, it has been unclear whether this 'Africanized' population has resulted from interbreeding between African and domestic European bees, or is an essentially pure African population. Also, it has not been known whether this population expanded primarily by female or by male migration. Restriction site mapping of 62 mitochondrial DNAs of African bees from Brazil, Venezuela and Mexico reveals that 97% were of African (Apis mellifera scutellata) type. Although neotropical European apiary populations are rapidly Africanized by mating with neotropical African males, there is little reciprocal gene flow to the neotropical African population through European females. These are the first genetic data to indicate that the neotropical African population could be expanding its range by female migration.

  9. Diffuse Reflectance Spectroscopy Versus Mexameter(®) MX18 Measurements of Melanin and Erythema in an African Population.

    PubMed

    Wright, Caradee Y; Karsten, Aletta E; Wilkes, Marcus; Singh, Ann; du Plessis, Johan; Albers, Patricia N; Karsten, Petrus A

    2016-07-01

    Melanin provides protection against excess exposure to solar ultraviolet radiation (UVR) and related adverse health effects. Diffuse reflectance spectroscopy (DRS) can be used to calculate cutaneous melanin and erythema, but this is complex and has been mostly used for light-to-medium pigmented skin. Handheld reflectance spectrophotometers, such as the Mexameter(®) MX18, can also be used. We compared DRS-calculated melanin and erythema values with Mexameter melanin and erythema index values to understand how these techniques/measurements correlate in an African population of predominantly deeply pigmented skin. Five hundred and three participants comprised 68.5% self-identified Black African, 9.9% Indian/Asian, 18.4% White and 2.9% Colored. The majority of Black African (45%), Indian/Asian (34%) and Colored (53%) participants self-identified their skin as being "brown." Measured melanin levels increased with darker self-reported skin color. DRS-calculated and Mexameter melanin values demonstrated a positive correlation (Spearman rho = 0.87, P < 0.001). The results from both instruments showed erythema values were strongly correlated with their own melanin values. This finding is considered spurious and may result from the complexity of separating brown and red pigment when using narrowband reflectance techniques. Further work is needed to understand melanin, erythema and color in Black skin given sun-related health risks in vulnerable groups in Africa.

  10. Five novel missense mutations of the Lewis gene (FUT3) in African (Xhosa) and Caucasian populations in South Africa.

    PubMed

    Pang, H; Liu, Y; Koda, Y; Soejima, M; Jia, J; Schlaphoff, T; Du Toit, E D; Kimura, H

    1998-06-01

    Five novel missense mutations, viz., C304 A, T370 G, G484 A, G667 A, and G808 A, in the Lewis gene (FUT3) were detected in African (Xhosa) and Caucasian individuals in South Africa. These single base substitutions may result in changes in amino acid residues from Gln102 to Lys in the 304 mutation, Ser124 to Ala in the 370 mutation, Asp162 to Asn in the 484 mutation, Gly223 to Arg in the 667 mutation, and Val270 to Met in the 808 mutation. Out of the five novel mutations identified in this investigation, four new alleles (le484,667, le484,667,808, Le304, and Le370) were determined in the Xhosa population and two new alleles (le202,314,484 and Le304) in the Caucasian population. The determination of alpha(1,3/1,4)fucosyltransferase activity, after transfection of plasmids containing the new alleles into COS7 cells, suggested that alleles le484,667 and le484,667,808 encoded an inactive enzyme, and that alleles Le304 and Le370 encoded a functional enzyme. In addition, we also examined the incidence of five common alleles, Le59, le59,508 le59,1067, le202,314, and le1067 in two populations by the polymerase chain reaction/restriction fragment length polymorphism method and compared differences in the allele frequencies of FUT3 among three ethnic groups (Orientals, Africans, and Caucasians).

  11. Theodore E. Woodward Award: lactase persistence SNPs in African populations regulate promoter activity in intestinal cell culture.

    PubMed

    Sibley, Eric; Ahn, Jong Kun

    2011-01-01

    Lactase-phlorizin hydrolase, lactase, is the intestinal enzyme responsible for the digestion of the milk sugar lactose. The majority of the world's human population experiences a decline in expression of the lactase gene by late childhood (lactase non-persistence). Individuals with lactase persistence, however, continue to express high levels of the lactase gene throughout adulthood. Lactase persistence is a heritable autosomal dominant condition and has been strongly correlated with several single nucleotide polymorphisms (SNPs) located ∼14 kb upstream of the lactase gene in different ethnic populations: -13910*T in Europeans and -13907*G, -13915*G, and -14010*C in several African populations. The coincidence of the four SNPs clustering within 100 bp strongly suggests that this region mediates the lactase non-persistence/persistence phenotype. Having previously characterized the European SNP, we aimed to determine whether the African SNPs similarly mediate a functional role in regulating the lactase promoter. Human intestinal Caco-2 cells were transfected with lactase SNP/promoter-reporter constructs and assayed for promoter activity. The -13907*G and -13915*G SNPs result in a significant enhancement of lactase promoter activity relative to the ancestral lactase non-persistence genotype. Such differential regulation by the SNPs is consistent with a causative role in the mechanism specifying the lactase persistence phenotype.

  12. A prospective study of childhood and adolescent antecedents of homelessness among a community population of African Americans.

    PubMed

    Fothergill, Kate E; Doherty, Elaine E; Robertson, Judith A; Ensminger, Margaret E

    2012-06-01

    Much is known about contemporaneous correlates of homelessness from studies of homeless individuals. However, few studies have prospectively examined early antecedents and prevalence of homelessness in community populations. We use data from a 35-year study of a community population of African Americans to examine relationships between homelessness and prior structural, family, school, and behavioral influences. Nearly 22% of males and 16% of females reported homelessness between ages 15 and 42, providing a rare estimate within an African American urban community population. In bivariate analyses, lower school bonds, depressed mood, violent behavior, and running away in adolescence are predictive for both males and females. Teen parenting and angry mood are unique influences for females, while for males, poor first grade classroom conduct and adolescent substance use are unique risks. In multivariate analyses, poor classroom conduct and weaker school bonds predict homelessness among males, while teen parenting does so for females. Running away before age 15 is strongly predictive of later homelessness for both males and females. These results reveal the relative influence of multiple, interrelated early risks on homelessness and confirm our hypothesis that factors linked to other poor outcomes also relate to homelessness, underscoring another benefit to early prevention efforts.

  13. Monitoring of African swine fever in the wild boar population of the most recent endemic area of Spain.

    PubMed

    Mur, L; Boadella, M; Martínez-López, B; Gallardo, C; Gortazar, C; Sánchez-Vizcaíno, J M

    2012-12-01

    Wild boars are natural hosts for African swine fever (ASF). The ASF virus (ASFV) can persist for long periods in the environment, such as in ticks and contaminated products, which may be sources of infection for wild boar populations. African swine fever was eradicated in domestic pig populations in Spain in 1995, after 35 years of significant effort. To determine whether ASFV can persist in wild boar hosts after it has been eradicated from domestic pigs and to study the role of wild boar in helping ASFV persist in the environment, we checked for the presence of ASFV in wild boars in Doñana National Park, one of the largest natural habitats of wild boar in Spain and one of the last areas where ASF was endemic prior its eradication. Samples from 158 animals collected between 2006 and 2010 were analysed using serological and nucleic acid-based diagnostic techniques recommended by the World Organization for Animal Health (OIE). None of the samples was found to be positive. These results confirm the absence of disease in wildlife in what was once one of the areas most affected by ASF in Spain, and they suggest that wild boars play a limited role in ASFV persistence. These results confirm that ASFV cannot persist in isolated wild boar populations for long periods of time without the interaction of other factors such as re-infection by contact with domestic pigs or by feeding on contaminated swill.

  14. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance.

    PubMed

    Yao, Nasser; Lee, Cheng-Ruei; Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders.

  15. Eliminating Health Disparities in the African American Population: The Interface of Culture, Gender, and Power

    ERIC Educational Resources Information Center

    Airhihenbuwa, Collins O.; Liburd, Leandris

    2006-01-01

    Since the release of former Secretary Margaret Heckler's "Secretary's Task Force Report on Black and Minority Health" more than two decades ago, excess death from chronic diseases and other conditions between African Americans and Whites have increased. The conclusion of that report emphasized excess death and thus clinical care, paying…

  16. Suicide Attempts in an African Schizophrenia Population: An Assessment of Demographic Risk Factors

    ERIC Educational Resources Information Center

    Niehaus, D.J.H.; Laurent, C.; Jordaan, E.; Koen, L.; Oosthuizen, P.; Keyter, N.; Muller, J. E.; Mbanga, N. I.; Deleuze, J.-F.; Mallet, J.; Stein, D. J.; Emsley, R.

    2004-01-01

    This study investigated demographic variables, including affected sibling pair status, as risk factors for suicidal behavior in schizophrenia patients of African (Xhosa) descent. Xhosa subjects with schizophrenia were interviewed with the Diagnostic Interview for Genetic Studies (DIGS) and then stratified into two groups: those with ( n = 90) and…

  17. Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow.

    PubMed

    Pinto, J; Egyir-Yawson, A; Vicente, Jl; Gomes, B; Santolamazza, F; Moreno, M; Charlwood, Jd; Simard, F; Elissa, N; Weetman, D; Donnelly, Mj; Caccone, A; Della Torre, A

    2013-09-01

    The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In west Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviors. To investigate patterns of macrogeographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west, central, and southern African genetic clusters. These clusters are coincident with the central African rainforest belt and northern and southern savannah biomes, which suggests restrictions to gene flow associated with the transition between these biomes. By contrast, geographically patterned population substructure appears much weaker within the S-form.

  18. Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow

    PubMed Central

    Pinto, J; Egyir-Yawson, A; Vicente, JL; Gomes, B; Santolamazza, F; Moreno, M; Charlwood, JD; Simard, F; Elissa, N; Weetman, D; Donnelly, MJ; Caccone, A; della Torre, A

    2013-01-01

    The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In west Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviors. To investigate patterns of macrogeographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west, central, and southern African genetic clusters. These clusters are coincident with the central African rainforest belt and northern and southern savannah biomes, which suggests restrictions to gene flow associated with the transition between these biomes. By contrast, geographically patterned population substructure appears much weaker within the S-form. PMID:24062800

  19. Overrepresented Minorities in Special Education in the United States and Romania: Comparison between African-American and Roma Populations in Disability Studies

    ERIC Educational Resources Information Center

    Walker, Gabriela

    2008-01-01

    This manuscript briefly examines minority participation within the school population that is eligible for special education services--namely, African Americans in the United States and the Roma population in Romania. A large percentage of students from both minorities come to school unprepared to learn and they remain behind because of the…

  20. The Climate-Population Nexus in the East African Horn: Emerging Degradation Trends in Rangeland and Pastoral Livelihood Zones

    NASA Astrophysics Data System (ADS)

    Pricope, N. G.; Husak, G. J.; Funk, C. C.; Lopez-Carr, D.

    2014-12-01

    Increasing climate variability and extreme weather conditions along with declining trends in both rainfall and temperature represent major risk factors affecting agricultural production and food security in many regions of the world. We identify regions where significant rainfall decrease from 1979-2011 over the entire continent of Africa couples with significant human population density increase. The rangelands of Ethiopia, Kenya, and Somalia in the East African Horn remain one of the world's most food insecure regions, yet have significantly increasing human populations predominantly dependent on pastoralist and agro-pastoralist livelihoods. Vegetation in this region is characterized by a variable mosaic of land covers, generally dominated by grasslands necessary for agro-pastoralism, interspersed by woody vegetation. Recent assessments indicate that widespread degradation is occurring, adversely impacting fragile ecosystems and human livelihoods. Using two underutilized MODIS products, we observe significant changes in vegetation patterns and productivity over the last decade all across the East African Horn. We observe significant vegetation browning trends in areas experiencing drying precipitation trends in addition to increasing population pressures. We also found that the drying precipitation trends only partially statistically explain the vegetation browning trends, further indicating that other factors such as population pressures and land use changes are responsible for the observed declining vegetation health. Furthermore, we show that the general vegetation browning trends persist even during years with normal rainfall conditions such as 2012, indicating potential long-term degradation of rangelands on which approximately 10 million people depend. These findings have serious implications for current and future regional food security monitoring and forecasting as well as for mitigation and adaptation strategies in a region where population is expected

  1. Linkage disequilibrium analysis reveals an albuminuria risk haplotype containing three missense mutations in the cubilin gene with striking differences among European and African ancestry populations

    PubMed Central

    2012-01-01

    Background A recent meta-analysis described a variant (p.Ile2984Val) in the cubilin gene (CUBN) that is associated with levels of albuminuria in the general population and in diabetics. Methods We implemented a Linkage Disequilibrium (LD) search with data from the 1000 Genomes Project, on African and European population genomic sequences. Results We found that the p.Ile2984Val variation is part of a larger haplotype in European populations and it is almost absent in west Africans. This haplotype contains 19 single nucleotide polymorphisms (SNPs) in very high LD, three of which are missense mutations (p.Leu2153Phe, p.Ile2984Val, p.Glu3002Gly), and two have not been previously reported. Notably, this European haplotype is absent in west African populations, and the frequency of each individual polymorphism differs significantly in Africans. Conclusions Genotyping of these variants in existing African origin sample sets coupled to measurements of urine albumin excretion levels should reveal which is the most likely functional candidate for albuminuria risk. The unique haplotypic structure of CUBN in different populations may leverage the effort to identify the functional variant and to shed light on evolution of the CUBN gene locus. PMID:23114252

  2. Sociocultural Behavior, Sex-Biased Admixture, and Effective Population Sizes in Central African Pygmies and Non-Pygmies

    PubMed Central

    Verdu, Paul; Becker, Noémie S.A.; Froment, Alain; Georges, Myriam; Grugni, Viola; Quintana-Murci, Lluis; Hombert, Jean-Marie; Van der Veen, Lolke; Le Bomin, Sylvie; Bahuchet, Serge; Heyer, Evelyne; Austerlitz, Frédéric

    2013-01-01

    Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter–gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history. PMID:23300254

  3. Genetic structure analysis of a highly inbred captive population of the African antelope Addax nasomaculatus. Conservation and management implications.

    PubMed

    Armstrong, E; Leizagoyen, C; Martínez, A M; González, S; Delgado, J V; Postiglioni, A

    2011-01-01

    The African antelope Addax nasomaculatus is a rare mammal at high risk of extinction, with no more than 300 individuals in the wild and 1,700 captive animals distributed in zoos around the world. In this work, we combine genetic data and genealogical information to assess the structure and genetic diversity of a captive population located at Parque Lecocq Zoo (N=27), originated from only two founders. We amplified 39 microsatellites previously described in other Artiodactyls but new to this species. Seventeen markers were polymorphic, with 2-4 alleles per locus (mean=2.71). Mean expected heterozygosity (He) per locus was between 0.050 (marker ETH3) and 0.650 (marker D5S2), with a global He of 0.43. The mean inbreeding coefficient of the population computed from pedigree records of all registered individuals (N=53) was 0.222. The mean coancestry of the population was 0.298 and F(IS) index was -0.108. These results reflect the importance of an adequate breeding management on a severely bottlenecked captive population, which would benefit by the incorporation of unrelated individuals. Thanks to the successful amplification of a large number of microsatellites commonly used in domestic bovids, this study will provide useful information for the management of this population and serve as future reference for similar studies in other captive populations of this species.

  4. Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources.

    PubMed

    Mtileni, Bohani; Dzama, Kennedy; Nephawe, Khathutshelo; Rhode, Clint

    2016-06-01

    Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6-78.6) in comparison to the field populations (point estimate range 118.9-580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. F st estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, F st estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic

  5. Molecular anthropology meets genetic medicine to treat blindness in the North African Jewish population: human gene therapy initiated in Israel.

    PubMed

    Banin, Eyal; Bandah-Rozenfeld, Dikla; Obolensky, Alexey; Cideciyan, Artur V; Aleman, Tomas S; Marks-Ohana, Devora; Sela, Malka; Boye, Sanford; Sumaroka, Alexander; Roman, Alejandro J; Schwartz, Sharon B; Hauswirth, William W; Jacobson, Samuel G; Hemo, Itzhak; Sharon, Dror

    2010-12-01

    The history of the North African Jewish community is ancient and complicated with a number of immigration waves and persecutions dramatically affecting its population size. A decade-long process in Israel of clinical-molecular screening of North African Jews with incurable autosomal recessive blindness led to the identification of a homozygous splicing mutation (c.95-2A > T; IVS2-2A > T) in RPE65, the gene encoding the isomerase that catalyzes a key step in the retinoid-visual cycle, in patients from 10 unrelated families. A total of 33 patients (four now deceased) had the severe childhood blindness known as Leber congenital amaurosis (LCA), making it the most common cause of retinal degeneration in this population. Haplotype analysis in seven of the patients revealed a shared homozygous region, indicating a population-specific founder mutation. The age of the RPE65 founder mutation was estimated to have emerged 100-230 (mean, 153) generations ago, suggesting it originated before the establishment of the Jewish community in North Africa. Individuals with this RPE65 mutation were characterized with retinal studies to determine if they were candidates for gene replacement, the recent and only therapy to date for this otherwise incurable blindness. The step from molecular anthropological studies to application of genetic medicine was then taken, and a representative of this patient subgroup was treated with subretinal rAAV2-RPE65 gene therapy. An increase in vision was present in the treated area as early as 15 days after the intervention. This process of genetically analyzing affected isolated populations as a screen for gene-based therapy suggests a new paradigm for disease diagnosis and treatment.

  6. Genetic Variation and Reproductive Timing: African American Women from the Population Architecture Using Genomics and Epidemiology (PAGE) Study

    PubMed Central

    Carty, Cara L.; Franceschini, Nora; Fernández-Rhodes, Lindsay; Young, Alicia; Cheng, Iona; Ritchie, Marylyn D.; Haiman, Christopher A.; Wilkens, Lynne; ChunyuanWu; Matise, Tara C.; Carlson, Christopher S.; Brennan, Kathleen; Park, Amy; Rajkovic, Aleksandar; Hindorff, Lucia A.

    2013-01-01

    Age at menarche (AM) and age at natural menopause (ANM) define the boundaries of the reproductive lifespan in women. Their timing is associated with various diseases, including cancer and cardiovascular disease. Genome-wide association studies have identified several genetic variants associated with either AM or ANM in populations of largely European or Asian descent women. The extent to which these associations generalize to diverse populations remains unknown. Therefore, we sought to replicate previously reported AM and ANM findings and to identify novel AM and ANM variants using the Metabochip (n = 161,098 SNPs) in 4,159 and 1,860 African American women, respectively, in the Women’s Health Initiative (WHI) and Atherosclerosis Risk in Communities (ARIC) studies, as part of the Population Architecture using Genomics and Epidemiology (PAGE) Study. We replicated or generalized one previously identified variant for AM, rs1361108/CENPW, and two variants for ANM, rs897798/BRSK1 and rs769450/APOE, to our African American cohort. Overall, generalization of the majority of previously-identified variants for AM and ANM, including LIN28B and MCM8, was not observed in this African American sample. We identified three novel loci associated with ANM that reached significance after multiple testing correction (LDLR rs189596789, p = 5×10−08; KCNQ1 rs79972789, p = 1.9×10−07; COL4A3BP rs181686584, p = 2.9×10−07). Our most significant AM association was upstream of RSF1, a gene implicated in ovarian and breast cancers (rs11604207, p = 1.6×10−06). While most associations were identified in either AM or ANM, we did identify genes suggestively associated with both: PHACTR1 and ARHGAP42. The lack of generalization coupled with the potentially novel associations identified here emphasize the need for additional genetic discovery efforts for AM and ANM in diverse populations. PMID:23424626

  7. Comparative assessment of absolute cardiovascular disease risk characterization from non-laboratory-based risk assessment in South African populations

    PubMed Central

    2013-01-01

    Background All rigorous primary cardiovascular disease (CVD) prevention guidelines recommend absolute CVD risk scores to identify high- and low-risk patients, but laboratory testing can be impractical in low- and middle-income countries. The purpose of this study was to compare the ranking performance of a simple, non-laboratory-based risk score to laboratory-based scores in various South African populations. Methods We calculated and compared 10-year CVD (or coronary heart disease (CHD)) risk for 14,772 adults from thirteen cross-sectional South African populations (data collected from 1987 to 2009). Risk characterization performance for the non-laboratory-based score was assessed by comparing rankings of risk with six laboratory-based scores (three versions of Framingham risk, SCORE for high- and low-risk countries, and CUORE) using Spearman rank correlation and percent of population equivalently characterized as ‘high’ or ‘low’ risk. Total 10-year non-laboratory-based risk of CVD death was also calculated for a representative cross-section from the 1998 South African Demographic Health Survey (DHS, n = 9,379) to estimate the national burden of CVD mortality risk. Results Spearman correlation coefficients for the non-laboratory-based score with the laboratory-based scores ranged from 0.88 to 0.986. Using conventional thresholds for CVD risk (10% to 20% 10-year CVD risk), 90% to 92% of men and 94% to 97% of women were equivalently characterized as ‘high’ or ‘low’ risk using the non-laboratory-based and Framingham (2008) CVD risk score. These results were robust across the six risk scores evaluated and the thirteen cross-sectional datasets, with few exceptions (lower agreement between the non-laboratory-based and Framingham (1991) CHD risk scores). Approximately 18% of adults in the DHS population were characterized as ‘high CVD risk’ (10-year CVD death risk >20%) using the non-laboratory-based score. Conclusions We found a high level of

  8. African ancestry is associated with risk of asthma and high total serum IgE in a population from the Caribbean Coast of Colombia.

    PubMed

    Vergara, Candelaria; Caraballo, Luis; Mercado, Dilia; Jimenez, Silvia; Rojas, Winston; Rafaels, Nicholas; Hand, Tracey; Campbell, Monica; Tsai, Yuhjung J; Gao, Li; Duque, Constanza; Lopez, Sergio; Bedoya, Gabriel; Ruiz-Linares, Andrés; Barnes, Kathleen C

    2009-06-01

    African descended populations exhibit an increased prevalence of asthma and allergies compared to Europeans. One approach to distinguish between environmental and genetic explanations for this difference is to study relationships of asthma risk to individual admixture. We aimed to determine the admixture proportions of a case-control sample from the Caribbean Coast of Colombia currently participating in genetic studies for asthma, and to test for population stratification and association between African ancestry and asthma and total serum IgE levels (tIgE). We genotyped 368 asthmatics and 365 non-asthmatics for 52 autosomal ancestry informative markers, six mtDNA haplogroups and nine haplogroups and five microsatellites in Y chromosome. Autosomal admixture proportions, population stratification, and associations between ancestry and the phenotypes were estimated by ADMIXMAP. The average admixture proportions among asthmatics were 42.8% European, 39.9% African and 17.2% Native American and among non-asthmatics they were 44.2% (P = 0.068), 37.6% (P = 0.007) and 18.1% (P = 0.050), respectively. In the total sample, the paternal contributions were 71% European, 25% African and 4.0% Native American and the maternal lineages were 56.8% Native American, and 20.2% African; 22.9% of the individuals carried other non-Native American mtDNA haplogroups. African ancestry was significantly associated with asthma (OR: 2.97; 95% CI: 1.08-8.08), high tIgE (OR: 1.9; 95% CI: 1.17-3.12) and socioeconomic status (OR = 0.64; 95% CI: 0.47-0.87). Significant population stratification was observed in this sample. Our findings indicate that genetic factors can explain the association between asthma and African ancestry and suggest that this sample is a useful resource for performing admixture mapping for asthma.

  9. Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles.

    PubMed

    Demos, Terrence C; Kerbis Peterhans, Julian C; Joseph, Tyler A; Robinson, John D; Agwanda, Bernard; Hickerson, Michael J

    2015-01-01

    The Eastern Afromontane biodiversity hotspot (EABH) has the highest concentration of biodiversity in tropical Africa, yet few studies have investigated recent historical diversification processes in EABH lineages. Herein, we analyze restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH's high diversity. We analyzed complete SNP matrices of > 50,000 RAD loci to delineate populations, reconstruct the history of isolation and admixture, and discover geographic patterns of genetic partitioning. These analyses demonstrate that persistently unsuitable habitat may have isolated multiple populations distributed across montane habitat islands in the Itombwe Massif and Albertine Rift to the west as well as Mt Elgon and Kenyan Highlands to the east. We detected low genetic diversity in Kenyan Highland populations of both genera, consistent with smaller historical population sizes in this region. We additionally tested predictions that Albertine Rift populations are older and more persistently isolated compared to the Kenyan Highlands. Phylogenetic analyses support greater historical isolation among Albertine Rift populations of both shrews and mice compared to the Kenyan Highlands and suggest that there are genetically isolated populations from both focal genera in the Itombwe Massif, Democratic Republic of Congo. The Albertine Rift ecoregion has the highest mammalian tropical forest species richness per unit area on earth. Our results clearly support accelerating efforts to conserve this diversity.

  10. Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles

    PubMed Central

    Demos, Terrence C.; Kerbis Peterhans, Julian C.; Joseph, Tyler A.; Robinson, John D.; Agwanda, Bernard; Hickerson, Michael J.

    2015-01-01

    The Eastern Afromontane biodiversity hotspot (EABH) has the highest concentration of biodiversity in tropical Africa, yet few studies have investigated recent historical diversification processes in EABH lineages. Herein, we analyze restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity. We analyzed complete SNP matrices of > 50,000 RAD loci to delineate populations, reconstruct the history of isolation and admixture, and discover geographic patterns of genetic partitioning. These analyses demonstrate that persistently unsuitable habitat may have isolated multiple populations distributed across montane habitat islands in the Itombwe Massif and Albertine Rift to the west as well as Mt Elgon and Kenyan Highlands to the east. We detected low genetic diversity in Kenyan Highland populations of both genera, consistent with smaller historical population sizes in this region. We additionally tested predictions that Albertine Rift populations are older and more persistently isolated compared to the Kenyan Highlands. Phylogenetic analyses support greater historical isolation among Albertine Rift populations of both shrews and mice compared to the Kenyan Highlands and suggest that there are genetically isolated populations from both focal genera in the Itombwe Massif, Democratic Republic of Congo. The Albertine Rift ecoregion has the highest mammalian tropical forest species richness per unit area on earth. Our results clearly support accelerating efforts to conserve this diversity. PMID:26394036

  11. Association between Paraoxonase 1 (PON1) Polymorphisms and the Risk of Acute Coronary Syndrome in a North African Population

    PubMed Central

    Bounafaa, Abdelghani; Berrougui, Hicham; Ghalim, Noreddine; Nasser, Boubker; Bagri, Abdallah; Moujahid, Abderrahmane; Ikhlef, Souad; Camponova, Pamela; Yamoul, Najoua; Simo, Olivier Kamtchueng; Essamadi, Abdelkhalid; Khalil, Abdelouahed

    2015-01-01

    The purpose of the present study was to investigate the distribution of PON1 Q192R and L55M polymorphisms and activities in a North African population and to determine their association with cardiovascular complications. The prevalence of the QQ, QR, RR, LL, LM, and MM genotypes in the study population was 55.4%, 34.09%, 9.83%, 41.97%, 48.20%, and 9.83% respectively. The Q, R, L, and M alleles had a gene frequency of 0.755, 0.245, 0.67, and 0.33, respectively. The PON1 192 RR genotype was significantly more prevalent among ACS patients than among healthy subjects. There was a 4.33-fold increase in the risk of ACS in subjects presenting the PON1 192 RR genotype compared to those with the QQ genotype (OR=4.33; 95% CI=1.27–17.7). There was a significantly different distribution of PON1 L55M in the ACS patient groups (UA, STEMI, NSTEMI). Moreover, individuals presenting the PON1 55MM genotype present a higher risk for ACS than those with LL genotype (OR=3.69; 95% CI=1.61–11.80). Paraoxonase activities were significantly lower in coronary patients than in healthy subjects. The decrease in PON1 activity was inversely correlated with the number of concomitant risk factors for CVD (r=0.57, p<0.0001). The results of the present study suggested that the PON1 R and M alleles may play a role in the pathogenesis of cardiac ischemia in our North African population and that a decrease in PON1 activity may be a valuable marker for monitoring the development of the atherosclerosis process and the associated cardiovascular complications. PMID:26241956

  12. Coffee consumption and prostate cancer aggressiveness among African and Caucasian Americans in a population-based study.

    PubMed

    Arab, Lenore; Su, L Joseph; Steck, Susan E; Ang, Alfonso; Fontham, Elizabeth T H; Bensen, Jeannette T; Mohler, James L

    2012-01-01

    This study evaluated the relationship between caffeinated and decaffeinated coffee and prostate cancer (CaP) aggressiveness using data from a population-based incident CaP study within the North Carolina-Louisiana Prostate Cancer Project (PCaP). Classification of CaP aggressiveness at diagnosis was based on clinical criteria for 1,049 African-American (AA) and 1,083 Caucasian-American (CA) research subjects. Coffee consumption was measured using a modified NCI Dietary History Questionnaire. No significant associations were found between CaP aggressiveness and consumption of either caffeinated or decaffeinated coffee. The OR for high aggressive CaP among consumers of more than 4 cups per day was 0.92 (95%CI = 0.61, 1.39), compared to non-coffee-drinkers. Results stratified by race found no significant associations and no noticeable trends in either AAs (P for trend = 0. 62) or CAs (P for trend = 0.42). In contrast to a recent report on a select population that has less complete information on CaP aggressiveness suggesting that coffee prevents aggressive CaP, this rapid case ascertainment population-based study, in a biracial population with differing risks of CaP did not demonstrate a protective relationship between high coffee consumption and risk of high aggressive CaP.

  13. Staphylococcus aureus in Animals and Food: Methicillin Resistance, Prevalence and Population Structure. A Review in the African Continent

    PubMed Central

    Lozano, Carmen; Gharsa, Haythem; Ben Slama, Karim; Zarazaga, Myriam; Torres, Carmen

    2016-01-01

    The interest about Staphylococcus aureus (S. aureus) and methicillin resistant S. aureus (MRSA) in livestock, and domestic and wild animals has significantly increased. The spread of different clonal complexes related to livestock animals, mainly CC398, and the recent description of the new mecC gene, make it necessary to know more about the epidemiology and population structure of this microorganism all over the world. Nowadays, there are several descriptions about the presence of S. aureus and/or MRSA in different animal species (dogs, sheep, donkeys, bats, pigs, and monkeys), and in food of animal origin in African countries. In this continent, there is a high diversity of ethnicities, cultures or religions, as well as a high number of wild animal species and close contact between humans and animals, which can have a relevant impact in the epidemiology of this microorganism. This review shows that some clonal lineages associated with humans (CC1, CC15, CC72, CC80, CC101, and CC152) and animals (CC398, CC130 and CC133) are present in this continent in animal isolates, although the mecC gene has not been detected yet. However, available studies are limited to a few countries, very often with incomplete information, and many more studies are necessary to cover a larger number of African countries. PMID:27681906

  14. 25-Hydroxyvitamin D in African-origin populations at varying latitudes challenges the construct of a physiologic norm123

    PubMed Central

    Durazo-Arvizu, Ramon A; Camacho, Pauline; Bovet, Pascal; Forrester, Terrence; Lambert, Estelle V; Plange-Rhule, Jacob; Hoofnagle, Andrew N; Aloia, John; Tayo, Bamidele; Dugas, Lara R; Cooper, Richard S; Luke, Amy

    2014-01-01

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

  15. Establishment of a self-propagating population of the African malaria vector Anopheles arabiensis under semi-field conditions

    PubMed Central

    2010-01-01

    Background The successful control of insect disease vectors relies on a thorough understanding of their ecology and behaviour. However, knowledge of the ecology of many human disease vectors lags behind that of agricultural pests. This is partially due to the paucity of experimental tools for investigating their ecology under natural conditions without risk of exposure to disease. Assessment of vector life-history and demographic traits under natural conditions has also been hindered by the inherent difficulty of sampling these seasonally and temporally varying populations with the limited range of currently available tools. Consequently much of our knowledge of vector biology comes from studies of laboratory colonies, which may not accurately represent the genetic and behavioural diversity of natural populations. Contained semi-field systems (SFS) have been proposed as more appropriate tools for the study of vector ecology. SFS are relatively large, netting-enclosed, mesocosms in which vectors can fly freely, feed on natural plant and vertebrate host sources, and access realistic resting and oviposition sites. Methods A self-replicating population of the malaria vector Anopheles arabiensis was established within a large field cage (21 × 9.1 × 7.1 m) at the Ifakara Health Institute, Tanzania that mimics the natural habitat features of the rural village environments where these vectors naturally occur. Offspring from wild females were used to establish this population whose life-history, behaviour and demography under semi-field conditions was monitored over 24 generations. Results This study reports the first successful establishment and maintenance of an African malaria vector population under SFS conditions for multiple generations (> 24). The host-seeking behaviour, time from blood feeding to oviposition, larval development, adult resting and swarming behaviour exhibited by An. arabiensis under SFS conditions were similar to those seen in nature. Conclusions

  16. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance

    PubMed Central

    Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders. PMID:27508500

  17. The imprint of the Slave Trade in an African American population: mitochondrial DNA, Y chromosome and HTLV-1 analysis in the Noir Marron of French Guiana

    PubMed Central

    2010-01-01

    Background Retracing the genetic histories of the descendant populations of the Slave Trade (16th-19th centuries) is particularly challenging due to the diversity of African ethnic groups involved and the different hybridisation processes with Europeans and Amerindians, which have blurred their original genetic inheritances. The Noir Marron in French Guiana are the direct descendants of maroons who escaped from Dutch plantations in the current day Surinam. They represent an original ethnic group with a highly blended culture. Uniparental markers (mtDNA and NRY) coupled with HTLV-1 sequences (env and LTR) were studied to establish the genetic relationships linking them to African American and African populations. Results All genetic systems presented a high conservation of the African gene pool (African ancestry: mtDNA = 99.3%; NRY = 97.6%; HTLV-1 env = 20/23; HTLV-1 LTR = 6/8). Neither founder effect nor genetic drift was detected and the genetic diversity is within a range commonly observed in Africa. Higher genetic similarities were observed with the populations inhabiting the Bight of Benin (from Ivory Coast to Benin). Other ancestries were identified but they presented an interesting sex-bias. Whilst male origins spread throughout the north of the bight (from Benin to Senegal), female origins were spread throughout the south (from the Ivory Coast to Angola). Conclusions The Noir Marron are unique in having conserved their African genetic ancestry, despite major cultural exchanges with Amerindians and Europeans through inhabiting the same region for four centuries. Their maroon identity and the important number of slaves deported in this region have maintained the original African diversity. All these characteristics permit to identify a major origin located in the former region of the Gold Coast and the Bight of Benin; regions highly impacted by slavery, from which goes a sex-biased longitudinal gradient of ancestry. PMID:20958967

  18. Autoantibodies in malaria, tuberculosis and hepatitis B in a west African population.

    PubMed Central

    Adebajo, A O; Charles, P; Maini, R N; Hazleman, B L

    1993-01-01

    Following reports of associations between autoantibodies and living in the tropics, we have studied the seroprevalence and nature of anti-nuclear antibodies, anti-cardiolipin antibodies, antibodies to extractable nuclear antigens and anti-neutrophilic cytoplasmic antibodies in 351 West Africans with malaria, tuberculosis or hepatitis B, or in good health. Amongst healthy West Africans we found a seroprevalence of 7% for anti-nuclear antibodies with several staining patterns, and of 30.3% for anti-cardiolipin antibodies. Among patients with tuberculosis and malaria there was twice that frequency of anti-nuclear antibodies (predominantly speckled in pattern), and anti-neutrophil cytoplasmic antibodies (predominantly IgM) were demonstrated in a few cases. A possible association between IgG anti-cardiolipin antibodies and tuberculosis was observed (P < 0.05), but antibodies to double-stranded DNA were not elevated and no antibodies to extractable nuclear antigens were found in any of the patients or healthy individuals studied. Our findings suggest the need for caution in the interpretation of autoantibody tests in subjects from or living in the tropics, as well as in patients with tropical infections. PMID:8467567

  19. Acyclovir achieves a lower concentration in African HIV-seronegative, herpes simplex virus 2-seropositive women than in non-African populations.

    PubMed

    Lu, Yanhui; Celum, Connie; Wald, Anna; Baeten, Jared M; Cowan, Frances; Delany-Moretlwe, Sinead; Reid, Stewart E; Hughes, James P; Wilcox, Ellen; Corey, Lawrence; Hendrix, Craig W

    2012-05-01

    Acyclovir pharmacokinetics was evaluated in 68 HIV-seronegative, herpes simplex virus 2 (HSV-2)-seropositive African women, who received a single oral 400-mg dose of acyclovir, with plasma acyclovir concentrations measured over 8 h. Geometric mean peak concentration and area under the concentration-time curve were 0.31 μg/ml and 1.59 h · μg/ml, respectively, 54% and 52% lower than values from non-Africans. Lower acyclovir concentrations may partly explain the reduced acyclovir suppression of HSV-2 genital ulcer recurrence in HPTN 039 African women participants.

  20. Pharmacogenetics of CYP2B6, CYP2A6 and UGT2B7 in HIV treatment in African populations: focus on efavirenz and nevirapine.

    PubMed

    Čolić, Antoinette; Alessandrini, Marco; Pepper, Michael S

    2015-05-01

    The CYP450 and UGT enzymes are involved in phase I and phase II metabolism of the majority of clinically prescribed drugs, including the non-nucleoside reverse transcriptase inhibitors, efavirenz and nevirapine, used in the treatment of HIV/AIDS. Variations in the activity of these enzymes due to gene polymorphisms can affect an individual's drug response or may lead to adverse drug reactions. There is an inter-ethnic distribution in the frequency of these polymorphisms, with African populations exhibiting higher genetic diversity compared to other populations. African specific alleles with clinical relevance have also emerged. Given the high prevalence of HIV/AIDS in sub-Saharan Africa, understanding the frequency of pharmacogenetically relevant alleles in populations of African origin, and their impact on efavirenz and nevirapine metabolism, is becoming increasingly critical. This review aims to investigate ethnic variation of CYP2B6, CYP2A6 and UGT2B7, and to understand the pharmacogenetic relevance when comparing frequencies in African populations to other populations worldwide.

  1. Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles.

    PubMed

    Velo-Antón, Guillermo; Godinho, Raquel; Campos, João Carlos; Brito, José Carlos

    2014-01-01

    The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12-0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.

  2. Should I Stay or Should I Go? Dispersal and Population Structure in Small, Isolated Desert Populations of West African Crocodiles

    PubMed Central

    Campos, João Carlos; Brito, José Carlos

    2014-01-01

    The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12–0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments. PMID:24740183

  3. Origin, evolution, and population genetics of the selfish Segregation Distorter gene duplication in European and African populations of Drosophila melanogaster.

    PubMed

    Brand, Cara L; Larracuente, Amanda M; Presgraves, Daven C

    2015-05-01

    Meiotic drive elements are a special class of evolutionarily "selfish genes" that subvert Mendelian segregation to gain preferential transmission at the expense of homologous loci. Many drive elements appear to be maintained in populations as stable polymorphisms, their equilibrium frequencies determined by the balance between drive (increasing frequency) and selection (decreasing frequency). Here we show that a classic, seemingly balanced, drive system is instead characterized by frequent evolutionary turnover giving rise to dynamic, rather than stable, equilibrium frequencies. The autosomal Segregation Distorter (SD) system of the fruit fly Drosophila melanogaster is a selfish coadapted meiotic drive gene complex in which the major driver corresponds to a partial duplication of the gene Ran-GTPase activating protein (RanGAP). SD chromosomes segregate at similar, low frequencies of 1-5% in natural populations worldwide, consistent with a balanced polymorphism. Surprisingly, our population genetic analyses reveal evidence for parallel, independent selective sweeps of different SD chromosomes in populations on different continents. These findings suggest that, rather than persisting at a single stable equilibrium, SD chromosomes turn over frequently within populations.

  4. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data.

    PubMed

    Mdladla, K; Dzomba, E F; Huson, H J; Muchadeyi, F C

    2016-08-01

    The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)  = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of <150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances >100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in

  5. Current status of African swine fever virus in a population of wild boar in eastern Poland (2014-2015).

    PubMed

    Woźniakowski, Grzegorz; Kozak, Edyta; Kowalczyk, Andrzej; Łyjak, Magdalena; Pomorska-Mól, Małgorzata; Niemczuk, Krzysztof; Pejsak, Zygmunt

    2016-01-01

    African swine fever virus (ASFV) was detected in wild boar in eastern Poland in early 2014. So far, 65 cases of ASFV infection in wild boar have been recognised. The methods used for ASFV detection included highly specific real-time PCR with a universal probe library (UPL), enzyme-linked immunosorbent assay (ELISA), and an immunoperoxidase test (IPT) for identification of anti-ASFV antibodies. The positive ASF cases were located near the border with Belarus in Sokółka and Białystok counties. Some of the countermeasures for disease prevention include early ASF diagnosis by ASFV DNA identification as well as detection of specific antibodies by systematic screening. The aim of this study was to assess the current ASF status in a Polish population of wild boar during the last two years (2014-2015).

  6. A pharmacogenetic study of CD4 recovery in response to HIV antiretroviral therapy in two South African population groups.

    PubMed

    Parathyras, John; Gebhardt, Stefan; Hillermann-Rebello, Renate; Grobbelaar, Nelis; Venter, Mauritz; Warnich, Louise

    2009-05-01

    South Africa, like many other Southern African countries, has one of the highest HIV infection rates in the world and many individuals consequently receive antiretroviral therapy (ART). However, knowledge regarding (i) the prevalence of functional single nucleotide polymorphisms (SNPs) in pharmacologically relevant genes, and (ii) variance in pharmacotherapy both within and between different populations and ethnic groups is limited. The aim of this study was to determine whether selected polymorphisms in cytochrome P450 (CYP) genes (CYP2B6 and CYP3A4) and the multidrug-resistance 1 (ABCB1) gene underlie altered antiretroviral (ARV) drug response in two South African populations. DNA samples from 182 HIV-positive individuals of Mixed-Ancestry and Xhosa ethnicity on ART were genotyped for the A-392G SNP in CYP3A4, the G516T and A785G SNPs in CYP2B6, and the T-129C, C1236T, G2677T/A and C3435T SNPs in ABCB1. Univariate two-way analysis of variance (ANOVA) testing revealed no apparent effect of ethnicity on immune recovery (in terms of CD4-cell count) in response to ART. Univariate one-way ANOVA testing revealed a discernible effect of genotype on immune recovery in the cases of the T-129C (P=0.03) and G2677A (P<0.01) polymorphisms in the ABCB1 gene. This study serves as a basis for better understanding and possible prediction of pharmacogenetic risk profiles and drug response in individuals and ethnic groups in South Africa.

  7. Beyond the black box: a systematic review of breast, prostate, colorectal, and cervical screening among native and immigrant African-descent Caribbean populations.

    PubMed

    Consedine, Nathan S; Tuck, Natalie L; Ragin, Camille R; Spencer, Benjamin A

    2015-06-01

    Cancer screening disparities between black and white groupings are well-documented. Less is known regarding African-descent subpopulations despite elevated risk, distinct cultural backgrounds, and increasing numbers of Caribbean migrants. A systematic search of Medline, Web of Science, PubMed and SCOPUS databases (1980-2012) identified 53 studies reporting rates of breast, prostate, cervical, and colorectal screening behavior among immigrant and non-immigrant Caribbean groups. Few studies were conducted within the Caribbean itself; most work is US-based, and the majority stem from Brooklyn, New York. In general, African-descent Caribbean populations screen for breast, prostate, colorectal, and cervical cancers less frequently than US-born African-Americans and at lower rates than recommendations and guidelines. Haitian immigrants, in particular, screen at very low frequencies. Both immigrant and non-immigrant African-descent Caribbean groups participate in screening less frequently than recommended. Studying screening among specific Caribbean groups of African-descent may yield data that both clarifies health disparities between US-born African-Americans and whites and illuminates the specific subpopulations at risk in these growing immigrant communities.

  8. Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe

    PubMed Central

    Der Sarkissian, Clio; Balanovsky, Oleg; Brandt, Guido; Khartanovich, Valery; Buzhilova, Alexandra; Koshel, Sergey; Zaporozhchenko, Valery; Gronenborn, Detlef; Moiseyev, Vyacheslav; Kolpakov, Eugen; Shumkin, Vladimir; Alt, Kurt W.; Balanovska, Elena; Cooper, Alan; Haak, Wolfgang

    2013-01-01

    North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across

  9. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    PubMed

    Der Sarkissian, Clio; Balanovsky, Oleg; Brandt, Guido; Khartanovich, Valery; Buzhilova, Alexandra; Koshel, Sergey; Zaporozhchenko, Valery; Gronenborn, Detlef; Moiseyev, Vyacheslav; Kolpakov, Eugen; Shumkin, Vladimir; Alt, Kurt W; Balanovska, Elena; Cooper, Alan; Haak, Wolfgang

    2013-01-01

    North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across

  10. The virus's tooth: cyanophages affect an African flamingo population in a bottom-up cascade

    PubMed Central

    Peduzzi, Peter; Gruber, Martin; Gruber, Michael; Schagerl, Michael

    2014-01-01

    Trophic cascade effects occur when a food web is disrupted by loss or significant reduction of one or more of its members. In East African Rift Valley lakes, the Lesser Flamingo is on top of a short food chain. At irregular intervals, the dominance of their most important food source, the cyanobacterium Arthrospira fusiformis, is interrupted. Bacteriophages are known as potentially controlling photoautotrophic bacterioplankton. In Lake Nakuru (Kenya), we found the highest abundance of suspended viruses ever recorded in a natural aquatic system. We document that cyanophage infection and the related breakdown of A. fusiformis biomass led to a dramatic reduction in flamingo abundance. This documents that virus infection at the very base of a food chain can affect, in a bottom-up cascade, the distribution of end consumers. We anticipate this as an important example for virus-mediated cascading effects, potentially occurring also in various other aquatic food webs. PMID:24430484

  11. The virus's tooth: cyanophages affect an African flamingo population in a bottom-up cascade.

    PubMed

    Peduzzi, Peter; Gruber, Martin; Gruber, Michael; Schagerl, Michael

    2014-06-01

    Trophic cascade effects occur when a food web is disrupted by loss or significant reduction of one or more of its members. In East African Rift Valley lakes, the Lesser Flamingo is on top of a short food chain. At irregular intervals, the dominance of their most important food source, the cyanobacterium Arthrospira fusiformis, is interrupted. Bacteriophages are known as potentially controlling photoautotrophic bacterioplankton. In Lake Nakuru (Kenya), we found the highest abundance of suspended viruses ever recorded in a natural aquatic system. We document that cyanophage infection and the related breakdown of A. fusiformis biomass led to a dramatic reduction in flamingo abundance. This documents that virus infection at the very base of a food chain can affect, in a bottom-up cascade, the distribution of end consumers. We anticipate this as an important example for virus-mediated cascading effects, potentially occurring also in various other aquatic food webs.

  12. The African contribution to the present-day population of the Azores Islands (Portugal): analysis of the Y chromosome haplogroup E.

    PubMed

    Neto, Domingos; Montiel, Rafael; Bettencourt, Conceição; Santos, Cristina; Prata, Maria J; Lima, Manuela

    2007-01-01

    Among the settlers that, from 1432 onwards, arrived to the Azores Islands were individuals of North and sub-Saharan African origin. A previous study of markers of the Y chromosome revealed that haplogroup E is the second more frequent in the Azores (13%). Since this haplogroup is heterogeneous and may contain subtypes of African or non-African origin, we analyzed an extended sample of 319 Azoreans, originating from the three groups of islands (Eastern, Central, and Western), to evaluate the African contribution to the present-day population of the Azores. Samples belonging to the E clade were distributed into six haplogroups, from which the most frequent was E3b1a, representing 47.2% of the E chromosomes (6.3% of the total sample). The sub-Saharan haplogroup E3a was found in 7.1% of E chromosomes (0.9% of the total), corresponding to the highest frequency reported so far in a Portuguese population. No significant differences were detected in the haplogroup distribution among groups of islands, as well as between Azores and most of other European populations compared. The present-day representation of sub-Saharan lineages in Azores, although reduced, is higher than in other Portuguese populations, where the demographic representation of sub-Saharan slaves is reported as similar.

  13. Psychological Factors in Deliberate Self-Harm as Seen in an Urban African Population in Uganda: A Case-Control Study

    ERIC Educational Resources Information Center

    Kinyanda, Eugene; Hjelmeland, Heidi; Musisi, Seggane

    2005-01-01

    Psychological factors associated with deliberate self-harm (DSH) as seen in an African population in Uganda are described. A case-control study design was employed in which a Luganda version (predominant language in the study area) of the modified European Parasuicide Interview Schedule I (EPSIS I) was used to collect data. The controls were…

  14. Context-dependent survival, fecundity and predicted population-level consequences of brucellosis in African buffalo

    USGS Publications Warehouse

    Gorsich, Erin E.; Ezenwa, Vanessa O.; Cross, Paul C.; Bengis, Roy G.; Jolles, Anna E.

    2015-01-01

    Our results suggest that brucellosis infection can potentially result in reduced population growth rates, but because these effects varied with demographic and environmental conditions, they may remain unseen without intensive, longitudinal monitoring.

  15. Henipavirus neutralising antibodies in an isolated island population of African fruit bats.

    PubMed

    Peel, Alison J; Baker, Kate S; Crameri, Gary; Barr, Jennifer A; Hayman, David T S; Wright, Edward; Broder, Christopher C; Fernández-Loras, Andrés; Fooks, Anthony R; Wang, Lin-Fa; Cunningham, Andrew A; Wood, James L N

    2012-01-01

    Isolated islands provide valuable opportunities to study the persistence of viruses in wildlife populations, including population size thresholds such as the critical community size. The straw-coloured fruit bat, Eidolon helvum, has been identified as a reservoir for henipaviruses (serological evidence) and Lagos bat virus (LBV; virus isolation and serological evidence) in continental Africa. Here, we sampled from a remote population of E. helvum annobonensis fruit bats on Annobón island in the Gulf of Guinea to investigate whether antibodies to these viruses also exist in this isolated subspecies. Henipavirus serological analyses (Luminex multiplexed binding and inhibition assays, virus neutralisation tests and western blots) and lyssavirus serological analyses (LBV: modified Fluorescent Antibody Virus Neutralisation test, LBV and Mokola virus: lentivirus pseudovirus neutralisation assay) were undertaken on 73 and 70 samples respectively. Given the isolation of fruit bats on Annobón and their lack of connectivity with other populations, it was expected that the population size on the island would be too small to allow persistence of viruses that are thought to cause acute and immunising infections. However, the presence of antibodies against henipaviruses was detected using the Luminex binding assay and confirmed using alternative assays. Neutralising antibodies to LBV were detected in one bat using both assays. We demonstrate clear evidence for exposure of multiple individuals to henipaviruses in this remote population of E. helvum annobonensis fruit bats on Annobón island. The situation is less clear for LBV. Seroprevalences to henipaviruses and LBV in Annobón are notably different to those in E. helvum in continental locations studied using the same sampling techniques and assays. Whilst cross-sectional serological studies in wildlife populations cannot provide details on viral dynamics within populations, valuable information on the presence or absence of

  16. Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds.

    PubMed

    Edea, Z; Bhuiyan, M S A; Dessie, T; Rothschild, M F; Dadi, H; Kim, K S

    2015-02-01

    Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69,903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

  17. Mortgage foreclosure and health disparities: serial displacement as asset extraction in African American populations.

    PubMed

    Saegert, Susan; Fields, Desiree; Libman, Kimberly

    2011-06-01

    In this paper we offer a conceptualization of mortgage foreclosure as serial displacement by highlighting the current crisis in the context of historically repeated extraction of capital-economic, social, and human-from communities defined at different scales: geographically, socially, and that of embodied individuals. We argue that serial displacement is the loss of capital, physical resources, social integration and collective capacity, and psycho-social resources at each of these scales, with losses at one level affecting other levels. The repeated extraction of resources has negative implications for the health of individuals and groups, within generations as well as across generations, through the accumulation of loss over time. Our analysis of the foreclosure crisis as serial displacement for African American households in the United States begins with the "housing niche" model. We focus on the foreclosure crisis as an example of the interconnectedness of structured inequality in health and housing. Then we briefly review the history of policies related to racial inequality in homeownership in the twentieth and twenty-first centuries. We end with an analysis of the scales of displacement and the human, social, and capital asset extraction that accompany them.

  18. Trajectories of Multiple Adolescent Health Risk Behaviors in a Low-Income African American Population

    PubMed Central

    Mustanski, Brian; Byck, Gayle R.; Dymnicki, Allison; Sterrett, Emma; Henry, David; Bolland, John

    2014-01-01

    This study examined interdependent trajectories of sexual risk, substance use, and conduct problems among 12–18 year-old African American youth who were followed annually as part of the Mobile Youth Study (MYS). We used growth-mixture modeling (GMM) to model the development of these three outcomes in the 1406 participants who met the inclusion criteria. Results indicate that there were four distinct classes: normative low risk (74.3% of sample); increasing high risk takers (11.9%); adolescent-limited conduct problems and drug risk with high risky sex (8.0%); and early experimenters (5.8%) The higher risk classes had higher rates of pregnancy and Sexually Transmitted Infections (STI) diagnoses than the normative sample at each of the ages we examined. Differing somewhat from our hypothesis, all of the non-normative classes exhibited high sexual risk behavior. While prevention efforts should be focused on addressing all three risk behaviors, the high rate of risky sexual behavior in the 25% of the sample that fall into the three non-normative classes, underscores an urgent need for improved sex education, including teen pregnancy and HIV/STI prevention, in this community. PMID:24229555

  19. Candida antifungal drug resistance in sub-Saharan African populations: A systematic review

    PubMed Central

    Africa, Charlene Wilma Joyce; Abrantes, Pedro Miguel dos Santos

    2017-01-01

    Background: Candida infections are responsible for increased morbidity and mortality rates in at-risk patients, especially in developing countries where there is limited access to antifungal drugs and a high burden of HIV co-infection.  Objectives: This study aimed to identify antifungal drug resistance patterns within the subcontinent of Africa.  Methods: A literature search was conducted on published studies that employed antifungal susceptibility testing on clinical Candida isolates from sub-Saharan African countries using Pubmed and Google Scholar.  Results: A total of 21 studies from 8 countries constituted this review. Only studies conducted in sub-Saharan Africa and employing antifungal drug susceptibility testing were included. Regional differences in Candida species prevalence and resistance patterns were identified.  Discussion: The outcomes of this review highlight the need for a revision of antifungal therapy guidelines in regions most affected by Candida drug resistance.  Better controls in antimicrobial drug distribution and the implementation of regional antimicrobial susceptibility surveillance programmes are required in order to reduce the high Candida drug resistance levels seen to be emerging in sub-Saharan Africa. PMID:28154753

  20. Glibenclamide population pharmacokinetic/pharmacodynamic modeling in South African type 2 diabetic subjects

    PubMed Central

    Rambiritch, Virendra; Naidoo, Poobalan; Pillai, Goonaseelan

    2016-01-01

    Aim To determine the effective dose of glibenclamide by quantifying the dose–response relationship in South African type 2 diabetic patients. Patients and methods A total of 24 type 2 diabetic patients participated in a glibenclamide dose-escalation study during which glibenclamide, glucose, and insulin concentrations were quantified, while the dose of glibenclamide was progressively increased. All except four subjects contributed data on all dose-escalation steps; however, data from all 24 patients were included in the model-based analysis. Pharmacokinetic/pharmacodynamic (PKPD) relationships were modeled using the software Nonmem®. Six models were utilized to explore the effect of alternative glibenclamide dose and plasma concentration inputs on various metrics of glucose response. Results Six models adequately described the experimental data. The effective dose for a glucose-lowering effect suggested by PKPD modeling is less than 5 mg/day. Doses beyond 5 mg/day do not meaningfully add to glibenclamide effects on blood-glucose response. Conclusion The effective dose of glibenclamide, suggested by PKPD modeling, is less than 5 mg/day. Higher doses of glibenclamide, eg, 15 mg/day as originally recommended by the manufacturer, do not produce further decrease in the blood glucose level but may predispose the patients to adverse effects. PMID:27713650

  1. Forecasting Human African Trypanosomiasis Prevalences from Population Screening Data Using Continuous Time Models

    PubMed Central

    Hasker, Epco; Lumbala, Crispin; Lutumba, Pascal; de Vlas, Sake J.; van de Klundert, Joris

    2016-01-01

    To eliminate and eradicate gambiense human African trypanosomiasis (HAT), maximizing the effectiveness of active case finding is of key importance. The progression of the epidemic is largely influenced by the planning of these operations. This paper introduces and analyzes five models for predicting HAT prevalence in a given village based on past observed prevalence levels and past screening activities in that village. Based on the quality of prevalence level predictions in 143 villages in Kwamouth (DRC), and based on the theoretical foundation underlying the models, we consider variants of the Logistic Model—a model inspired by the SIS epidemic model—to be most suitable for predicting HAT prevalence levels. Furthermore, we demonstrate the applicability of this model to predict the effects of planning policies for screening operations. Our analysis yields an analytical expression for the screening frequency required to reach eradication (zero prevalence) and a simple approach for determining the frequency required to reach elimination within a given time frame (one case per 10000). Furthermore, the model predictions suggest that annual screening is only expected to lead to eradication if at least half of the cases are detected during the screening rounds. This paper extends knowledge on control strategies for HAT and serves as a basis for further modeling and optimization studies. PMID:27657937

  2. Updating the African human mitochondrial DNA tree: Relevance to forensic and population genetics.

    PubMed

    Heinz, Tanja; Pala, Maria; Gómez-Carballa, Alberto; Richards, Martin B; Salas, Antonio

    2017-03-01

    Analysis of human mitochondrial DNA (mtDNA) variation plays an important role in forensic genetic investigations, especially in degraded biological samples and hair shafts. There are many issues of the mtDNA phylogeny that are of special interest to the forensic community, such as haplogroup classification or the post hoc investigation of potential errors in mtDNA datasets. We have analyzed >2200 mitogenomes of African ancestry with the aim of improving the known worldwide phylogeny. More than 300 new minor subclades were identified, and the Time to the Most Recent Common Ancestor (TMRCA) was estimated for each node of the phylogeny. Phylogeographic details are provided which might also be relevant to forensic genetics. The present study has special interest for forensic investigations because current analysis and interpretation of mtDNA casework rest on a solid worldwide phylogeny, as is evident from the role that phylogeny plays in popular resources in the field (e.g. PhyloTree), software (e.g. Haplogrep 2), and databases (e.g. EMPOP). Apart from this forensic genetic interest, we also highlight the impact of this research in anthropological studies, such as those related to the reconstruction of the transatlantic slave trade.

  3. Do species populations really start small? New perspectives from the Late Neogene fossil record of African mammals.

    PubMed Central

    Vrba, E S; DeGusta, D

    2004-01-01

    This analysis of all known African larger mammals of the past 10 Myr offers new perspectives on the geographical circumstances of speciation. Our central question is: does the fossil evidence support the idea that most new species start as small populations and, if true, how long is the average growth interval until species are established at their mean later size? This simple question is important to unravelling the competing claims of rival models of speciation. We approached it by direct use of fossil data, which, to our knowledge, has not been done previously. We compared the numbers of fossil site records, as a proxy for magnitude of geographical spread, between survivorship intervals across all species. The results show that the average mammal species has indeed started its life in a relatively small population, and thereafter increased rapidly in geographical spread to reach its long-term equilibrium abundance by about 1 million years after origin. Some theoretical implications of these results are discussed. PMID:15101584

  4. Molecular and Bioenergetic Differences between Cells with African versus European Inherited Mitochondrial DNA Haplogroups: Implications for Population Susceptibility to Diseases

    PubMed Central

    Kenney, M. Cristina; Chwa, Marilyn; Atilano, Shari R.; Falatoonzadeh, Payam; Ramirez, Claudio; Malik, Deepika; Tarek, Mohamed; Cáceres del Carpio, Javier; Nesburn, Anthony B.; Boyer, David S.; Kuppermann, Baruch D.; Vawter, Marquis P.; Jazwinski, S. Michal; Miceli, Michael V.; Wallace, Douglas C.; Udar, Nitin

    2015-01-01

    The geographic origins of populations can be identified by their maternally inherited mitochondrial DNA (mtDNA) haplogroups. This study compared human cybrids (cytoplasmic hybrids), which are cell lines with identical nuclei but mitochondria from different individuals with mtDNA from either the H haplogroup or L haplogroup backgrounds. The most common European haplogroup is H while individuals of maternal African origin are of the L haplogroup. Despite lower mtDNA copy numbers, L cybrids had higher expression levels for nine mtDNA-encoded respiratory complex genes, decreased ATP turnover rates and lower levels of ROS production, parameters which are consistent with more efficient oxidative phosphorylation. Surprisingly, GeneChip arrays showed that the L and H cybrids had major differences in expression of genes of the canonical complement system (5 genes), dermatan/chondroitin sulfate biosynthesis (5 genes) and CCR3 signaling (9 genes). Quantitative nuclear gene expression studies confirmed that L cybrids had (a) lower expression levels of complement pathway and innate immunity genes and (b) increased levels of inflammation-related signaling genes, which are critical in human diseases. Our data support the hypothesis that mtDNA haplogroups representing populations from different geographic origins may play a role in differential susceptibilities to diseases. PMID:24200652

  5. Differentiation of African Components of Ancestry to Stratify Groups in a Case–Control Study of a Brazilian Urban Population

    PubMed Central

    Hirata, Mario H.; Luchessi, Andre D.; Genvigir, Fabiana D.V.; Cerda, Alvaro; Rodrigues, Alice C.; Willrich, Maria A.V.; Arazi, Simone S.; Dorea, Egidio L.; Bernik, Marcia M.S.; Faludi, Andre A.; Bertolami, Marcelo C.; Santos, Carla; Carracedo, Ángel; Salas, Antonio; Freire, Ana; Lareu, Maria Victoria; Phillips, Christopher; Porras-Hurtado, Liliana; Fondevila, Manuel; Hirata, Rosario D.C.

    2012-01-01

    Background: Balancing the subject composition of case and control groups to create homogenous ancestries between each group is essential for medical association studies. Methods: We explored the applicability of single-tube 34-plex ancestry informative markers (AIM) single nucleotide polymorphisms (SNPs) to estimate the African Component of Ancestry (ACA) to design a future case–control association study of a Brazilian urban sample. Results: One hundred eighty individuals (107 case group; 73 control group) self-described as white, brown-intermediate or black were selected. The proportions of the relative contribution of a variable number of ancestral population components were similar between case and control groups. Moreover, the case and control groups demonstrated similar distributions for ACA <0.25 and >0.50 categories. Notably a high number of outlier values (23 samples) were observed among individuals with ACA <0.25. These individuals presented a high probability of Native American and East Asian ancestral components; however, no individuals originally giving these self-described ancestries were observed in this study. Conclusions: The strategy proposed for the assessment of ancestry and adjustment of case and control groups for an association study is an important step for the proper construction of the study, particularly when subjects are taken from a complex urban population. This can be achieved using a straight forward multiplexed AIM-SNPs assay of highly discriminatory ancestry markers. PMID:22288895

  6. Problems in determination of skeletal lead burden in archaeological samples: An example from the First African Baptist Church population

    SciTech Connect

    Whittmers Jr., L. E.; Aufderheide, A. C.; Pounds, Joel G.; Jones, Keith W.; Angel, J. L.

    2008-08-01

    Human bone lead content has been demonstrated to be related to socioeconomic status, occupation and other social and environmental correlates. Skeletal tissue samples from 135 individuals from an early nineteenth century Philadelphia cemetery (First African Baptist Church) were studied by electrothermal atomic absorption spectrometry and x-ray fluorescence for lead content. High bone lead levels led to investigation of possible diagenetic effects. These were investigated by several different approaches including distribution of lead within bone by x-ray fluorescence, histological preservation, soil lead concentration and acidity as well as location and depth of burial. Bone lead levels were very high in the children, exceeding those of the adult population that were buried in the cemetery, and also those of present day adults. The antemortem age-related increase in bone lead, reported in other studies, was not evidenced in this population. Lead was even deposited in areas of taphonomic bone destruction. Synchrotron x-ray fluorescence studies revealed no consistent pattern of lead microdistribution within the bone. Our conclusions are that postmortem diagenesis of lead ion has penetrated these archaeological bones to a degree that makes their original bone lead content irretrievable by any known method. Increased bone porosity is most likely responsible for the very high levels of lead found in bones of newborns and children.

  7. Problems in Determination of Skeletal Lead Burden in Archaeological Samples: An Example From the First African Baptist Church Population

    SciTech Connect

    Whittmers Jr., L. E.; Aufderheide, A. C.; Pounds, Joel G.; JONES, Keith; Angel, J. L.

    2008-08-01

    ABSTRACT Human bone lead content has been demonstrated to be related to socioeconomic status, occupation and other social and environmental correlates. Skeletal tissue samples from 135 individuals from an early nineteenth century Philadelphia cemetery (First African Baptist Church) were studied by electrothermal atomic absorption spectrometry and x-ray fluorescence for lead content. High bone lead levels led to investigation of possible diagenetic effects. These were investigated by several different approaches including distribution of lead within bone by x-ray fluorescence, histological preservation, soil lead concentration and acidity as well as location and depth of burial. Bone lead levels were very high in children, exceeding those of the adult population that were buried in the cemetery, and also those of present day adults. The antemortem age-related increase in bone lead, reported in other studies, was not evidenced in this population. Lead was even deposited in areas of taphonomic bone destruction. Synchrotron x-ray fluorescence studies revealed no consistent pattern of lead microdistribution within the bone. Our conclusions are that postmortem diagenesis of lead ion has penetrated these archaeological bones to a degree that makes their original bone lead content irretrievable by any known method. Increased bone porosity is most likely responsible for the very high levels of lead found in bones of newborns and children.

  8. Psychometric properties of the Social Problem Solving Inventory-Revised Short-Form in a South African population.

    PubMed

    Sorsdahl, Katherine; Stein, Dan J; Myers, Bronwyn

    2017-04-01

    The Social Problem Solving Inventory-Revised Short-Form (SPSI-R:SF) has been used in several countries to identify problem-solving deficits among clinical and general populations in order to guide cognitive-behavioural interventions. Yet, very few studies have evaluated its psychometric properties. Three language versions of the questionnaire were administered to a general population sample comprising 1000 participants (771 English-, 178 Afrikaans- and 101 Xhosa-speakers). Of these participants, 210 were randomly selected to establish test-retest reliability (70 in each language). Principal component analysis was performed to examine the applicability of the factor structure of the original questionnaire to the South African data. Supplementary psychometric analyses were performed, including internal consistency and test-retest reliability. Collectively, results provide initial evidence of the reliability and validity of the SPSI-R:SF for the assessment of problem solving deficits in South Africa. Further studies that explore how the Afrikaans language version of the SPSI-R:SF can be improved and that establish the predictive validity of scores on the SPSI-R:SF are needed.

  9. Transformation of a cadaver population: Analysis of a South African cadaver program, 1921-2013.

    PubMed

    Kramer, Beverley; Hutchinson, Erin F

    2015-01-01

    Anatomy has served as a cornerstone in the training of various allied and clinical disciplines and has traditionally been based on dissection of the human body. Thus, to pursue this method of teaching and learning, access to cadavers is of continuing importance. Over a significant period of time unclaimed cadavers have performed an essential role in the teaching of anatomy in South Africa and in Africa. As recent cadaver numbers were declining at the School of Anatomical Sciences, University of the Witwatersrand, Johannesburg and difficulty in procurement was being experienced, the purpose of this study was to critically evaluate the composition of our cadaver population over time so as to provide possible strategies to arrest the decline. A retrospective, quantitative analysis of cadaver records from the School of Anatomical Sciences between 1921 and 2013 was undertaken. Analysis included a comparison of Poisson counts and Fischer's exact test. A significant decrease in the number of cadavers received during the period 2000-2013 and a slow bequest program over the same period of time has led to concerns about the sustainability of teaching anatomy through dissection. Decreases in the numbers of males and cadavers of the black population group occurred between 1990 and 2013, and of bequests from 2000 to 2013. An influence on the cadaver population from a changing political climate and change in socioeconomic status of part of the population was perceived. Changes in sex and population group of the cadavers may have a long-term effect on teaching and research.

  10. Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations

    PubMed Central

    Band, Gavin; Le, Quang Si; Jostins, Luke; Pirinen, Matti; Kivinen, Katja; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bojang, Kalifa; Pinder, Margaret; Sirugo, Giorgio; Conway, David J.; Nyirongo, Vysaul; Kachala, David; Molyneux, Malcolm; Taylor, Terrie; Ndila, Carolyne; Peshu, Norbert; Marsh, Kevin; Williams, Thomas N.; Alcock, Daniel; Andrews, Robert; Edkins, Sarah; Gray, Emma; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Schuldt, Kathrin; Clark, Taane G.; Small, Kerrin S.; Teo, Yik Ying; Kwiatkowski, Dominic P.; Rockett, Kirk A.; Barrett, Jeffrey C.; Spencer, Chris C. A.

    2013-01-01

    Combining data from genome-wide association studies (GWAS) conducted at different locations, using genotype imputation and fixed-effects meta-analysis, has been a powerful approach for dissecting complex disease genetics in populations of European ancestry. Here we investigate the feasibility of applying the same approach in Africa, where genetic diversity, both within and between populations, is far more extensive. We analyse genome-wide data from approximately 5,000 individuals with severe malaria and 7,000 population controls from three different locations in Africa. Our results show that the standard approach is well powered to detect known malaria susceptibility loci when sample sizes are large, and that modern methods for association analysis can control the potential confounding effects of population structure. We show that pattern of association around the haemoglobin S allele differs substantially across populations due to differences in haplotype structure. Motivated by these observations we consider new approaches to association analysis that might prove valuable for multicentre GWAS in Africa: we relax the assumptions of SNP–based fixed effect analysis; we apply Bayesian approaches to allow for heterogeneity in the effect of an allele on risk across studies; and we introduce a region-based test to allow for heterogeneity in the location of causal alleles. PMID:23717212

  11. Population Genetics and Reproductive Strategies of African Trypanosomes: Revisiting Available Published Data.

    PubMed

    Koffi, Mathurin; De Meeûs, Thierry; Séré, Modou; Bucheton, Bruno; Simo, Gustave; Njiokou, Flobert; Salim, Bashir; Kaboré, Jacques; MacLeod, Annette; Camara, Mamadou; Solano, Philippe; Belem, Adrien Marie Gaston; Jamonneau, Vincent

    2015-01-01

    Trypanosomatidae are a dangerous family of Euglenobionta parasites that threaten the health and economy of millions of people around the world. More precisely describing the population biology and reproductive mode of such pests is not only a matter of pure science, but can also be useful for understanding parasite adaptation, as well as how parasitism, specialization (parasite specificity), and complex life cycles evolve over time. Studying this parasite's reproductive strategies and population structure can also contribute key information to the understanding of the epidemiology of associated diseases; it can also provide clues for elaborating control programs and predicting the probability of success for control campaigns (such as vaccines and drug therapies), along with emergence or re-emergence risks. Population genetics tools, if appropriately used, can provide precise and useful information in these investigations. In this paper, we revisit recent data collected during population genetics surveys of different Trypanosoma species in sub-Saharan Africa. Reproductive modes and population structure depend not only on the taxon but also on the geographical location and data quality (absence or presence of DNA amplification failures). We conclude on issues regarding future directions of research, in particular vis-à-vis genotyping and sampling strategies, which are still relevant yet, too often, neglected issues.

  12. Influence of two Wolbachia strains on population structure of East African Drosophila simulans.

    PubMed Central

    Dean, Matthew D; Ballard, Kirrie J; Glass, Anne; Ballard, J William O

    2003-01-01

    Drosophila simulans is hypothesized to have originated in continental East Africa or Madagascar. In this study, we investigated evolutionary forces operating on mitochondrial DNA (mtDNA) in populations of D. simulans from Zimbabwe, Malawi, Tanzania, and Kenya. Variation in mtDNA may be affected by positive selection, background selection, demographic history, and/or any maternally inherited factor such as the bacterial symbiont Wolbachia. In East Africa, the wRi and wMa Wolbachia strains associate with the siII or siIII mitochondrial haplogroups, respectively. To ask how polymorphism relates to Wolbachia infection status, we sequenced 1776 bp of mitochondrial DNA and 1029 bp of the X-linked per locus from 79 lines. The two southern populations were infected with wRi and exhibited significantly reduced mtDNA variation, while Wolbachia-uninfected siII flies from Tanzania and Kenya showed high levels of mtDNA polymorphism. These are the first known populations of D. simulans that do not exhibit reduced mtDNA variation. We observed no mitochondrial variation in the siIII haplogroup regardless of Wolbachia infection status, suggesting positive or background selection. These populations offer a unique opportunity to monitor evolutionary dynamics in ancestral populations that harbor multiple strains of Wolbachia. PMID:14704179

  13. Epidemiology of an intestinal parasite (Spirometra spp.) in two populations of African lions (Panthera leo).

    PubMed

    Müller-Graf, C D; Woolhouse, M E; Packer, C

    1999-04-01

    Infection with the cestode Spirometra spp. was studied in 2 populations of lions in the Serengeti and the Ngorongoro Crater in Tanzania, East Africa. These 2 lion populations lived in different habitats and were known to differ genetically: lions in the Serengeti were outbred, whereas lions in the Ngorongoro Crater were inbred. Faecal samples were collected from 112 individually known lions between March 1991 and November 1992. Over 60% of lions were infected and the median intensity of infection was 975 eggs per g of faeces. The distribution of egg counts was overdispersed. There was variability through time, though this was unrelated to seasons delimited by rainfall. There were no significant differences in levels of infection between age classes; cubs less than 9 months were already heavily infected. Sex and reproductive status did not have a significant effect. However, there were significant differences in intensities of infection between the Crater and the Serengeti populations--Spirometra spp. showed a higher level of infection intensity in the Crater population--with some variation between prides within these populations. Allozyme heterozygosity scores were available for a subset of 28 lions but were unrelated to levels of Spirometra infection. It was not possible to ascribe differences in levels of parasite infection to genetic rather than ecological factors.

  14. Prevalence and characteristics of aquagenic pruritus in a young African population

    PubMed Central

    Salami, TA; Samuel, SO; Eze, KC; Irekpita, E; Oziegbe, E; Momoh, MO

    2009-01-01

    Background Aquagenic pruritus (AP) occurs during or after contact of the skin with water such as occurs in bathing. Methods This study aims to describe the prevalence of aquagenic pruritus in a young adult population and describe the circumstances of bathing. A Population-based cross sectional study involving administration of Questionnaires to young adult Nigerians on the occurrence of pruritus associated with bathing. Results The prevalence of bathing pruritus among respondents in this study was 23.8%. The commonest type of water respondents itch to was rain water (23%) followed by cold water (19%). 8.33% of respondents feels like avoiding bathing because of these. Conclusion Bathing pruritus is a common finding among young adult Nigerians in the general population. PMID:19374742

  15. Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

    PubMed

    Makina, Sithembile O; Taylor, Jeremy F; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; MacNeil, Michael D; Maiwashe, Azwihangwisi

    2015-01-01

    Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

  16. Genetic Testing for the Susceptibility to Alcohol Dependence: Interest and Concerns in an African American Population

    PubMed Central

    Nwulia, Evaristus; Kwagyan, John; Cain, Gloria; Marshall, Vanessa J.; Kalu, Nnenna; Ewing, Altovise; Taylor, Robert E.

    2014-01-01

    Background: The search to identify genes for the susceptibility to alcohol dependence (AD) is generating interest for genetic risk assessment. The purpose of this study is to examine the level of interest and concerns for genetic testing for susceptibility to AD. Methods: Three hundred four African American adults were recruited through public advertisement. All participants were administered the Genetic Psycho-Social Implication (GPSI) questionnaire, which surveyed their interests in hypothetical genetic testing for AD, as well as their perception of ethical and legal concerns. Results: Over 85% of participants were interested in susceptibility genetic testing; however, persons with higher education (p=0.002) and income (p=0.008) were less willing to receive testing. Perception of AD as a deadly disease (48.60%) and wanting to know for their children (47.90%) were the strongest reasons for interest in testing. Among those not interested in testing, the belief that they were currently acting to lower their risk was the most prevalent. The most widely expressed concern in the entire sample was the accuracy of testing (35.50%). Other notable concerns, such as issues with the method of testing, side effects of venipuncture, falsely reassuring results, and lack of guidelines on “what to do next” following test results, were significantly associated with willingness to receive testing. Conclusion: Although an overwhelming majority of participants expressed an interest in genetic testing for AD, there is an understandable high level of methodological and ethical concerns. Such information should form the basis of policies to guide future genetic testing of AD. PMID:24926856

  17. Frequency-Dependent Social Transmission and the Interethnic Transfer of Female Genital Modification in the African Diaspora and Indigenous Populations of Colombia.

    PubMed

    Ross, Cody T; Campiño, Patricia Joyas; Winterhalder, Bruce

    2015-12-01

    We present a quantitative account based on ethnographic and documentary research of the prevalence of female genital modification (FGMo) in the African diaspora and indigenous populations of Colombia. We use these data to test hypotheses concerning the cultural evolutionary drivers of costly trait persistence, attenuation, and intergroup transmission. The uptake of FGMo by indigenous populations in Colombia is consistent with frequency-dependent hypotheses for the social transmission of the FGMo trait from the African diaspora population in the period following the era of slavery in Colombia. The prevalence and severity of practices related to FGMo decline with level of sociocultural integration into mainstream Colombian culture. Our results provide empirical support for the cultural evolutionary models proposed by Ross et al. (2015) to describe the transmission dynamics of FGMo and other costly traits. Analysis of costly trait dynamics contributes knowledge useful to applied anthropology and may be of interest in policy design and human rights monitoring in Colombia and elsewhere.

  18. Stochastic seasonality and nonlinear density-dependent factors regulate population size in an African rodent

    USGS Publications Warehouse

    Leirs, H.; Stenseth, N.C.; Nichols, J.D.; Hines, J.E.; Verhagen, R.; Verheyen, W.

    1997-01-01

    Ecology has long been troubled by the controversy over how populations are regulated. Some ecologists focus on the role of environmental effects, whereas others argue that density-dependent feedback mechanisms are central. The relative importance of both processes is still hotly debated, but clear examples of both processes acting in the same population are rare. Keyfactor analysis (regression of population changes on possible causal factors) and time-series analysis are often used to investigate the presence of density dependence, but such approaches may be biased and provide no information on actual demographic rates. Here we report on both density-dependent and density-independent effects in a murid rodent pest species, the multimammate rat Mastomys natalensis (Smith, 1834), using statistical capture-recapture models. Both effects occur simultaneously, but we also demonstrate that they do not affect all demographic rates in the same way. We have incorporated the obtained estimates of demographic rates in a population dynamics model and show that the observed dynamics are affected by stabilizing nonlinear density-dependent components coupled with strong deterministic and stochastic seasonal components.

  19. Disease, predation and demography: Assessing the impacts of bovine tuberculosis on African buffalo by monitoring at individual and population levels

    USGS Publications Warehouse

    Cross, P.C.; Heisey, D.M.; Bowers, J.A.; Hay, C.T.; Wolhuter, J.; Buss, P.; Hofmeyr, M.; Michel, A.L.; Bengis, Roy G.; Bird, T.L.F.; Du Toit, J.T.; Getz, W.M.

    2009-01-01

    1. Understanding the effects of disease is critical to determining appropriate management responses, but estimating those effects in wildlife species is challenging. We used bovine tuberculosis (BTB) in the African buffalo Syncerus caffer population of Kruger National Park, South Africa, as a case study to highlight the issues associated with estimating chronic disease effects in a long-lived host. 2. We used known and radiocollared buffalo, aerial census data, and a natural gradient in pathogen prevalence to investigate if: (i) at the individual level, BTB infection reduces reproduction; (ii) BTB infection increases vulnerability to predation; and (iii) at the population level, increased BTB prevalence causes reduced population growth. 3. There was only a marginal reduction in calving success associated with BTB infection, as indexed by the probability of sighting a known adult female with or without a calf (P = 0??065). 4. Since 1991, BTB prevalence increased from 27 to 45% in the southern region and from 4 to 28% in the central region of Kruger National Park. The prevalence in the northern regions was only 1??5% in 1998. Buffalo population growth rates, however, were neither statistically different among regions nor declining over time. 5. Lions Panthera leo did not appear to preferentially kill test-positive buffalo. The best (Akaike's Information Criterion corrected for small sample size) AICc model with BTB as a covariate [exp(??) = 0??49; 95% CI = (0??24-1??02)] suggested that the mortality hazard for positive individuals was no greater than for test-negative individuals. 6. Synthesis and applications. Test accuracy, time-varying disease status, and movement among populations are some of the issues that make the detection of chronic disease impacts challenging. For these reasons, the demographic impacts of bovine tuberculosis in the Kruger National Park remain undetectable despite 6 years of study on known individuals and 40 years of population counts

  20. Smoking and genetic risk variation across populations of European, Asian, and African American ancestry--a meta-analysis of chromosome 15q25.

    PubMed

    Chen, Li-Shiun; Saccone, Nancy L; Culverhouse, Robert C; Bracci, Paige M; Chen, Chien-Hsiun; Dueker, Nicole; Han, Younghun; Huang, Hongyan; Jin, Guangfu; Kohno, Takashi; Ma, Jennie Z; Przybeck, Thomas R; Sanders, Alan R; Smith, Jennifer A; Sung, Yun Ju; Wenzlaff, Angie S; Wu, Chen; Yoon, Dankyu; Chen, Ying-Ting; Cheng, Yu-Ching; Cho, Yoon Shin; David, Sean P; Duan, Jubao; Eaton, Charles B; Furberg, Helena; Goate, Alison M; Gu, Dongfeng; Hansen, Helen M; Hartz, Sarah; Hu, Zhibin; Kim, Young Jin; Kittner, Steven J; Levinson, Douglas F; Mosley, Thomas H; Payne, Thomas J; Rao, D C; Rice, John P; Rice, Treva K; Schwantes-An, Tae-Hwi; Shete, Sanjay S; Shi, Jianxin; Spitz, Margaret R; Sun, Yan V; Tsai, Fuu-Jen; Wang, Jen C; Wrensch, Margaret R; Xian, Hong; Gejman, Pablo V; He, Jiang; Hunt, Steven C; Kardia, Sharon L; Li, Ming D; Lin, Dongxin; Mitchell, Braxton D; Park, Taesung; Schwartz, Ann G; Shen, Hongbing; Wiencke, John K; Wu, Jer-Yuarn; Yokota, Jun; Amos, Christopher I; Bierut, Laura J

    2012-05-01

    Recent meta-analyses of European ancestry subjects show strong evidence for association between smoking quantity and multiple genetic variants on chromosome 15q25. This meta-analysis extends the examination of association between distinct genes in the CHRNA5-CHRNA3-CHRNB4 region and smoking quantity to Asian and African American populations to confirm and refine specific reported associations. Association results for a dichotomized cigarettes smoked per day phenotype in 27 datasets (European ancestry (N = 14,786), Asian (N = 6,889), and African American (N = 10,912) for a total of 32,587 smokers) were meta-analyzed by population and results were compared across all three populations. We demonstrate association between smoking quantity and markers in the chromosome 15q25 region across all three populations, and narrow the region of association. Of the variants tested, only rs16969968 is associated with smoking (P < 0.01) in each of these three populations (odds ratio [OR] = 1.33, 95% CI = 1.25-1.42, P = 1.1 × 10(-17) in meta-analysis across all population samples). Additional variants displayed a consistent signal in both European ancestry and Asian datasets, but not in African Americans. The observed consistent association of rs16969968 with heavy smoking across multiple populations, combined with its known biological significance, suggests rs16969968 is most likely a functional variant that alters risk for heavy smoking. We interpret additional association results that differ across populations as providing evidence for additional functional variants, but we are unable to further localize the source of this association. Using the cross-population study paradigm provides valuable insights to narrow regions of interest and inform future biological experiments.

  1. Hypertension in the African American population: A succinct look at its epidemiology, pathogenesis, and therapy.

    PubMed

    Ortega, Luis M; Sedki, Emad; Nayer, Ali

    2015-01-01

    Arterial hypertension is prevalent in the black population in the United States. It is directly related to cardiovascular and kidney damage. Its pathogenesis is complex and includes the high incidence of obesity, salt sensitivity and the activation of the renin-angiotensin-aldosterone system. This complexity requires a therapeutic combination that includes changes in dietary habits and appropriate antihypertensive regimes. The International Society of Hypertension in Blacks recommends initiating dietary intervention for values of systolic/diastolic arterial blood pressure above 115/75 mmHg and maintaining arterial blood pressure below 135/85 mmHg using appropiate antihypertensive medication. The most adequate antihypertensive drug for this population has yet to be determined.

  2. Verification of serum reference intervals for free light chains in a local South African population.

    PubMed

    Zemlin, Annalise E; Rensburg, Megan A; Ipp, Hayley; Germishuys, Jurie J; Erasmus, Rajiv T

    2013-11-01

    Monoclonal serum free light chain measurements are used to follow up and manage patients with monoclonal gammopathies, and abnormal serum free light chain ratios are associated with risk of progression in certain diseases. We aimed to validate the reference intervals in our population. Reference intervals for κ and λ free light chains were established on 120 healthy adults. Creatinine levels were measured to exclude renal dysfunction and serum protein electrophoresis was performed. All creatinine values were within normal limits. After exclusion of subjects with abnormal serum protein electrophoreses, 113 subjects were available for analysis. The 95% reference interval was 6.3-20.6 mg/L for κ free light chains, 8.7-25.9 mg/L for λ free light chains and 0.46-1.23 for free light chain ratio. Most of the values fell within the manufacturer's recommended limits and therefore could be used for our population.

  3. Co-circulation of diverse paramyxoviruses in an urban African fruit bat population

    PubMed Central

    Baker, K. S.; Todd, S.; Marsh, G.; Fernandez-Loras, A.; Suu-Ire, R.; Wood, J. L. N.; Wang, L. F.

    2012-01-01

    Bats constitute a reservoir of zoonotic infections and some bat paramyxoviruses are capable of cross-species transmission, often with fatal consequences. Determining the level of viral diversity in reservoir populations is fundamental to understanding and predicting viral emergence. This is particularly relevant for RNA viruses where the adaptive mutations required for cross-species transmission can be present in the reservoir host. We report the use of non-invasively collected, pooled, neat urine samples as a robust sample type for investigating paramyxoviruses in bat populations. Using consensus PCR assays we have detected a high incidence and genetic diversity of novel paramyxoviruses in an urban fruit bat population over a short period of time. This may suggest a similarly unique relationship between bats and the members of the family Paramyxoviridae as proposed for some other viral families. Additionally, the high rate of bat–human contact at the study site calls for the zoonotic potential of the detected viruses to be investigated further. PMID:22205718

  4. Chronic Airflow Obstruction in a Black African Population: Results of BOLD Study, Ile-Ife, Nigeria.

    PubMed

    Obaseki, Daniel O; Erhabor, Gregory E; Gnatiuc, Louisa; Adewole, Olufemi O; Buist, Sonia A; Burney, Peter G

    2016-01-01

    Global estimates suggest that Chronic Obstructive Pulmonary Disease (COPD) is emerging as a leading cause of death in developing countries but there are few spirometry-based general population data on its prevalence and risk factors in sub-Saharan Africa. We used the Burden of Obstructive Lung Disease (BOLD) protocol to select a representative sample of adults aged 40 years and above in Ile-Ife, Nigeria. All the participants underwent spirometry and provided information on smoking history, biomass and occupational exposures as well as diagnosed respiratory diseases and symptoms. Chronic Airflow Obstruction (CAO) was defined as the ratio of post-bronchodilator (BD) one second Forced Expiratory Volume (FEV1) to Forced Vital Capacity (FVC) below the lower limit of normal (LLN) of the population distribution for FEV1/FVC. The overall prevalence of obstruction (post-BD FEV1/FVC < LLN) was 7.7% (2.7% above LLN) using Global Lung Function Initiative (GLI) equations. It was associated with few respiratory symptoms; 0.3% reported a previous doctor-diagnosed chronic bronchitis, emphysema or COPD. Independent predictors included a lack of education (OR 2.5, 95% CI: 1.0, 6.4) and a diagnosis of either TB (OR 23.4, 95% CI: 2.0, 278.6) or asthma (OR 35.4, 95%CI: 4.9, 255.8). There was no association with the use of firewood or coal for cooking or heating. The vast majority of this population (89%) are never smokers. We conclude that the prevalence of CAO is low in Ile-Ife, Nigeria and unrelated to biomass exposure. The key independent predictors are poor education, and previous diagnosis of tuberculosis or asthma.

  5. Lung cancer, tobacco, and environmental factors in the African population of the Northern Province, South Africa

    PubMed Central

    Mzileni, O.; Sitas, F.; Steyn, K.; Carrara, H.; Bekker, P.

    1999-01-01

    DESIGN—Case-control study among incident African patients with cancer. Questionnaire assessment of exposure to tobacco, occupation, and place of birth.
SETTING—Northern Province, South Africa.
SUBJECTS—Between 1993 and 1995, 288 men and 60 women with lung cancer and 183 male and 197 female controls (consisting of patients newly diagnosed with cancers other than those known to be associated with smoking) were interviewed. Unmatched, unconditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs) of developing lung cancer in relation to a number of variables.
MAIN OUTCOME MEASURE—Risk of developing lung cancer related to exposure to tobacco, indoor pollution, dusty work environment, and residential exposure to asbestos.
RESULTS—There was a significant increase in the risk of developing lung cancer through smoking. In men, the ORs were 2.2 (95% CI = 1.0 to 4.6) in ex-smokers, 9.8 (95% CI = 5.9 to 16.4) in light smokers (0-14 g/day), and 12.0 (95% CI = 6.5 to 22.3) in heavy smokers. In women, the ORs were 5.8 (95% CI = 1.3 to 25.8) in ex-smokers and 5.5 (95% CI = 2.6 to 11.3) in current smokers. Work in a dusty industry showed an elevated risk (OR = 3.2, 95% CI = 1.8 to 5.8) for lung cancer only in men. Male residents of areas where asbestos was shipped for distribution (termed moderately polluted asbestos areas) had a 2.5-fold increase (95% CI = 1.0 to 4.4) in the risk (OR) of developing lung cancer, and residents of areas where asbestos was mined (termed heavily polluted asbestos areas) had a 2.8-fold increase in risk (95% CI = 0.7 to 10.4). Female residents of heavily polluted asbestos areas showed elevated risks of 5.4 (95% CI = 1.3 to 22.5) of developing lung cancer.
CONCLUSION—The data suggest that tobacco smoking is the most important risk factor for the development of lung cancer in this setting. Risks for lung cancer are reminiscent of those

  6. The Paternal Landscape along the Bight of Benin – Testing Regional Representativeness of West-African Population Samples Using Y-Chromosomal Markers

    PubMed Central

    Larmuseau, Maarten H. D.; Vessi, Andrea; Jobling, Mark A.; Van Geystelen, Anneleen; Primativo, Giuseppina; Biondi, Gianfranco; Martínez-Labarga, Cristina; Ottoni, Claudio; Decorte, Ronny; Rickards, Olga

    2015-01-01

    Patterns of genetic variation in human populations across the African continent are still not well studied in comparison with Eurasia and America, despite the high genetic and cultural diversity among African populations. In population and forensic genetic studies a single sample is often used to represent a complete African region. In such a scenario, inappropriate sampling strategies and/or the use of local, isolated populations may bias interpretations and pose questions of representativeness at a macrogeographic-scale. The non-recombining region of the Y-chromosome (NRY) has great potential to reveal the regional representation of a sample due to its powerful phylogeographic information content. An area poorly characterized for Y-chromosomal data is the West-African region along the Bight of Benin, despite its important history in the trans-Atlantic slave trade and its large number of ethnic groups, languages and lifestyles. In this study, Y-chromosomal haplotypes from four Beninese populations were determined and a global meta-analysis with available Y-SNP and Y-STR data from populations along the Bight of Benin and surrounding areas was performed. A thorough methodology was developed allowing comparison of population samples using Y-chromosomal lineage data based on different Y-SNP panels and phylogenies. Geographic proximity turned out to be the best predictor of genetic affinity between populations along the Bight of Benin. Nevertheless, based on Y-chromosomal data from the literature two population samples differed strongly from others from the same or neighbouring areas and are not regionally representative within large-scale studies. Furthermore, the analysis of the HapMap sample YRI of a Yoruban population from South-western Nigeria based on Y-SNPs and Y-STR data showed for the first time its regional representativeness, a result which is important for standard population and forensic genetic applications using the YRI sample. Therefore, the uniquely

  7. Seasonal variation in attention and spatial performance in a wild population of the African striped mouse (Rhabdomys pumilio).

    PubMed

    Maille, Audrey; Pillay, Neville; Schradin, Carsten

    2015-11-01

    Cognitive flexibility describes the reversible changes of cognition in response to environmental changes. Although various environmental factors such as temperature, photoperiod and rainfall change seasonally, seasonal variation in cognitive performance has been reported in merely a few birds and mammals. We assessed whether cognitive performance in a wild population of African striped mice Rhabdomys pumilio, from the Succulent Karoo semidesert of South Africa, differed between summer and winter. In order to measure cognitive performance, striped mice were trapped in the field, tested under laboratory conditions at our research station and returned to the field within 5 h. We measured attention and spatial memory using the standardized orientation response test and the Barnes maze test. Males tested during summer oriented faster toward a predator-stimulus but made more errors and took longer to locate a shelter than males tested during winter. In contrast, females' performance did not differ between the two seasons. We discuss how the faster orientation in males during winter might be the consequence of lower temperatures and/or prolonged food restriction. We suggest that the enhancement of spatial performance during winter might be due to a greater motivation for future dispersal in male striped mice, as spring represents the breeding season.

  8. Envelope-specific B-cell populations in African green monkeys chronically infected with simian immunodeficiency virus

    PubMed Central

    Zhang, Ruijun; Martinez, David R.; Nguyen, Quang N.; Pollara, Justin; Arifin, Trina; Stolarchuk, Christina; Foulger, Andrew; Amos, Josh D.; Parks, Robert; Himes, Jonathon E.; Wang, Minyue; Edwards, Regina W.; Trama, Ashley M.; Vandergrift, Nathan; Colvin, Lisa; Dewar, Ken; Juretic, Nikoleta; Wasserscheid, Jessica; Ferrari, Guido; Liao, Hua-Xin; Permar, Sallie R.

    2016-01-01

    African green monkeys (AGMs) are natural primate hosts of simian immunodeficiency virus (SIV). Interestingly, features of the envelope-specific antibody responses in SIV-infected AGMs are distinct from that of HIV-infected humans and SIV-infected rhesus monkeys, including gp120-focused responses and rapid development of autologous neutralization. Yet, the lack of genetic tools to evaluate B-cell lineages hinders potential use of this unique non-human primate model for HIV vaccine development. Here we define features of the AGM Ig loci and compare the proportion of Env-specific memory B-cell populations to that of HIV-infected humans and SIV-infected rhesus monkeys. AGMs appear to have a higher proportion of Env-specific memory B cells that are mainly gp120 directed. Furthermore, AGM gp120-specific monoclonal antibodies display robust antibody-dependent cellular cytotoxicity and CD4-dependent virion capture activity. Our results support the use of AGMs to model induction of functional gp120-specific antibodies by HIV vaccine strategies. PMID:27381634

  9. Amerindian (but not African or European) ancestry is significantly associated with diurnal preference within an admixed Brazilian population.

    PubMed

    Egan, Kieren J; Campos Santos, Hadassa; Beijamini, Felipe; Duarte, Núbia E; Horimoto, Andréa R V R; Taporoski, Tâmara P; Vallada, Homero; Negrão, André B; Krieger, José E; Pedrazzoli, Mário; Knutson, Kristen L; Pereira, Alexandre C; von Schantz, Malcolm

    2017-01-01

    Significant questions remain unanswered regarding the genetic versus environmental contributions to racial/ethnic differences in sleep and circadian rhythms. We addressed this question by investigating the association between diurnal preference, using the morningness-eveningness questionnaire (MEQ), and genetic ancestry within the Baependi Heart Study cohort, a highly admixed Brazilian population based in a rural town. Analysis was performed using measures of ancestry, using the Admixture program, and MEQ from 1,453 individuals. We found an association between the degree of Amerindian (but not European of African) ancestry and morningness, equating to 0.16 units for each additional percent of Amerindian ancestry, after adjustment for age, sex, education, and residential zone. To our knowledge, this is the first published report identifying an association between genetic ancestry and MEQ, and above all, the first one based on ancestral contributions within individuals living in the same community. This previously unknown ancestral dimension of diurnal preference suggests a stratification between racial/ethnic groups in an as yet unknown number of genetic polymorphisms.

  10. Functional Dyspepsia: Subtypes, Risk Factors, and Overlap with Irritable Bowel Syndrome in a Population of African Patients

    PubMed Central

    Nwokediuko, Sylvester Chuks; Ijoma, Uchenna; Obienu, Olive

    2012-01-01

    Background. Functional dyspepsia is the prototype functional gastrointestinal disorder. This study was designed to determine its prevalence, subtypes, and risk factors associated with the subtypes. Method. Patients with upper gastrointestinal symptoms who presented for endoscopy were administered a questionnaire containing the functional dyspepsia and irritable bowel syndrome modules of the Rome III diagnostic criteria. Results. Of 192 patients who had functional dyspepsia, epigastric pain syndrome, postprandial distress syndrome, and combination of the two subtypes accounted for 79.2%, 62.5%, and 50%, respectively. Multivariate analysis of the risk factors showed that independent predictors of postprandial distress syndrome were alcohol and irritable bowel syndrome while irritable bowel syndrome was independent predictor of epigastric pain syndrome. Alcohol, smoking, and use of nonsteroidal anti-inflammatory drugs were independent predictors of cooccurrence of postprandial distress syndrome and epigastric pain syndrome. Conclusion. Functional dyspepsia accounts for 62.5% of dyspepsia in a population of black African patients. Regarding symptomatology, epigastric pain syndrome, postprandial distress syndrome, and combination of the two subtypes account for 79.2%, 62.5%, and 50%, respectively. Risk factors for functional dyspepsia are irritable bowel syndrome, alcohol, smoking, and use of nonsteroidal anti-inflammatory drugs. PMID:23213327

  11. Estimating the net effect of HIV on child mortality in African populations affected by generalized HIV epidemics.

    PubMed

    Marston, Milly; Zaba, Basia; Salomon, Joshua A; Brahmbhatt, Heena; Bagenda, Danstan

    2005-02-01

    For a given prevalence, HIV has a relatively higher impact on child mortality when mortality from other causes is low. To project the effect of the epidemic on child mortality, it is necessary to estimate a realistic schedule of "net" age-specific mortality rates that would operate if HIV were the only cause of child death observable. We assume that this net pattern would be independent of mortality from other causes. We used African studies that measured the survival of HIV-infected children (direct data) or survival of children of HIV-infected mothers (indirect data). We developed a mathematic procedure to estimate the mortality of infected children from indirect data sources and obtained net HIV mortality patterns for each study population. The net age-specific HIV mortality pattern for infected children can be described by a double Weibull curve fitted to empiric data; this gives a functional representation of age-specific mortality rates that decline after infancy and rise in the preteens. The fitted curve that we would expect if HIV were the only effective cause of death shows 67% net survival at 1 year and 39% at 5 years. The curve also predicts 13% net survival at 10 years using constraints based on survival of infected adults.

  12. CD1A, D and E gene polymorphisms in a North African population from Morocco.

    PubMed

    Aureli, Anna; Oumhani, Khadija; Del Beato, Tiziana; El Aouad, Rajae; Piancatelli, Daniela

    2016-07-01

    CD1 molecules are specialized in capturing and presenting lipids and glycolipids to distinct subsets of T and NKT cells. Glycolipid presentation could play a significant role in the immune response against microbial infections. There are five closely linked CD1 genes in humans, named CD1A, B, C, D, and E, which all show a limited polymorphism. In this study, exon 2 polymorphisms of CD1A, CD1D and CD1E were investigated and allele, genotype and haplotype frequencies of these loci were reported in a Moroccan population. A comparison with allele, genotype and haplotype frequencies observed in other geographic areas was also performed. Results confirmed the presence of ethnic differences in CD1 polymorphism, mainly in CD1D (in this population two additional CD1D variant alleles, CD1D(∗)03 and CD1D(∗)04, were described) and E genes. These data could be useful to evaluate a possible pathogenetic role of CD1 in diseases. Increasing the knowledge in this field may offer possibilities for the development of new immunotherapeutic approaches.

  13. As Latino Populations Grow, So Does Their Power. Will They Compete or Cooperate with African Americans for Academic Clout?

    ERIC Educational Resources Information Center

    Weiger, Pamela R.

    2000-01-01

    Examines perceptions that African Americans must compete with Hispanics for faculty and administrative positions at Arizona State University. School officials deny replacing African American employees with Hispanics, suggesting that isolated incidents might make people believe this is occurring. Data are provided on Hispanic higher education…

  14. Familial Factors in the Early Life Experiences of a Population of African American Crack-Cocaine Users: The Father Link?

    ERIC Educational Resources Information Center

    Dixon, Patricia

    1998-01-01

    Explored factors contributing to addiction in 140 African-American males in an inner-city homeless shelter. A common theme in their life stories is that of negative and painful experiences with father figures. Suggestions are made for research into this area and policy strategies to enhance the African-American father's role. (SLD)

  15. Mental Health and African Americans

    MedlinePlus

    ... Minority Population Profiles > Black/African American > Mental Health Mental Health and African Americans Poverty level affects mental health ... compared to 120% of non-Hispanic whites. 1 MENTAL HEALTH STATUS Serious psychological distress among adults 18 years ...

  16. Hunter-gatherer adaptations and environmental change in the southern Great Basin: The evidence from Pahute and Rainier mesas

    SciTech Connect

    Pippin, L.C.

    1998-06-01

    This paper reviews the evidence for fluctuations in past environments in the southern Great Basin and examines how these changes may have affected the strategies followed by past hunter and gatherers in their utilization of the resources available on a highland in this region. The evidence used to reconstruct past environments for the region include botanical remains from packrat middens, pollen spectra from lake and spring deposits, faunal remains recovered from archaeological and geologic contexts, tree-ring indices from trees located in sensitive (tree-line) environments, and eolian, alluvial and fluvial sediments deposited in a variety of contexts. Interpretations of past hunter and gatherer adaptive strategies are based on a sample of 1,311 archaeological sites recorded during preconstruction surveys on Pahute and Rainier mesas in advance of the US Department of Energy`s nuclear weapons testing program. Projectile point chronologies and available tree-ring, radiocarbon, thermoluminescence and obsidian hydration dates were used to assign these archaeological sites to specific periods of use.

  17. Sex-biased weaning and early childhood diet among middle holocene hunter-gatherers in Central California.

    PubMed

    Eerkens, Jelmer W; Bartelink, Eric J

    2013-12-01

    This article evaluates age of weaning and early childhood diets of eight males and nine females from a Middle Holocene (4300-3000 BP) site in Central California, CA-CCO-548. All individuals died as adults. δ(15) N values from serial sections of dentin collagen in first molars suggest females were fully weaned, on average, by 3.6 years of age, about 0.4 years later than males in the sample, suggesting possible greater parental investment in female offspring. However, throughout childhood females consumed lower trophic-level foods than males. This could indicate greater investment in males through provisioning of higher quality foods, or alternatively, some degree of independent foraging by males starting as early as 2 to 3 years of age. Even as adults, these same males and females consumed a different range of foods as indicated by their bone collagen δ(13) C and δ(15) N values. Overall, the data suggest children were enculturated early into their respective gendered diets, with girls consuming greater amounts of plant foods and boys consuming greater amounts of higher-trophic level fish and meat protein.

  18. The Modern Obesity Epidemic, Ancestral Hunter-Gatherers, and the Sensory/Reward Control of Food Intake

    ERIC Educational Resources Information Center

    King, Bruce M.

    2013-01-01

    Obesity has become a true pandemic. In the United States, over two thirds of adults are obese or overweight. The prevalence of obesity has doubled since 1980. The increase in the prevalence of obese and overweight individuals has happened too rapidly for it to be due to an alteration in the genome. The gastrointestinal, sensory (taste and…

  19. The South African and Namibian populations of the resurrection plant Myrothamnus flabellifolius are genetically distinct and display variation in their galloylquinic acid composition.

    PubMed

    Moore, John P; Farrant, Jill M; Lindsey, George G; Brandt, Wolf F

    2005-12-01

    The polyphenol contents and compositions in desiccated leaves of Myrothamnus flabellifolius plants collected in various locations in Namibia and South Africa were analyzed using UV spectroscopy and high-performance liquid chromatography-mass spectrometry. A study of the genetic relatedness of these populations was also performed by determination of the DNA sequence of the intergenic spacer region between the psbA and the trnH genes in the chloroplast genome. Namibian M. flabellifolius plants contained significantly more polyphenols than South African plants. Namibian plants essentially contained a single polyphenol, 3,4,5-tri-O-galloylquinic acid, whereas South African plants contained a variety of galloylquinic acids including 3,4,5-tri-O-galloylquinic acid together with higher molecular weight galloylquinic acids. Sequence analysis revealed a 1.4% divergence between Namibian and South African plants corresponding to the separation of these populations of approximately 4 x 10(6) years. The significance of the poly-phenol content and composition to the desiccation tolerance of the two populations is discussed.

  20. Prevalence and predictors of concurrent sexual partnerships in a predominantly African American population in Jackson, Mississippi

    PubMed Central

    Nunn, Amy; MacCarthy, Sarah; Barnett, Nancy; Rose, Jennifer; Chan, Philip; Yolken, Annajane; Cornwall, Alexandra; Chamberlain, Nicholas; Barnes, Arti; Riggins, Reginald; Moore, Elya; Simmons, Dantrell; Parker, Sharon; Mena, Leandro

    2014-01-01

    Concurrent sexual partnerships, or sexual partnerships that overlap in time, have been associated with HIV and sexually transmitted infections (STI) infection. How best to measure concurrency and the personal characteristics and predictors of concurrency are not yet well understood. We compared two frequently used concurrency definitions, including a self-reported measure based on participant response regarding overlapping sex with partners, and the UNAIDS measure based on overlapping dates of last sex and intention to have sex again. We performed multivariable logistic regression analyses to identify socio-demographic, behavioral, and structural predictors of concurrency among 1,542 patients at an urban STI clinic in Jackson, Mississippi. Nearly half (44%) reported concurrency based on self-reported sex with other partners, and 26% reported concurrency according to the UNAIDS concurrency measure. Using the self-reported concurrency measure, the strongest predictors of concurrency were perceived partner concurrency, drug use at last sex, having more than 10 lifetime partners, and being recently incarcerated. Strongest predictors of concurrency using the UNAIDS measure were lifetime number of partners and perceived partner concurrency. Concurrency is highly prevalent in this population in the Deep South and social, structural and behavioral factors were important predictors of concurrency for both measures. Future research should use time anchored data collection methods and biomarkers to assess whether both definitions of concurrency are associated with HIV outcomes. PMID:24803130

  1. Frequency and predictors of suboptimal glycemic control in an African diabetic population

    PubMed Central

    Kibirige, Davis; Akabwai, George Patrick; Kampiire, Leaticia; Kiggundu, Daniel Ssekikubo; Lumu, William

    2017-01-01

    Background Persistent suboptimal glycemic control is invariably associated with onset and progression of acute and chronic diabetic complications in diabetic patients. In Uganda, studies documenting the magnitude and predictors of suboptimal glycemic control in adult ambulatory diabetic patients are limited. This study aimed at determining the frequency and predictors of suboptimal glycemic control in adult diabetic patients attending three urban outpatient diabetic clinics in Uganda. Methods In this hospital-based cross-sectional study, eligible ambulatory adult diabetic patients attending outpatient diabetic clinics of three urban hospitals were consecutively enrolled over 11 months. Suboptimal glycemic control was defined as glycated hemoglobin (HbA1c) level ≥7%. Multivariable analysis was applied to determine the predictors. Results The mean age of the study participants was 52.2±14.4 years, and the majority of them were females (283, 66.9%). The median (interquartile range) HbA1c level was 9% (6.8%–12.4%). Suboptimal glycemic control was noted in 311 study participants, accounting for 73.52% of the participants. HbA1c levels of 7%–8%, 8.1%–9.9%, and ≥10% were noted in 56 (13.24%), 76 (17.97%), and 179 (42.32%) study participants, respectively. The documented predictors of suboptimal glycemic control were metformin monotherapy (odds ratio: 0.36, 95% confidence interval: 0.21–0.63, p<0.005) and insulin therapy (odds ratio: 2.41, 95% confidence interval: 1.41–4.12, p=0.001). Conclusion Suboptimal glycemic control was highly prevalent in this study population with an association to metformin monotherapy and insulin therapy. Strategies aimed at improving glycemic control in diabetes care in Uganda should be enhanced. PMID:28260942

  2. Genetic diversity of simian immunodeficiency viruses from West African green monkeys: evidence of multiple genotypes within populations from the same geographical locale.

    PubMed Central

    Bibollet-Ruche, F; Brengues, C; Galat-Luong, A; Galat, G; Pourrut, X; Vidal, N; Veas, F; Durand, J P; Cuny, G

    1997-01-01

    High simian immunodeficiency virus (SIV) seroprevalence rates have been reported in the different African green monkey (AGM) subspecies. Genetic diversity of these viruses far exceeds the diversity observed in the other lentivirus-infected human and nonhuman primates and is thought to reflect ancient introduction of SIV in the AGM population. We investigate here genetic diversity of SIVagm in wild-living AGM populations from the same geographical locale (i.e., sympatric population) in Senegal. For 11 new strains, we PCR amplified and sequenced two regions of the genome spanning the first tat exon and part of the transmembrane glycoprotein. Phylogenetic analysis of these sequences shows that viruses found in sympatric populations cluster into distinct lineages, with at least two distinct genotypes in each troop. These data strongly suggest an ancient introduction of these divergent viruses in the AGM population. PMID:8985351

  3. Polymorphisms in nucleotide excision repair genes, smoking and breast cancer in African Americans and whites: a population-based case-control study.

    PubMed

    Mechanic, Leah E; Millikan, Robert C; Player, Jon; de Cotret, Allan René; Winkel, Scott; Worley, Kendra; Heard, Kristin; Heard, Kimberley; Tse, Chiu-Kit; Keku, Temitope

    2006-07-01

    Polymorphisms exist in several genes involved in nucleotide excision repair (NER), the principal pathway for removal of smoking-induced DNA damage. An epidemiologic study was conducted to determine whether these polymorphisms modify the association between smoking and breast cancer. DNA samples and exposure histories were analyzed as part of a large population-based case-control study of breast cancer in North Carolina. The study population included 2311 cases (894 African Americans, 1417 whites) and 2022 controls (788 African Americans, 1234 whites). Odds ratios (ORs) were calculated for breast cancer and smoking, and for breast cancer and nine non-synonymous coding polymorphisms in six NER genes (XPD codons 312 and 751, RAD23B codon 249, XPG codon 1104, XPC codon 939, XPF codons 415 and 662, and ERCC6 codons 1213 and 1230). Modification of ORs for smoking by single and combined NER genotypes was investigated. In this study population, smoking was more strongly associated with breast cancer in African American women compared with white women. Among African American women, the association of breast cancer and smoking was strongest among women with specific combinations of NER genotypes. Evidence for multiplicative interaction was found between combined NER genotypes and smoking dose (likelihood ratio test P = 0.06), duration (P = 0.09), time since cessation (P = 0.02), age at initiation (P = 0.04) and former smoking (P = 0.03). No interactions were observed in white women. Therefore, polymorphisms in NER genes may modify the relationship between breast cancer and smoking. These results are consistent with previous evidence of exposure-specific p53 mutations in breast tumors from current and former smokers, suggesting that smoking may play a role in breast cancer etiology.

  4. The Association of C-Reactive Protein and Physical Activity Among a Church-Based Population of African Americans

    PubMed Central

    Adams, Swann Arp; Wirth, Michael D.; Khan, Samira; Murphy, E. Angela; Heiney, Sue P.; Davis, Lisa C.; Davis, Briana; Drayton, Ruby F.; Hurley, Thomas G.; Blair, Steven M.; Hébert, James R.

    2015-01-01

    Objective Regular physical activity can reduce systemic inflammation and, thereby, the burden of chronic inflammatory-related conditions. This study examined whether regular physical activity, measured subjectively (Rapid Assessment of Physical Activity [RAPA]) and objectively (Bodymedia’s SenseWear® activity monitor [SWA]), is associated with inflammatory or glycemic control markers. Methods Subjects were 345 participants of the Healthy Eating and Active Living in the Spirit (HEALS) lifestyle intervention among African-American (AA) churches in South Carolina in 2009. Linear regression analyses were performed to assess the relationship between both subjectively- and objectively- measured physical activity and inflammatory markers including high sensitivity c-reactive protein (CRP), interleukin-6 (IL-6), and glycosylated hemoglobin (HbA1c). Results Those who participated in regular physical activity (RAPA) had lower CRP values compared to those who were sedentary (2.3 vs. 3.8 mg/L, p<0.01). Lower levels of CRP or IL-6 were observed among those in the highest quartile of active energy expenditure (CRP: 2.0 vs. 3.6 mg/L, p=0.01) or moderate-vigorous physical activity minutes (CRP=1.7 vs. 4.5 mg/L, p<0.01; IL-6=1.5 vs. 2.1 pg/mL, p=0.01) compared to their lowest respective quartiles as measured by the SWA. Conclusion Physical activity may improve chronic inflammation, which is a primary pathophysiological mechanism for numerous chronic disorders, especially among minority populations. PMID:26007295

  5. Temporal variation in the genetic structure of a drone congregation area: an insight into the population dynamics of wild African honeybees (Apis mellifera scutellata).

    PubMed

    Jaffé, R; Dietemann, V; Crewe, R M; Moritz, R F A

    2009-04-01

    The mating system of the honeybee (Apis mellifera) has been regarded as one of the most panmictic in the animal kingdom, with thousands of males aggregating in drone congregation areas (DCAs) that virgin queens visit to mate with tens of partners. Although males from many colonies gather at such congregations, the temporal changes in the colonies contributing drones remain unknown. Yet, changes in the DCAs' genetic structure will ultimately determine population gene flow and effective population size. By repeatedly sampling drones from an African DCA over a period of 3 years, we studied the temporal changes in the genetic structure of a wild honeybee population. Using three sets of tightly linked microsatellite markers, we were able to reconstruct individual queen genotypes with a high accuracy, follow them through time and estimate their rate of replacement. The number of queens contributing drones to the DCA varied from 12 to 72 and was correlated with temperature and rainfall. We found that more than 80% of these queens were replaced by mostly unrelated ones in successive eight months sampling intervals, which resulted in a clear temporal genetic differentiation of the DCA. Our results suggest that the frequent long-range migration of colonies without nest-site fidelity is the main driver of this high queen turnover. DCAs of African honeybees should thus be regarded as extremely dynamic systems which together with migration boost the effective population size and maintain a high genetic diversity in the population.

  6. Assessing the maximum contribution from ancient populations.

    PubMed

    Sjödin, Per; Skoglund, Pontus; Jakobsson, Mattias

    2014-05-01

    Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of "level of contribution" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmström H, Gilbert MTP, Thomas MG, Brandström M, Storå J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Götherström A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Gröcke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326).

  7. Growth and fat-body cycles in feral populations of the African clawed frog, Xenopus laevis (Pipidae), in California with comments on reproduction

    USGS Publications Warehouse

    McCoid, Michael J.; Fritts, Thomas H.

    1989-01-01

    Feral populations of the African clawed frog (Xenopus laevis) exist in several areas of southern California. By following the first cohort of progeny produced by African clawed frogs at a recently colonized site, data on the growth rates and age at first maturity were obtained in field conditions. Females reached maturity at an earlier age than males, grew faster than males, and attained body lengths up to 25% larger than males. Larger females were capable of producing larger numbers of eggs than small females and, therefore, had greater reproductive potential. The relatively stable ambient temperatures of southern California contributed to the possibility of reproduction of clawed frogs during all but the coolest periods of the year. Cycles detected in the mass of fatbodies suggested that nutrients were mobilized from fat prior to and during ovulation. The amount of fat in females varies widely, but fat in males tended to accumulate as the males grew during the study period.

  8. Growth and fatbody cycles in feral populations of the African clawed frog, Xenopus laevis (Pipidae), in California with comments on reproduction

    USGS Publications Warehouse

    McCoid, M.J.; Fritts, T.H.

    1989-01-01

    Feral populations of the African clawed frog (Xenopus laevis) exist in several areas of southern California. By following the first cohort of progeny produced by African clawed frogs at a recently colonized site, data on the growth rates and age at first maturity were obtained in field conditions. Females reached maturity at an earlier age than males, grew faster than males, and attained body lengths up to 25% larger than males. Larger females were capable of producing larger numbers of eggs than small females and, therefore, had greater reproductive potential. The relatively stable ambient temperatures of southern California contributed to the possibility of reproduction of clawed frogs during all but the coolest periods of the year. Cycles detected in the mass of fatbodies suggested that nutrients were mobilized from fat prior to and during ovulation. The amount of fat in females varied widely, but fat in males tended to accumulate as the males grew during the study period.

  9. The birth prevalence of PKU in populations of European, South Asian and sub-Saharan African ancestry living in South East England.

    PubMed

    Hardelid, P; Cortina-Borja, M; Munro, A; Jones, H; Cleary, M; Champion, M P; Foo, Y; Scriver, C R; Dezateux, C

    2008-01-01

    Phenylketonuria (PKU) is an autosomal recessive inborn error of metabolism (OMIM 261600). Treatment with a low-phenylalanine diet following early ascertainment by newborn screening prevents impaired cognitive development, the major disease phenotype in PKU. The overall birth prevalence of PKU in European, Chinese and Korean populations is approximately 1/10,000. Since the human PAH locus contains PKU-causing alleles and polymorphic core haplotypes that describe and corroborate an out-of-Africa range expansion in modern human populations, it is of interest to know the prevalence of PKU in different ethnic groups with diverse geographical origin. We estimated PKU prevalence in South East England, where a sizeable proportion of the population are of Sub-Saharan African or South Asian ancestry. Over the period 1994 to 2004 167 children were diagnosed with PKU. Using birth registration and census data to derive denominators, PKU birth prevalence per 10,000 live births (95% Bayesian credible intervals) was estimated to be 1.14 (0.96-1.33) among white, 0.11 (0.02-0.37) among black, and 0.29 (0.10-0.63) among Asian ethnic groups. This suggests that PKU is up to an order of magnitude less prevalent in populations with Sub-Saharan African and South Asian ancestry that have migrated to the UK.

  10. Molecular Variation of Adh and P6 Genes in an African Population of Drosophila Melanogaster and Its Relation to Chromosomal Inversions

    PubMed Central

    Benassi, V.; Aulard, S.; Mazeau, S.; Veuille, M.

    1993-01-01

    Four-cutter molecular polymorphism of Adh and P6, and chromosome inversion polymorphism of chromosome II were investigated in 95 isogenic lines of an Ivory Coast population of Drosophila melanogaster, a species assumed to have recently spread throughout the world from a West African origin. The P6 gene showed little linkage disequilibrium with the In(2L)t inversion, although it is located within this inversion. This suggests that the inversion and the P6 locus have extensively exchanged genetic information through either double crossover or gene conversion. Allozymic variation in ADH was in linkage disequilibrium with In(2L)t and In(2R)NS inversions. Evidence suggests either that inversion linkage with the Fast allele is selectively maintained, or that this allele only recently appeared. Molecular polymorphism at the Adh locus in the Ivory Coast is not higher than in North American populations. New haplotypes specific to the African population were found, some of them connect the ``Wa(s)-like'' haplotypes found at high frequencies in the United States to the other slow haplotypes. Their relation with In(2L)t supports the hypothesis that Wa(s) recently recombined away from an In(2L)t chromosome which may be the cause of its divergence from the other haplotypes. PMID:8349110

  11. Evidence of common signatures of selection in the genomes of West African cattle and the Yoruba human population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 1954, Allison found that the sickle-cell anemia mutation in the beta hemoglobin gene was highly prevalent in West African people because it is protective against malaria, so carriers would thrive and leave offspring in spite of the genetic disease. This is one of the earliest evidences of an envi...

  12. Genetic diversity and natural selection footprints of the glycine amidinotransferase gene in various human populations.

    PubMed

    Khan, Asifullah; Tian, Lei; Zhang, Chao; Yuan, Kai; Xu, Shuhua

    2016-01-05

    The glycine amidinotransferase gene (GATM) plays a vital role in energy metabolism in muscle tissues and is associated with multiple clinically important phenotypes. However, the genetic diversity of the GATM gene remains poorly understood within and between human populations. Here we analyzed the 1,000 Genomes Project data through population genetics approaches and observed significant genetic diversity across the GATM gene among various continental human populations. We observed considerable variations in GATM allele frequencies and haplotype composition among different populations. Substantial genetic differences were observed between East Asian and European populations (FST = 0.56). In addition, the frequency of a distinct major GATM haplotype in these groups was congruent with population-wide diversity at this locus. Furthermore, we identified GATM as the top differentiated gene compared to the other statin drug response-associated genes. Composite multiple analyses identified signatures of positive selection at the GATM locus, which was estimated to have occurred around 850 generations ago in European populations. As GATM catalyzes the key step of creatine biosynthesis involved in energy metabolism, we speculate that the European prehistorical demographic transition from hunter-gatherer to farming cultures was the driving force of selection that fulfilled creatine-based metabolic requirement of the populations.

  13. TESTING POPULATION-SPECIFIC QUANTITATIVE TRAIT ASSOCIATIONS FOR CLINICAL OUTCOME RELEVANCE IN A BIOREPOSITORY LINKED TO ELECTRONIC HEALTH RECORDS: LPA AND MYOCARDIAL INFARCTION IN AFRICAN AMERICANS

    PubMed Central

    Dumitrescu, Logan; Diggins, Kirsten E.; Goodloe, Robert; Crawford, Dana C.

    2015-01-01

    Previous candidate gene and genome-wide association studies have identified common genetic variants in LPA associated with the quantitative trait Lp(a), an emerging risk factor for cardiovascular disease. These associations are population-specific and many have not yet been tested for association with the clinical outcome of interest. To fill this gap in knowledge, we accessed the epidemiologic Third National Health and Nutrition Examination Surveys (NHANES III) and BioVU, the Vanderbilt University Medical Center biorepository linked to de-identified electronic health records (EHRs), including billing codes (ICD-9-CM) and clinical notes, to test population-specific Lp(a)-associated variants for an association with myocardial infarction (MI) among African Americans. We performed electronic phenotyping among African Americans in BioVU ≥40 years of age using billing codes. At total of 93 cases and 522 controls were identified in NHANES III and 265 cases and 363 controls were identified in BioVU. We tested five known Lp(a)-associated genetic variants (rs1367211, rs41271028, rs6907156, rs10945682, and rs1652507) in both NHANES III and BioVU for association with myocardial infarction. We also tested LPA rs3798220 (I4399M), previously associated with increased levels of Lp(a), MI, and coronary artery disease in European Americans, in BioVU. After meta-analysis, tests of association using logistic regression assuming an additive genetic model revealed no significant associations (p<0.05) for any of the five LPA variants previously associated with Lp(a) levels in African Americans. Also, I4399M rs3798220 was not associated with MI in African Americans (odds ratio = 0.51; 95% confidence interval: 0.16 – 1.65; p=0.26) despite strong, replicated associations with MI and coronary artery disease in European American genome-wide association studies. These data highlight the challenges in translating quantitative trait associations to clinical outcomes in diverse populations

  14. Transcriptome sequencing reveals population differentiation in gene expression linked to functional traits and environmental gradients in the South African shrub Protea repens.

    PubMed

    Akman, Melis; Carlson, Jane E; Holsinger, Kent E; Latimer, Andrew M

    2016-04-01

    Understanding the environmental and genetic mechanisms underlying locally adaptive trait variation across the ranges of species is a major focus of evolutionary biology. Combining transcriptome sequencing with common garden experiments on populations spanning geographical and environmental gradients holds promise for identifying such mechanisms. The South African shrub Protea repens displays diverse phenotypes in the wild along drought and temperature gradients. We grew plants from seeds collected at 19 populations spanning this species' range, and sequenced the transcriptomes of these plants to reveal gene pathways associated with adaptive trait variation. We related expression in co-expressed gene networks to trait phenotypes measured in the common garden and to source population climate. We found that expression in gene networks correlated with source-population environment and with plant traits. In particular, the activity of gene networks enriched for growth related pathways correlated strongly with source site minimum winter temperature and with leaf size, stem diameter and height in the garden. Other gene networks with enrichments for photosynthesis related genes showed associations with precipitation. Our results strongly suggest that this species displays population-level differences in gene expression that have been shaped by source population site climate, and that are reflected in trait variation along environmental gradients.

  15. Neurodevelopmental outcome and risk factors for impaired development of African American infants in an underserved urban population: a population-based study.

    PubMed

    Perenyi, Agnes; Katz, Joanne S; Sklar, Tzipporah; Flom, Peter

    2011-08-01

    We aimed 1) to define risk factors for adverse outcome in urban African American patients, 2) to determine whether clinical variables as risk factors are congruent with previously published data, and 3) to identify the proportion of infants with different outcomes. The study included African American infants who were born and participated in neurodevelopmental follow-up. Infants with gestational age range of 23 to 41 weeks, and birth weight (BW) range of 495 to 3,965 g were classified by developmental outcome. Among the smallest infants, BW, gestational age, gender and respiratory distress syndrome were significantly (p<.05) associated with adverse outcome. No significant risk factors were identified for adverse outcome in the two other birth weight categories. Adverse outcomes were seen more frequently in infants with BW ≤1,500 g than in larger infants. The number of infants with severe outcome was found higher than previously reported and may be related to different racial/generational origin.

  16. Familial clustering of risk factors for cardiovascular disease among first-degree relatives of patients with chronic kidney disease in a sub-Saharan African population

    PubMed Central

    Raji, Yemi; Mabayoje, Omolara; Bello, Taslim

    2015-01-01

    Summary Objective To determine the prevalence of risk factors for cardiovascular disease (CVD) in first-degree relatives (FDRs) of patients with chronic kidney disease (CKD) in a sub-Saharan African population. Methods This was a cross-sectional survey of 460 subjects (230 FDRs of patients with CKD and 230 healthy controls). Anthropometrics and blood pressures were measured. Spot urine and fasting venous blood samples were obtained for biochemical analysis. Results The prevalence of hypertension, diabetes mellitus, obesity and dyslipidaemia were significantly higher in FDRs of patients with CKD compared with the controls: 56 (24.3%) vs 29 (12.6%), p = 0.01; 20 (8.7%) vs 6 (2.6%), p = 0.01; 40 (17.4%) vs 24 (10.4%), p = 0.03 and 171 (74.3%) vs 138 (60.0%), p = 0.01, respectively. Hypertension (OR, 1.65), dyslipidaemia (OR, 1.72) and albuminuria (OR, 1.61) were independently associated with being a FDR of patients with CKD. Conclusion In this sub-Saharan African population, risk factors for CVD were more prevalent in the FDRs of patients with CKD than in healthy controls. PMID:25962941

  17. Radiocarbon dating of seized ivory confirms rapid decline in African elephant populations and provides insight into illegal trade.

    PubMed

    Cerling, Thure E; Barnette, Janet E; Chesson, Lesley A; Douglas-Hamilton, Iain; Gobush, Kathleen S; Uno, Kevin T; Wasser, Samuel K; Xu, Xiaomei

    2016-11-22

    Carbon-14 measurements on 231 elephant ivory specimens from 14 large ivory seizures (≥0.5 ton) made between 2002 and 2014 show that most ivory (ca 90%) was derived from animals that had died less than 3 y before ivory was confiscated. This indicates that the assumption of recent elephant death for mortality estimates of African elephants is correct: Very little "old" ivory is included in large ivory shipments from Africa. We found only one specimen of the 231 analyzed to have a lag time longer than 6 y. Patterns of trade differ by regions: East African ivory, based on genetic assignments of geographic origin, has a much higher fraction of "rapid" transit than ivory originating in the Tridom region of Cameroon-Gabon-Congo. Carbon-14 is an important tool in understanding patterns of movement of illegal wildlife products.

  18. Radiocarbon dating of seized ivory confirms rapid decline in African elephant populations and provides insight into illegal trade

    NASA Astrophysics Data System (ADS)

    Cerling, Thure E.; Barnette, Janet E.; Chesson, Lesley A.; Douglas-Hamilton, Iain; Gobush, Kathleen S.; Uno, Kevin T.; Wasser, Samuel K.; Xu, Xiaomei

    2016-11-01

    Carbon-14 measurements on 231 elephant ivory specimens from 14 large ivory seizures (≥0.5 ton) made between 2002 and 2014 show that most ivory (ca. 90%) was derived from animals that had died less than 3 y before ivory was confiscated. This indicates that the assumption of recent elephant death for mortality estimates of African elephants is correct: Very little “old” ivory is included in large ivory shipments from Africa. We found only one specimen of the 231 analyzed to have a lag time longer than 6 y. Patterns of trade differ by regions: East African ivory, based on genetic assignments of geographic origin, has a much higher fraction of “rapid” transit than ivory originating in the Tridom region of Cameroon-Gabon-Congo. Carbon-14 is an important tool in understanding patterns of movement of illegal wildlife products.

  19. Radiocarbon dating of seized ivory confirms rapid decline in African elephant populations and provides insight into illegal trade

    PubMed Central

    Cerling, Thure E.; Barnette, Janet E.; Chesson, Lesley A.; Douglas-Hamilton, Iain; Gobush, Kathleen S.; Wasser, Samuel K.; Xu, Xiaomei

    2016-01-01

    Carbon-14 measurements on 231 elephant ivory specimens from 14 large ivory seizures (≥0.5 ton) made between 2002 and 2014 show that most ivory (ca. 90%) was derived from animals that had died less than 3 y before ivory was confiscated. This indicates that the assumption of recent elephant death for mortality estimates of African elephants is correct: Very little “old” ivory is included in large ivory shipments from Africa. We found only one specimen of the 231 analyzed to have a lag time longer than 6 y. Patterns of trade differ by regions: East African ivory, based on genetic assignments of geographic origin, has a much higher fraction of “rapid” transit than ivory originating in the Tridom region of Cameroon–Gabon–Congo. Carbon-14 is an important tool in understanding patterns of movement of illegal wildlife products. PMID:27821744

  20. Genomic insights into the origin of farming in the ancient Near East

    PubMed Central

    Lazaridis, Iosif; Nadel, Dani; Rollefson, Gary; Merrett, Deborah C.; Rohland, Nadin; Mallick, Swapan; Fernandes, Daniel; Novak, Mario; Gamarra, Beatriz; Sirak, Kendra; Connell, Sarah; Stewardson, Kristin; Harney, Eadaoin; Fu, Qiaomei; Gonzalez-Fortes, Gloria; Jones, Eppie R.; Roodenberg, Songül Alpaslan; Lengyel, György; Bocquentin, Fanny; Gasparian, Boris; Monge, Janet M.; Gregg, Michael; Eshed, Vered; Mizrahi, Ahuva-Sivan; Meiklejohn, Christopher; Gerritsen, Fokke; Bejenaru, Luminita; Blüher, Matthias; Campbell, Archie; Cavalleri, Gianpiero; Comas, David; Froguel, Philippe; Gilbert, Edmund; Kerr, Shona M.; Kovacs, Peter; Krause, Johannes; McGettigan, Darren; Merrigan, Michael; Merriwether, D. Andrew; O'Reilly, Seamus; Richards, Martin B.; Semino, Ornella; Shamoon-Pour, Michel; Stefanescu, Gheorghe; Stumvoll, Michael; Tönjes, Anke; Torroni, Antonio; Wilson, James F.; Yengo, Loic; Hovhannisyan, Nelli A.; Patterson, Nick; Pinhasi, Ron; Reich, David

    2016-01-01

    We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia. PMID:27459054

  1. Genomic insights into the origin of farming in the ancient Near East.

    PubMed

    Lazaridis, Iosif; Nadel, Dani; Rollefson, Gary; Merrett, Deborah C; Rohland, Nadin; Mallick, Swapan; Fernandes, Daniel; Novak, Mario; Gamarra, Beatriz; Sirak, Kendra; Connell, Sarah; Stewardson, Kristin; Harney, Eadaoin; Fu, Qiaomei; Gonzalez-Fortes, Gloria; Jones, Eppie R; Roodenberg, Songül Alpaslan; Lengyel, György; Bocquentin, Fanny; Gasparian, Boris; Monge, Janet M; Gregg, Michael; Eshed, Vered; Mizrahi, Ahuva-Sivan; Meiklejohn, Christopher; Gerritsen, Fokke; Bejenaru, Luminita; Blüher, Matthias; Campbell, Archie; Cavalleri, Gianpiero; Comas, David; Froguel, Philippe; Gilbert, Edmund; Kerr, Shona M; Kovacs, Peter; Krause, Johannes; McGettigan, Darren; Merrigan, Michael; Merriwether, D Andrew; O'Reilly, Seamus; Richards, Martin B; Semino, Ornella; Shamoon-Pour, Michel; Stefanescu, Gheorghe; Stumvoll, Michael; Tönjes, Anke; Torroni, Antonio; Wilson, James F; Yengo, Loic; Hovhannisyan, Nelli A; Patterson, Nick; Pinhasi, Ron; Reich, David

    2016-08-25

    We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

  2. Population structure of the African Clawed Frog (Xenopus laevis) in maize-growing areas with atrazine application versus non-maize-growing areas in South Africa

    USGS Publications Warehouse

    Du Preez, L.H.; Solomon, K.R.; Carr, J.A.; Giesy, J.P.; Gross, T.S.; Kendall, R.J.; Smith, E.E.; Van Der Kraak, G. L.; Weldon, C.

    2005-01-01

    The herbicide atrazine has been suggested to cause gonadal deformities in frogs and could possibly impact on reproduction. Since the early 1960s, atrazine has been used in large amounts in maize production areas of South Africa. These areas overlap with populations of the African Clawed Frog (Xenopus laevis) that has a wide distribution in southern Africa and is found in most water-bodies including those where atrazine residues are detected. The aim of this study was to compare various attributes of individual- and population-level responses of X. laevis from maize-growing and non-maize-growing areas. Xenopus laevis were studied in three reference and five maize-growing sites. Sex ratio, snout-vent length, body-mass and age profiles were found to be similar for populations in maize-growing and non-maize-growing areas. Our mark-recapture data indicated that all sites had robust populations. There were no significant relationships between exposure to atrazine and any of the parameters investigated in populations of X. laevis.

  3. Population-specific prognostic models are needed to stratify outcomes for African-Americans with diffuse large B-cell lymphoma.

    PubMed

    Chen, Qiushi; Ayer, Turgay; Nastoupil, Loretta J; Koff, Jean L; Staton, Ashley D; Chhatwal, Jagpreet; Flowers, Christopher R

    2016-01-01

    Diffuse large B-cell lymphoma (DLBCL) demonstrates significant racial differences in age of onset, stage, and survival. To examine whether population-specific models improve prediction of outcomes for African-American (AA) patients with DLBCL, we utilized Surveillance, Epidemiology, and End Results data and compared stratification by the international prognostic index (IPI) in general and AA populations. We also constructed and compared prognostic models for general and AA populations using multivariable logistic regression (LR) and artificial neural network approaches. While the IPI adequately stratified outcomes for the general population, it failed to separate AA DLBCL patients into distinct risk groups. Our AA LR model identified age ≥ 55 (odds ratio 0.45, [95% CI: 0.36, 0.56], male sex (0.75, [0.60, 0.93]), and stage III/IV disease (0.43, [0.34, 0.54]) as adverse predictors of 5-year survival for AA patients. In addition, general-population prognostic models were poorly calibrated for AAs with DLBCL, indicating a need for validated AA-specific prognostic models.

  4. Pregnancy Associated Plasma Protein-A and Placental Growth Factor in a Sub-Saharan African Population: A Nested Cross-Sectional Study

    PubMed Central

    Klipstein-Grobusch, Kerstin; Koster, Maria P. H.; Ramamoorthy, Dhivya; Antwi, Edward; Belmouden, Idder; Franx, Arie; Grobbee, Diederick E.; Schielen, Peter C. J. I.

    2016-01-01

    Background Baseline distributions of pregnancy disorders’ biomarkers PlGF and PAPP-A levels are primarily based on Western European populations of Caucasian ethnicity. Differences in PAPP-A and PlGF concentrations by ethnicity have been observed, with increased levels in Afro-Caribbean, East Asian, and South Asian women. Baseline concentrations of sub-Saharan African women have not been evaluated. Objectives To investigate PlGF and PAPP-A in a sub-Saharan African population and assess the performance of existing reference values of PAPP-A and PlGF. Methods A nested cross-sectional study was conducted in two public hospitals in Accra, Ghana. Out of the original 1010 women enrolled in the cohort, 398 participants were eligible for inclusion with a normotensive singleton gestation and serum samples taken between 56–97 days of pregnancy. PAPP-A and PlGF concentrations were measured with an automated immunoassay. Multiple of the median (MoM) values corrected for gestation and maternal weight for PAPP-A and PlGF were calculated using reference values of a Dutch perinatal screening laboratory based on over 10.000 samples, and PlGF manufacturer reference values, respectively. Results The PAPP-A median MoM was 2.34 (interquartile range (IQR) 1.24–3.97). Median PlGF MoM was 1.25 (IQR 0.95–1.80). Median MoM values for PAPP-A and PlGF tended to be slightly different for various Ghanaian ethnic subgroups. Conclusions PAPP-A and PlGF MoM values appear to be substantially higher in a sub-Saharan African population compared to the Caucasian or Afro-Caribbean MoM values previously reported. The difference suggests the need for a specific correction factor for this population to avoid underestimation of risk for fetal aneuploidies or placental disorders when using PAPP-A and PlGF MoM for screening purposes. PMID:27532602

  5. Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests

    PubMed Central

    Duminil, J; Daïnou, K; Kaviriri, D K; Gillet, P; Loo, J; Doucet, J-L; Hardy, O J

    2016-01-01

    Owing to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low-quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide indirect evidence of the potential impacts of logging. Here, we analysed patterns of genetic diversity, mating system and gene flow in three Central African populations of the self-compatible legume timber species Erythrophleum suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha). The comparison of inbreeding levels among cohorts suggests that selfing is detrimental as inbred individuals are eliminated between seedling and adult stages. Levels of genetic diversity, selfing rates (∼16%) and patterns of spatial genetic structure (Sp ∼0.006) were similar in all three populations. However, the extent of gene dispersal differed markedly among populations: the average distance of pollen dispersal increased with decreasing density (from 200 m in the high-density population to 1000 m in the low-density one). Overall, our results suggest that the reproductive biology and genetic diversity of the species are not affected by current logging practices. However, further investigations need to be conducted in low-density populations to evaluate (1) whether pollen limitation may reduce seed production and (2) the regeneration potential of the species. PMID:26696137

  6. Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests.

    PubMed

    Duminil, J; Daïnou, K; Kaviriri, D K; Gillet, P; Loo, J; Doucet, J-L; Hardy, O J

    2016-03-01

    Owing to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low-quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide indirect evidence of the potential impacts of logging. Here, we analysed patterns of genetic diversity, mating system and gene flow in three Central African populations of the self-compatible legume timber species Erythrophleum suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha). The comparison of inbreeding levels among cohorts suggests that selfing is detrimental as inbred individuals are eliminated between seedling and adult stages. Levels of genetic diversity, selfing rates (∼16%) and patterns of spatial genetic structure (Sp ∼0.006) were similar in all three populations. However, the extent of gene dispersal differed markedly among populations: the average distance of pollen dispersal increased with decreasing density (from 200 m in the high-density population to 1000 m in the low-density one). Overall, our results suggest that the reproductive biology and genetic diversity of the species are not affected by current logging practices. However, further investigations need to be conducted in low-density populations to evaluate (1) whether pollen limitation may reduce seed production and (2) the regeneration potential of the species.

  7. Demographic Ageing of the South African Population: Past (1945-1985) and Expected Trends (1985-2035). Report S-190.

    ERIC Educational Resources Information Center

    Hofmeyr, B. E.; Mostert, W. P.

    This report presents demographic data for four racial populations in South Africa (Blacks, Whites, Coloureds, and Asians) and examines trends in the aging of each of these populations. The age structure of a population is determined most directly by fertility and mortality. The findings of this report support a general theory to the effect that…

  8. SURVEILLANCE FOR VIRAL AND PARASITIC PATHOGENS IN A VULNERABLE AFRICAN LION (PANTHERA LEO) POPULATION IN THE NORTHERN TULI GAME RESERVE, BOTSWANA.

    PubMed

    McDermid, Kimberly R; Snyman, Andrei; Verreynne, Frederick J; Carroll, John P; Penzhorn, Banie L; Yabsley, Michael J

    2017-01-01

    African lion ( Panthera leo ) numbers are decreasing rapidly and populations are becoming smaller and more fragmented. Infectious diseases are one of numerous issues threatening free-ranging lion populations, and low-density populations are particularly at risk. We collected data on the prevalence and diversity of viral and parasitic pathogens in a small lion population in eastern Botswana. During 2012 and 2014, blood samples were collected from 59% (n=13) of the adult-subadult lions in the Northern Tuli Game Reserve in eastern Botswana. One lion had antibodies to feline panleukopenia virus, two had antibodies to canine distemper virus, and two had feline calicivirus antibodies. Ten of the 13 had antibodies to feline immunodeficiency virus and 11 had feline herpesvirus antibodies. All lions were negative for antibodies to feline coronavirus. Blood samples from all lions were negative for Trypanosoma, Anaplasma, Theileria, and Ehrlichia spp. by molecular testing; however, all lions were positive for Babesia spp. by reverse line blot hybridization assay. Sequencing of amplicons from four lions revealed four groups of Babesia spp. including several genetic variants of Babesia felis , Babesia lengau, and Babesia canis and a group of novel Babesia sequences which were only 96% similar to other Babesia spp. Six lions were infested with four species of ticks (Rhipicentor nuttalli, Rhipicephalus simus, Rhipicephalus sulcatus, and Rhipicephalus appendiculatus). These data provide the first health assessment of this population and can be used to identify management and conservation strategies to decrease the impact of pathogens on this population. This is particularly important as there is an initiative to incorporate this population into a larger metapopulation of lions from adjacent South Africa and Zimbabwe.

  9. West African and Amerindian ancestry and risk of myocardial infarction and metabolic syndrome in the Central Valley population of Costa Rica.

    PubMed

    Ruiz-Narváez, Edward A; Bare, Lance; Arellano, Andre; Catanese, Joseph; Campos, Hannia

    2010-06-01

    Genetic ancestry and environmental factors may contribute to the ethnic differences in risk of coronary heart disease (CHD), metabolic syndrome (MS) or its individual components. The population of the Central Valley of Costa Rica offers a unique opportunity to assess the role of genetic ancestry in these chronic diseases because it derived from the admixture of a relatively small number of founders of Southern European, Amerindian, and West African origin. We aimed to determine whether genetic ancestry is associated with risk of myocardial infarction (MI), MS and its individual components in the Central Valley of Costa Rica. We genotyped 39 ancestral informative markers in cases (n = 1,998) with a first non-fatal acute MI and population-based controls (n = 1,998) matched for age, sex, and area of residence, to estimate individual ancestry proportions. Odds ratios (ORs) and 95% confidence intervals (95% CI) were estimated using conditional (MI) and unconditional (MS and its components) logistic regression adjusting for relevant confounders. Mean individual ancestry proportions in cases and controls were 57.5 versus 57.8% for the Southern European, 38.4 versus 38.3% for the Amerindian and 4.1 versus 3.8% for the West African ancestry. Compared with Southern European ancestry, each 10% increase in West African ancestry was associated with a 29% increase in MI, OR (95% CI) = 1.29 (1.07, 1.56), and with a 30% increase on the risk of hypertension, OR (95% CI) = 1.30 (1.00, 1.70). Each 10% increase in Amerindian ancestry was associated with a 14% increase on the risk of MS, OR (95% CI) = 1.14 (1.00, 1.30), and 20% increase on the risk of impaired fasting glucose, OR (95% CI) = 1.20 (1.01, 1.42). These results show that the high variability of admixture proportions in the Central Valley population offers a unique opportunity to uncover the genetic basis of ethnic differences on the risk of disease.

  10. Differentiation in putative male sex pheromone components across and within populations of the African butterfly Bicyclus anynana as a potential driver of reproductive isolation.

    PubMed

    Bacquet, Paul M B; de Jong, Maaike A; Brattström, Oskar; Wang, Hong-Lei; Molleman, Freerk; Heuskin, Stéphanie; Lognay, George; Löfstedt, Christer; Brakefield, Paul M; Vanderpoorten, Alain; Nieberding, Caroline M

    2016-09-01

    Sexual traits are often the most divergent characters among closely related species, suggesting an important role of sexual traits in speciation. However, to prove this, we need to show that sexual trait differences accumulate before or during the speciation process, rather than being a consequence of it. Here, we contrast patterns of divergence among putative male sex pheromone (pMSP) composition and the genetic structure inferred from variation in the mitochondrial cytochrome oxidase 1 and nuclear CAD loci in the African butterfly Bicyclus anynana (Butler, 1879) to determine whether the evolution of "pheromonal dialects" occurs before or after the differentiation process. We observed differences in abundance of some shared pMSP components as well as differences in the composition of the pMSP among B. anynana populations. In addition, B. anynana individuals from Kenya displayed differences in the pMSP composition within a single population that appeared not associated with genetic differences. These differences in pMSP composition both between and within B. anynana populations were as large as those found between different Bicyclus species. Our results suggest that "pheromonal dialects" evolved within and among populations of B. anynana and may therefore act as precursors of an ongoing speciation process.

  11. Developing a computer touch-screen interactive colorectal screening decision aid for a low-literacy African American population: lessons learned.

    PubMed

    Bass, Sarah Bauerle; Gordon, Thomas F; Ruzek, Sheryl Burt; Wolak, Caitlin; Ruggieri, Dominique; Mora, Gabriella; Rovito, Michael J; Britto, Johnson; Parameswaran, Lalitha; Abedin, Zainab; Ward, Stephanie; Paranjape, Anuradha; Lin, Karen; Meyer, Brian; Pitts, Khaliah

    2013-07-01

    African Americans have higher colorectal cancer (CRC) mortality than White Americans and yet have lower rates of CRC screening. Increased screening aids in early detection and higher survival rates. Coupled with low literacy rates, the burden of CRC morbidity and mortality is exacerbated in this population, making it important to develop culturally and literacy appropriate aids to help low-literacy African Americans make informed decisions about CRC screening. This article outlines the development of a low-literacy computer touch-screen colonoscopy decision aid using an innovative marketing method called perceptual mapping and message vector modeling. This method was used to mathematically model key messages for the decision aid, which were then used to modify an existing CRC screening tutorial with different messages. The final tutorial was delivered through computer touch-screen technology to increase access and ease of use for participants. Testing showed users were not only more comfortable with the touch-screen technology but were also significantly more willing to have a colonoscopy compared with a "usual care group." Results confirm the importance of including participants in planning and that the use of these innovative mapping and message design methods can lead to significant CRC screening attitude change.

  12. HLA-E coding and 3' untranslated region variability determined by next-generation sequencing in two West-African population samples.

    PubMed

    Castelli, Erick C; Mendes-Junior, Celso T; Sabbagh, Audrey; Porto, Iane O P; Garcia, André; Ramalho, Jaqueline; Lima, Thálitta H A; Massaro, Juliana D; Dias, Fabrício C; Collares, Cristhianna V A; Jamonneau, Vincent; Bucheton, Bruno; Camara, Mamadou; Donadi, Eduardo A

    2015-12-01

    HLA-E is a non-classical Human Leucocyte Antigen class I gene with immunomodulatory properties. Whereas HLA-E expression usually occurs at low levels, it is widely distributed amongst human tissues, has the ability to bind self and non-self antigens and to interact with NK cells and T lymphocytes, being important for immunosurveillance and also for fighting against infections. HLA-E is usually the most conserved locus among all class I genes. However, most of the previous studies evaluating HLA-E variability sequenced only a few exons or genotyped known polymorphisms. Here we report a strategy to evaluate HLA-E variability by next-generation sequencing (NGS) that might be used to other HLA loci and present the HLA-E haplotype diversity considering the segment encoding the entire HLA-E mRNA (including 5'UTR, introns and the 3'UTR) in two African population samples, Susu from Guinea-Conakry and Lobi from Burkina Faso. Our results indicate that (a) the HLA-E gene is indeed conserved, encoding mainly two different protein molecules; (b) Africans do present several unknown HLA-E alleles presenting synonymous mutations; (c) the HLA-E 3'UTR is quite polymorphic and (d) haplotypes in the HLA-E 3'UTR are in close association with HLA-E coding alleles. NGS has proved to be an important tool on data generation for future studies evaluating variability in non-classical MHC genes.

  13. Delayed diagnosis of pancreatic cancer reported as more common in a population of North African young adults

    PubMed Central

    Harir, Noria; Khaled, Méghit B.; Mrabent, Nesrine M.; Salah, Rachida; Benchouk, Arslane; Diaf, Mustapha

    2015-01-01

    Background Pancreatic cancer is one of the most challenging tumor entities worldwide, characterized as a highly aggressive disease with dismal overall prognosis and an incidence rate equaling mortality rate. Objective In order to have an update about pancreatic cancer incidence and evolution in North Africa, we conducted an epidemiological analytical retrospective study at the level of three Algerian regions: Sidi-bel-Abbes, Oran and Tlemcen along the last eight years [2006-2013]. Methods We performed a retrospective hospital-based study in which we analyzed the records of 160 pancreatic cancer patients registered, evaluated and treated in a Northern African region; at the level of hospital centers of the three western Algerian regions from 2006 to 2013. Results Along the period of study, 160 patients were diagnosed with pancreatic cancer; with a mean age of 66.2 years, and a sex ratio of 1.65; other parameters such as a medical history smoking and alcoholism history, tumor site; histological type as well as the stage of diagnosis were also enrolled in the study. Our statistical analyses reported a very significant correlation between patients who belonged to the age group of 21-40 years and the advanced stage of diagnosis (basing on TNM classification) with P=0.02. Conclusions Pancreatic cancer is increasingly diagnosed in young adults at an advanced stage in North African regions. PMID:26487944

  14. Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

    PubMed Central

    Lashmar, Simon F.; Van Marle-Köster, Este; Poli, Mario A.

    2016-01-01

    The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations. PMID:27171175

  15. Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data.

    PubMed

    Visser, Carina; Lashmar, Simon F; Van Marle-Köster, Este; Poli, Mario A; Allain, Daniel

    2016-01-01

    The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.

  16. African American Female Offender’s Use of Alternative and Traditional Health Services After Re-Entry: Examining the Behavioral Model for Vulnerable Populations

    PubMed Central

    Oser, Carrie B.; Bunting, Amanda M.; Pullen, Erin; Stevens-Watkins, Danelle

    2016-01-01

    This is the first known study to use the Gelberg-Andersen Behavioral Model for Vulnerable Populations to predict African American women’s use of three types of health services (alternative, hospitalization, and ambulatory) in the 18 months after release from prison. In the multivariate models, the most robust predictors of all three types of service utilization were in the vulnerable theoretical domains. Alternative health services were predicted by ethnic community membership, higher religiosity, and HIV/HCV. Hospitalizations were predicted by the lack of barriers to health care and disability. Ambulatory office visits were predicted by more experiences of gendered racism, a greater number of physical health problems, and HIV/HCV. Findings highlight the importance of cultural factors and HIV/HCV in obtaining both alternative and formal health care during community re-entry. Clinicians and policy makers should consider the salient role that the vulnerable domain plays in offender’s accessing health services. PMID:27133515

  17. High-resolution African population projections from radiative forcing and socio-economic models, 2000 to 2100

    NASA Astrophysics Data System (ADS)

    Boke-Olén, Niklas; Abdi, Abdulhakim M.; Hall, Ola; Lehsten, Veiko

    2017-01-01

    For its fifth assessment report, the Intergovernmental Panel on Climate Change divided future scenario projections (2005-2100) into two groups: Socio-Economic Pathways (SSPs) and Representative Concentration Pathways (RCPs). Each SSP has country-level urban and rural population projections, while the RCPs are based on radiative forcing caused by greenhouse gases, aerosols and associated land-use change. In order for these projections to be applicable in earth system models, SSP and RCP population projections must be at the same spatial scale. Thus, a gridded population dataset that takes into account both RCP-based urban fractions and SSP-based population projection is needed. To support this need, an annual (2000-2100) high resolution (approximately 1km at the equator) gridded population dataset conforming to both RCPs (urban land use) and SSPs (population) country level scenario data were created.

  18. High-resolution African population projections from radiative forcing and socio-economic models, 2000 to 2100

    PubMed Central

    Boke-Olén, Niklas; Abdi, Abdulhakim M.; Hall, Ola; Lehsten, Veiko

    2017-01-01

    For its fifth assessment report, the Intergovernmental Panel on Climate Change divided future scenario projections (2005–2100) into two groups: Socio-Economic Pathways (SSPs) and Representative Concentration Pathways (RCPs). Each SSP has country-level urban and rural population projections, while the RCPs are based on radiative forcing caused by greenhouse gases, aerosols and associated land-use change. In order for these projections to be applicable in earth system models, SSP and RCP population projections must be at the same spatial scale. Thus, a gridded population dataset that takes into account both RCP-based urban fractions and SSP-based population projection is needed. To support this need, an annual (2000–2100) high resolution (approximately 1km at the equator) gridded population dataset conforming to both RCPs (urban land use) and SSPs (population) country level scenario data were created. PMID:28094785

  19. High-resolution African population projections from radiative forcing and socio-economic models, 2000 to 2100.

    PubMed

    Boke-Olén, Niklas; Abdi, Abdulhakim M; Hall, Ola; Lehsten, Veiko

    2017-01-17

    For its fifth assessment report, the Intergovernmental Panel on Climate Change divided future scenario projections (2005-2100) into two groups: Socio-Economic Pathways (SSPs) and Representative Concentration Pathways (RCPs). Each SSP has country-level urban and rural population projections, while the RCPs are based on radiative forcing caused by greenhouse gases, aerosols and associated land-use change. In order for these projections to be applicable in earth system models, SSP and RCP population projections must be at the same spatial scale. Thus, a gridded population dataset that takes into account both RCP-based urban fractions and SSP-based population projection is needed. To support this need, an annual (2000-2100) high resolution (approximately 1km at the equator) gridded population dataset conforming to both RCPs (urban land use) and SSPs (population) country level scenario data were created.

  20. Climate and demography in early prehistory: using calibrated (14)C dates as population proxies.

    PubMed

    Riede, Felix

    2009-04-01

    Although difficult to estimate for prehistoric hunter-gatherer populations, demographic variables-population size, density, and the connectedness of demes-are critical for a better understanding of the processes of material culture change, especially in deep prehistory. Demography is the middle-range link between climatic changes and both biological and cultural evolutionary trajectories of human populations. Much of human material culture functions as a buffer against climatic changes, and the study of prehistoric population dynamics, estimated through changing frequencies of calibrated radiocarbon dates, therefore affords insights into how effectively such buffers operated and when they failed. In reviewing a number of case studies (Mesolithic Ireland, the origin of the Bromme culture, and the earliest late glacial human recolonization of southern Scandinavia), I suggest that a greater awareness of demographic processes, and in particular of demographic declines, provides many fresh insights into what structured the archaeological record. I argue that we cannot sideline climatic and environmental factors or extreme geophysical events in our reconstructions of prehistoric culture change. The implications of accepting demographic variability as a departure point for evaluating the archaeological record are discussed.

  1. Climate change influenced female population sizes through time across the Indonesian archipelago.

    PubMed

    Guillot, Elsa G; Tumonggor, Meryanne K; Lansing, J Stephen; Sudoyo, Herawati; Cox, Murray P

    2013-01-01

    Lying at the crossroads of Asia and the Pacific world, the Indonesian archipelago hosts one of the world's richest accumulations of cultural, linguistic, and genetic variation. While the role of human migration into and around the archipelago is now known in some detail, other aspects of Indonesia's complex history are less understood. Here, we focus on population size changes from the first settlement of Indonesia nearly 50 kya up to the historic era. We reconstructed the past effective population sizes of Indonesian women using mitochondrial DNA sequences from 2,104 individuals in 55 village communities on four islands spanning the Indonesian archipelago (Bali, Flores, Sumba, and Timor). We found little evidence for large fluctuations in effective population size. Most communities grew slowly during the late Pleistocene, peaked 15-20 kya, and subsequently declined slowly into the Holocene. This unexpected pattern may reflect population declines caused by the flooding of lowland hunter/gatherer habitat during sea-level rises following the last glacial maximum.

  2. Detection of molecular signatures of selection at microsatellite loci in the South African abalone (Haliotis midae) using a population genomic approach.

    PubMed

    Rhode, Clint; Vervalle, Jessica; Bester-van der Merwe, Aletta E; Roodt-Wilding, Rouvay

    2013-06-01

    Identifying genomic regions that may be under selection is important for elucidating the genetic architecture of complex phenotypes underlying adaptation to heterogeneous environments. A population genomic approach, using a classical neutrality test and various Fst-outlier detection methods was employed to evaluate genome-wide polymorphism data in order to identify loci that may be candidates for selection amongst six populations (three cultured and three wild) of the South African abalone, Haliotis midae. Approximately 9% of the genome-wide microsatellite markers were putatively subject to directional selection, whilst 6-18% of the genome is thought to be influenced by balancing selection. Genetic diversity estimates for candidate loci under directional selection was significantly reduced in comparison to candidate neutral loci, whilst candidate balancing selection loci demonstrated significantly higher levels of genetic diversity (Kruskal-Wallis test, P<0.05). Pairwise Fst estimates based on candidate directional selection loci also demonstrated increased levels of differentiation between study populations. Various candidate loci under selection showed significant inter-chromosomal linkage disequilibrium, suggesting possible gene-networks underling adaptive phenotypes. Furthermore, several loci had significant hits to known genes when performing BLAST searches to NCBI's non-redundant databases, whilst others are known to be derived from expressed sequences even though homology to a known gene could not be established. A number of loci also demonstrated relatively high similarity to transposable elements. The association of these loci to functional and genomically active sequences could in part explain the observed signatures of selection.

  3. Genetic variants determining survival and fertility in an adverse African environment: a population-based large-scale candidate gene association study

    PubMed Central

    Koopman, Jacob J.E.; Pijpe, Jeroen; Böhringer, Stefan; van Bodegom, David; Eriksson, Ulrika K.; Sanchez-Faddeev, Hernando; Ziem, Juventus B.; Zwaan, Bas; Slagboom, P. Eline; de Knijff, Peter; Westendorp, Rudi G.J.

    2016-01-01

    Human survival probability and fertility decline strongly with age. These life history traits have been shaped by evolution. However, research has failed to uncover a consistent genetic determination of variation in survival and fertility. As an explanation, such genetic determinants have been selected in adverse environments, in which humans have lived during most of their history, but are almost exclusively studied in populations in modern affluent environments. Here, we present a large-scale candidate gene association study in a rural African population living in an adverse environment. In 4387 individuals, we studied 4052 SNPs in 148 genes that have previously been identified as possible determinants of survival or fertility in animals or humans. We studied their associations with survival comparing newborns, middle-age adults, and old individuals. In women, we assessed their associations with reported and observed numbers of children. We found no statistically significant associations of these SNPs with survival between the three age groups nor with women's reported and observed fertility. Population stratification was unlikely to explain these results. Apart from a lack of power, we hypothesise that genetic heterogeneity of complex phenotypes and gene-environment interactions prevent the identification of genetic variants explaining variation in survival and fertility in humans. PMID:27356285

  4. Multilocus ISSR Markers Reveal Two Major Genetic Groups in Spanish and South African Populations of the Grapevine Fungal Pathogen Cadophora luteo-olivacea

    PubMed Central

    Gramaje, David; León, Maela; Santana, Marcela; Crous, Pedro W.; Armengol, Josep

    2014-01-01

    Cadophora luteo-olivacea is a lesser-known fungal trunk pathogen of grapevine which has been recently isolated from vines showing decline symptoms in grape growing regions worldwide. In this study, 80 C. luteo-olivacea isolates (65 from Spain and 15 from South Africa) were studied. Inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR) generated 55 polymorphic loci from four ISSR primers selected from an initial screen of 13 ISSR primers. The ISSR markers revealed 40 multilocus genotypes (MLGs) in the global population. Minimum spanning network analysis showed that the MLGs from South Africa clustered around the most frequent genotype, while the genotypes from Spain were distributed all across the network. Principal component analysis and dendrograms based on genetic distance and bootstrapping identified two highly differentiated genetic clusters in the Spanish and South African C. luteo-olivacea populations, with no intermediate genotypes between these clusters. Movement within the Spanish provinces may have occurred repeatedly given the frequent retrieval of the same genotype in distant locations. The results obtained in this study provide new insights into the population genetic structure of C. luteo-olivacea in Spain and highlights the need to produce healthy and quality planting material in grapevine nurseries to avoid the spread of this fungus throughout different grape growing regions. PMID:25310345

  5. Multilocus ISSR markers reveal two major genetic groups in Spanish and South African populations of the grapevine fungal pathogen Cadophora luteo-olivacea.

    PubMed

    Gramaje, David; León, Maela; Santana, Marcela; Crous, Pedro W; Armengol, Josep

    2014-01-01

    Cadophora luteo-olivacea is a lesser-known fungal trunk pathogen of grapevine which has been recently isolated from vines showing decline symptoms in grape growing regions worldwide. In this study, 80 C. luteo-olivacea isolates (65 from Spain and 15 from South Africa) were studied. Inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR) generated 55 polymorphic loci from four ISSR primers selected from an initial screen of 13 ISSR primers. The ISSR markers revealed 40 multilocus genotypes (MLGs) in the global population. Minimum spanning network analysis showed that the MLGs from South Africa clustered around the most frequent genotype, while the genotypes from Spain were distributed all across the network. Principal component analysis and dendrograms based on genetic distance and bootstrapping identified two highly differentiated genetic clusters in the Spanish and South African C. luteo-olivacea populations, with no intermediate genotypes between these clusters. Movement within the Spanish provinces may have occurred repeatedly given the frequent retrieval of the same genotype in distant locations. The results obtained in this study provide new insights into the population genetic structure of C. luteo-olivacea in Spain and highlights the need to produce healthy and quality planting material in grapevine nurseries to avoid the spread of this fungus throughout different grape growing regions.

  6. Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians.

    PubMed

    Budowle, B; Moretti, T R; Baumstark, A L; Defenbaugh, D A; Keys, K M

    1999-11-01

    Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p = 0.010, Bahamians); CSF1PO (p = 0.014, Trinidadians); TPOX (p = 0.011, Jamaicans and p = 0.035, U.S. Caucasians); and D16S539 (p = 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group.

  7. The clinical surface anatomy anomalies of the palmaris longus muscle in the Black African population of Zimbabwe and a proposed new testing technique.

    PubMed

    Gangata, Hope

    2009-03-01

    The presence of the palmaris longus muscle (PLM) is highly variable. Rates of absence vary from 0.6% in the Korean population to as high as 63.9% in the Turkish population. The tendon of PLM may be absent on one or both forearms, may have duplicated tendons on one forearm or may be laterally shifted to the extent that the tendon of the PLM lies superficial to that of flexor carpi radialis muscle. Among Black American populations, in which there is usually mixed ancestry, rates of absence are 3.5%. Only two studies have been performed on Black African populations: in Republic of Congo and Uganda, and each showed widely differing rates of absence of 3.0% and 14.6%, respectively. In this study, a total of 890 Black Zimbabwean subjects in Harare aged between 8 and 13 years, were examined for clinical surface anatomy anomalies of the tendon of PLM. The results showed that the tendon of the PLM was absent unilaterally in 0.9% of the population, and bilaterally absent in 0.6% with an overall rate of absence of 1.5%. Other variations noted were a laterally shifted PLM in 1.1% of subjects and duplicated tendons on one forearm, which was the least prevalent anomaly, in 0.2% of subjects. The author proposes a new technique to test the tendon of PLM, which combines resisted thumb abduction and resisted wrist flexion. The proposed technique capitalizes on the role of the PLM as an important abductor of the thumb.

  8. Association of polymorphisms at the ADIPOR1 regulatory region with type 2 diabetes and body mass index in a Brazilian population with European or African ancestry.

    PubMed

    Yeh, E; Kimura, L; Errera, F I V; Angeli, C B; Mingroni-Netto, R C; Silva, M E R; Canani, L H S; Passos-Bueno, M R

    2008-06-01

    Association studies between ADIPOR1 genetic variants and predisposition to type 2 diabetes (DM2) have provided contradictory results. We determined if two single nucleotide polymorphisms (SNP c.-8503G>A and SNP c.10225C>G) in regulatory regions of ADIPOR1 in 567 Brazilian individuals of European (EA; N = 443) or African (AfA; N = 124) ancestry from rural (quilombo remnants; N = 439) and urban (N = 567) areas. We detected a significant effect of ethnicity on the distribution of the allelic frequencies of both SNPs in these populations (EA: -8503A = 0.27; AfA: -8503A = 0.16; P = 0.001 and EA: 10225G = 0.35; AfA: 10225G = 0.51; P < 0.001). Neither of the polymorphisms were associated with DM2 in the case-control study in EA (SNP c.-8503G>A: DM2 group -8503A = 0.26; control group -8503A = 0.30; P = 0.14/SNP 10225C>G: DM2 group 10225G = 0.37; control group 10225G = 0.32; P = 0.40) and AfA populations (SNP c.-8503G>A: DM2 group -8503A = 0.16; control group -8503A = 0.15; P = 0.34/SNP 10225C>G: DM2 group 10225G = 0.51; control group 10225G = 0.52; P = 0.50). Similarly, none of the polymorphisms were associated with metabolic/anthropometric risk factors for DM2 in any of the three populations, except for HDL cholesterol, which was significantly higher in AfA heterozygotes (GC = 53.75 +/- 17.26 mg/dL) than in homozygotes. We conclude that ADIPOR1 polymorphisms are unlikely to be major risk factors for DM2 or for metabolic/anthropometric measurements that represent risk factors for DM2 in populations of European and African ancestries.

  9. Resource variability, aggregation and direct density dependence in an open context: the local regulation of an African elephant population.

    PubMed

    Chamaillé-Jammes, Simon; Fritz, Hervé; Valeix, Marion; Murindagomo, Felix; Clobert, Jean

    2008-01-01

    1. An emerging perspective in the study of density dependence is the importance of the spatial and temporal heterogeneity of resources. Although this is well understood in temperate ungulates, few studies have been conducted in tropical environments where both food and water are limiting resources. 2. We studied the regulation of one of the world's largest elephant populations in Hwange National Park, Zimbabwe. The study period started in 1986 when the population was released from culling. Using census data we investigated changes in elephant abundance with respect to rainfall and density across the entire park and across waterholes. 3. The population more than doubled since culling stopped. The population increased continuously during the first 6 years, and then fluctuated widely at about 30,000 individuals. Immigration processes must have been involved in the increase of the population size. 4. Population growth rates were negatively related to previous population density by a convex relationship, and negatively related to the ratio of previous population density on annual rainfall by a linear relationship. However, only this latter model (i.e. assuming a fluctuating carrying capacity related to annual rainfall) produced realistic dynamics. Overall, population decreased during dry years when the elephant density was high. 5. During dry years there were fewer waterholes retaining water during the dry season and consequently elephant numbers at waterholes increased, while their aggregation level across waterholes decreased. On the long-run elephant numbers increased only at the less crowded waterholes. 6. We suggest that the interaction between population size and the available foraging range determined by the number of active waterholes during the dry season controls the park population. 7. Our results emphasize the need to understand how key-resource areas cause resource-based aggregation, which ultimately influences the strength of density dependence. More

  10. Variation in responses to susceptible and resistant cowpeas among West African populations of Callosobruchus maculatus (Coleoptera: Bruchidae).

    PubMed

    Appleby, J H; Credland, P F

    2003-04-01

    The cowpea seed beetle, sometimes also known as the cowpea weevil, Callosobruchus maculatus (F.), is a major pest of stored cowpeas (Vigna unguiculata Walpers) in West Africa. Control methods have included development of 'resistant' varieties as an environmentally benign alternative to insecticides, but there is concern over their effectiveness because of population variation among the insects and the possibility of adaptation overcoming seed resistance. Populations of C. maculatus from Nigeria, Ghana, Benin, and Niger, were used to examine variation in response to resistant and susceptible cowpea varieties at two geographical scales. Among seven Nigerian populations, there were significant differences in development times, the pattern of adult emergence, adult weights, and female fecundity when reared under identical conditions. Development in the resistant variety was retarded, produced higher mortality and lower adult weights. Significant interactions between variety and population were evident in terms of their effects on adult weight and development time; development times in the resistant variety were longer and emergences occurred over a longer period in some populations than in others. Population responses to resistant seeds were therefore unpredictable, but there was no evidence to suggest adaptation to overcome seed resistance within three generations. On a larger geographical scale, variation in performance was much greater and therefore, even less predictable. Mortality in resistant seeds was also higher among populations collected from outside Nigeria and may be explained by significant adaptation among Nigerian populations to previous release of resistant varieties. The findings are discussed in relation to understanding the extent of intraspecific variation in C. maculatus and its implications for future pest management.

  11. Evolutionary demography and the population history of the European early Neolithic.

    PubMed

    Shennan, Stephen

    2009-04-01

    In this paper I propose that evolutionary demography and associated theory from human behavioral ecology provide a strong basis for explaining the available evidence for the patterns observed in the first agricultural settlement of Europe in the 7th-5th millennium cal. BC, linking together a variety of what have previously been disconnected observations and casting doubt on some long-standing existing models. An outline of relevant aspects of life history theory, which provides the foundation for understanding demography, is followed by a review of large-scale demographic patterns in the early Neolithic, which point to rapid population increase and a process of demic diffusion. More localized socioeconomic and demographic patterns suggesting rapid expansion to local carrying capacities and an associated growth of inequality in the earliest farming communities of central Europe (the Linear Pottery Culture, or LBK) are then outlined and shown to correspond to predictions of spatial population ecology and reproductive skew theory. Existing models of why it took so long for farming to spread to northern and northwest Europe, which explain the spread in terms of the gradual disruption of hunter-gatherer ways of life, are then questioned in light of evidence for population collapse at the end of the LBK. Finally, some broader implications of the study are presented, including the suggestion that the pattern of an initial agricultural boom followed by a bust may be relevant in other parts of the world.

  12. Diet and nutrition of prehistoric populations at the alluvial banks of the Parana River.

    PubMed