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Sample records for islands genetic african

  1. African Journals Online: Turks and Caicos Islands

    African Journals Online (AJOL)

    African Journals Online: Turks and Caicos Islands. Home > African Journals Online: Turks and Caicos Islands. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register · Browse By Category · Browse Alphabetically · Browse By Country · List All Titles · Free to read Titles This ...

  2. African Journals Online: Northern Mariana Islands

    African Journals Online (AJOL)

    African Journals Online: Northern Mariana Islands. Home > African Journals Online: Northern Mariana Islands. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register · Browse By Category · Browse Alphabetically · Browse By Country · List All Titles · Free to read Titles This ...

  3. African Journals Online: Virgin Islands (British)

    African Journals Online (AJOL)

    African Journals Online: Virgin Islands (British). Home > African Journals Online: Virgin Islands (British). Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register · Browse By Category · Browse Alphabetically · Browse By Country · List All Titles · Free to read Titles This Journal ...

  4. The genetic origins of the Andaman Islanders

    DEFF Research Database (Denmark)

    Endicott, Phillip; Gilbert, M Thomas P; Stringer, Chris

    2002-01-01

    Mitochondrial sequences were retrieved from museum specimens of the enigmatic Andaman Islanders to analyze their evolutionary history. D-loop and protein-coding data reveal that phenotypic similarities with African pygmoid groups are convergent. Genetic and epigenetic data are interpreted as favo...... of humans through Asia. The results demonstrate that Victorian anthropological collections can be used to study extinct, or seriously admixed populations, to provide new data about early human origins....

  5. African Journals Online: United States Minor Outlying Islands

    African Journals Online (AJOL)

    African Journals Online: United States Minor Outlying Islands. Home > African Journals Online: United States Minor Outlying Islands. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register · Browse By Category · Browse Alphabetically · Browse By Country · List All Titles ...

  6. The Genetic Structure and History of Africans and African Americans

    Science.gov (United States)

    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.

    2010-01-01

    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 (~71%), European (~13%), and other African (~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. PMID:19407144

  7. Pollinating fig wasps: genetic consequences of island recolonization

    NARCIS (Netherlands)

    Zavodna, M.; Arens, P.; Partomihardjo, T.; Vosman, B.; van Dijk, P.J.; Van Damme, J.M.M.

    2005-01-01

    The levels of genetic diversity and gene flow may influence the long-term persistence of populations. Using microsatellite markers, we investigated genetic diversity and genetic differentiation in island (Krakatau archipelago, Indonesia) and mainland (Java and Sumatra, Indonesia) populations of

  8. Population genetics of African ungulates

    DEFF Research Database (Denmark)

    Lorenzen, Eline

    -specific data sets, which are used to elucidate evolutionary processes of importance to the savannah ungulate community. Patterns of DNA variation were analyzed to assess the genetic signatures of Pleistocene refugia and investigate aspects of speciation, intraspecific structuring, hybridization, and historic...

  9. Mitochondrial DNA heritage of Cres Islanders--example of Croatian genetic outliers.

    Science.gov (United States)

    Jeran, Nina; Havas Augustin, Dubravka; Grahovac, Blaienka; Kapović, Miljenko; Metspalu, Ene; Villems, Richard; Rudan, Pavao

    2009-12-01

    Diversity of mitochondrial DNA (mtDNA) lineages of the Island of Cres was determined by high-resolution phylogenetic analysis on a sample of 119 adult unrelated individuals from eight settlements. The composition of mtDNA pool of this Island population is in contrast with other Croatian and European populations. The analysis revealed the highest frequency of haplogroup U (29.4%) with the predominance of one single lineage of subhaplogroup U2e (20.2%). Haplogroup H is the second most prevalent one with only 27.7%. Other very interesting features of contemporary Island population are extremely low frequency of haplogroup J (only 0.84%), and much higher frequency of haplogroup W (12.6%) comparing to other Croatian and European populations. Especially interesting finding is a strikingly higher frequency of haplogroup N1a (9.24%) presented with African/south Asian branch almost absent in Europeans, while its European sister-branch, proved to be highly prevalent among Neolithic farmers, is present in contemporary Europeans with only 0.2%. Haplotype analysis revealed that only five mtDNA lineages account for almost 50% of maternal genetic heritage of this island and they present supposed founder lineages. All presented findings confirm that genetic drift, especially founder effect, has played significant role in shaping genetic composition of the isolated population of the Island of Cres. Due to presented data contemporary population of Cres Island can be considered as genetic "outlier" among Croatian populations.

  10. Genetic history of the African Sahelian populations.

    Science.gov (United States)

    Černý, V; Kulichová, I; Poloni, E S; Nunes, J M; Pereira, L; Mayor, A; Sanchez-Mazas, A

    2018-03-01

    From a biogeographic perspective, Africa is subdivided into distinct horizontal belts. Human populations living along the Sahel/Savannah belt south of the Sahara desert have often been overshadowed by extensive studies focusing on other African populations such as hunter-gatherers or Bantu in particular. However, the Sahel together with the Savannah bordering it in the south is a challenging region where people had and still have to cope with harsh climatic conditions and show resilient behaviours. Besides exponentially growing urban populations, several local groups leading various lifestyles and speaking languages belonging to three main linguistic families still live in rural localities across that region today. Thanks to several years of consistent population sampling throughout this area, the genetic history of the African Sahelian populations has been largely reconstructed and a deeper knowledge has been acquired regarding their adaptation to peculiar environments and/or subsistence modes. Distinct exposures to pathogens-in particular, malaria-likely contributed to their genetic differentiation for HLA genes. In addition, although food-producing strategies spread within the Sahel/Savannah belt relatively recently, during the last five millennia according to recent archaeological and archaeobotanical studies, remarkable amounts of genetic differences are also observed between sedentary farmers and more mobile pastoralists at multiple neutral and selected loci, reflecting both demographic effects and genetic adaptations to distinct cultural traits, such as dietary habits. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

    Science.gov (United States)

    Galindo-Cardona, Alberto; Acevedo-Gonzalez, Jenny P; Rivera-Marchand, Bert; Giray, Tugrul

    2013-08-06

    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. 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. Genetic structure of Puerto Rico gAHB differs from mainland AHB populations, probably representing evolutionary processes on the island.

  12. Genetic analyses for conformation traits in South African Jersey and ...

    African Journals Online (AJOL)

    JACO

    Genetic trends for conformation traits of the South African Holstein show that ... conformation traits can be used to improve stayability, fertility and disease resistance (Rogers et al., 1999; .... Genetic correlations among protein yield, productive.

  13. Genetic and linguistic coevolution in Northern Island Melanesia.

    Science.gov (United States)

    Hunley, Keith; Dunn, Michael; Lindström, Eva; Reesink, Ger; Terrill, Angela; Healy, Meghan E; Koki, George; Friedlaender, Françoise R; Friedlaender, Jonathan S

    2008-10-01

    Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may

  14. Genetic and linguistic coevolution in Northern Island Melanesia.

    Directory of Open Access Journals (Sweden)

    Keith Hunley

    2008-10-01

    Full Text Available Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain. There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast

  15. Ichthyoplankton transport from the African coast to the Canary Islands

    Science.gov (United States)

    Brochier, Timothée; Mason, Evan; Moyano, Marta; Berraho, Amina; Colas, Francois; Sangrà, Pablo; Hernández-León, Santiago; Ettahiri, Omar; Lett, Christophe

    2011-08-01

    The Canary Upwelling System (CUS), a major eastern boundary upwelling system, sustains large cross-border fisheries of small pelagic fish, which poses the question of stock connectivity. Studies suggest that ichthyoplankton transport from the northwest African coast to the Canary Islands (CI) is facilitated by coastal-upwelling associated filaments. Here we analyze connections between larval supply to the CI and sardine and anchovy populations that spawn over the continental shelf. For both species, ichthyoplankton observations (1) at the shelf and (2) near the island of Gran Canaria (GC) are used. Predictions of ichthyoplankton transport to GC are obtained from the Ichthyop Lagrangian transport model, which is forced by a high-resolution hydrodynamic model (ROMS) that reproduces the regional circulation. Results show that upwelling filaments play an important role in the transport of larvae to GC. However, (1) filaments are not the only mechanism, and (2) filament presence does not necessarily imply larval transport. Anchovy and sardine larval presence at GC appears to be independent of the respective adult spawning seasonality. Combining of observed and modeled data does not succeed in reproducing the observed larval patterns at GC. Various hypotheses are proposed to explain this discrepancy in larval transport to GC.

  16. Genetic studies on the South African Mutton Merino: growth traits

    African Journals Online (AJOL)

    Unknown

    breed has undergone such a metamorphosis that it no longer bears much, if any, resemblance to its European ancestor. The need for a separate genetic characterization of this distinct South African strain is therefore evident. The aim of this study was to determine the applicable non-genetic factors and to estimate genetic ...

  17. Genetic Counseling for Breast Cancer Susceptibility in African American Women

    National Research Council Canada - National Science Library

    Hughes, Chanita

    2004-01-01

    .... The objectives of this study are to develop a Culturally Tailored Genetic (CTGC) protocol for African American women and evaluate its impact on decision-making and satisfaction about BRCAl/2 testing, quality of life, and cancer control practices...

  18. Genetic analysis of three South African horse breeds

    Directory of Open Access Journals (Sweden)

    E.G. Cothran

    1998-07-01

    Full Text Available Genetic variability at 7 blood-group and 10 biochemical genetic loci was examined in 3 South African horse breeds, the Nooitgedacht, Boerperd and Basuto Pony. Observed heterozygosity for these breeds was intermediate for domestic horses, with the highest heterozygosity in the Boerperd and the lowest in the Basuto Pony. The 3 breeds show greater genetic similarity to each other than to other domestic horse breeds. Compared to other breeds, the South African breeds show greater genetic similarity to breeds such as the Thoroughbred, Holstein, Trakehner and Hanovarian and also to North American breeds such as the Saddlebred, Standardbred and Morgan Horse.

  19. Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome.

    Science.gov (United States)

    Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O'Connor, Timothy D; Abecasis, Gonçalo R; Wojcik, Genevieve L; Gignoux, Christopher R; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E; Bustamante, Carlos; Beaty, Terri H; Mathias, Rasika A; Barnes, Kathleen C; Qin, Zhaohui S

    2017-04-21

    A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

  20. Genetic African Ancestry and Markers of Mineral Metabolism in CKD.

    Science.gov (United States)

    Gutiérrez, Orlando M; Parsa, Afshin; Isakova, Tamara; Scialla, Julia J; Chen, Jing; Flack, John M; Nessel, Lisa C; Gupta, Jayanta; Bellovich, Keith A; Steigerwalt, Susan; Sondheimer, James H; Wright, Jackson T; Feldman, Harold I; Kusek, John W; Lash, James P; Wolf, Myles

    2016-04-07

    Disorders of mineral metabolism are more common in African Americans with CKD than in European Americans with CKD. Previous studies have focused on the differences in mineral metabolism by self-reported race, making it difficult to delineate the importance of environmental compared with biologic factors. In a cross-sectional analysis of 3013 participants of the Chronic Renal Insufficiency Cohort study with complete data, we compared markers of mineral metabolism (phosphorus, calcium, alkaline phosphatase, parathyroid hormone, fibroblast growth factor 23, and urine calcium and phosphorus excretion) in European Americans versus African Americans and separately, across quartiles of genetic African ancestry in African Americans (n=1490). Compared with European Americans, African Americans had higher blood concentrations of phosphorus, alkaline phosphatase, fibroblast growth factor 23, and parathyroid hormone, lower 24-hour urinary excretion of calcium and phosphorus, and lower urinary fractional excretion of calcium and phosphorus at baseline (PAfrican Americans, a higher percentage of African ancestry was associated with lower 24-hour urinary excretion of phosphorus (PtrendAfrican ancestry was significantly associated with lower 24-hour urinary phosphorus excretion (each 10% higher African ancestry was associated with 39.6 mg lower 24-hour urinary phosphorus, PAfrican ancestry was associated with an absolute 1.1% lower fractional excretion of phosphorus, P=0.01). A higher percentage of African ancestry was independently associated with lower 24-hour urinary phosphorus excretion and lower fractional excretion of phosphorus among African Americans with CKD. These findings suggest that genetic variability might contribute to racial differences in urinary phosphorus excretion in CKD. Copyright © 2016 by the American Society of Nephrology.

  1. Genetic analysis of rock hole and domestic Aedes aegypti on the Caribbean island of Anguilla.

    Science.gov (United States)

    Wallis, G P; Tabachnick, W J

    1990-12-01

    Genetic variation was characterized at 11 enzyme coding loci in Aedes aegypti collected from 3 rock hole and 4 domestic sites on the island of Anguilla, West Indies. The pattern of gene frequency variation suggests that these mosquito samples do not constitute a single panmictic population, but there are no large consistent differences between rock hole and domestic forms to parallel the East African sylvan-domestic dichotomy. With the exception of one of the domestic populations, two loci did however show some gene frequency differences consistent with genetic differentiation between the 2 habitat types. We conclude that whereas there may be some degree of differentiation between the 2 habitat types, local eradication attempts and sporadic gene flow cause temporal and spatial volatility that is sufficient to swamp these differences.

  2. Genetic epidemiology of hypertension: an update on the African diaspora.

    Science.gov (United States)

    Daniel, Harold I; Rotimi, Charles N

    2003-01-01

    Hypertension is a serious global public health problem, affecting approximately 600 million people worldwide. The lifetime risk of developing the condition exceeds 50% in most populations. Despite considerable success in the pharmacological treatment of hypertension in all-human populations, the health-care community still lacks understanding of how and why individuals develop chronically elevated blood pressure. This gap in knowledge, and the high prevalence of hypertension and associated complications in some populations of African descent, have led some to conclude that hypertension is a "different disease" in people of African descent. Despite considerable evidence from epidemiologic studies showing that blood pressure distribution in populations of the African diaspora spans the known spectrum for all human populations, theories in support of unique "defects" among populations of African descent continue to gain wide acceptance. To date, no known environmental factors or genetic variants relevant to the pathophysiology of human hypertension have been found to be unique to Black populations. However, available genetic epidemiologic data demonstrate differential distributions of risk factors that are consistent with current environmental and geographic origins. This review summarizes the available evidence and demonstrates that as the exposure to known risk factors for hypertension (eg, excess consumption of salt and calories, stress, sedentary lifestyle, and degree of urbanization) increases among genetically susceptible individuals, the prevalence of hypertension and associated complications also increases across populations of the African diaspora. This observation is true for all human populations.

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

    Science.gov (United States)

    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.

    2014-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterisation of African genetic diversity is needed. The African Genome Variation Project (AGVP) provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. The AGVP represents dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across SSA. We identify new loci under selection, including for malaria and hypertension. We show that modern imputation panels can identify association signals at highly differentiated loci across populations in SSA. Using WGS, we show further improvement in imputation accuracy supporting efforts for large-scale sequencing of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa, showing for the first time that such designs are feasible. PMID:25470054

  4. Genetic structure and diversity of East African taro [ Colocasia ...

    African Journals Online (AJOL)

    Taro [Colocasia esculenta (L) Schott] is mainly produced in Africa by small holder farmers and plays an important role in the livelihood of millions of poor people in less developed countries. The genetic diversity of East African taro has not been determined. This study utilizes six microsatellite primers to analyze five ...

  5. Population structure and genetic trends for indigenous African beef ...

    African Journals Online (AJOL)

    The aim of this study was to investigate population structure and genetic trends based on pedigree and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger, Nguni and Tuli) in South Africa. Pedigree completeness over six generations was higher than 88.5% in the first ...

  6. Genetic Counseling for Breast Cancer Susceptibility in African American Women

    National Research Council Canada - National Science Library

    Hughes, Chanita

    2005-01-01

    .... The objectives of this study are to develop a Culturally Tailored Genetic (CTGC) protocol for African American women and evaluate its impact on decision-making and satisfaction about BRCA1/2 testing, quality of life, and cancer control practices...

  7. Understanding participation by African Americans in cancer genetics research.

    Science.gov (United States)

    McDonald, Jasmine A; Barg, Frances K; Weathers, Benita; Guerra, Carmen E; Troxel, Andrea B; Domchek, Susan; Bowen, Deborah; Shea, Judy A; Halbert, Chanita Hughes

    2012-01-01

    Understanding genetic factors that contribute to racial differences in cancer outcomes may reduce racial disparities in cancer morbidity and mortality. Achieving this goal will be limited by low rates of African American participation in cancer genetics research. We conducted a qualitative study with African American adults (n = 91) to understand attitudes about participating in cancer genetics research and to identify factors that are considered when making a decision about participating in this type of research. Participants would consider the potential benefits to themselves, family members, and their community when making a decision to participate in cancer genetics research. However, concerns about exploitation, distrust of researchers, and investigators' motives were also important to participation decisions. Individuals would also consider who has access to their personal information and what would happen to these data. Side effects, logistical issues, and the potential to gain knowledge about health issues were also described as important factors in decision making. African Americans may consider a number of ethical, legal, and social issues when making a decision to participate in cancer genetics research. These issues should be addressed as part of recruitment efforts.

  8. African, Amerindian and European hepatitis B virus strains circulate on the Caribbean Island of Martinique.

    Science.gov (United States)

    Brichler, Ségolène; Lagathu, Gisèle; Chekaraou, Mariama Abdou; Le Gal, Frédéric; Edouard, André; Dény, Paul; Césaire, Raymond; Gordien, Emmanuel

    2013-10-01

    Ten Hepatitis B virus (HBV) genotypes, as well as numerous subgenotypes, have been described in well-characterized ethnogeographical populations. Martinique has been at a crossroads between Africa, Europe, India and the Americas because of the slave trade (17th-19th centuries), followed by an important immigration of Indian and West African workers. In this work, we aimed to study the molecular epidemiology of HBV infection in Martinique according to this unique settlement pattern. To that end, blood samples from 86 consecutive HBV-infected patients from the main hospitals of the island, were retrospectively analysed. Direct sequencing of the pre-S1 or pre-C-C region or complete genome sequencing, followed by phylogenetic analyses were performed. HBV genotypes were: HBV/A1 (68.6 %), HBV/A2 (10.5 %), HBV/D, mainly HBV/D3 and HBV/D4 (8.1 %), HBV/F (3.5 %), and also HBV/E (2.3 %), two strains isolated from two West-African patients. Moreover, 74 % of the HBeAg-negative strains harboured classical pre-C-C mutations, and most HBV/A1 strains also containing specific mutations. Finally, various patterns of deletion mutants in pre-S and pre-C-C regions were found. In conclusion, our findings point to historical and migration-related issues in HBV-genotype distribution suggesting that HBV/A1, but not HBV/E, was imported from Africa during the slave trade, and further supporting the hypothesis that HBV/E has emerged recently in West Africa (<150 years). Potential origins of 'European' HBV/A2 and HBV/D3, 'Amerindian' HBV/F, and HBV/D4 strains are also discussed. Such HBV genetic diversity, beyond its epidemiological interest, may have a clinical impact on the natural history of HBV infection in Martinique.

  9. Genetically depauperate in the continent but rich in oceanic islands: Cistus monspeliensis (Cistaceae in the Canary Islands.

    Directory of Open Access Journals (Sweden)

    Mario Fernández-Mazuecos

    Full Text Available BACKGROUND: Population genetic theory holds that oceanic island populations are expected to have lower levels of genetic variation than their mainland counterparts, due to founder effect after island colonization from the continent. Cistus monspeliensis (Cistaceae is distributed in both the Canary Islands and the Mediterranean region. Numerous phylogenetic results obtained in the last years allow performing further phylogeographic analyses in Cistus. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed sequences from multiple plastid DNA regions in 47 populations of Cistus monspeliensis from the Canary Islands (21 populations and the Mediterranean basin (26 populations. The time-calibrated phylogeny and phylogeographic analyses yielded the following results: (1 a single, ancestral haplotype is distributed across the Mediterranean, whereas 10 haplotypes in the Canary Islands; (2 four haplotype lineages are present in the Canarian Islands; (3 multiple colonization events across the archipelago are inferred; (4 the earliest split of intraspecific lineages occurred in the Early to Middle Pleistocene (<930,000 years BP. CONCLUSIONS/SIGNIFICANCE: The contrasting pattern of cpDNA variation is best explained by genetic bottlenecks in the Mediterranean during Quaternary glaciations, while the Canarian archipelago acted as a refugium of high levels of genetic diversity. Active colonization across the Canarian islands is supported not only by the distribution of C. monspeliensis in five of the seven islands, but also by our phylogeographic reconstruction in which unrelated haplotypes are present on the same island. Widespread distribution of thermophilous habitats on every island, as those found throughout the Mediterranean, has likely been responsible for the successful colonization of C. monspeliensis, despite the absence of a long-distance dispersal mechanism. This is the first example of a plant species with higher genetic variation among oceanic island

  10. African Americans' opinions about human-genetics research.

    Science.gov (United States)

    Achter, Paul; Parrott, Roxanne; Silk, Kami

    2004-03-01

    Research on attitudes toward genetics and medicine registers skepticism among minority communities, but the reasons for this skepticism are not well known. In the past, studies linked mistrust of the medical system to historical ethics violations involving minority groups and to suspicions about ideological premise and political intent. To assess public knowledge, attitudes, and behavior regarding human-genetics research, we surveyed 858 Americans onsite in four community settings or online in a geographically nonspecific manner. Compared to participants as a whole, African Americans were significantly more likely to believe that clinical trials might be dangerous and that the federal government knowingly conducted unethical research, including studies in which risky vaccines were administered to prison populations. However, African Americans were also significantly more likely to believe that the federal government worked to prevent environmental exposure to toxicants harmful to people with genetic vulnerabilities. Our data suggest that most Americans trust government to act ethically in sponsoring and conducting research, including genetics research, but that African Americans are particularly likely to see government as powerfully protective in some settings yet selectively disingenuous in others.

  11. Genetic Programming for Sea Level Predictions in an Island Environment

    Directory of Open Access Journals (Sweden)

    M.A. Ghorbani

    2010-03-01

    Full Text Available Accurate predictions of sea-level are important for geodetic applications, navigation, coastal, industrial and tourist activities. In the current work, the Genetic Programming (GP and artificial neural networks (ANNs were applied to forecast half-daily and daily sea-level variations from 12 hours to 5 days ahead. The measurements at the Cocos (Keeling Islands in the Indian Ocean were used for training and testing of the employed artificial intelligence techniques. A comparison was performed of the predictions from the GP model and the ANN simulations. Based on the comparison outcomes, it was found that the Genetic Programming approach can be successfully employed in forecasting of sea level variations.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. An Institutional Approach to Bordering in Islands: The Canary Islands on the African-European Migration Routes

    Directory of Open Access Journals (Sweden)

    Dirk Godenau

    2012-05-01

    Full Text Available Islands play a significant role in international irregular maritime migration. Frequently they are part of maritime interstitial spaces between states, and their location, combined with institutional membership, makes them part of international migration routes and subject to border management strategies. In this paper borders are analysed as social institutions used for regulating relative permeability through rules of entry and exit for persons, goods and capital. Borders institutionalize territoriality and are politically implemented by states. They are selective, also in migration, and irregular border transit is not always indicative of an inability to control. The Canary Islands are used as an illustrative example of how border management at the southern edge of the European Union has evolved towards more coercive deterrence and tighter surveillance. The Canary Islands experienced irregular maritime immigration from the west African coasts during the first decade of the 21st century and most of these migrants intended to use the islands as transit space towards the European continent. Increasing surveillance in countries of origin, enforcement of border controls and stricter return policies were used to stop flows. The so-called “cayuco crisis” in 2006 induced institutional change in border management and forced the active involvement of the EU through FRONTEX.

  15. Forecasting tourist arrivals to balearic islands using genetic programming

    Directory of Open Access Journals (Sweden)

    Rosselló-Nadal, Jaume

    2007-01-01

    Full Text Available Traditionally, univariate time-series models have largely dominated forecasting for international tourism demand. In this paper, the ability of a Genetic Program (GP to predict monthly tourist arrivals from UK and Germany to Balearic Islands (Spain is explored. GP has already been employed satisfactorily in different scientific areas, including economics. The technique shows different advantages regarding to other forecasting methods. Firstly, it does not assume a priori a rigid functional form of the model. Secondly, it is more robust and easy-to-use than other non-parametric methods. Finally, it provides explicitly a mathematical equation which allows a simple ad hoc interpretation of the results. Comparing the performance of the proposed technique against other method commonly used in tourism forecasting (no-change model, Moving Average and ARIMA, the empirical results reveal that GP can be a valuable tool in this field.

  16. Low Genetic Variation of Red-Crowned Cranes on Hokkaido Island, Japan, Over the Hundred Years.

    Science.gov (United States)

    Akiyama, Takuya; Momose, Kunikazu; Onuma, Manabu; Matsumoto, Fumio; Masuda, Ryuichi

    2017-06-01

    The red-crowned crane (Grus japonensis) is recognized internationally as an endangered species. Migratory populations breed in eastern Russia and northeastern China, whereas the resident population inhabits the island of Hokkaido, Japan. Although the population inhabiting Hokkaido had experienced a severe bottleneck by the end of the 19th century, the population size has recovered to about 1500 and continues to increase now thanks to conservation efforts. A previous study reported that no marked genetic differences were seen in the island population, and that the genetic variation of the whole population on Hokkaido was lower than that of the continental population. However, the precise genetic structure of the island population in the past or near present remains unclear. To better understand the spatiotemporal changes in the genetic structure of the island population, we performed mitochondrial DNA (mtDNA) analyses using stuffed specimens (years 1878-2001) and tissue or blood samples (years 1970-2014). We found three haplotypes in the island population, one of which was a novel mtDNA haplotype in 1997 and 2007 samples. In addition, there was no clear difference in the haplotype frequency through the time span. These results suggest that the low genetic variation of the island population persisted for the last hundred years. It is thus nearly impossible for the island population to recover its genetic variation in isolation. Conservation plans for this species should therefore include the promotion of genetic exchanges between the continental and island populations, such as through artificial introduction to Hokkaido.

  17. Association of substance use disorders with childhood trauma but not African genetic heritage in an African American cohort.

    Science.gov (United States)

    Ducci, Francesca; Roy, Alec; Shen, Pei-Hong; Yuan, Qiaoping; Yuan, Nicole P; Hodgkinson, Colin A; Goldman, Lynn R; Goldman, David

    2009-09-01

    Genetic variation influences differential vulnerability to addiction within populations. However, it remains unclear whether differences in frequencies of vulnerability alleles contribute to disparities between populations and to what extent ancestry correlates with differential exposure to environmental risk factors, including poverty and trauma. The authors used 186 ancestry-informative markers to measure African ancestry in 407 addicts and 457 comparison subjects self-identified as African Americans. The reference group was 1,051 individuals from the Human Genome Diversity Cell Line Panel, which includes 51 diverse populations representing most worldwide genetic diversity. African Americans varied in degrees of African, European, Middle Eastern, and Central Asian genetic heritage. The overall level of African ancestry was actually smaller among cocaine, opiate, and alcohol addicts (proportion=0.76-0.78) than nonaddicted African American comparison subjects (proportion=0.81). African ancestry was associated with living in impoverished neighborhoods, a factor previously associated with risk. There was no association between African ancestry and exposure to childhood abuse or neglect, a factor that strongly predicted all types of addictions. These results suggest that African genetic heritage does not increase the likelihood of genetic risk for addictions. They highlight the complex interrelation between genetic ancestry and social, economic, and environmental conditions and the strong relation of those factors to addiction. Studies of epidemiological samples characterized for genetic ancestry and social, psychological, demographic, economic, cultural, and historical factors are needed to better disentangle the effects of genetic and environmental factors underlying interpopulation differences in vulnerability to addiction and other health disparities.

  18. Genetic aspects of athletic performance: the African runners phenomenon

    Directory of Open Access Journals (Sweden)

    Vancini RL

    2014-05-01

    Full Text Available Rodrigo Luiz Vancini,1 João Bosco Pesquero,2 Rafael Júlio Fachina,3,4 Marília dos Santos Andrade,1 João Paulo Borin,3 Paulo César Montagner,3 Claudio Andre Barbosa de Lira51Centro de Educação Física e Desportos, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil; 2Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil; 3Departamento de Ciência do Esporte, Faculdade de Educação Física, Universidade Estadual de Campinas, Campinas, Brazil; 4Confederação Brasileira de Basquetebol, Rio de Janeiro, Brazil; 5Setor de Fisiologia Humana e do Exercício, Faculdade de Educação Física, Universidade Federal de Goiás, Goiânia, BrazilAbstract: The current dominance of African runners in long-distance running is an intriguing phenomenon that highlights the close relationship between genetics and physical performance. Many factors in the interesting interaction between genotype and phenotype (eg, high cardiorespiratory fitness, higher hemoglobin concentration, good metabolic efficiency, muscle fiber composition, enzyme profile, diet, altitude training, and psychological aspects have been proposed in the attempt to explain the extraordinary success of these runners. Increasing evidence shows that genetics may be a determining factor in physical and athletic performance. But, could this also be true for African long-distance runners? Based on this question, this brief review proposed the role of genetic factors (mitochondrial deoxyribonucleic acid, the Y chromosome, and the angiotensin-converting enzyme and the alpha-actinin-3 genes in the amazing athletic performance observed in African runners, especially the Kenyans and Ethiopians, despite their environmental constraints.Keywords: genes, genotype, physical exercise, endurance runners

  19. Anagenetic speciation in Ullung Island, Korea: genetic diversity and structure in the island endemic species, Acer takesimense (Sapindaceae).

    Science.gov (United States)

    Takayama, Koji; Sun, Byung-Yun; Stuessy, Tod F

    2013-05-01

    Anagenetic speciation is an important mode of speciation in oceanic islands; one-fourth of the endemic plants are estimated to have been derived via this process. Few studies, however, have critically examined the genetic consequences of anagenesis in comparison with cladogenesis (involved with adaptive radiation). We hypothesize that endemic species originating via anagenetic speciation in a relatively uniform environment should accumulate genetic variation with limited populational differentiation. We undertook a population genetic analysis using nine nuclear microsatellite loci of Acer takesimense, an anagenetically derived species endemic to Ullung Island, Korea, and its continental progenitor A. pseudosieboldianum on the Korean Peninsula. Microsatellite data reveal a clear genetic distinction between the two species. A high F value in the cluster of A. takesimense was found by Bayesian clustering analysis, suggesting a strong episode of genetic drift during colonization and speciation. In comparison with A. pseudosieboldianum, A. takesimense has slightly lower genetic diversity and possesses less than half the number of private and rare alleles. Consistent with predictions, weak geographical genetic structure within the island was found in A. takesimense. These results imply that anagenetic speciation leads to a different pattern of specific and genetic diversity than often seen with cladogenesis.

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

    Science.gov (United States)

    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. Conservation genetics of the critically endangered Round Island bottle palm, Hyophorbe lagenicaulis (Arecaceae)

    DEFF Research Database (Denmark)

    Lange, Conny Bruun Asmussen; Maunder, Michael; Fay, Michael F.

    2011-01-01

    The amplified fragment length polymorphism (AFLP) technique was used to examine genetic variation among old and newly emerged individuals of Hyophorbe lagenicaulis (the Round Island bottle palm) on Round Island to assess surviving levels of diversity in the wild population and to evaluate...... monomorphic bands. Analysis of molecular variance (AMOVA) and Shannon’s indices showed a high level of genetic variation within the wild population on Round Island and a smaller amount of genetic variation among cultivated individuals. A neighbor joining analysis resulted in an unrooted network of genetic...... distances in which the five Hyophorbe spp. were separated and much variation within H. lagenicaulis was recovered. The Round Island populations of H. lagenicaulis contain representatives of the genetic variation found within the species as a whole. However, a few individuals, both wild and cultivated...

  2. A Mainly Circum-Mediterranean Origin for West Eurasian and North African mtDNAs in Puerto Rico with Strong Contributions from the Canary Islands and West Africa.

    Science.gov (United States)

    Díaz-Zabala, Héctor J; Nieves-Colón, María A; Martínez-Cruzado, Juan C

    2017-04-01

    Maternal lineages of West Eurasian and North African origin account for 11.5% of total mitochondrial ancestry in Puerto Rico. Historical sources suggest that this ancestry arrived mostly from European migrations that took place during the four centuries of the Spanish colonization of Puerto Rico. This study analyzed 101 mitochondrial control region sequences and diagnostic coding region variants from a sample set randomly and systematically selected using a census-based sampling frame to be representative of the Puerto Rican population, with the goal of defining West Eurasian-North African maternal clades and estimating their possible geographical origin. Median-joining haplotype networks were constructed using hypervariable regions 1 and 2 sequences from various reference populations in search of shared haplotypes. A posterior probability analysis was performed to estimate the percentage of possible origins across wide geographic regions for the entire sample set and for the most common haplogroups on the island. Principal component analyses were conducted to place the Puerto Rican mtDNA set within the variation present among all reference populations. Our study shows that up to 38% of West Eurasian and North African mitochondrial ancestry in Puerto Rico most likely migrated from the Canary Islands. However, most of those haplotypes had previously migrated to the Canary Islands from elsewhere, and there are substantial contributions from various populations across the circum-Mediterranean region and from West African populations related to the modern Wolof and Serer peoples from Senegal and the nomad Fulani who extend up to Cameroon. In conclusion, the West Eurasian mitochondrial ancestry in Puerto Ricans is geographically diverse. However, haplotype diversity seems to be low, and frequencies have been shaped by population bottlenecks, migration waves, and random genetic drift. Consequently, approximately 47% of mtDNAs of West Eurasian and North African ancestry

  3. Genetic and morphological differences among populations of the Bonin Islands White-eye in Japan.

    Science.gov (United States)

    Kawakami, Kazuto; Harada, Sachiko; Suzuki, Tadashi; Higuchi, Hiroyoshi

    2008-09-01

    The Bonin Islands White-eye, Apalopteron familiare , is the sole endemic avian species surviving on the Bonin Islands. The current distribution of this species is limited to only three islands of the Hahajima Island group: Hahajima, Imotojima, and Mukohjima. Imotojima and Mukohjima, which are small satellite islands of Hahajima, are about 3.6 km and 5.5 km, respectively, from the larger island. To investigate genetic and morphological differences among A. familiare populations on these islands, we assayed 634 bp of mitochondrial control region sequence for 132 birds from five locations among the three islands. We detected five haplotypes: two endemic haplotypes each on Hahajima and Imotojima and one on Mukohjima. Principal component analysis based on eight morphological characters of 162 birds from the three island populations revealed that birds from the small satellite islands had significantly different beak morphological characters. Our findings indicate that over-sea dispersal is rare in A. familiare , even when islands are separated by only a few kilometers, and suggest that little movement occurs on Hahajima. Thus, each population on each island should be conserved as an evolutionarily significant unit. The low dispersal ability of this species suggests that it is vulnerable to habitat fragmentation. Although the populations are currently stable and do not require rapid countermeasures, they should be monitored, especially those on the smaller islands.

  4. Effects of religion, economics, and geography on genetic structure of Fogo Island, Newfoundland.

    Science.gov (United States)

    Crawford, M H; Koertevlyessy, T; Huntsman, R G; Collins, M; Duggirala, R; Martin, L; Keeping, D

    1995-01-01

    The population structure of Fogo Island, Newfoundland is described using geography, religious affiliation, economic factors (such as the presence of a fish-packing plant), and genetic markers. Five different analytic methods, R-matrix analysis, r ii VS. mean per locus heterozygosity, predicted kinship (ϕ), mean first passage time, and Mantel matrix comparisons, were applied to the Fogo Island genetic and demographic data. The results suggest that geography plays a role on Fogo Island in the distribution of genes, while religion, ethnicity, and economic factors play less significant roles. The communities with fish-packing plants and tourism serve as migratory "sinks" for Fogo islanders seeking employment. Reproductively, the most isolated village on Fogo Island is Tilting, and this is reflected in its genetic uniqueness, initially caused by Irish settlement and subsequently the action of stochastic processes. © 1995 Wiley-Liss, Inc. Copyright © 1995 Wiley-Liss, Inc., A Wiley Company.

  5. Systematic review on the conservation genetics of African savannah elephants.

    Science.gov (United States)

    Zacarias, Daniel; Bini, Luis Mauricio; Loyola, Rafael

    2016-01-01

    In this paper we review the conservation genetics of African savannah elephants, aiming to understand the spatio-temporal research trends and their underlying factors. As such, we explore three questions associated to the conservation genetics and molecular ecology of these elephants: (1) what are the research trends concerning the conservation genetics of Loxodonta africana ? (2) Do richer countries conduct more research on the genetics of African elephants? (3) Which attributes influence where scholars conduct their research? We examined available peer-reviewed publications from 1993 to 2014 in complementary online databases, including the ISI/Web of Science (WoS), Scopus and Google Scholar (GS), and searched for publications in scientific journals as well as in the reference section of these publications. We analyzed the annual trend of publications in this field of research, including the number of authors, levels of collaboration among authors, year of publication, publishing journal and the countries from where genetic samples were collected. Additionally, we identified main research clusters, authors, and institutional collaborations, based on co-citation and co-occurrence networks. We found that during the study period there was a positive trend in the number of publications and a reduction in the number of authors per paper. Twenty-five countries contributed, with the majority of publications authored by researchers in the USA, Kenya and South Africa. The majority of samples were collected in Kenya, Tanzania and South Africa. Research outputs are associated with the existence of long-term conservation/research projects and research potential as measured by the literacy rate and the number of higher education institutions in a country. Five research clusters were identified, focusing on the origin and evolution of the species, methodological issues and the relatedness among elephant species. Research in this field should be expanded to additional countries

  6. Systematic review on the conservation genetics of African savannah elephants

    Directory of Open Access Journals (Sweden)

    Daniel Zacarias

    2016-10-01

    Full Text Available Background In this paper we review the conservation genetics of African savannah elephants, aiming to understand the spatio-temporal research trends and their underlying factors. As such, we explore three questions associated to the conservation genetics and molecular ecology of these elephants: (1 what are the research trends concerning the conservation genetics of Loxodonta africana? (2 Do richer countries conduct more research on the genetics of African elephants? (3 Which attributes influence where scholars conduct their research? Materials and Methods We examined available peer-reviewed publications from 1993 to 2014 in complementary online databases, including the ISI/Web of Science (WoS, Scopus and Google Scholar (GS, and searched for publications in scientific journals as well as in the reference section of these publications. We analyzed the annual trend of publications in this field of research, including the number of authors, levels of collaboration among authors, year of publication, publishing journal and the countries from where genetic samples were collected. Additionally, we identified main research clusters, authors, and institutional collaborations, based on co-citation and co-occurrence networks. Results We found that during the study period there was a positive trend in the number of publications and a reduction in the number of authors per paper. Twenty-five countries contributed, with the majority of publications authored by researchers in the USA, Kenya and South Africa. The majority of samples were collected in Kenya, Tanzania and South Africa. Research outputs are associated with the existence of long-term conservation/research projects and research potential as measured by the literacy rate and the number of higher education institutions in a country. Five research clusters were identified, focusing on the origin and evolution of the species, methodological issues and the relatedness among elephant species. Conclusions

  7. Functional analysis of the Gonococcal Genetic Island of Neisseria gonorrhoeae.

    Directory of Open Access Journals (Sweden)

    Emilia Pachulec

    Full Text Available Neisseria gonorrhoeae is an obligate human pathogen that is responsible for the sexually-transmitted disease gonorrhea. N. gonorrhoeae encodes a T4SS within the Gonococcal Genetic Island (GGI, which secretes ssDNA directly into the external milieu. Type IV secretion systems (T4SSs play a role in horizontal gene transfer and delivery of effector molecules into target cells. We demonstrate that GGI-like T4SSs are present in other β-proteobacteria, as well as in α- and γ-proteobacteria. Sequence comparison of GGI-like T4SSs reveals that the GGI-like T4SSs form a highly conserved unit that can be found located both on chromosomes and on plasmids. To better understand the mechanism of DNA secretion by N. gonorrhoeae, we performed mutagenesis of all genes encoded within the GGI, and studied the effects of these mutations on DNA secretion. We show that genes required for DNA secretion are encoded within the yaa-atlA and parA-parB regions, while genes encoded in the yfeB-exp1 region could be deleted without any effect on DNA secretion. Genes essential for DNA secretion are encoded within at least four different operons.

  8. The Cape Verde Islands are home to a small and genetically distinct humpback whale breeding population

    NARCIS (Netherlands)

    Bérubé, Martine; Ryan, Conor; Berrow, Simon D.; Suarez, Pedro Lopez; Monteiro, Vanda; Wenzel, Frederick; Robbins, Jooke; Mattila, David; Vikingsson, G.A.; Øien, Nils; Palsboll, Per

    2013-01-01

    The Cape Verde Islands appear to be winter breeding ground of the smallest humpback whale population yet known. However, it is unclear whether the humpback whales at the Cape Verde Islands interbreed with those in the West Indies. Here we present the results of the genetic analysis of 50 humpback

  9. AFSC/REFM: Pacific cod genetics in the Aleutian Islands 2004-2007

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Landscape genetics of Pacific cod Gadus macrocephalus within the Bering Sea and Aleutian Islands (BSAI) management area of Alaska was examined in samples from nine...

  10. Genetic determination of adiponectin and its relationship with body fat topography in multigenerational families of African heritage.

    Science.gov (United States)

    Miljkovic-Gacic, Iva; Wang, Xiaojing; Kammerer, Candace M; Bunker, Clareann H; Wheeler, Victor W; Patrick, Alan L; Kuller, Lewis H; Evans, Rhobert W; Zmuda, Joseph M

    2007-02-01

    Adiponectin, an adipose-specific protein, is negatively associated with adiposity, insulin sensitivity, and diabetes. Very few studies have examined the role of heredity in the regulation of adiponectin and its association with body fat among individuals of African heritage. Thus, we measured fasting serum adiponectin levels by radioimmunoassay and body composition by dual-energy x-ray absorptiometry (DEXA) in 402 individuals aged 18 to 103 years belonging to 7 multigenerational families of African heritage in the relatively homogeneous island population of Tobago. Heritability of adiponectin was 33.2% (P genetic factors are a significant source of interindividual differences in circulating adiponectin among Afro-Caribbeans. Adiponectin may serve as a promising quantitative intermediate trait in studies designed to map the genes underlying diabetes and obesity in this population.

  11. Microsatellite Analysis of the Population Genetic Structure of Anolis carolinensis Introduced to the Ogasawara Islands.

    Science.gov (United States)

    Sugawara, Hirotaka; Takahashi, Hiroo; Hayashi, Fumio

    2015-01-01

    DNA analysis can reveal the origins and dispersal patterns of invasive species. The green anole Anolis carolinensis is one such alien animal, which has been dispersed widely by humans from its native North America to many Pacific Ocean islands. In the Ogasawara (Bonin) Islands, this anole was recorded from Chichi-jima at the end of the 1960s, and then from Haha-jima in the early 1980s. These two islands are inhabited. In 2013, it was also found on the uninhabited Ani-jima, close to Chichi-jima. Humans are thought to have introduced the anole to Haha-jima, while the mode of introduction to Ani-jima is unknown. To clarify its dispersal patterns within and among these three islands, we assessed the fine-scale population genetic structure using five microsatellite loci. The results show a homogeneous genetic structure within islands, but different genetic structures among islands, suggesting that limited gene flow occurs between islands. The recently established Ani-jima population may have originated from several individuals simultaneously, or by repeated immigration from Chichi-jima. We must consider frequent incursions among these islands to control these invasive lizard populations and prevent their negative impact on native biodiversity.

  12. Population genetics of the potentially invasive African fruit fly species, Ceratitis rosa and Ceratitis fasciventris (Diptera: Tephritidae).

    Science.gov (United States)

    Baliraine, F N; Bonizzoni, M; Guglielmino, C R; Osir, E O; Lux, S A; Mulaa, F J; Gomulski, L M; Zheng, L; Quilici, S; Gasperi, G; Malacrida, A R

    2004-03-01

    A set of 10 microsatellite markers was used to survey the levels of genetic variability and to analyse the genetic aspects of the population dynamics of two potentially invasive pest fruit fly species, Ceratitis rosa and C. fasciventris, in Africa. The loci were derived from the closely related species, C. capitata. The degree of microsatellite polymorphism in C. rosa and C. fasciventris was extensive and comparable to that of C. capitata. In C. rosa, the evolution of microsatellite polymorphism in its distribution area reflects the colonization history of this species. The mainland populations are more polymorphic than the island populations. Low levels of differentiation were found within the Africa mainland area, while greater levels of differentiation affect the islands. Ceratitis fasciventris is a central-east African species. The microsatellite data over the Uganda/Kenya spatial scale suggest a recent expansion and possibly continuing gene flow within this area. The microsatellite variability data from C. rosa and C. fasciventris, together with those of C. capitata, support the hypothesis of an east African origin of the Ceratitis spp.

  13. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline

    2017-02-15

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

  14. [Gene geography of Chile: regional distribution of American, European and African genetic contributions].

    Science.gov (United States)

    Fuentes, Macarena; Pulgar, Iván; Gallo, Carla; Bortolini, María-Cátira; Canizales-Quinteros, Samuel; Bedoya, Gabriel; González-José, Rolando; Ruiz-Linares, Andrés; Rothhammer, Francisco

    2014-03-01

    The geographical distribution of genes plays a key role in genetic epidemiology. The Chilean population has three major stem groups (Native American, European and African). To estimate the regional rate of American, European and African admixture of the Chilean population. Forty single nucleotide polymorphisms (SNP´s) which exhibit substantially different frequencies between Amerindian populations (ancestry-informative markers or AIM´s), were genotyped in a sample of 923 Chilean participants to estimate individual genetic ancestry. The American, European and African individual average admixture estimates for the 15 Chilean Regions were relatively homogeneous and not statistically different. However, higher American components were found in northern and southern Chile and higher European components were found in central Chile. A negative correlation between African admixture and latitude was observed. On the average, American and European genetic contributions were similar and significantly higher than the African contribution. Weighted mean American, European and African genetic contributions of 44.34% ± 3 9%, 51.85% ± 5.44% and 3.81% ± 0.45%, were estimated. Fifty two percent of subjects harbor African genes. Individuals with Aymara and Mapuche surnames have an American admixture of 58.64% and 68.33%, respectively. Half of the Chilean population harbors African genes. Participants with Aymara and Mapuche surnames had a higher American genetic contribution than the general Chilean population. These results confirm the usefulness of surnames as a first approximation to determine genetic ancestry.

  15. Genetic structure of the Common Eider in the western Aleutian Islands prior to fox eradication

    Science.gov (United States)

    Sonsthagen, Sarah A.; Talbot, Sandra L.; Wilson, Robert E.; Petersen, Margaret R.; Williams, Jeffrey C.; Byrd, G. Vernon; McCracken, Kevin G.

    2013-01-01

    Since the late 18th century bird populations residing in the Aleutian Archipelago have been greatly reduced by introduced arctic foxes (Alopex lagopus). We analyzed data from microsatellite, nuclear intron, and mitochondrial (mtDNA) loci to examine the spatial genetic structure, demography, and gene flow among four Aleutian Island populations of the Common Eider (Somateria mollissima) much reduced by introduced foxes. In mtDNA, we found high levels of genetic structure within and between island groups (ΦST = 0.643), but we found no population subdivision in microsatellites or nuclear introns. Differences in genetic structure between the mitochondrial and nuclear genomes are consistent with the Common Eider's breeding and winter biology, as females are highly philopatric and males disperse. Nevertheless, significant differences between islands in the mtDNA of males and marginal significance (P =0.07) in the Z-linked locus Smo 1 suggest that males may also have some level of fidelity to island groups. Severe reduction of populations by the fox, coupled with females' high philopatry, may have left the genetic signature of a bottleneck effect, resulting in the high levels of genetic differentiation observed in mtDNA (ΦST = 0.460–0.807) between islands only 440 km apart. Reestablishment of the Common Eider following the fox's eradication was likely through recruitment from within the islands and bolstered by dispersal from neighboring islands, as suggested by the lack of genetic structure and asymmetry in gene flow between Attu and the other Near Islands.

  16. A new servaline genet (Carnivora, Viverridae) from Zanzibar Island

    African Journals Online (AJOL)

    1997-09-23

    Sep 23, 1997 ... Adult of unknown sex: badly damaged skin with head + body length of 55 ..... Department of Biological Science, University of Swaziland,. Private Bag 4 ... ative brain sizes of some southern African myomorph rodents based on ...

  17. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands.

    Science.gov (United States)

    Sun, Ye; Vargas-Mendoza, Carlos F

    2017-01-01

    Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  18. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae on the Canary Islands

    Directory of Open Access Journals (Sweden)

    Ye Sun

    2017-06-01

    Full Text Available Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat. The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote and western islands (EI Hierro, La Palma, La Gomera, Tenerife, this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  19. The Robben Island diversity experience. An exploration of South African diversity dynamics

    Directory of Open Access Journals (Sweden)

    Marius Pretorius

    2012-03-01

    Research purpose: The purpose of the research was to describe the experiences of participants attending the Robben Island Diversity Experience (RIDE in order to understand South African diversity dynamics from a depth psychology perspective. Motivation for the study: Of the many and different diversity events presented in South African organisations, RIDE is the only annual systems psycho-dynamically designed and presented event. This research was an effort to explore the nature of these dynamics which manifest themselves from below the surface. Research design, approach and method: Qualitative and descriptive research from a hermeneutic phenomenology paradigm was used. The 15 participants who attended a RIDE event formed a case study. The data from an unstructured interview was content-analysed and interpreted using the systems psychodynamic perspective. The themes were integrated into a research hypothesis. Main findings: Five themes manifested themselves, namely, crossing boundaries, engaging the brave new world, ties that bind, being imprisoned and the struggle. Practical/managerial implications: The research highlighted the importance of understanding unconscious dynamics in the context of diversity in order to inform consultants about diversity management interventions in organisations. Contribution/value-add: The research contributed towards how South African diversity dynamics manifest themselves and how that can be addressed in organisations.

  20. Geochemical evidence for African dust inputs to soils of western Atlantic islands: Barbados, the Bahamas, and Florida

    Science.gov (United States)

    Muhs, D.R.; Budahn, J.R.; Prospero, J.M.; Carey, S.N.

    2007-01-01

    We studied soils on high-purity limestones of Quaternary age on the western Atlantic Ocean islands of Barbados, the Florida Keys, and the Bahamas. Potential soil parent materials in this region, external to the carbonate substrate, include volcanic ash from the island of St. Vincent (near Barbados), volcanic ash from the islands of Dominica and St. Lucia (somewhat farther from Barbados), the fine-grained component of distal loess from the lower Mississippi River Valley, and wind-transported dust from Africa. These four parent materials can be differentiated using trace elements (Sc, Cr, Th, and Zr) and rare earth elements that have minimal mobility in the soil-forming environment. Barbados soils have compositions that indicate a complex derivation. Volcanic ash from the island of St. Vincent appears to have been the most important influence, but African dust is a significant contributor, and even Mississippi River valley loess may be a very minor contributor to Barbados soils. Soils on the Florida Keys and islands in the Bahamas appear to have developed mostly from African dust, but Mississippi River valley loess may be a significant contributor. Our results indicate that inputs of African dust are more important to the genesis of soils on islands in the western Atlantic Ocean than previously supposed. We hypothesize that African dust may also be a major contributor to soils on other islands of the Caribbean and to soils in northern South America, central America, Mexico, and the southeastern United States. Dust inputs to subtropical and tropical soils in this region increase both nutrient-holding capacity and nutrient status and thus may be critical in sustaining vegetation. Copyright 2007 by the American Geophysical Union.

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

    NARCIS (Netherlands)

    De Candia, T.r.; Lee, S.H.; Yang, J.; Browning, B.L.; Gejman, P. V.; Levinson, D. F.; Mowry, B. J.; Hewitt, J.K.; Goddard, M.E.; O'Donovan, M.C.; Purcell, S.M.; Posthuma, D.; Visscher, P. M.; Wray, N.R.; Keller, M. C.

    2013-01-01

    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

  2. Analysis of the genetic diversity of selected East African sweet potato

    African Journals Online (AJOL)

    Aghomotsegin

    Taiwan. Orange. 65. Mugande x New kawogo 2. Uganda. Cream. 66. Bungoma. Uganda .... African countries is still very slow due to financial and technical .... IPGRI, Rome,. Italy and Institute for Genetic Diversity, Ithaca, New York, USA. ISBN:.

  3. Genetic tests for ecological and allopatric speciation in anoles on an island archipelago.

    Science.gov (United States)

    Thorpe, Roger S; Surget-Groba, Yann; Johansson, Helena

    2010-04-29

    From Darwin's study of the Galapagos and Wallace's study of Indonesia, islands have played an important role in evolutionary investigations, and radiations within archipelagos are readily interpreted as supporting the conventional view of allopatric speciation. Even during the ongoing paradigm shift towards other modes of speciation, island radiations, such as the Lesser Antillean anoles, are thought to exemplify this process. Geological and molecular phylogenetic evidence show that, in this archipelago, Martinique anoles provide several examples of secondary contact of island species. Four precursor island species, with up to 8 mybp divergence, met when their islands coalesced to form the current island of Martinique. Moreover, adjacent anole populations also show marked adaptation to distinct habitat zonation, allowing both allopatric and ecological speciation to be tested in this system. We take advantage of this opportunity of replicated island coalescence and independent ecological adaptation to carry out an extensive population genetic study of hypervariable neutral nuclear markers to show that even after these very substantial periods of spatial isolation these putative allospecies show less reproductive isolation than conspecific populations in adjacent habitats in all three cases of subsequent island coalescence. The degree of genetic interchange shows that while there is always a significant genetic signature of past allopatry, and this may be quite strong if the selection regime allows, there is no case of complete allopatric speciation, in spite of the strong primae facie case for it. Importantly there is greater genetic isolation across the xeric/rainforest ecotone than is associated with any secondary contact. This rejects the development of reproductive isolation in allopatric divergence, but supports the potential for ecological speciation, even though full speciation has not been achieved in this case. It also explains the paucity of anole species

  4. Genetic affinities between the Yami tribe people of Orchid Island and the Philippine Islanders of the Batanes archipelago

    Science.gov (United States)

    2011-01-01

    Background Yami and Ivatan islanders are Austronesian speakers from Orchid Island and the Batanes archipelago that are located between Taiwan and the Philippines. The paternal genealogies of the Yami tribe from 1962 monograph of Wei and Liu were compared with our dataset of non-recombining Y (NRY) chromosomes from the corresponding families. Then mitochondrial DNA polymorphism was also analyzed to determine the matrilineal relationships between Yami, Ivatan, and other East Asian populations. Results The family relationships inferred from the NRY Phylogeny suggested a low number of paternal founders and agreed with the genealogy of Wei and Liu (P Philippine people was closer than that between Yami and Ivatan, suggesting that the Orchid islanders were colonized separately by their nearest neighbors and bred in isolation. However a northward gene flow to Orchid Island from the Philippines was suspected as Yami and Ivatan peoples both speak Western Malayo-Polynesian languages which are not spoken in Taiwan. Actually, only very little gene flow was observed between Yami and Ivatan or between Yami and the Philippines as indicated by the sharing of mtDNA haplogroup B4a1a4 and one O1a1* Y-STR lineage. Conclusions The NRY and mtDNA genetic information among Yami tribe peoples fitted well the patrilocal society model proposed by Wei and Liu. In this proposal, there were likely few genetic exchanges among Yami and the Philippine people. Trading activities may have contributed to the diffusion of Malayo-Polynesian languages among them. Finally, artifacts dating 4,000 YBP, found on Orchid Island and indicating association with the Out of Taiwan hypothesis might be related to a pioneering stage of settlement, as most dating estimates inferred from DNA variation in our data set ranged between 100-3,000 YBP. PMID:21281460

  5. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Science.gov (United States)

    Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

    2016-01-01

    Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic

  6. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Directory of Open Access Journals (Sweden)

    Shiori Yabe

    Full Text Available Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS, which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the

  7. Genetic consequences of anagenetic speciation in Acer okamotoanum (Sapindaceae) on Ullung Island, Korea.

    Science.gov (United States)

    Takayama, Koji; Sun, Byung-Yun; Stuessy, Tod F

    2012-02-01

    Anagenesis (also known as phyletic speciation) is an important process of speciation in endemic species of oceanic islands. We investigated genetic variation in Acer okamotoanum, an anagenetically derived species endemic to Ullung Island, South Korea, to infer genetic consequences of anagenesis in comparison with other groups that have undergone cladogenesis (and adaptive radiation). We examined genetic variation based on eight polymorphic microsatellite markers from 145 individuals of A. okamotoanum and 134 individuals of its putative progenitor A. mono. We employed standard population genetic analyses, clustering analyses, Bayesian clustering analyses in STRUCTURE and bottleneck analyses. Based on both the Neighbor-Joining tree and Bayesian clustering analyses, clear genetic distinctions were found between the two species. Genetic diversity in terms of allelic richness and heterozygosity shows slightly lower levels in A. okamotoanum in comparison with A. mono. Bayesian clustering analyses showed a relatively high F-value in the cluster of A. okamotoanum, suggesting a strong episode of genetic drift during colonization and speciation. There was no clear evidence of a bottleneck based on allelic frequency distribution and excess of observed heterozygotes, but the M-ratio indicated a historical bottleneck in several populations of A. okamotoanum. No geographical genetic structure within the island was found, and the genetic variation among populations of A. okamotoanum was quite low. We hypothesized that genetic consequences of oceanic-endemic plants derived via anagenesis would be quite different from those derived via cladogenesis. Populations of A. okamotoanum form a cluster and are clearly differentiated from A. mono, which suggests a single origin for the anagenetically derived island endemic. No pattern of geographical differentiation of populations occurs in A. okamotoanum, which supports the concept of initial founder populations diverging through time by

  8. Phylogeography and genetic structure of endemic Acmispon argophyllus and A. dendroideus (Fabaceae) across the California Channel Islands.

    Science.gov (United States)

    Wallace, Lisa E; Wheeler, Gregory L; McGlaughlin, Mitchell E; Bresowar, Gerald; Helenurm, Kaius

    2017-05-01

    Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. DNA sequences were collected from nuclear (ADH) and plastid genomes ( rpL16 , ndhA , psbD-trnT ) from >450 samples on the Channel Islands and California. We estimated population genetic diversity and structure, phylogenetic patterns among populations, and migration rates, and tested for population growth. Populations of northern island A. argophyllus var. niveus are genetically distinct from conspecific populations on southern islands. On the southern islands, A. argophyllus var. argenteus populations on Santa Catalina are phylogenetically distinct from populations of var. argenteus and var. adsurgens on the other southern islands. For A. dendroideus , we found the varieties to be monophyletic. Populations of A. dendroideus var. traskiae on San Clemente are genetically differentiated from other conspecific populations, whereas populations on the northern islands and Santa Catalina show varying degrees of gene flow. Evidence of population growth was found in both species. Oceanic barriers between islands have had a strong influence on population genetic structure in both Acmispon species, although the species have differing phylogeographic patterns. This study provides a contrasting pattern of dispersal on a near island system that does not follow a strict stepping-stone model, commonly found on isolated island systems. © 2017 Botanical Society of America.

  9. Integrating paleoecology and genetics of bird populations in two sky island archipelagos.

    Science.gov (United States)

    McCormack, John E; Bowen, Bonnie S; Smith, Thomas B

    2008-06-27

    Genetic tests of paleoecological hypotheses have been rare, partly because recent genetic divergence is difficult to detect and time. According to fossil plant data, continuous woodland in the southwestern USA and northern Mexico became fragmented during the last 10,000 years, as warming caused cool-adapted species to retreat to high elevations. Most genetic studies of resulting 'sky islands' have either failed to detect recent divergence or have found discordant evidence for ancient divergence. We test this paleoecological hypothesis for the region with intraspecific mitochondrial DNA and microsatellite data from sky-island populations of a sedentary bird, the Mexican jay (Aphelocoma ultramarina). We predicted that populations on different sky islands would share common, ancestral alleles that existed during the last glaciation, but that populations on each sky island, owing to their isolation, would contain unique variants of postglacial origin. We also predicted that divergence times estimated from corrected genetic distance and a coalescence model would post-date the last glacial maximum. Our results provide multiple independent lines of support for postglacial divergence, with the predicted pattern of shared and unique mitochondrial DNA haplotypes appearing in two independent sky-island archipelagos, and most estimates of divergence time based on corrected genetic distance post-dating the last glacial maximum. Likewise, an isolation model based on multilocus gene coalescence indicated postglacial divergence of five pairs of sky islands. In contrast to their similar recent histories, the two archipelagos had dissimilar historical patterns in that sky islands in Arizona showed evidence for older divergence, suggesting different responses to the last glaciation. This study is one of the first to provide explicit support from genetic data for a postglacial divergence scenario predicted by one of the best paleoecological records in the world. Our results

  10. African American Women’s Limited Knowledge and Experiences with Genetic Counseling for Hereditary Breast Cancer

    Science.gov (United States)

    Sheppard, Vanessa B.; Graves, Kristi D.; Christopher, Juleen; Hurtado-de-Mendoza, Alejandra; Talley, Costellia; Williams, Karen Patricia

    2014-01-01

    Genetic counseling and testing for hereditary breast cancer have the potential benefit of early detection and early interventions in African American women. However, African American women have low use of these services compared to White women. We conducted two focus groups with African American women diagnosed with breast cancer (affected group, n=13) and women with at least one first-degree relative with breast/ovarian cancer (unaffected group, n= 8). A content analysis approach was employed to analyze interview data. Breast cancer survivors had more knowledge about genetic counseling and testing than participants who were unaffected with cancer. However, knowledge about genetic counseling was limited in both groups. Barriers to pursuing genetic counseling and testing included poor understanding of the genetic counseling and testing process, fear of carrying the mutation, concerns about discrimination, and cost. Motivators to participate in genetic counseling and testing included desire to help family members, insurance coverage, and potential of benefiting the larger African American community. Education efforts are needed to increase genetic counseling and testing awareness in the African American community. PMID:24186304

  11. African American women's limited knowledge and experiences with genetic counseling for hereditary breast cancer.

    Science.gov (United States)

    Sheppard, Vanessa B; Graves, Kristi D; Christopher, Juleen; Hurtado-de-Mendoza, Alejandra; Talley, Costellia; Williams, Karen Patricia

    2014-06-01

    Genetic counseling and testing for hereditary breast cancer have the potential benefit of early detection and early interventions in African American women. However, African American women have low use of these services compared to White women. We conducted two focus groups with African American women diagnosed with breast cancer (affected group, n = 13) and women with at least one first-degree relative with breast/ovarian cancer (unaffected group, n = 8). A content analysis approach was employed to analyze interview data. Breast cancer survivors had more knowledge about genetic counseling and testing than participants who were unaffected with cancer. However, knowledge about genetic counseling was limited in both groups. Barriers to pursuing genetic counseling and testing included poor understanding of the genetic counseling and testing process, fear of carrying the mutation, concerns about discrimination, and cost. Motivators to participate in genetic counseling and testing included desire to help family members, insurance coverage, and potential of benefiting the larger African American community. Education efforts are needed to increase genetic counseling and testing awareness in the African American community.

  12. Genetics, geography, and culture: the population of S. Pietro Island (Sardinia, Italy).

    Science.gov (United States)

    Vona, G; Calò, C M; Lucia, G; Mameli, G E; Succa, V; Esteban, E; Moral, P

    1996-08-01

    An interesting aspect of the island of Sardinia (Italy) is the wide range of genetic variability within the island itself. The variability is widened by the presence of some populations of different ethnic origin who speak a language other than Sardinian. This work deals with the study of the genetic structure of the Carloforte population which inhabits the tiny island of S. Pietro 4 km off the southwest coast of Sardinia. S. Pietro was first populated in 1738 by emigrants coming from the island of Tabarka (Tunisia) who spoke an archaic form of the Ligurian dialect. Data on genetic polymorphisms in the Carloforte population are presented and discussed in relation to some Sardinian and Italian populations. Data on demographic and matrimonial structure are also presented. The genetic analyses show the Carloforte population as being clearly separated from both Sardinians and continental Italians. The isolation of Carloforte, highlighted by language diversity, endogamy, and consanguinity levels and marriage area, supports the idea of genetic diversity linked to cultural peculiarity.

  13. A hybrid niched-island genetic algorithm applied to a nuclear core optimization problem

    International Nuclear Information System (INIS)

    Pereira, Claudio M.N.A.

    2005-01-01

    Diversity maintenance is a key-feature in most genetic-based optimization processes. The quest for such characteristic, has been motivating improvements in the original genetic algorithm (GA). The use of multiple populations (called islands) has demonstrating to increase diversity, delaying the genetic drift. Island Genetic Algorithms (IGA) lead to better results, however, the drift is only delayed, but not avoided. An important advantage of this approach is the simplicity and efficiency for parallel processing. Diversity can also be improved by the use of niching techniques. Niched Genetic Algorithms (NGA) are able to avoid the genetic drift, by containing evolution in niches of a single-population GA, however computational cost is increased. In this work it is investigated the use of a hybrid Niched-Island Genetic Algorithm (NIGA) in a nuclear core optimization problem found in literature. Computational experiments demonstrate that it is possible to take advantage of both, performance enhancement due to the parallelism and drift avoidance due to the use of niches. Comparative results shown that the proposed NIGA demonstrated to be more efficient and robust than an IGA and a NGA for solving the proposed optimization problem. (author)

  14. Introduction to the Arizona Sky Island Arthropod Project (ASAP): Systematics, biogeography, ecology, and population genetics of arthropods of the Madrean Sky Islands

    Science.gov (United States)

    Wendy Moore; Wallace M. Meyer; Jeffrey A. Eble; Kimberly Franklin; John F. Wiens; Richard C. Brusca

    2013-01-01

    The Arizona Sky Island Arthropod Project (ASAP) is a new multi-disciplinary research program at the University of Arizona that combines systematics, biogeography, ecology, and population genetics to study origins and patterns of arthropod diversity along elevation gradients and among mountain ranges in the Madrean Sky Island Region. Arthropods represent taxonomically...

  15. Genetic diversity of a clonal angiosperm near its range limit: The case of Cymodocea nodosa at the Canary Islands

    OpenAIRE

    Alberto, Filipe; Arnaud-Haond, Sophie; Duarte, Carlos M.; Serrao, Ester Álvares

    2006-01-01

    The seagrass Cymodocea nodosa forms a unique community in the Canary Islands, where it is classified as an endangered species. Biogeographic theory predicts that clonal species on islands near their distributional limits might show lower proportions of sexual (versus clonal) reproduction, lower genetic diversity, and higher differentiation. We addressed these hypotheses by comparing the genetic structure of C. nodosa from 10 meadows in the 4 main Canary Islands with 2 Iberian sites (Atlantic ...

  16. Genetic ancestry-smoking interactions and lung function in African Americans: a cohort study.

    Directory of Open Access Journals (Sweden)

    Melinda C Aldrich

    Full Text Available BACKGROUND: Smoking tobacco reduces lung function. African Americans have both lower lung function and decreased metabolism of tobacco smoke compared to European Americans. African ancestry is also associated with lower pulmonary function in African Americans. We aimed to determine whether African ancestry modifies the association between smoking and lung function and its rate of decline in African Americans. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated a prospective ongoing cohort of 1,281 African Americans participating in the Health, Aging, and Body Composition (Health ABC Study initiated in 1997. We also examined an ongoing prospective cohort initiated in 1985 of 1,223 African Americans in the Coronary Artery Disease in Young Adults (CARDIA Study. Pulmonary function and tobacco smoking exposure were measured at baseline and repeatedly over the follow-up period. Individual genetic ancestry proportions were estimated using ancestry informative markers selected to distinguish European and West African ancestry. African Americans with a high proportion of African ancestry had lower baseline forced expiratory volume in one second (FEV₁ per pack-year of smoking (-5.7 ml FEV₁/ smoking pack-year compared with smokers with lower African ancestry (-4.6 ml in FEV₁/ smoking pack-year (interaction P value  = 0.17. Longitudinal analyses revealed a suggestive interaction between smoking, and African ancestry on the rate of FEV(1 decline in Health ABC and independently replicated in CARDIA. CONCLUSIONS/SIGNIFICANCE: African American individuals with a high proportion of African ancestry are at greater risk for losing lung function while smoking.

  17. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

    Science.gov (United States)

    FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

    2016-01-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

  18. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

    Science.gov (United States)

    Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

    2016-05-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

  19. Effect of Genetic African Ancestry on eGFR and Kidney Disease

    Science.gov (United States)

    Nadkarni, Girish N.; Belbin, Gillian; Lotay, Vaneet; Wyatt, Christina; Gottesman, Omri; Bottinger, Erwin P.; Kenny, Eimear E.; Peter, Inga

    2015-01-01

    Self-reported ancestry, genetically determined ancestry, and APOL1 polymorphisms are associated with variation in kidney function and related disease risk, but the relative importance of these factors remains unclear. We estimated the global proportion of African ancestry for 9048 individuals at Mount Sinai Medical Center in Manhattan (3189 African Americans, 1721 European Americans, and 4138 Hispanic/Latino Americans by self-report) using genome-wide genotype data. CKD-EPI eGFR and genotypes of three APOL1 coding variants were available. In admixed African Americans and Hispanic/Latino Americans, serum creatinine values increased as African ancestry increased (per 10% increase in African ancestry, creatinine values increased 1% in African Americans and 0.9% in Hispanic/Latino Americans; P≤1x10−7). eGFR was likewise significantly associated with African genetic ancestry in both populations. In contrast, APOL1 risk haplotypes were significantly associated with CKD, eGFRblack on the basis of ≥50% African ancestry resulted in higher eGFR for 14.7% of Hispanic/Latino Americans and lower eGFR for 4.1% of African Americans, affecting CKD staging in 4.3% and 1% of participants, respectively. Reclassified individuals had electrolyte values consistent with their newly assigned CKD stage. In summary, proportion of African ancestry was significantly associated with normal-range creatinine and eGFR, whereas APOL1 risk haplotypes drove the associations with CKD. Recalculation of eGFR on the basis of genetic ancestry affected CKD staging and warrants additional investigation. PMID:25349204

  20. Grandmothers as gems of genetic wisdom: exploring South African traditional beliefs about the causes of childhood genetic disorders.

    Science.gov (United States)

    Penn, Claire; Watermeyer, Jennifer; MacDonald, Carol; Moabelo, Colleen

    2010-02-01

    With its diverse cultural and linguistic profile, South Africa provides a unique context to explore contextual influences on the process of genetic counseling. Prior research suggests intergenerational differences regarding models of causation which influence treatment-seeking paths. This pilot study therefore aimed to explore South African traditional beliefs regarding common childhood genetic disorders. Three focus groups were conducted with fifteen grandmothers from different cultural backgrounds in an urban community. Questions pertained to the role of the grandmother, traditional beliefs regarding causes of genetic disorders, explanations of heredity, and prevention and management of genetic disorders. Results indicate a variety of cultural explanations for causes of childhood genetic disorders. These causes can be classified into categories related to lifestyle, behavior, social issues, culture, religion, genetic, and familial causes. Prevention and treatment issues are also highlighted. These findings have implications for genetic counseling practice, which needs to include a greater focus on cultural issues.

  1. Directed genetic modification of African horse sickness virus by reverse genetics

    Directory of Open Access Journals (Sweden)

    Elaine Vermaak

    2015-07-01

    Full Text Available African horse sickness virus (AHSV, a member of the Orbivirus genus in the family Reoviridae, is an arthropod-transmitted pathogen that causes a devastating disease in horses with a mortality rate greater than 90%. Fundamental research on AHSV and the development of safe, efficacious vaccines could benefit greatly from an uncomplicated genetic modification method to generate recombinant AHSV. We demonstrate that infectious AHSV can be recovered by transfection of permissive mammalian cells with transcripts derived in vitro from purified AHSV core particles. These findings were expanded to establish a genetic modification system for AHSV that is based on transfection of the cells with a mixture of purified core transcripts and a synthetic T7 transcript. This approach was applied successfully to recover a directed cross-serotype reassortant AHSV and to introduce a marker sequence into the viral genome. The ability to manipulate the AHSV genome and engineer specific mutants will increase understanding of AHSV replication and pathogenicity, as well as provide a tool for generating designer vaccine strains.

  2. Restricted genetic variation in populations of Achatina (Lissachatina) fulica outside of East Africa and the Indian Ocean Islands points to the Indian Ocean Islands as the earliest known common source.

    Science.gov (United States)

    Fontanilla, Ian Kendrich C; Sta Maria, Inna Mikaella P; Garcia, James Rainier M; Ghate, Hemant; Naggs, Fred; Wade, Christopher M

    2014-01-01

    The Giant African Land Snail, Achatina ( =  Lissachatina) fulica Bowdich, 1822, is a tropical crop pest species with a widespread distribution across East Africa, the Indian subcontinent, Southeast Asia, the Pacific, the Caribbean, and North and South America. Its current distribution is attributed primarily to the introduction of the snail to new areas by Man within the last 200 years. This study determined the extent of genetic diversity in global A. fulica populations using the mitochondrial 16S ribosomal RNA gene. A total of 560 individuals were evaluated from 39 global populations obtained from 26 territories. Results reveal 18 distinct A. fulica haplotypes; 14 are found in East Africa and the Indian Ocean islands, but only two haplotypes from the Indian Ocean islands emerged from this region, the C haplotype, now distributed across the tropics, and the D haplotype in Ecuador and Bolivia. Haplotype E from the Philippines, F from New Caledonia and Barbados, O from India and Q from Ecuador are variants of the emergent C haplotype. For the non-native populations, the lack of genetic variation points to founder effects due to the lack of multiple introductions from the native range. Our current data could only point with certainty to the Indian Ocean islands as the earliest known common source of A. fulica across the globe, which necessitates further sampling in East Africa to determine the source populations of the emergent haplotypes.

  3. Restricted genetic variation in populations of Achatina (Lissachatina fulica outside of East Africa and the Indian Ocean Islands points to the Indian Ocean Islands as the earliest known common source.

    Directory of Open Access Journals (Sweden)

    Ian Kendrich C Fontanilla

    Full Text Available The Giant African Land Snail, Achatina ( =  Lissachatina fulica Bowdich, 1822, is a tropical crop pest species with a widespread distribution across East Africa, the Indian subcontinent, Southeast Asia, the Pacific, the Caribbean, and North and South America. Its current distribution is attributed primarily to the introduction of the snail to new areas by Man within the last 200 years. This study determined the extent of genetic diversity in global A. fulica populations using the mitochondrial 16S ribosomal RNA gene. A total of 560 individuals were evaluated from 39 global populations obtained from 26 territories. Results reveal 18 distinct A. fulica haplotypes; 14 are found in East Africa and the Indian Ocean islands, but only two haplotypes from the Indian Ocean islands emerged from this region, the C haplotype, now distributed across the tropics, and the D haplotype in Ecuador and Bolivia. Haplotype E from the Philippines, F from New Caledonia and Barbados, O from India and Q from Ecuador are variants of the emergent C haplotype. For the non-native populations, the lack of genetic variation points to founder effects due to the lack of multiple introductions from the native range. Our current data could only point with certainty to the Indian Ocean islands as the earliest known common source of A. fulica across the globe, which necessitates further sampling in East Africa to determine the source populations of the emergent haplotypes.

  4. Genetic differentiation of the Kittlitz's Murrelet Brachyramphus brevirostris in the Aleutian Islands and Gulf of Alaska

    Science.gov (United States)

    Birt, T.P.; Mackinnon, D.; Piatt, John F.; Friesen, Vicki L.

    2011-01-01

    Information about the distribution of genetic variation within and among local populations of the Kittlitz's Murrelet Brachyramphus brevirostris is needed for effective conservation of this rare and declining species. We compared variation in a 429 base pair fragment of the mitochondrial control region and 11 microsatellite loci among 53 Kittlitz's Murrelets from three sites in the western Aleutian Islands (Attu Island) and Gulf of Alaska (Glacier Bay and Kachemak Bay). We found that birds in these two regions differ genetically in three assessments: (1) global and pairwise indices of genetic differentiation were significantly greater than zero, (2) mitochondrial haplotypes differed by a minimum of nine substitutions, and (3) molecular assignments indicated little gene flow between regions. The data suggest that birds in these regions have been genetically isolated for an extended period. We conclude that Kittlitz's Murrelets from Attu Island and from the Gulf of Alaska represent separate evolutionarily significant units, and should be treated as such for conservation. Genetic data for Kittlitz's Murrelets from the remainder of the breeding range are urgently needed.

  5. Molecular genetic variation in the African wild rice Oryza ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-05-16

    May 16, 2008 ... Eastern Coasts in Kenya, the South West and North East of Zambia .... 22a - Mosaic of dry deciduous forest and secondary grassland (a) Zambezian .... mopane, a woodland tree species. ..... Island Press, Washington D.C..

  6. North African genetic variation of cytochrome and sulfotransferase ...

    African Journals Online (AJOL)

    in these genes have shown relevant ethnic differences among Sub-Saharan .... This cytochrome catalyzes a big amount of oxidative reactions of substances like ... with samples of European and African origin (because of the scarce data ...

  7. Ethical, legal and social issues of genetic studies with African immigrants as research subjects.

    Science.gov (United States)

    Gong, Gordon; Kosoko-Lasaki, Sade; Haynatzki, Gleb; Cook, Cynthia; O'Brien, Richard L; Houtz, Lynne E

    2008-09-01

    There is growing interest in exploring gene-environment interactions in the etiology of diseases in immigrants from sub-Saharan Africa. Our experience working with the Sudanese immigrant population in Omaha, NE, makes clear the pressing need for geneticists and federal and local funding agencies to address the ethical, legal and social implications of genetic research with such vulnerable populations. Our work raises several questions. How does one design research with African immigrant participants to assure it is ethical? Many immigrants may not understand the purposes, risks and benefits involved in research because of low literacy rates, one of the results of civil wars, or concepts of biologic science foreign to their cultures. Is it possible to obtain truly informed consent? Do African immigrants perceive genetic research using them as subjects as racist? Is genetic research on minorities "biopiracy" or "bio-colonialism?" In our experience, some Sudanese immigrants have challenged the legality and ethics of genetic studies with profit-making as an end. We have concluded that it is essential to educate African immigrant or any other non-English-speaking immigrant participants in research using lay language and graphic illustrations before obtaining consent. Cultural proficiency is important in gaining the trust of African immigrants; profit-sharing may encourage their participation in genetic research to benefit all; involvement of African immigrant community leaders in planning, delivery and evaluation using the community-based participatory research approach will facilitate healthcare promotion, health literacy education, as well as genetic research. It is crucial to address the ethical, legal and social implications of genetic studies with African immigrants as research subjects.

  8. Wolves Recolonizing Islands: Genetic Consequences and Implications for Conservation and Management.

    Directory of Open Access Journals (Sweden)

    Liivi Plumer

    Full Text Available After a long and deliberate persecution, the grey wolf (Canis lupus is slowly recolonizing its former areas in Europe, and the genetic consequences of this process are of particular interest. Wolves, though present in mainland Estonia for a long time, have only recently started to recolonize the country's two largest islands, Saaremaa and Hiiumaa. The main objective of this study was to analyse wolf population structure and processes in Estonia, with particular attention to the recolonization of islands. Fifteen microsatellite loci were genotyped for 185 individuals across Estonia. As a methodological novelty, all putative wolf-dog hybrids were identified and removed (n = 17 from the dataset beforehand to avoid interference of dog alleles in wolf population analysis. After the preliminary filtering, our final dataset comprised of 168 "pure" wolves. We recommend using hybrid-removal step as a standard precautionary procedure not only for wolf population studies, but also for other taxa prone to hybridization. STRUCTURE indicated four genetic groups in Estonia. Spatially explicit DResD analysis identified two areas, one of them on Saaremaa island and the other in southwestern Estonia, where neighbouring individuals were genetically more similar than expected from an isolation-by-distance null model. Three blending areas and two contrasting transition zones were identified in central Estonia, where the sampled individuals exhibited strong local differentiation over relatively short distance. Wolves on the largest Estonian islands are part of human-wildlife conflict due to livestock depredation. Negative public attitude, especially on Saaremaa where sheep herding is widespread, poses a significant threat for island wolves. To maintain the long-term viability of the wolf population on Estonian islands, not only wolf hunting quota should be targeted with extreme care, but effective measures should be applied to avoid inbreeding and minimize conflicts

  9. Alpha-thalassemia genetic testing: an important anemia diagnostic tool in patients of African heritage.

    Science.gov (United States)

    Dasanu, Constantin A

    2010-01-01

    Inherited alpha-thalassemia genotypes have been shown to have a rather high prevalence in some patient populations of African heritage. These genotypes lead to mild anemia with microcytic indices and a normal hemoglobin electrophoresis. In our outpatient department, we analyzed 54 consecutive patients of African descent with longstanding microcytic anemia, but no evidence of iron deficiency. We detected alpha-thalassemia gene deletions in 94 percent of these patients. Alpha-thalassemia genetic testing appears cost-effective in an otherwise unexplained, longstanding microcytic anemia in patients of African origin.

  10. Polymorphic microsatellite markers for genetic studies of African ...

    African Journals Online (AJOL)

    Administrator

    2011-09-26

    Sep 26, 2011 ... Many wild animal species lack informative genetic markers for analysing genetic variation and ... which act as important buffer zones between human and wildlife. ..... amplification tests of ungulate primers in the endangered.

  11. Rabbit defensin (NP-1) genetic engineering of plant | Ting | African ...

    African Journals Online (AJOL)

    Rabbit defensin (NP-1) genetic engineering of plant. ... Log in or Register to get access to full text downloads. ... defensin genetic engineering of plant in recent years, and also focuses on the existing problems and new strategies in this area.

  12. Genetic structure of drone congregation areas of Africanized honeybees in southern Brazil

    Directory of Open Access Journals (Sweden)

    Thais Collet

    2009-01-01

    Full Text Available As yet, certain aspects of the Africanization process are not well understood, for example, the reproductive behavior of African and European honeybees and how the first Africanized swarms were formed and spread. Drone congregation areas (DCAs are the ideal place to study honeybee reproduction under natural conditions since hundreds of drones from various colonies gather together in the same geographical area for mating. In the present study, we assessed the genetic structure of seven drone congregations and four commercial European-derived and Africanized apiaries in southern Brazil, employing seven microsatellite loci for this purpose. We also estimated the number of mother-colonies that drones of a specific DCA originated from. Pairwise comparison failed to reveal any population sub-structuring among the DCAs, thus indicating low mutual genetic differentiation. We also observed high genetic similarity between colonies of commercial apiaries and DCAs, besides a slight contribution from a European-derived apiary to a DCA formed nearby. Africanized DCAs seem to have a somewhat different genetic structure when compared to the European.

  13. Genetic structure of drone congregation areas of Africanized honeybees in southern Brazil.

    Science.gov (United States)

    Collet, Thais; Cristino, Alexandre Santos; Quiroga, Carlos Fernando Prada; Soares, Ademilson Espencer Egea; Del Lama, Marco Antônio

    2009-10-01

    As yet, certain aspects of the Africanization process are not well understood, for example, the reproductive behavior of African and European honeybees and how the first Africanized swarms were formed and spread. Drone congregation areas (DCAs) are the ideal place to study honeybee reproduction under natural conditions since hundreds of drones from various colonies gather together in the same geographical area for mating. In the present study, we assessed the genetic structure of seven drone congregations and four commercial European-derived and Africanized apiaries in southern Brazil, employing seven microsatellite loci for this purpose. We also estimated the number of mother-colonies that drones of a specific DCA originated from. Pairwise comparison failed to reveal any population sub-structuring among the DCAs, thus indicating low mutual genetic differentiation. We also observed high genetic similarity between colonies of commercial apiaries and DCAs, besides a slight contribution from a European-derived apiary to a DCA formed nearby. Africanized DCAs seem to have a somewhat different genetic structure when compared to the European.

  14. Genetic transformation of forest trees | Diouf | African Journal of ...

    African Journals Online (AJOL)

    In this review, the recent progress on genetic transformation of forest trees were discussed. Its described also, different applications of genetic engineering for improving forest trees or understanding the mechanisms governing genes expression in woody plants. Key words: Genetic transformation, transgenic forest trees, ...

  15. Community leaders' perspectives on engaging African Americans in biobanks and other human genetics initiatives.

    Science.gov (United States)

    Buseh, Aaron G; Stevens, Patricia E; Millon-Underwood, Sandra; Townsend, Leolia; Kelber, Sheryl T

    2013-10-01

    There is limited information about what African Americans think about biobanks and the ethical questions surrounding them. Likewise, there is a gap in capacity to successfully enroll African Americans as biobank donors. The purposes of this community-based participatory study were to: (a) explore African Americans' perspectives on genetics/genomic research, (b) understand facilitators and barriers to participation in such studies, and (c) enlist their ideas about how to attract and sustain engagement of African Americans in genetics initiatives. As the first phase in a mixed methods study, we conducted four focus groups with 21 African American community leaders in one US Midwest city. The sample consisted of executive directors of community organizations and prominent community activists. Data were analyzed thematically. Skepticism about biomedical research and lack of trust characterized discussions about biomedical research and biobanks. The Tuskegee Untreated Syphilis Study and the Henrietta Lacks case influenced their desire to protect their community from harm and exploitation. Connections between genetics and family history made genetics/genomics research personal, pitting intrusion into private affairs against solutions. Participants also expressed concerns about ethical issues involved in genomics research, calling attention to how research had previously been conducted in their community. Participants hoped personalized medicine might bring health benefits to their people and proposed African American communities have a "seat at the table." They called for basic respect, authentic collaboration, bidirectional education, transparency and prerogative, and meaningful benefits and remuneration. Key to building trust and overcoming African Americans' trepidation and resistance to participation in biobanks are early and persistent engagement with the community, partnerships with community stakeholders to map research priorities, ethical conduct of research, and

  16. The African Lupus Genetics Network (ALUGEN) registry: standardized, prospective follow-up studies in African patients with systemic lupus erythematosus.

    Science.gov (United States)

    Hodkinson, B; Mapiye, D; Jayne, D; Kalla, A; Tiffin, N; Okpechi, I

    2016-03-01

    The prevalence and severity of systemic lupus erythematosus (SLE) differs between ethnic groups and geographical regions. Although initially reported as rare, there is growing evidence that SLE is prevalent and runs a severe course in Africa. There is a paucity of prospective studies on African SLE patients. The African Lupus Genetics Network (ALUGEN) is a multicentred framework seeking to prospectively assess outcomes in SLE patients in Africa. Outcomes measured will be death, hospital admission, disease activity flares, and SLE-related damage. We will explore predictors for these outcomes including clinical, serological, socio-demographic, therapeutic and genetic factors. Further, we will investigate comorbidities and health-related quality of life amongst these patients. Data of patients recently (≤ 5 yrs) diagnosed with SLE will be collected at baseline and annual follow-up visits, and captured electronically. The ALUGEN project will facilitate standardized data capture for SLE cases in Africa, allowing participating centres to develop their own SLE registries, and enabling collaboration to enrich our understanding of inter-ethnic and regional variations in disease expression. Comprehensive, high-quality multi-ethnic data on African SLE patients will expand knowledge of the disease and inform clinical practice, in addition to augmenting research capacity and networking links and providing a platform for future biomarker and interventional studies. © The Author(s) 2015.

  17. Distribution and genetic variation of hymenolepidid cestodes in murid rodents on the Canary Islands (Spain).

    Science.gov (United States)

    Foronda, Pilar; López-González, Mercedes; Hernández, Mariano; Haukisalmi, Voitto; Feliu, Carlos

    2011-09-26

    In the Canary Islands there are no previous data about tapeworms (Cestoda) of rodents. In order to identify the hymenolepidid species present in these hosts, a survey of 1,017 murine (349 Rattus rattus, 13 Rattus norvegicus and 655 Mus musculus domesticus) was carried out in the whole Archipelago. Molecular studies based on nuclear ITS1 and mitochondrial COI loci were performed to confirm the identifications and to analyse the levels of genetic variation and differentiation. Three species of hymenolepidids were identified: Hymenolepis diminuta, Rodentolepis microstoma and Rodentolepis fraterna. Hymenolepis diminuta (in rats) and R. microstoma (in mice) showed a widespread distribution in the Archipelago, and R. fraterna was the least spread species, appearing only on five of the islands. The hymenolepidids found on Fuerteventura, Lanzarote and La Graciosa were restricted to one area. The COI network of H. diminuta showed that the haplotypes from Lanzarote and Fuerteventura are the most distant with respect to the other islands, but clearly related among them. Founder effects and biotic and abiotic factors could have played important role in the presence/absence of the hymenolepidid species in determined locations. The haplotypes from the eastern islands (Fuerteventura and Lanzarote) seem to have shared an ancestral haplotype very distant from the most frequent one that was found in the rest of the islands. Two colonization events or a single event with subsequent isolation and reduced gene flow between western-central and eastern islands, have taken place in the Archipelago. The three tapeworms detected are zoonotic species, and their presence among rodents from this Archipelago suggests a potential health risk to human via environmental contamination in high risk areas. However, the relatively low prevalence of infestations detected and the focal distribution of some of these species on certain islands reduce the general transmission risk to human.

  18. Distribution and genetic variation of hymenolepidid cestodes in murid rodents on the Canary Islands (Spain

    Directory of Open Access Journals (Sweden)

    Feliu Carlos

    2011-09-01

    Full Text Available Abstract Background In the Canary Islands there are no previous data about tapeworms (Cestoda of rodents. In order to identify the hymenolepidid species present in these hosts, a survey of 1,017 murine (349 Rattus rattus, 13 Rattus norvegicus and 655 Mus musculus domesticus was carried out in the whole Archipelago. Molecular studies based on nuclear ITS1 and mitochondrial COI loci were performed to confirm the identifications and to analyse the levels of genetic variation and differentiation. Results Three species of hymenolepidids were identified: Hymenolepis diminuta, Rodentolepis microstoma and Rodentolepis fraterna. Hymenolepis diminuta (in rats and R. microstoma (in mice showed a widespread distribution in the Archipelago, and R. fraterna was the least spread species, appearing only on five of the islands. The hymenolepidids found on Fuerteventura, Lanzarote and La Graciosa were restricted to one area. The COI network of H. diminuta showed that the haplotypes from Lanzarote and Fuerteventura are the most distant with respect to the other islands, but clearly related among them. Conclusions Founder effects and biotic and abiotic factors could have played important role in the presence/absence of the hymenolepidid species in determined locations. The haplotypes from the eastern islands (Fuerteventura and Lanzarote seem to have shared an ancestral haplotype very distant from the most frequent one that was found in the rest of the islands. Two colonization events or a single event with subsequent isolation and reduced gene flow between western-central and eastern islands, have taken place in the Archipelago. The three tapeworms detected are zoonotic species, and their presence among rodents from this Archipelago suggests a potential health risk to human via environmental contamination in high risk areas. However, the relatively low prevalence of infestations detected and the focal distribution of some of these species on certain islands reduce

  19. Characterization of the genetic variation present in CYP3A4 in three South African populations

    OpenAIRE

    Drögemöller, Britt; Plummer, Marieth; Korkie, Lundi; Agenbag, Gloudi; Dunaiski, Anke; Niehaus, Dana; Koen, Liezl; Gebhardt, Stefan; Schneider, Nicol; Olckers, Antonel; Wright, Galen; Warnich, Louise

    2013-01-01

    TThe CYP3A4 enzyme is the most abundant human cytochrome P450 and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study wa...

  20. Genetic diversity of sea-island cotton (Gossypium barbadense) revealed by mapped SSRs.

    Science.gov (United States)

    Wang, X Q; Feng, C H; Lin, Z X; Zhang, X L

    2011-12-08

    In order to evaluate the genetic diversity of sea-island cotton (Gossypium barbadense), 237 commonly mapped SSR markers covering the cotton genome were used to genotype 56 sea-island cotton accessions. A total of 218 polymorphic primer pairs (91.98%) amplified 361 loci, with a mean of 1.66 loci. Polymorphism information content values of the SSR primers ranged from 0.035 to 0.862, with a mean of 0.320. The highest mean polymorphism information content value for the SSR motifs was from a compound motif (0.402), and for the chromosomes it was Chr10 (0.589); the highest ratio of polymorphic primers in Xinjiang accessions was from Chr21 (83.33%). Genetic diversity was high in Xinjiang accessions. AMOVA showed that variation was 8 and 92% among populations and within populations, respectively. The 56 sea-island accessions were divided into three groups in the UPGMA dendrogram: Xinhai5 was in the first group; accessions from Xinjiang, except the five main ones, were in the second group, and the other 34 accessions were in the third group. Accessions from the former Soviet Union and Xinjiang main accessions were closely related. Both PCA and UPGMA confirmed that Xinhai5 was distinct from the other accessions, and accessions from Xinjiang were in an independent group. Given the differences between principal components analysis and UPGMA results, it is necessary to combine molecular markers and pedigree information so that genetic diversity can be objectively analyzed.

  1. Will an "island" population of voles be recolonized if eradicated? Insights from molecular genetic analyses

    Science.gov (United States)

    Miller, Mark P.; Haig, Susan M.; Ledig, David B.; Vander Heyden, Madeleine F.; Bennett, Gregory

    2011-01-01

    We performed genetic analyses of Microtus longicaudus populations within the Crook Point Unit of the Oregon Islands National Wildlife Refuge. A M. longicaudus population at Saddle Rock (located approx. 65 m off-shore from the Crook Point mainland) is suspected to be partially responsible for declines of a Leach's storm-petrel colony at this important nesting site. Using Amplified Fragment Length Polymorphism markers and mitochondrial DNA, we illustrate that Saddle Rock and Crook Point function as separate island and mainland populations despite their close proximity. In addition to genetic structure, we also observed reduced genetic diversity at Saddle Rock, suggesting that little individual movement occurs between populations. If local resource managers decide to perform an eradication at Saddle Rock, we conclude that immediate recolonization of the island by M. longicaudus would be unlikely. Because M. longicaudus is native to Oregon, we also consider the degree with which the differentiation of Saddle Rock signifies the presence of a unique entity that warrants conservation rather than eradication. ?? The Wildlife Society, 2011.

  2. Aedes aegypti on Madeira Island (Portugal): genetic variation of a recently introduced dengue vector.

    Science.gov (United States)

    Seixas, Gonçalo; Salgueiro, Patrícia; Silva, Ana Clara; Campos, Melina; Spenassatto, Carine; Reyes-Lugo, Matías; Novo, Maria Teresa; Ribolla, Paulo Eduardo Martins; Silva Pinto, João Pedro Soares da; Sousa, Carla Alexandra

    2013-01-01

    The increasing population of Aedes aegypti mosquitoes on Madeira Island (Portugal) resulted in the first autochthonous dengue outbreak, which occurred in October 2012. Our study establishes the first genetic evaluation based on the mitochondrial DNA (mtDNA) genes [cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4)] and knockdown resistance (kdr) mutations exploring the colonisation history and the genetic diversity of this insular vector population. We included mosquito populations from Brazil and Venezuela in the analysis as putative geographic sources. The Ae. aegypti population from Madeira showed extremely low mtDNA genetic variability, with a single haplotype for COI and ND4. We also detected the presence of two important kdr mutations and the quasi-fixation of one of these mutations (F1534C). These results are consistent with a unique recent founder event that occurred on the island of Ae. aegypti mosquitoes that carry kdr mutations associated with insecticide resistance. Finally, we also report the presence of the F1534C kdr mutation in the Brazil and Venezuela populations. To our knowledge, this is the first time this mutation has been found in South American Ae. aegypti mosquitoes. Given the present risk of Ae. aegypti re-invading continental Europe from Madeira and the recent dengue outbreaks on the island, this information is important to plan surveillance and control measures.

  3. Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

    Science.gov (United States)

    Diefenbach, Duane R.; Hansen, Leslie A.; Bohling, Justin H.; Miller-Butterworth, Cassandra

    2015-01-01

    In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (Ne) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a

  4. Genetic variability of South African fiscal shrikes ( Lanius collaris ...

    African Journals Online (AJOL)

    Rogers' (1972) mean genetic distance (D) was 0.094, and Nei's (1978) mean unbiased genetic distance was 0.019. A phenogram (unweighted pair group method) and a phylogenetic tree (distance Wagner network), both based on Rogers' (1972) distance, showed some degree of geographical subgrouping. The high ...

  5. Animal models for human genetic diseases | Sharif | African Journal ...

    African Journals Online (AJOL)

    The study of human genetic diseases can be greatly aided by animal models because of their similarity to humans in terms of genetics. In addition to understand diverse aspects of basic biology, model organisms are extensively used in applied research in agriculture, industry, and also in medicine, where they are used to ...

  6. Maintaining genetic stability in a control flock of South African ...

    African Journals Online (AJOL)

    means of whole progeny and replacement groups for the measured characters ... The whole problem of the estimation of genetic change was ... that a genetic control flock is a segregating population in which ... 5,5 years, were divided into five equal groups by stratified ..... A note on tests of significance and optimal ex-.

  7. Phylogeography and conservation genetics of the common wall lizard, Podarcis muralis, on islands at its northern range.

    Directory of Open Access Journals (Sweden)

    Sozos Michaelides

    Full Text Available Populations at range limits are often characterized by lower genetic diversity, increased genetic isolation and differentiation relative to populations at the core of geographical ranges. Furthermore, it is increasingly recognized that populations situated at range limits might be the result of human introductions rather than natural dispersal. It is therefore important to document the origin and genetic diversity of marginal populations to establish conservation priorities. In this study, we investigate the phylogeography and genetic structure of peripheral populations of the common European wall lizard, Podarcis muralis, on Jersey (Channel Islands, UK and in the Chausey archipelago. We sequenced a fragment of the mitochondrial cytochrome b gene in 200 individuals of P. muralis to infer the phylogeography of the island populations using Bayesian approaches. We also genotyped 484 individuals from 21 populations at 10 polymorphic microsatellite loci to evaluate the genetic structure and diversity of island and mainland (Western France populations. We detected four unique haplotypes in the island populations that formed a sub-clade within the Western France clade. There was a significant reduction in genetic diversity (HO, HE and AR of the island populations in relation to the mainland. The small fragmented island populations at the northern range margin of the common wall lizard distribution are most likely native, with genetic differentiation reflecting isolation following sea level increase approximately 7000 BP. Genetic diversity is lower on islands than in marginal populations on the mainland, potentially as a result of early founder effects or long-term isolation. The combination of restriction to specific localities and an inability to expand their range into adjacent suitable locations might make the island populations more vulnerable to extinction.

  8. Genetic polymorphism of CSN1S2 in South African dairy goat ...

    African Journals Online (AJOL)

    The aim of this study was to investigate the polymorphism and genetic variation of CSN1S2 in South African dairy goats, using DNA sequencing technology. Sixty dairy goats (20 Saanes, 20 British Alpine, and 20 Toggenburg) and 20 meat-type goats were sequenced with four primers to distinguish among the seven known ...

  9. Genetic differentiation in Elaeocarpus photiniifolia (Elaeocarpaceae) associated with geographic distribution and habitat variation in the Bonin (Ogasawara) Islands.

    Science.gov (United States)

    Sugai, Kyoko; Setsuko, Suzuki; Nagamitsu, Teruyoshi; Murakami, Noriaki; Kato, Hidetoshi; Yoshimaru, Hiroshi

    2013-11-01

    Gene flow between populations in different environmental conditions can be limited due to divergent natural selection, thus promoting genetic differentiation. Elaeocarpus photiniifolia, an endemic tree species in the Bonin Islands, is distributed in two types of habitats, dry scrubs and mesic forests. We aim to elucidate the genetic differentiation in E. photiniifolia within and between islands and between the habitat types. We investigated genotypes of 639 individuals from 19 populations of E. photiniifolia and its closely-related E. sylvestris at 24 microsatellite loci derived from expressed sequence tags. The data revealed genetic differentiation (1) between E. photiniifolia and E. sylvestris (0.307 ≤ F ST ≤ 0.470), (2) between the E. photiniifolia populations of the Chichijima and Hahajima Island Groups in the Bonin Islands (0.033 ≤ F ST ≤ 0.121) and (3) between E. photiniifolia populations associated with dry scrubs and mesic forests in the Chichijima Island Group (0.005 ≤ F ST ≤ 0.071). Principal coordinate analysis and Bayesian clustering analysis also showed that genetically distinct groups were associated with the habitat types, and isolation by distance was not responsible for the genetic differentiation. These findings suggest that E. photiniifolia is divided into genetically differentiated groups associated with different environmental conditions in the Bonin Islands.

  10. Serological survey of antibodies to Toxoplasma gondii and Coxiella burnetii in rodents in north-western African islands (Canary Islands and Cape Verde).

    Science.gov (United States)

    Foronda, Pilar; Plata-Luis, Josué; del Castillo-Figueruelo, Borja; Fernández-Álvarez, Ángela; Martín-Alonso, Aarón; Feliu, Carlos; Cabral, Marilena D; Valladares, Basilio

    2015-05-29

    Coxiella burnetii and Toxoplasma gondii are intracellular parasites that cause important reproductive disorders in animals and humans worldwide, resulting in high economic losses. The aim of the present study was to analyse the possible role of peridomestic small mammals in the maintenance and transmission of C. burnetii and T. gondii in the north-western African archipelagos of the Canary Islands and Cape Verde, where these species are commonly found affecting humans and farm animals. Between 2009 and 2013, 108 black rats (Rattus rattus) and 77 mice (Mus musculus) were analysed for the presence of Coxiella and Toxoplasma antibodies by enzyme-linked immunosorbent assay (ELISA) and indirect immunofluorescence (IFA), respectively. Our results showed a wide distribution of C. burnetii and T. gondii, except for T. gondii in Cape Verde, in both rodent species. The overall seroprevalence of C. burnetii antibodies was 12.4%; 21.1% for Cape Verde and 10.2% for the Canary Islands. With respect to T. gondii, seropositive rodents were only observed in the Canary Islands, with an overall seroprevalence of 15%. Considering the fact that both pathogens can infect a large range of hosts, including livestock and humans, the results are of public health and veterinary importance and could be used by governmental entities to manage risk factors and to prevent future cases of Q fever and toxoplasmosis.

  11. Limited overwater dispersal and genetic differentiation of the snake-eyed skink (Cryptoblepharus nigropunctatus) in the Oceanic Ogasawara Islands, Japan.

    Science.gov (United States)

    Hayashi, Fumio; Shima, Akina; Horikoshi, Kazuo; Kawakami, Kazuto; Segawa, Ryoko D; Aotsuka, Tadashi; Suzuki, Tadashi

    2009-08-01

    The genetic differentiation and speciation of lizards on oceanic islands may be affected by their rate of overwater dispersal. Cryptoblepharus is one of the most geographically widespread scincid lizards throughout the Indo-Pacific and Australian regions. Cryptoblepharus nigropunctatus is the northernmost species of the genus, dwelling on several small Pacific islands. To examine the colonization history of this lizard, mitochondrial 16S rDNA and D-loop sequences were compared among populations of the Ogasawara Islands consisting of four island groups (the Muko-jima, Chichi-jima, Haha-jima, and Kazan groups), and an isolated island, Minamitori-shima (Marcus Island). These four groups and Minamitori-shima have not been connected to each other because each is surrounded by deep sea (>100 m). DNA analyses showed that the lizard populations on individual islands had each representative haplotypes. The ancestors of C. nigropunctatus probably arrived on the islands from the southern Pacific Ocean via wave dispersal and differentiated to produce the present state. They appear to have dispersed from their origin along two independent pathways: one between Kitaiwo-to (Kazan group) and the Muko-jima and Chichi-jima groups, and the other among the Minamitori-shima, Minamiiwo-to (Kazan group), and Haha-jima groups. Limited long-distance overwater dispersal may be responsible for the genetic structure of the C. nigropunctatus populations on these oceanic islands. However, among the small islands within the same island group, D-loop haplotypes were shared and the local genetic diversity was usually high, suggesting frequent gene flow across the same group of islands.

  12. Patterns of genetic diversity in three plant lineages endemic to the Cape Verde Islands.

    Science.gov (United States)

    Romeiras, Maria M; Monteiro, Filipa; Duarte, M Cristina; Schaefer, Hanno; Carine, Mark

    2015-05-15

    Conservation of plant diversity on islands relies on a good knowledge of the taxonomy, distribution and genetic diversity of species. In recent decades, a combination of morphology- and DNA-based approaches has become the standard for investigating island plant lineages and this has led, in some cases, to the discovery of previously overlooked diversity, including 'cryptic species'. The flora of the Cape Verde archipelago in the North Atlantic is currently thought to comprise ∼740 vascular plant species, 92 of them endemics. Despite the fact that it is considered relatively well known, there has been a 12 % increase in the number of endemics in the last two decades. Relatively few of the Cape Verde plant lineages have been included in genetic studies so far and little is known about the patterns of diversification in the archipelago. Here we present an updated list for the endemic Cape Verde flora and analyse diversity patterns for three endemic plant lineages (Cynanchum, Globularia and Umbilicus) based on one nuclear (ITS) and four plastid DNA regions. In all three lineages, we find genetic variation. In Cynanchum, we find two distinct haplotypes with no clear geographical pattern, possibly reflecting different ploidy levels. In Globularia and Umbilicus, differentiation is evident between populations from northern and southern islands. Isolation and drift resulting from the small and fragmented distributions, coupled with the significant distances separating the northern and southern islands, could explain this pattern. Overall, our study suggests that the diversity in the endemic vascular flora of Cape Verde is higher than previously thought and further work is necessary to characterize the flora. Published by Oxford University Press on behalf of the Annals of Botany Company.

  13. Genetic relationships among West African okra ( Abelmoschus caillei )

    African Journals Online (AJOL)

    Abelmoschus caillei) and 43 Asian genotypes (A. esculentus) were assessed for genetic distinctiveness and relationships using random amplified polymorphic DNA (RAPD). The molecular analysis showed that all the thirteen primers used ...

  14. Molecular Identification and Genetic Diversity of Acropora hyacinthus from Boo and Deer Island, Raja Ampat, West Papua

    Science.gov (United States)

    Wijayanti, DP; Indrayanti, E.; Nuryadi, H.; Dewi, RA; Sabdono, A.

    2018-02-01

    Indonesia lies at the centre of biodiversity for corals. However, the reefs suffered from extensive human exploitation. Marine Protected Areas is thought to be best solution to protect coral reefs ecosystem. Understanding genetic diversity is crucial for effective management of the MPAs, however genetic diversity is rarely been corporate in designing an MPA. Moreover, many MPAs are uneffectively manage due to poor designated and demarcated.Raja Ampat which is located in western tip of West Papua, was designated as a park to mitigatethreatsand protect the valuable marine resources.Scleractinian corals in the genus Acropora are among the most dominant distributed in Raja Ampat waters, including the species of Acroporahyacinthus. The research aimed to analyze genetic diversity and to describe the kinship relationship of Acroporahyacinthus between 2 populations: Boo Island and Deer Island, Raja Ampat. Genetic marker Cytochrome Oxidase I (CO I) of the mitochondrial genome DNA (mtDNA) was used to analyze genetic diversity. Reconstruction of phylogenetic tree and genetic diversity were made by usingsoftware MEGA 5.05 (Moleculer Evolutionary Genetics Analysis). The results of this research indicatecorals A. hyacinthus from Boo Island and Deer Island Raja Ampat are in the low category of genetic diversity and overall had a close genetic relationship of kinship. This is likely due to the small size of the population and few numbers of samples that may not represent the population.

  15. Degree of European Genetic Ancestry is Associated with Serum Vitamin D Levelsin African Americans.

    Science.gov (United States)

    Haddad, Stephen A; Ruiz-Narváez, Edward A; Cozier, Yvette C; Gerlovin, Hanna; Rosenberg, Lynn; Palmer, Julie R

    2018-01-30

    Circulating levels of vitamin D are generally lower in African Americans compared to U.S. whites, and one prior analysis in a small number of African Americans suggested that, within this population, vitamin D levels may be related to the degree of genetic admixture. We assessed the association of percent European ancestry with serum vitamin D levels in 2183 African American women from the Black Women's Health Study in 2013-2015, whose DNA had been genotyped for ancestry informative markers. ADMIXMAP software was used to estimate percent European versus African ancestry in each individual. In linear regression analyses with adjustment for genotype batch, age, body mass index, supplemental vitamin D use, UVB flux in state of residence, and season of blood draw, each 10% increase in European ancestry was associated with a 0.672 ng/mL increase in serum vitamin D concentration (95% confidence interval 0.173, 1.170). The association was statistically significant only among women who were not taking vitamin D supplements (beta coefficient for 10% increase in European ancestry 0.855, 95% confidence interval 0.139, 1.571). Among African Americans, use of vitamin D supplementation may help to reduce vitamin D deficiency due to genetic ancestry. © The Author(s) 2018. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. The first joint congress of the South African Biochemical Society, South African Genetics Society and the South African Society for Microbiology at the University of the Witwatersrand, 29 June-4 July 1986

    International Nuclear Information System (INIS)

    1986-01-01

    The South African Biochemical Society, South African Genetics Society and the South African Society for Microbiology held a joint congress at the University of the Witwatersrand from 29 June - 4 July 1986. The papers delivered cover subjects such as Molecular biology, Genetics, Biochemistry, Medical biochemistry, Physiology, Zoology and Isotope and radiation sciences. Different isotopes are used in labelling studies of enzymes, nutrition, metabolism, viruses, bacteria and other biological assays done in the fields of Biochenmistry, Genetics and Microbiology. This work contains only the abstracts of these papers

  17. Assessment of Genetic Variation Among East African Cercospora ...

    African Journals Online (AJOL)

    Rapid flagement length polymorphism (RFLP) and amplified flagement length polymorphism (AFLP) analyses were used to study genetic diversity of Cercospora zeae-maydis isolates collected from Uganda, Kenya and Rwanda. For comparative purposes, isolates from Zimbabwe and the United States of America (USA) ...

  18. Genetic transformation of moss plant | Jing | African Journal of ...

    African Journals Online (AJOL)

    Thus, in recent times mosses such as Physcomitrella patens, Funaria hygrometrica, Ceratodon purpureus, and Tortula ruralis are being developed for genetic engineering studies. Recently, the finding of efficient homologous recombination of P. patens and yeast and murine cells could be comparable. So, the moss, P.

  19. Huntington\\'s disease: Genetic heterogeneity in black African patients

    African Journals Online (AJOL)

    Objective. Huntington's disease (HD) has been reported to occur rarely in black patients. A new genetic variant– Huntington's disease-like 2 (HDL2) – occurring more frequently in blacks, has recently been described. The absence of an expanded trinucleotide repeat at the chromosome 4 HD locus was previously regarded ...

  20. Risks and benefits of genetically modified foods | Amin | African ...

    African Journals Online (AJOL)

    There are claims that fear towards new technology has been caused by the lack of information and education on the subject to the public. Modern biotechnology and its applications have been receiving the same criticism. Thus, the objective of this study is to analyze the trends and coverage of genetically modified food ...

  1. A critical scientific review on South African governance of genetically ...

    African Journals Online (AJOL)

    Credible governance of genetically modified organisms (GMOs) is essential because of public concerns in South Africa (SA) and internationally. In this preliminary study, the opinions of a number of scientists with experience and/or interest in GMO governance were determined by means of two questionnaires to determine ...

  2. Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus

    Directory of Open Access Journals (Sweden)

    Martin Faye

    2018-04-01

    Full Text Available Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014. Parameters such as genetic distances, N-glycosylation patterns, recombination events, selective pressures, and its codon adaptation to human genes are assessed. Our study is noteworthy for the observation of N-glycosylation and recombination in Bagaza virus and provides insight into its Indian origin from the 13th century. Interestingly, evidence of Bagaza virus codon adaptation to human house-keeping genes is also observed to be higher than those of other flaviviruses well known in human infections. Genetic variations on genome of West African Bagaza virus could play an important role in generating diversity and may promote Bagaza virus adaptation to other vertebrates and become an important threat in human health.

  3. Characterization of the genetic variation present in CYP3A4 in three South African populations

    Directory of Open Access Journals (Sweden)

    Britt Ingrid Drögemöller

    2013-02-01

    Full Text Available TThe CYP3A4 enzyme is the most abundant human cytochrome P450 and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study was to identify genetic variation within CYP3A4 in three South African population groups comprising of 29 Khoisan, 65 Xhosa and 65 Mixed Ancestry individuals. To identify known and novel CYP3A4 variants, 15 individuals were randomly selected from each of the population groups for bi-directional Sanger sequencing of approximately 600 bp of the 5’-upstream region and all thirteen exons including flanking intronic regions. Genetic variants detected were genotyped in the rest of the cohort. In total, 24 SNPs were detected, including CYP3A4*12, CYP3A4*15, and the reportedly functional CYP3A4*1B promoter polymorphism, as well as two novel non-synonymous variants. These putatively functional variants, p.R162W and p.Q200H, were present in two of the three populations and all three populations, respectively, and in silico analysis predicted that the former would damage the protein product. Furthermore, the three populations were shown to exhibit distinct genetic profiles. These results confirm that South African populations show unique patterns of variation in the genes encoding xenobiotic metabolizing enzymes. This research suggests that population-specific genetic profiles for CYP3A4 and other drug metabolizing genes would be essential to make full use of pharmacogenetics in Southern Africa. Further investigation is needed to determine if the identified genetic variants influence CYP3A4 metabolism phenotype in these populations.

  4. Characterization of the genetic variation present in CYP3A4 in three South African populations.

    Science.gov (United States)

    Drögemöller, Britt; Plummer, Marieth; Korkie, Lundi; Agenbag, Gloudi; Dunaiski, Anke; Niehaus, Dana; Koen, Liezl; Gebhardt, Stefan; Schneider, Nicol; Olckers, Antonel; Wright, Galen; Warnich, Louise

    2013-01-01

    The CYP3A4 enzyme is the most abundant human cytochrome P450 (CYP) and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study was to identify genetic variation within CYP3A4 in three South African population groups comprising of 29 Khoisan, 65 Xhosa and 65 Mixed Ancestry (MA) individuals. To identify known and novel CYP3A4 variants, 15 individuals were randomly selected from each of the population groups for bi-directional Sanger sequencing of ~600 bp of the 5'-upstream region and all thirteen exons including flanking intronic regions. Genetic variants detected were genotyped in the rest of the cohort. In total, 24 SNPs were detected, including CYP3A4(*)12, CYP3A4(*)15, and the reportedly functional CYP3A4(*)1B promoter polymorphism, as well as two novel non-synonymous variants. These putatively functional variants, p.R162W and p.Q200H, were present in two of the three populations and all three populations, respectively, and in silico analysis predicted that the former would damage the protein product. Furthermore, the three populations were shown to exhibit distinct genetic profiles. These results confirm that South African populations show unique patterns of variation in the genes encoding xenobiotic metabolizing enzymes. This research suggests that population-specific genetic profiles for CYP3A4 and other drug metabolizing genes would be essential to make full use of pharmacogenetics in Southern Africa. Further investigation is needed to determine if the identified genetic variants influence CYP3A4 metabolism phenotype in these populations.

  5. Current situation, genetic relationship and control measures of infectious bronchitis virus variants circulating in African regions

    Directory of Open Access Journals (Sweden)

    Khadija Khataby

    2016-08-01

    Three S1 gene hypervariable regions were studied and compared to the reference genotypes/serotypes that found emerging in African regions. This comparison was based on phylogenetic trees, nucleotide and amino-acid sequence analysis. It clearly appears that IBV variants reported in Africa, display a low genetic relationship between them and with the majority of the reference strains emerging in neighboring countries, except the case of variants from Libya and Egypt that show a high relatedness. Also the Massachusetts serotypes were the most prevalent co-circulating with both serotypes, Italy02 type in Morocco and Qx-like genotype in South part of the African continent. In order to control the IBV variants in African regions, an efficient vaccination strategy program should be implemented.

  6. Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean.

    Science.gov (United States)

    Davies, S W; Treml, E A; Kenkel, C D; Matz, M V

    2015-01-01

    Understanding how genetic diversity is maintained across patchy marine environments remains a fundamental problem in marine biology. The Coral Triangle, located in the Indo-West Pacific, is the centre of marine biodiversity and has been proposed as an important source of genetic diversity for remote Pacific reefs. Several studies highlight Micronesia, a scattering of hundreds of small islands situated within the North Equatorial Counter Current, as a potentially important migration corridor. To test this hypothesis, we characterized the population genetic structure of two ecologically important congeneric species of reef-building corals across greater Micronesia, from Palau to the Marshall Islands. Genetic divergences between islands followed an isolation-by-distance pattern, with Acropora hyacinthus exhibiting greater genetic divergences than A. digitifera, suggesting different migration capabilities or different effective population sizes for these closely related species. We inferred dispersal distance using a biophysical larval transport model, which explained an additional 15-21% of the observed genetic variation compared to between-island geographical distance alone. For both species, genetic divergence accumulates and genetic diversity diminishes with distance from the Coral Triangle, supporting the hypothesis that Micronesian islands act as important stepping stones connecting the central Pacific with the species-rich Coral Triangle. However, for A. hyacinthus, the species with lower genetic connectivity, immigration from the subequatorial Pacific begins to play a larger role in shaping diversity than input from the Coral Triangle. This work highlights the enormous dispersal potential of broadcast-spawning corals and identifies the biological and physical drivers that influence coral genetic diversity on a regional scale. © 2014 John Wiley & Sons Ltd.

  7. Bio science: genetic genealogy testing and the pursuit of African ancestry.

    Science.gov (United States)

    Nelson, Alondra

    2008-10-01

    This paper considers the extent to which the geneticization of 'race' and ethnicity is the prevailing outcome of genetic testing for genealogical purposes. The decoding of the human genome precipitated a change of paradigms in genetics research, from an emphasis on genetic similarity to a focus on molecular-level differences among individuals and groups. This shift from lumping to splitting spurred ongoing disagreements among scholars about the significance of 'race' and ethnicity in the genetics era. I characterize these divergent perspectives as 'pragmatism' and 'naturalism'. Drawing upon ethnographic fieldwork and interviews, I argue that neither position fully accounts for how understandings of 'race' and ethnicity are being transformed with genetic genealogy testing. While there is some acquiescence to genetic thinking about ancestry, and by implication, 'race', among African-American and black British consumers of genetic genealogy testing, test-takers also adjudicate between sources of genealogical information and from these construct meaningful biographical narratives. Consumers engage in highly situated 'objective' and 'affiliative' self-fashioning, interpreting genetic test results in the context of their 'genealogical aspirations'. I conclude that issues of site, scale, and subjectification must be attended to if scholars are to understand whether and to what extent social identities are being transformed by recent developments in genetic science.

  8. The Genetic Contribution of West-African Ancestry to Protection against Central Obesity in African-American Men but Not Women: Results from the ARIC and MESA Studies.

    Science.gov (United States)

    Klimentidis, Yann C; Arora, Amit; Zhou, Jin; Kittles, Rick; Allison, David B

    2016-01-01

    Over 80% of African-American (AA) women are overweight or obese. A large racial disparity between AA and European-Americans (EA) in obesity rates exists among women, but curiously not among men. Although socio-economic and/or cultural factors may partly account for this race-by-sex interaction, the potential involvement of genetic factors has not yet been investigated. Among 2814 self-identified AA in the Atherosclerosis Risk in Communities study, we estimated each individual's degree of West-African genetic ancestry using 3437 ancestry informative markers. We then tested whether sex modifies the association between West-African genetic ancestry and body mass index (BMI), waist-circumference (WC), and waist-to-hip ratio (WHR), adjusting for income and education levels, and examined associations of ancestry with the phenotypes separately in males and females. We replicated our findings in the Multi-Ethnic Study of Atherosclerosis (n = 1611 AA). In both studies, we find that West-African ancestry is negatively associated with obesity, especially central obesity, among AA men, but not among AA women (pinteraction = 4.14 × 10(-5) in pooled analysis of WHR). In conclusion, our results suggest that the combination of male gender and West-African genetic ancestry is associated with protection against central adiposity, and suggest that the large racial disparity that exists among women, but not men, may be at least partly attributed to genetic factors.

  9. Genetics of Genome-Wide Recombination Rate Evolution in Mice from an Isolated Island.

    Science.gov (United States)

    Wang, Richard J; Payseur, Bret A

    2017-08-01

    Recombination rate is a heritable quantitative trait that evolves despite the fundamentally conserved role that recombination plays in meiosis. Differences in recombination rate can alter the landscape of the genome and the genetic diversity of populations. Yet our understanding of the genetic basis of recombination rate evolution in nature remains limited. We used wild house mice ( Mus musculus domesticus ) from Gough Island (GI), which diverged recently from their mainland counterparts, to characterize the genetics of recombination rate evolution. We quantified genome-wide autosomal recombination rates by immunofluorescence cytology in spermatocytes from 240 F 2 males generated from intercrosses between GI-derived mice and the wild-derived inbred strain WSB/EiJ. We identified four quantitative trait loci (QTL) responsible for inter-F 2 variation in this trait, the strongest of which had effects that opposed the direction of the parental trait differences. Candidate genes and mutations for these QTL were identified by overlapping the detected intervals with whole-genome sequencing data and publicly available transcriptomic profiles from spermatocytes. Combined with existing studies, our findings suggest that genome-wide recombination rate divergence is not directional and its evolution within and between subspecies proceeds from distinct genetic loci. Copyright © 2017 by the Genetics Society of America.

  10. Integrated analysis of genetic variation and gene expression reveals novel variant for increased warfarin dose requirement in African Americans

    NARCIS (Netherlands)

    Hernandez, W.; Gamazon, E. R.; Aquino-Michaels, K.; Smithberger, E.; O'Brien, T. J.; Harralson, A. F.; Tuck, M.; Barbour, A.; Cavallari, L. H.; Perera, M. A.

    2017-01-01

    Essentials Genetic variants controlling gene regulation have not been explored in pharmacogenomics. We tested liver expression quantitative trait loci for association with warfarin dose response. A novel predictor for increased warfarin dose response in African Americans was identified. Precision

  11. Islands in a desert : breeding ecology of the African Reed Warbler Acrocephalus baeticatus in Namibia

    NARCIS (Netherlands)

    Eising, CM; Komdeur, J; Buys, J; Reemer, M; Richardson, DS; Richardson, David S.

    The continental African Reed Warbler Acrocephalus baeticatus, like its relative the Seychelles Warbler Acrocephalus sechellensis, breeds in isolated patches. We studied the mating system of the African Reed Warbler to see whether this species, like the Seychelles Warbler, shows co-operative

  12. Paraoxonase1 Genetic Polymorphisms in a Mixed Ancestry African Population

    Directory of Open Access Journals (Sweden)

    M. Macharia

    2014-01-01

    Full Text Available Paraoxonase 1 (PON1 activity is markedly influenced by coding polymorphisms, Q/R at position 192 and M/L at position 55 of the PON1 gene. We investigated the frequencies of these polymorphisms and their effects on PON1 and antioxidant activities in 844 South African mixed ancestry individuals. Genotyping was done using allele-specific TaqMan technology, PON1 activities were measured using paraoxon and phenylacetate, oxidative status was determined by measuring the antioxidant activities of ferric reducing antioxidant power and trolox equivalent antioxidant capacity, and lipid peroxidation markers included malondialdehyde and oxidized LDL. The frequencies of Q192R and L55M were 47.6% and 28.8%, respectively, and the most common corresponding alleles were 192R (60.4% and 55M (82.6%. The Q192 was significantly associated with 5.8 units’ increase in PON1 concentration and 15.4 units’ decrease in PONase activity after adjustment for age, sex, BMI, and diabetes, with suggestion of differential effects by diabetes status. The PON1 L55 variant was associated with none of the measured indices. In conclusion, we have shown that the Q192R polymorphism is a determinant of both PON1 concentration and activity and this association appeared to be enhanced in subjects with diabetes.

  13. Characterizing genetic risk at known prostate cancer susceptibility loci in African Americans.

    Directory of Open Access Journals (Sweden)

    Christopher A Haiman

    2011-05-01

    Full Text Available GWAS of prostate cancer have been remarkably successful in revealing common genetic variants and novel biological pathways that are linked with its etiology. A more complete understanding of inherited susceptibility to prostate cancer in the general population will come from continuing such discovery efforts and from testing known risk alleles in diverse racial and ethnic groups. In this large study of prostate cancer in African American men (3,425 prostate cancer cases and 3,290 controls, we tested 49 risk variants located in 28 genomic regions identified through GWAS in men of European and Asian descent, and we replicated associations (at p≤0.05 with roughly half of these markers. Through fine-mapping, we identified nearby markers in many regions that better define associations in African Americans. At 8q24, we found 9 variants (p≤6×10(-4 that best capture risk of prostate cancer in African Americans, many of which are more common in men of African than European descent. The markers found to be associated with risk at each locus improved risk modeling in African Americans (per allele OR = 1.17 over the alleles reported in the original GWAS (OR = 1.08. In summary, in this detailed analysis of the prostate cancer risk loci reported from GWAS, we have validated and improved upon markers of risk in some regions that better define the association with prostate cancer in African Americans. Our findings with variants at 8q24 also reinforce the importance of this region as a major risk locus for prostate cancer in men of African ancestry.

  14. Genetic variants determining survival and fertility in an adverse African environment

    DEFF Research Database (Denmark)

    Koopman, Jacob J E; Pijpe, Jeroen; Böhringer, Stefan

    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...

  15. Island Rule, quantitative genetics and brain-body size evolution in Homo floresiensis.

    Science.gov (United States)

    Diniz-Filho, José Alexandre Felizola; Raia, Pasquale

    2017-06-28

    Colonization of islands often activate a complex chain of adaptive events that, over a relatively short evolutionary time, may drive strong shifts in body size, a pattern known as the Island Rule. It is arguably difficult to perform a direct analysis of the natural selection forces behind such a change in body size. Here, we used quantitative evolutionary genetic models, coupled with simulations and pattern-oriented modelling, to analyse the evolution of brain and body size in Homo floresiensis , a diminutive hominin species that appeared around 700 kya and survived up to relatively recent times (60-90 kya) on Flores Island, Indonesia. The hypothesis of neutral evolution was rejected in 97% of the simulations, and estimated selection gradients are within the range found in living natural populations. We showed that insularity may have triggered slightly different evolutionary trajectories for body and brain size, which means explaining the exceedingly small cranial volume of H. floresiensis requires additional selective forces acting on brain size alone. Our analyses also support previous conclusions that H. floresiensis may be most likely derived from an early Indonesian H. erectus , which is coherent with currently accepted biogeographical scenario for Homo expansion out of Africa. © 2017 The Author(s).

  16. Genetic islands in pome fruit pathogenic and nonpathogenic Erwinia species and related plasmids

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    Pablo eLlop

    2015-08-01

    Full Text Available New pathogenic bacteria species belonging to the genus Erwinia associated with pome fruit trees (Erwinia pyrifoliae, E. piriflorinigrans, E. uzenensis have been increasingly described in the last years, and comparative analyses have found that all these species share several genetic characteristics. Studies at different level (whole genome comparison, virulence genes, plasmid content, etc. show a high intraspecies homogeneity (i.e. among E. amylovora strains and also abundant similarities appear between the different Erwinia species: presence of plasmids of similar size in the pathogenic species; high similarity in several genes associated with exopolysaccharide production and hence, with virulence, as well as in some other genes, in the chromosomes. Many genetic similarities have been observed also among some of the plasmids (and genomes from the pathogenic species and E. tasmaniensis or E. billingiae, two epiphytic species on the same hosts. The amount of genetic material shared in this genus varies from individual genes to clusters, genomic islands and genetic material that even may constitute a whole plasmid. Recent research on evolution of erwinias point out the horizontal transfer acquisition of some genomic islands that were subsequently lost in some species and several pathogenic traits that are still present. How this common material has been obtained and is efficiently maintained in different species belonging to the same genus sharing a common ecological niche provides an idea of the origin and evolution of the pathogenic Erwinia and the interaction with nonpathogenic species present in the same niche, and the role of the genes that are conserved in all of them.

  17. Significant genetic differentiation within the population of the Island of Corsica (France) revealed by y-chromosome analysis.

    Science.gov (United States)

    Ghiani, Maria Elena; Varesi, Laurent; Mitchell, Robert John; Vona, Giuseppe

    2009-12-01

    Using 10 Y-chromosome short tandem repeat allelic and haplotypic frequencies, we examined genetic variation within the population of Corsica and its relationship with other Mediterranean populations. The most significant finding is the high level of genetic differentiation within Corsica, with strong evidence of an effective barrier to male-mediated gene flow between the south and the rest of the island. This internal differentiation most probably results from low exogamy among small isolated populations and also from the orography of the island, with a central mountain chain running the length of the island restricting human movement. This physical barrier is reflected not only in present-day intraisland linguistic and genetic differences but also in the relatedness of Corsican regions to other Mediterranean groups. Northwest and Central Corsica are much closer to West Mediterranean populations, whereas South Corsica is closer to Central-North Sardinia and East Mediterranean populations.

  18. Genetic diversity of Bactrocera dorsalis (Diptera: Tephritidae) on the Hawaiian islands: Implications for an introduction pathway into California

    International Nuclear Information System (INIS)

    Barr, Norman B.; Ledezma, Lisa A.; Bartels, David W.; Garza, Daniel; Leblanc, Luc; Jose, Michael San; Rubinoff, Daniel; Geib, Scott M.; Fujita, Brian; Kerr, Peter; Hauser, Martin; Gaimari, Stephen

    2015-01-01

    Population genetic diversity of the oriental fruit fly, Bactrocera dorsalis (Hendel), on the Hawaiian islands of Oahu, Maui, Kauai, and Hawaii (the Big Island) was estimated using DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene. In total, 932 flies representing 36 sampled sites across the four islands were sequenced for a 1,500-bp fragment of the gene named the C1500 marker. Genetic variation was low on the Hawaiian Islands with >96% of flies having just two haplotypes: C1500- Haplotype 1 (63.2%) or C1500-Haplotype 2 (33.3%). The other 33 flies (3.5%) had haplotypes similar to the two dominant haplotypes. No population structure was detected among the islands or within islands. The two haplotypes were present at similar frequencies at each sample site, suggesting that flies on the various islands can be considered one population. Comparison of the Hawaiian data set to DNA sequences of 165 flies from outbreaks in California between 2006 and 2012 indicates that a single-source introduction pathway of Hawaiian origin cannot explain many of the flies in California. Hawaii, however, could not be excluded as a maternal source for 69 flies. There was no clear geographic association for Hawaiian or non-Hawaiian haplotypes in the Bay Area or Los Angeles Basin over time. This suggests that California experienced multiple, independent introductions from different sources. (author)

  19. Insecticide-driven patterns of genetic variation in the dengue vector Aedes aegypti in Martinique Island.

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    Sébastien Marcombe

    Full Text Available Effective vector control is currently challenged worldwide by the evolution of resistance to all classes of chemical insecticides in mosquitoes. In Martinique, populations of the dengue vector Aedes aegypti have been intensively treated with temephos and deltamethrin insecticides over the last fifty years, resulting in heterogeneous levels of resistance across the island. Resistance spreading depends on standing genetic variation, selection intensity and gene flow among populations. To determine gene flow intensity, we first investigated neutral patterns of genetic variability in sixteen populations representative of the many environments found in Martinique and experiencing various levels of insecticide pressure, using 6 microsatellites. Allelic richness was lower in populations resistant to deltamethrin, and consanguinity was higher in populations resistant to temephos, consistent with a negative effect of insecticide pressure on neutral genetic diversity. The global genetic differentiation was low, suggesting high gene flow among populations, but significant structure was found, with a pattern of isolation-by-distance at the global scale. Then, we investigated adaptive patterns of divergence in six out of the 16 populations using 319 single nucleotide polymorphisms (SNPs. Five SNP outliers displaying levels of genetic differentiation out of neutral expectations were detected, including the kdr-V1016I mutation in the voltage-gated sodium channel gene. Association tests revealed a total of seven SNPs associated with deltamethrin resistance. Six other SNPs were associated with temephos resistance, including two non-synonymous substitutions in an alkaline phosphatase and in a sulfotransferase respectively. Altogether, both neutral and adaptive patterns of genetic variation in mosquito populations appear to be largely driven by insecticide pressure in Martinique.

  20. The early colonial atlantic world: New insights on the African Diaspora from isotopic and ancient DNA analyses of a multiethnic 15th-17th century burial population from the Canary Islands, Spain.

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    Santana, Jonathan; Fregel, Rosa; Lightfoot, Emma; Morales, Jacob; Alamón, Martha; Guillén, José; Moreno, Marco; Rodríguez, Amelia

    2016-02-01

    The Canary Islands are considered one of the first places where Atlantic slave plantations with labourers of African origin were established, during the 15th century AD. In Gran Canaria (Canary Islands, Spain), a unique cemetery dated to the 15th and 17th centuries was discovered adjacent to an ancient sugar plantation with funerary practices that could be related to enslaved people. In this article, we investigate the origin and possible birthplace of each individual buried in this cemetery, as well as the identity and social status of these people. The sample consists of 14 individuals radiocarbon dated to the 15th and 17th centuries AD. We have employed several methods, including the analysis of ancient human DNA, stable isotopes, and skeletal markers of physical activity. 1) the funerary practices indicate a set of rituals not previously recorded in the Canary Islands; 2) genetic data show that some people buried in the cemetery could have North-African and sub-Saharan African lineages; 3) isotopic results suggest that some individuals were born outside Gran Canaria; and 4) markers of physical activity show a pattern of labour involving high levels of effort. This set of evidence, along with information from historical sources, suggests that Finca Clavijo was a cemetery for a multiethnic marginalized population that had being likely enslaved. Results also indicate that this population kept practicing non-Christian rituals well into the 17th century. We propose that this was possible because the location of the Canaries, far from mainland Spain and the control of the Spanish Crown, allowed the emergence of a new society with multicultural origins that was more tolerant to foreign rituals and syncretism. © 2015 Wiley Periodicals, Inc.

  1. Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds.

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    Selepe, Mokhethi Matthews; Ceccobelli, Simone; Lasagna, Emiliano; Kunene, Nokuthula Winfred

    2018-01-01

    The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69) and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu) had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

  2. Genetic structure of South African Nguni (Zulu sheep populations reveals admixture with exotic breeds.

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    Mokhethi Matthews Selepe

    Full Text Available The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69 and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

  3. Introduction to the Arizona Sky Island Arthropod Project (ASAP): Systematics, Biogeography, Ecology, and Population Genetics of Arthropods of the Madrean Sky Islands.

    Science.gov (United States)

    Moore, Wendy; Meyer, Wallace M; Eble, Jeffrey A; Franklin, Kimberly; Wiens, John F; Brusca, Richard C

    2013-01-01

    The Arizona Sky Island Arthropod Project (ASAP) is a new multi-disciplinary research program at the University of Arizona that combines systematics, biogeography, ecology, and population genetics to study origins and patterns of arthropod diversity along elevation gradients and among mountain ranges in the Madrean Sky Island Region. Arthropods represent taxonomically and ecologically diverse organisms that drive key ecosystem processes in this mountain archipelago. Using data from museum specimens and specimens we obtain during long-term collecting and monitoring programs, ASAP will document arthropod species across Arizona's Sky Islands to address a number of fundamental questions about arthropods of this region. Baseline data will be used to determine climatic boundaries for target species, which will then be integrated with climatological models to predict future changes in arthropod communities and distributions in the wake of rapid climate change. ASAP also makes use of the natural laboratory provided by the Sky Islands to investigate ecological and genetic factors that influence diversification and patterns of community assembly. Here, we introduce the project, outline overarching goals, and describe preliminary data from the first year of sampling ground-dwelling beetles and ants in the Santa Catalina Mountains.

  4. Genetic diversity and population differentiation of small giant clam Tridacna maxima in Comoros islands assessed by microsatellite markers.

    Science.gov (United States)

    Ahmed Mohamed, Nadjim; Yu, Qian; Chanfi, Mohamed Ibrahim; Li, Yangping; Wang, Shi; Huang, Xiaoting; Bao, Zhenmin

    2016-01-01

    Small giant clam, Tridacna maxima , widely distributed from French Polynesia to East Africa, has faced population declines due to over-exploitation. Comoros islands are an important biogeographic region due to potential richness of marine species, but no relevant information is available. In order to facilitate devising effective conservation management plan for T. maxima , nine microsatellite markers were used to survey genetic diversity and population differentiation of 72 specimens collected from three Comoros islands, Grande Comore, Moheli and Anjouan. A total of 51 alleles were detected ranged from 2 to 8 per locus. Observed and expected heterozygosity varied from 0.260 to 0.790 and from 0.542 to 0.830, respectively. All populations have high genetic diversity, especially the population in Moheli, a protected area, has higher genetic diversity than the others. Significant heterozygote deficiencies were recorded, and null alleles were probably the main factor leading to these deficits. F ST value indicated medium genetic differentiation among the populations. Although significant, AMOVA revealed 48.9 % of genetic variation within individuals and only a small variation of 8.9 % was found between populations. Gene flow was high ( Nm  = 12.40) between Grande Comore and Moheli, while lower ( Nm  = 1.80) between Grande Comore and Anjouan, explaining geographic barriers to genetic exchanges might exist in these two islands. Global gene flow analysis ( Nm  = 5.50) showed that larval dispersal is enough to move between the islands. The high genetic diversity and medium population differentiation revealed in the present study offer useful information on genetic conservation of small giant clams.

  5. Genetic differentiation between marine iguanas from different breeding sites on the island of Santa Fe (Galapagos Archipelago).

    Science.gov (United States)

    Lanterbecq, Deborah; Glaberman, Scott; Vitousek, Maren Noelani; Steinfartz, Sebastian; Benavides, Edgar; Wikelski, Martin; Caccone, Adalgisa

    2010-01-01

    We studied patterns of genetic diversity within and among 5 populations (318 individuals) of Galápagos marine iguanas (Amblyrhynchus cristatus) from the island Santa Fé. Populations were separated by distances of 0.2 to 9.9 km. We sequenced 1182 base pairs of the mitochondrial control region and screened 13 microsatellite loci for variability. We also added data from 5 populations (397 individuals) sampled on 4 neighboring islands (Santa Cruz, Floreana, Espanola, and San Cristobal). The 5 Santa Fé populations, revealed as genetically distinct from populations on other islands, present relatively low levels of genetic diversity, which are similar for both microsatellite (average observed heterozygosity from 0.7686 to 0.7773) and mitochondrial DNA (mtDNA) markers (haplotypic and nucleotide diversity from 0.587 to 0.728 and from 0.00079 to 0.00293, respectively), and comparable with those observed in similar-sized sampling sites on other islands. There was frequency-based evidence of genetic structure between northern and southern sites on Santa Fé (F(st) of 0.0027-0.0115 for microsatellite and 0.0447-0.2391 for mtDNA), but the 4 southern sites showed little differentiation. Most of the intra-island genetic variation was allocated within rather than between sites. There was no evidence of sex-biased dispersal or population substructuring due to lek-mating behavior, suggesting that these 2 observed behaviors are not strong enough to leave an evolutionary signal on genetic patterns in this species.

  6. Evaluation of genetic susceptibility to childhood allergy and asthma in an African American urban population

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    Hudgens Edward E

    2011-02-01

    Full Text Available Abstract Background Asthma and allergy represent complex phenotypes, which disproportionately burden ethnic minorities in the United States. Strong evidence for genomic factors predisposing subjects to asthma/allergy is available. However, methods to utilize this information to identify high risk groups are variable and replication of genetic associations in African Americans is warranted. Methods We evaluated 41 single nucleotide polymorphisms (SNP and a deletion corresponding to 11 genes demonstrating association with asthma in the literature, for association with asthma, atopy, testing positive for food allergens, eosinophilia, and total serum IgE among 141 African American children living in Detroit, Michigan. Independent SNP and haplotype associations were investigated for association with each trait, and subsequently assessed in concert using a genetic risk score (GRS. Results Statistically significant associations with asthma were observed for SNPs in GSTM1, MS4A2, and GSTP1 genes, after correction for multiple testing. Chromosome 11 haplotype CTACGAGGCC (corresponding to MS4A2 rs574700, rs1441586, rs556917, rs502581, rs502419 and GSTP1 rs6591256, rs17593068, rs1695, rs1871042, rs947895 was associated with a nearly five-fold increase in the odds of asthma (Odds Ratio (OR = 4.8, p = 0.007. The GRS was significantly associated with a higher odds of asthma (OR = 1.61, 95% Confidence Interval = 1.21, 2.13; p = 0.001. Conclusions Variation in genes associated with asthma in predominantly non-African ethnic groups contributed to increased odds of asthma in this African American study population. Evaluating all significant variants in concert helped to identify the highest risk subset of this group.

  7. The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States

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    Bryc, Katarzyna; Durand, Eric Y.; Macpherson, J. Michael; Reich, David; Mountain, Joanna L.

    2015-01-01

    Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry. PMID:25529636

  8. African ancestry and its correlation to type 2 diabetes in African Americans: a genetic admixture analysis in three U.S. population cohorts.

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    Ching-Yu Cheng

    Full Text Available The risk of type 2 diabetes is approximately 2-fold higher in African Americans than in European Americans even after adjusting for known environmental risk factors, including socioeconomic status (SES, suggesting that genetic factors may explain some of this population difference in disease risk. However, relatively few genetic studies have examined this hypothesis in a large sample of African Americans with and without diabetes. Therefore, we performed an admixture analysis using 2,189 ancestry-informative markers in 7,021 African Americans (2,373 with type 2 diabetes and 4,648 without from the Atherosclerosis Risk in Communities Study, the Jackson Heart Study, and the Multiethnic Cohort to 1 determine the association of type 2 diabetes and its related quantitative traits with African ancestry controlling for measures of SES and 2 identify genetic loci for type 2 diabetes through a genome-wide admixture mapping scan. The median percentage of African ancestry of diabetic participants was slightly greater than that of non-diabetic participants (study-adjusted difference = 1.6%, P<0.001. The odds ratio for diabetes comparing participants in the highest vs. lowest tertile of African ancestry was 1.33 (95% confidence interval 1.13-1.55, after adjustment for age, sex, study, body mass index (BMI, and SES. Admixture scans identified two potential loci for diabetes at 12p13.31 (LOD = 4.0 and 13q14.3 (Z score = 4.5, P = 6.6 × 10(-6. In conclusion, genetic ancestry has a significant association with type 2 diabetes above and beyond its association with non-genetic risk factors for type 2 diabetes in African Americans, but no single gene with a major effect is sufficient to explain a large portion of the observed population difference in risk of diabetes. There undoubtedly is a complex interplay among specific genetic loci and non-genetic factors, which may both be associated with overall admixture, leading to the observed ethnic differences in diabetes

  9. Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations.

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    Haber, Marc; Mezzavilla, Massimo; Bergström, Anders; Prado-Martinez, Javier; Hallast, Pille; Saif-Ali, Riyadh; Al-Habori, Molham; Dedoussis, George; Zeggini, Eleftheria; Blue-Smith, Jason; Wells, R Spencer; Xue, Yali; Zalloua, Pierre A; Tyler-Smith, Chris

    2016-12-01

    Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750-7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700-7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%-30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  10. A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island

    Science.gov (United States)

    Moodley, Yoshan; Uhr, Markus; Stamer, Christiana; Vauterin, Marc; Suerbaum, Sebastian; Achtman, Mark

    2010-01-01

    The Helicobacter pylori cag pathogenicity island (cagPAI) encodes a type IV secretion system. Humans infected with cagPAI–carrying H. pylori are at increased risk for sequelae such as gastric cancer. Housekeeping genes in H. pylori show considerable genetic diversity; but the diversity of virulence factors such as the cagPAI, which transports the bacterial oncogene CagA into host cells, has not been systematically investigated. Here we compared the complete cagPAI sequences for 38 representative isolates from all known H. pylori biogeographic populations. Their gene content and gene order were highly conserved. The phylogeny of most cagPAI genes was similar to that of housekeeping genes, indicating that the cagPAI was probably acquired only once by H. pylori, and its genetic diversity reflects the isolation by distance that has shaped this bacterial species since modern humans migrated out of Africa. Most isolates induced IL-8 release in gastric epithelial cells, indicating that the function of the Cag secretion system has been conserved despite some genetic rearrangements. More than one third of cagPAI genes, in particular those encoding cell-surface exposed proteins, showed signatures of diversifying (Darwinian) selection at more than 5% of codons. Several unknown gene products predicted to be under Darwinian selection are also likely to be secreted proteins (e.g. HP0522, HP0535). One of these, HP0535, is predicted to code for either a new secreted candidate effector protein or a protein which interacts with CagA because it contains two genetic lineages, similar to cagA. Our study provides a resource that can guide future research on the biological roles and host interactions of cagPAI proteins, including several whose function is still unknown. PMID:20808891

  11. MICROSATELLITE GENETIC VARIATION IN CULTURED POPULATIONS OF AFRICAN CATFISH (Clarias gariepinus IN INDONESIA

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    Imron Imron

    2011-06-01

    Full Text Available African catfish, Clarias gariepinus, is one of economically important farmed species in Indonesia. To support the development of aquaculture industry, high genetic quality of both broodstock and seeds is required and breeding program is considered as viable option. Information on genetic variation of the populations being considered to form a base population may give insight toward the appropriate strategy to be implemented in breeding program. This study was aimed to assess genetic variation in farmed populations of catfish in Indonesia using microsatellite markers with special emphasis on their use to develop breeding program. Three populations of farmed catfish, namely Dumbo, Paiton, and Sangkuriang were collected. Fifteen individuals representing each population were screened for microsatellite variability using seven primer sets (cga01, cga02, cga03, cga05, cga06, cga09, cga10. Results found that with exception of two loci (cga01 and cg02 which had a slight increase, the other four loci showed reduction in the number of alleles ranging from 35% to 80% depending on loci. Farmed populations also showed heterozygote deficient and inbreeding level, being the highest was found in Sangkuriang and the least was observed in Dumbo population. Individuals within populations contributed most (95% while interpopulation variation accounted for only 5% of the total genetic variation. Populations of Dumbo and Sangkuriang were genetically similar while populations of Paiton were genetically different from both Dumbo and Sangkuriang. Viewed from genetic perspective, by combining all information emerging from this study, the best possible strategy to establish a base population with broad genetic base and less inbreeding would be to combine all the populations into a synthetic base population.

  12. Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana

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    Santie M. De Villiers

    2015-03-01

    Discussion: Five individual samples from an accession captured the largest number of alleles per locus compared to the four different bulked sampling strategies but this difference was not significant. The identified set comprised 20 markers: UGEP24, UGEP53, UGEP84, UGEP27, UGEP98, UGEP95, UGEP64, UGEP33, UGEP67, UGEP106, UGEP110, UGEP57, UGEP96, UGEP66, UGEP46, UGEP79, UGEP20, UGEP12, UGEP73 and UGEP5 and was since used to assess East African finger millet genetic diversity in two separate studies.

  13. A new phylogeographic pattern of endemic Bufo bankorensis in Taiwan Island is attributed to the genetic variation of populations.

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    Teng-Lang Yu

    Full Text Available To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1 the existence of various geological barriers (Central Mountain Ranges, CMRs; and (2 the genetic variation of Bufo bankorensis using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species B. gargarizans of mainland China.Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA D-loop gene (348 bp recovered a close relationship between B. bankorensis and B. gargarizans, identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp amplified (279 individuals, 27 localities from Taiwan Island indicated three divergent clades within B. bankorensis (Clade W, E and S, corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species B. bankorensis might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and co-distribution among clades.The multiple origins (different clades of B. bankorensis mtDNA sequences were first evident in this study. The divergent genetic clades found within B. bankorensis could be independent colonization by previously diverged lineages; inferring B. bankorensis originated from B. gargarizans of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of B

  14. Genetic network and breeding patterns of a sicklefin lemon shark (Negaprion acutidens population in the Society Islands, French Polynesia.

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    Johann Mourier

    Full Text Available Human pressures have put many top predator populations at risk of extinction. Recent years have seen alarming declines in sharks worldwide, while their resilience remains poorly understood. Studying the ecology of small populations of marine predators is a priority to better understand their ability to withstand anthropogenic and environmental stressors. In the present study, we monitored a naturally small island population of 40 adult sicklefin lemon sharks in Moorea, French Polynesia over 5 years. We reconstructed the genetic relationships among individuals and determined the population's mating system. The genetic network illustrates that all individuals, except one, are interconnected at least through one first order genetic relationship. While this species developed a clear inbreeding avoidance strategy involving dispersal and migration, the small population size, low number of breeders, and the fragmented environment characterizing these tropical islands, limits its complete effectiveness.

  15. Henipavirus neutralising antibodies in an isolated island population of African fruit bats.

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    Alison J Peel

    Full Text Available 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

  16. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries.

    Directory of Open Access Journals (Sweden)

    Erasto V Mbugi

    Full Text Available The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs were: SIT21/CAS1-Kili (n = 76; 25.94%, SIT59/LAM11-ZWE (n = 22; 7.51%, and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%. Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1. We noted that the East-African-Indian (EAI lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS lineage was more predominant in Dar es Salaam (p-value<0.0001. No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103. However, when grouping lineages as Principal Genetic Groups (PGG, we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu (p-value = 0.03. This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3

  17. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries.

    Science.gov (United States)

    Mbugi, Erasto V; Katale, Bugwesa Z; Streicher, Elizabeth M; Keyyu, Julius D; Kendall, Sharon L; Dockrell, Hazel M; Michel, Anita L; Rweyemamu, Mark M; Warren, Robin M; Matee, Mecky I; van Helden, Paul D; Couvin, David; Rastogi, Nalin

    2016-01-01

    The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA

  18. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries

    Science.gov (United States)

    Mbugi, Erasto V.; Katale, Bugwesa Z.; Streicher, Elizabeth M.; Keyyu, Julius D.; Kendall, Sharon L.; Dockrell, Hazel M.; Michel, Anita L.; Rweyemamu, Mark M.; Warren, Robin M.; Matee, Mecky I.; van Helden, Paul D.; Couvin, David; Rastogi, Nalin

    2016-01-01

    The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA

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

    Science.gov (United States)

    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.

  20. The African baobab (Adansonia digitata, Malvaceae): genetic resources in neglected populations of the Nuba Mountains, Sudan.

    Science.gov (United States)

    Wiehle, Martin; Prinz, Kathleen; Kehlenbeck, Katja; Goenster, Sven; Mohamed, Seifeldin Ali; Finkeldey, Reiner; Buerkert, Andreas; Gebauer, Jens

    2014-09-01

    • Adansonia digitata L. is one of the most important indigenous fruit trees of mainland Africa. Despite its significance for subsistence and income generation of local communities, little is known about the genetic and morphological variability of East African populations of A. digitata, including those of Sudan. The aim of the current study, therefore, was to analyze genetic and morphological variability of different baobab populations in Kordofan, Sudan and to estimate the effect of human intervention on genetic differentiation and diversity.• A total of 306 trees were randomly sampled from seven spatially separated locations in the Nuba Mountains, Sudan, to cover a wide range of differing environmental gradients and management regimes ('homesteads' and 'wild'). Genetic analyses were conducted using nine microsatellite markers. Because of the tetraploid nature of A. digitata, different approaches were applied to estimate patterns of genetic diversity. Investigations were completed by measurements of dendrometric and fruit morphological characters.• Genetic diversity was balanced and did not differ between locations or management regimes, although tendencies of higher diversity in 'homesteads' were observed. A Bayesian cluster approach detected two distinct gene pools in the sample set, mainly caused by one highly diverse population close to a main road. The variability of tree characters and fruit morphometries was high, and significantly different between locations.• Results indicated a rather positive effect with human intervention. The observed populations provide a promising gene pool and likely comprise ecotypes well-adapted to environmental conditions at the northern distribution range of the species, which should be considered in conservation and management programs. © 2014 Botanical Society of America, Inc.

  1. A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef

    Directory of Open Access Journals (Sweden)

    Madeleine J.H. van Oppen

    2015-07-01

    Full Text Available Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative

  2. Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss.

    Science.gov (United States)

    Sammler, Svenja; Ketmaier, Valerio; Havenstein, Katja; Krause, Ulrike; Curio, Eberhard; Tiedemann, Ralph

    2012-10-12

    The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow

  3. Reproductive biology and genetic diversity of the green turtle (Chelonia mydas) in Vamizi island, Mozambique.

    Science.gov (United States)

    Anastácio, Rita; Santos, Camila; Lopes, Cardoso; Moreira, Helena; Souto, Luis; Ferrão, Jorge; Garnier, Julie; Pereira, Mário J

    2014-01-01

    Vamizi, an Island located in the Western Indian Ocean, is visited by a small and not fully characterized green turtle (Chelonia mydas (L.)) population. This population is threatened by natural hazards and several human activities, which are used to identify conservation priorities for marine turtles. It was our aim to contribute to the knowledge of marine turtles that nest in Vamizi, with respect to its regional management, and to an area that may possibly be included on the UNESCO World Heritage List due to its potential Outstanding Universal Value. Here, we evaluate the nesting parameters (incubation period, clutch size, hatching and emergence successes rates) and patterns over an 8-year (2003 - 2010) conservation program. We also present the results of genetic diversity based on the analysis of approximately an 850 pb fragment of the mitochondrial DNA control region. We found that Vamizi beaches host a small number of nesting females, approximately 52 per year, but these have shown a reduction in their length. High hatching success (88.5 ± SD 17.2%, N = 649), emergence success rates (84.5 ± SD 20.4%, N = 649) were observed, and genetic diversity (N = 135), with 11 haplotypes found (7 new). It was also observed, in the later years of this study, a reduction in the incubation period, a dislocation of the nesting peak activity and an increase in the number of flooded nests and an increase of the number of nests in areas with lower human activity. Some resilience and behavioral plasticity seems to occur regarding human territory occupancy and climate changes. However, regardless of the results, aspects like what seems to be the reduction of some cohorts, the number of flooded nests and the diminishing of the incubation period (East and South facing beaches), show that conservation efforts have to be improved.

  4. The gonococcal genetic island and type IV secretion in the pathogenic Neisseria

    Directory of Open Access Journals (Sweden)

    Meghan E Ramsey

    2011-04-01

    Full Text Available Eighty percent of Neisseria gonorrhoeae strains and some Neisseria meningitidis strains encode a 57 kb gonococcal genetic island (GGI. The GGI was horizontally acquired and is inserted in the chromosome at the replication terminus. The GGI is flanked by direct repeats, and site-specific recombination at these sites results in excision of the GGI and may be responsible for its original acquisition. Although the role of the GGI in N. meningitidis is unclear, the GGI in N. gonorrhoeae encodes a type IV secretion system (T4SS. Type IV secretion systems are versatile multi-protein complexes and include both conjugation systems as well as effector systems that translocate either proteins or DNA-protein complexes. In N. gonorrhoeae, the T4SS secretes single-stranded chromosomal DNA into the extracellular milieu in a contact-independent manner. Importantly, the DNA secreted through the T4SS is effective in natural transformation and therefore contributes to the spread of genetic information through Neisseria populations. Mutagenesis experiments have identified genes for DNA secretion including those encoding putative structural components of the apparatus, peptidoglycanases which may act in assembly, and relaxosome components for processing the DNA and delivering it to the apparatus. The T4SS may also play a role in infection by N. gonorrhoeae. During intracellular infection, N. gonorrhoeae requires the Ton complex for iron acquisition and survival. However, N. gonorrhoeae strains that do not express the Ton complex can survive intracellularly if they express structural components of the T4SS. These data provide evidence that the T4SS is expressed during intracellular infection and suggest that the T4SS may provide an advantage for intracellular survival. Here we review our current understanding of how the GGI and type IV secretion affect natural transformation and pathogenesis in N. gonorrhoeae and N. meningitidis.

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

    Directory of Open Access Journals (Sweden)

    Sandra Beleza

    2013-03-01

    Full Text Available 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.

  6. Microbial flora in organic honey samples of africanized honeybees from Parana river islands

    Directory of Open Access Journals (Sweden)

    Maria Josiane Sereia

    2011-06-01

    Full Text Available The purpose of this study was to verify and compare the main contamination sources and the hygienic/sanitary conditions of organic honey samples of Apis mellifera from Parana River islands. Thirty-three (33 samples were analyzed between January 2005 and August 2006. Eleven (11 samples were collected by beekeepers and twenty-two (22 samples were collected and processed in accordance with ideal personal hygiene norms and good manufacturing practices. The samples underwent microbiological analysis in search of coliforms at 35 ºC and 45 ºC, as well as fungi enumeration analysis. As for fungi counting, the samples harvested by beekeepers showed values above the maximum established by Resolution nº 15/94 of Common Market Group - Mercosul. The results showed that secondary contamination sources are responsible for the reduction of organic honey quality.

  7. Genetic analysis of the isolated Faroe Islands reveals SORCS3 as a potential multiple sclerosis risk gene

    DEFF Research Database (Denmark)

    Binzer, Stefanie; Stenager, Egon; Binzer, Michael

    2016-01-01

    BACKGROUND: In search of the missing heritability in multiple sclerosis (MS), additional approaches adding to the genetic discoveries of large genome-wide association studies are warranted. OBJECTIVE: The objective of this research paper is to search for rare genetic MS risk variants...... in the genetically homogenous population of the isolated Faroe Islands. METHODS: Twenty-nine Faroese MS cases and 28 controls were genotyped with the HumanOmniExpressExome-chip. The individuals make up 1596 pair-combinations in which we searched for identical-by-descent shared segments using the PLINK...... of neurotrophin factors and involvement in glutamate homeostasis. Although additional work is needed to scrutinise the genetic effect of the SORCS3-covering haplotype, this study suggests that SORCS3 may also be important in MS pathogenesis....

  8. Genetic characterization and phylogenetic position of Echinococcus felidis (Cestoda: Taeniidae) from the African lion.

    Science.gov (United States)

    Hüttner, Marion; Nakao, Minoru; Wassermann, Torsten; Siefert, Ludwig; Boomker, Joop D F; Dinkel, Anke; Sako, Yasuhito; Mackenstedt, Ute; Romig, Thomas; Ito, Akira

    2008-06-01

    Echinococcus felidis had been described in 1937 from African lions, but was later included in Echinococcus granulosus as a subspecies or a strain. In the absence of any genetic characterization, most previous records of this taxon from a variety of large African mammals remained unconfirmed due to the lack of diagnostic criteria and the possible confusion with the sympatric E. granulosus sensu stricto, Echinococcus ortleppi and Echinococcus canadensis. In this study, we obtained taeniid eggs from lion feces in Uganda and amplified DNA from individual eggs. Mitochondrial and nuclear DNA sequences showed similarities with those of other Echinococcus spp., but high values of percentage divergence of mitochondrial genes indicated the presence of a distinct species. In a second step, we compared this material with the preserved specimens of adult E. granulosus felidis, which had been identified morphologically approximately 40 years ago in South Africa. All DNA fragments (<200 bp) that could be amplified from the adults showed 100% similarity with the Ugandan material. In the phylogenetic tree of Echinococcus which was constructed from the mitochondrial genes, E. felidis is positioned as a sister taxon of E. granulosus sensu stricto. The data obtained will facilitate the development of diagnostic tools necessary to study the epidemiology of this enigmatic parasite.

  9. NEIGHBORHOOD CRIME AND DEPRESSIVE SYMPTOMS AMONG AFRICAN AMERICAN WOMEN: GENETIC MODERATION AND EPIGENETIC MEDIATOIN OF EFFECTS

    Science.gov (United States)

    Lei, Man-Kit; Beach, Steven R. H.; Simons, Ronald L.; Philibert, Robert A.

    2015-01-01

    Introduction Social scientists have long recognized the important role that neighborhood crime can play in stress-related disease, but very little is known about potential biosocial mechanisms that may link the experience of living in high-crime neighborhoods with depression. Objective The current study introduces an integrated model that combines neighborhood, genetic, and epigenetic factors. Methods Hypotheses were tested with a sample of 99 African American women from the Family and Community Health Study (FACHS). Results Allele variants of the serotonin transporter gene (5-HTT) interact with neighborhood crime to predict depressive symptoms in a manner consonant with the differential susceptibility perspective. Furthermore, this association is mediated by DNA methylation of the promoter region of the serotonin transporter gene. Conclusion The findings provide support for an integrated model in which changes in DNA methylation, resulting from neighborhood crime, can result in an increase or decrease in gene activity which, in turn, influences depressive symptoms. PMID:26513121

  10. Neighborhood crime and depressive symptoms among African American women: Genetic moderation and epigenetic mediation of effects.

    Science.gov (United States)

    Lei, Man-Kit; Beach, Steven R H; Simons, Ronald L; Philibert, Robert A

    2015-12-01

    Social scientists have long recognized the important role that neighborhood crime can play in stress-related disease, but very little is known about potential biosocial mechanisms that may link the experience of living in high-crime neighborhoods with depression. The current study introduces an integrated model that combines neighborhood, genetic, and epigenetic factors. Hypotheses were tested with a sample of 99 African American women from the Family and Community Health Study (FACHS). Allele variants of the serotonin transporter gene (5-HTT) interact with neighborhood crime to predict depressive symptoms in a manner consonant with the differential susceptibility perspective. Furthermore, this association is mediated by DNA methylation of the promoter region of the serotonin transporter gene. The findings provide support for an integrated model in which changes in DNA methylation, resulting from neighborhood crime, can result in an increase or decrease in gene activity which, in turn, influences depressive symptoms. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss

    OpenAIRE

    Sammler, Svenja; Ketmaier, Valerio; Havenstein, Katja; Krause, Ulrike; Curio, Eberhard; Tiedemann, Ralph

    2012-01-01

    Abstract Background The Visayan Tarictic Hornbill (Penelopides panini) and the Walden’s Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp) of the mitochondrial control region I and at 12...

  12. Meta-Analysis of Genome-Wide Association Studies Identifies Genetic Risk Factors for Stroke in African Americans.

    Science.gov (United States)

    Carty, Cara L; Keene, Keith L; Cheng, Yu-Ching; Meschia, James F; Chen, Wei-Min; Nalls, Mike; Bis, Joshua C; Kittner, Steven J; Rich, Stephen S; Tajuddin, Salman; Zonderman, Alan B; Evans, Michele K; Langefeld, Carl D; Gottesman, Rebecca; Mosley, Thomas H; Shahar, Eyal; Woo, Daniel; Yaffe, Kristine; Liu, Yongmei; Sale, Michèle M; Dichgans, Martin; Malik, Rainer; Longstreth, W T; Mitchell, Braxton D; Psaty, Bruce M; Kooperberg, Charles; Reiner, Alexander; Worrall, Bradford B; Fornage, Myriam

    2015-08-01

    The majority of genome-wide association studies (GWAS) of stroke have focused on European-ancestry populations; however, none has been conducted in African Americans, despite the disproportionately high burden of stroke in this population. The Consortium of Minority Population Genome-Wide Association Studies of Stroke (COMPASS) was established to identify stroke susceptibility loci in minority populations. Using METAL, we conducted meta-analyses of GWAS in 14 746 African Americans (1365 ischemic and 1592 total stroke cases) from COMPASS, and tested genetic variants with Pstroke genetic studies in European-ancestry populations. We also evaluated stroke loci previously identified in European-ancestry populations. The 15q21.3 locus linked with lipid levels and hypertension was associated with total stroke (rs4471613; P=3.9×10(-8)) in African Americans. Nominal associations (Pstroke were observed for 18 variants in or near genes implicated in cell cycle/mRNA presplicing (PTPRG, CDC5L), platelet function (HPS4), blood-brain barrier permeability (CLDN17), immune response (ELTD1, WDFY4, and IL1F10-IL1RN), and histone modification (HDAC9). Two of these loci achieved nominal significance in METASTROKE: 5q35.2 (P=0.03), and 1p31.1 (P=0.018). Four of 7 previously reported ischemic stroke loci (PITX2, HDAC9, CDKN2A/CDKN2B, and ZFHX3) were nominally associated (Pstroke in COMPASS. We identified a novel genetic variant associated with total stroke in African Americans and found that ischemic stroke loci identified in European-ancestry populations may also be relevant for African Americans. Our findings support investigation of diverse populations to identify and characterize genetic risk factors, and the importance of shared genetic risk across populations. © 2015 American Heart Association, Inc.

  13. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium.

    Science.gov (United States)

    Ng, Maggie C Y; Graff, Mariaelisa; Lu, Yingchang; Justice, Anne E; Mudgal, Poorva; Liu, Ching-Ti; Young, Kristin; Yanek, Lisa R; Feitosa, Mary F; Wojczynski, Mary K; Rand, Kristin; Brody, Jennifer A; Cade, Brian E; Dimitrov, Latchezar; Duan, Qing; Guo, Xiuqing; Lange, Leslie A; Nalls, Michael A; Okut, Hayrettin; Tajuddin, Salman M; Tayo, Bamidele O; Vedantam, Sailaja; Bradfield, Jonathan P; Chen, Guanjie; Chen, Wei-Min; Chesi, Alessandra; Irvin, Marguerite R; Padhukasahasram, Badri; Smith, Jennifer A; Zheng, Wei; Allison, Matthew A; Ambrosone, Christine B; Bandera, Elisa V; Bartz, Traci M; Berndt, Sonja I; Bernstein, Leslie; Blot, William J; Bottinger, Erwin P; Carpten, John; Chanock, Stephen J; Chen, Yii-Der Ida; Conti, David V; Cooper, Richard S; Fornage, Myriam; Freedman, Barry I; Garcia, Melissa; Goodman, Phyllis J; Hsu, Yu-Han H; Hu, Jennifer; Huff, Chad D; Ingles, Sue A; John, Esther M; Kittles, Rick; Klein, Eric; Li, Jin; McKnight, Barbara; Nayak, Uma; Nemesure, Barbara; Ogunniyi, Adesola; Olshan, Andrew; Press, Michael F; Rohde, Rebecca; Rybicki, Benjamin A; Salako, Babatunde; Sanderson, Maureen; Shao, Yaming; Siscovick, David S; Stanford, Janet L; Stevens, Victoria L; Stram, Alex; Strom, Sara S; Vaidya, Dhananjay; Witte, John S; Yao, Jie; Zhu, Xiaofeng; Ziegler, Regina G; Zonderman, Alan B; Adeyemo, Adebowale; Ambs, Stefan; Cushman, Mary; Faul, Jessica D; Hakonarson, Hakon; Levin, Albert M; Nathanson, Katherine L; Ware, Erin B; Weir, David R; Zhao, Wei; Zhi, Degui; Arnett, Donna K; Grant, Struan F A; Kardia, Sharon L R; Oloapde, Olufunmilayo I; Rao, D C; Rotimi, Charles N; Sale, Michele M; Williams, L Keoki; Zemel, Babette S; Becker, Diane M; Borecki, Ingrid B; Evans, Michele K; Harris, Tamara B; Hirschhorn, Joel N; Li, Yun; Patel, Sanjay R; Psaty, Bruce M; Rotter, Jerome I; Wilson, James G; Bowden, Donald W; Cupples, L Adrienne; Haiman, Christopher A; Loos, Ruth J F; North, Kari E

    2017-04-01

    Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHRadjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHRadjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHRadjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations.

  14. Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes

    OpenAIRE

    Ng, Maggie C. Y.; Shriner, Daniel; Chen, Brian H.; Li, Jiang; Chen, Wei-Min; Guo, Xiuqing; Liu, Jiankang; Bielinski, Suzette J.; Yanek, Lisa R.; Nalls, Michael A.; Comeau, Mary E.; Rasmussen-Torvik, Laura J.; Jensen, Richard A.; Evans, Daniel S.; Sun, Yan V.

    2014-01-01

    Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 case...

  15. Population genetics of Glossina palpalis palpalis from central African sleeping sickness foci

    Directory of Open Access Journals (Sweden)

    Solano Philippe

    2011-07-01

    Full Text Available Abstract Background Glossina palpalis palpalis (Diptera: Glossinidae is widespread in west Africa, and is the main vector of sleeping sickness in Cameroon as well as in the Bas Congo Province of the Democratic Republic of Congo. However, little is known on the structure of its populations. We investigated G. p. palpalis population genetic structure in five sleeping sickness foci (four in Cameroon, one in Democratic Republic of Congo using eight microsatellite DNA markers. Results A strong isolation by distance explains most of the population structure observed in our sampling sites of Cameroon and DRC. The populations here are composed of panmictic subpopulations occupying fairly wide zones with a very strong isolation by distance. Effective population sizes are probably between 20 and 300 individuals and if we assume densities between 120 and 2000 individuals per km2, dispersal distance between reproducing adults and their parents extends between 60 and 300 meters. Conclusions This first investigation of population genetic structure of G. p. palpalis in Central Africa has evidenced random mating subpopulations over fairly large areas and is thus at variance with that found in West African populations of G. p. palpalis. This study brings new information on the isolation by distance at a macrogeographic scale which in turn brings useful information on how to organise regional tsetse control. Future investigations should be directed at temporal sampling to have more accurate measures of demographic parameters in order to help vector control decision.

  16. East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus

    Directory of Open Access Journals (Sweden)

    De Bruyn Alexandre

    2012-11-01

    Full Text Available Abstract Background Cassava (Manihot esculenta is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD. Caused by a complex of bipartite cassava mosaic geminiviruses (CMG species (Family: Geminivirideae; Genus: Begomovirus CMD has been widely described throughout Africa and it is apparent that CMG's are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO islands. Results The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV. Phylogeographic analyses suggest that CMG’s presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. While only two recombination events characteristic of SWIO islands isolates were identified, numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components. Conclusions Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain

  17. Genetic analysis of Saccharomyces cerevisiae strains isolated from palm wine in eastern Nigeria. Comparison with other African strains.

    Science.gov (United States)

    Ezeronye, O U; Legras, J-L

    2009-05-01

    To study the yeast diversity of Nigerian palm wines by comparison with other African strains. Twenty-three Saccharomyces cerevisiae strains were obtained from palm wine samples collected at four locations in eastern Nigeria, and characterized using different molecular techniques: internal transcribed spacer restriction fragment length polymorphism and sequence analysis, pulsed field gel electrophoresis, inter delta typing and microsatellite multilocus analysis. These techniques revealed that palm wine yeasts represent a group of closely related strains that includes other West African isolates (CBS400, NCYC110, DVPG6044). Population analysis revealed an excess of homozygote strains and an allelic richness similar to wine suggestive of local domestication. Several other African yeast strains were not connected to this group. Ghana sorghum beer strains and other African strains (DBVPG1853 and MUCL28071) displayed strikingly high relatedness with European bread, beer or wine strains, and the genome of strain MUCL30909 contained African and wine-type alleles, indicating its hybrid origin. Nigerian palm wine yeast represents a local specific yeast flora, whereas a European origin or hybrid was suspected for several other Africa isolates. This study presents the first genetic characterization of an autochthonous African palm wine yeast population and confirms the idea that human intervention has favoured yeast migration.

  18. Knowledge, group-based medical mistrust, future expectations, and perceived disadvantages of medical genetic testing: perspectives of Black African immigrants/refugees.

    Science.gov (United States)

    Buseh, A; Kelber, S; Millon-Underwood, S; Stevens, P; Townsend, L

    2014-01-01

    Reasons for low participation of ethnic minorities in genetic studies are multifactorial and often poorly understood. Based on published literature, participation in genetic testing is low among Black African immigrants/refugees although they are purported to bear disproportionate disease burden. Thus, research involving Black African immigrant/refugee populations that examine their perspectives on participating in genetic studies is needed. This report examines and describes the knowledge of medical genetics, group-based medical mistrust, and future expectations of genetic research and the influence of these measures on the perceived disadvantages of genetic testing among Black African immigrants/refugees. Using a cross-sectional survey design, a nonprobability sample (n = 212) of Black African immigrants/refugees was administered a questionnaire. Participants ranged in age from 18 to 61 years (mean = 38.91, SD = 9.78). The questionnaire consisted of 5 instruments: (a) sociodemographic characteristics, (b) Knowledge of Medical Genetics scale, (c) Group-Based Medical Mistrust Scale, (d) Future Expectations/Anticipated Consequences of Genetics Research scale, and (e) Perceived Disadvantages of Genetic Testing scale. Participants were concerned that genetic research may result in scientists 'playing God,' interfering with the natural order of life. In multivariate analyses, the perceived disadvantages of genetic testing increased as medical mistrust and anticipated negative impacts of genetic testing increased. Increase in genetic knowledge contributed to a decrease in perceived disadvantages. Our findings suggest that recruitment of Black African immigrants/refugees in genetic studies should address potential low knowledge of genetics, concerns about medical mistrust, the expectations/anticipated consequences of genetic research, and the perceived disadvantages of genetic testing.

  19. Genetic and environmental risk factors for rheumatoid arthritis in a UK African ancestry population: the GENRA case-control study.

    Science.gov (United States)

    Traylor, Matthew; Curtis, Charles; Patel, Hamel; Breen, Gerome; Hyuck Lee, Sang; Xu, Xiaohui; Newhouse, Stephen; Dobson, Richard; Steer, Sophia; Cope, Andrew P; Markus, Hugh S; Lewis, Cathryn M; Scott, Ian C

    2017-08-01

    To evaluate whether genetic and environmental factors associated with RA in European and Asian ancestry populations are also associated with RA in African ancestry individuals. A case-control study was undertaken in 197 RA cases and 868 controls of African ancestry (Black African, Black Caribbean or Black British ethnicity) from South London. Smoking and alcohol consumption data at RA diagnosis was captured. Genotyping was undertaken (Multi-Ethnic Genotyping Array) and human leukocyte antigen (HLA) alleles imputed. The following European/Asian RA susceptibility factors were tested: 99 genome-wide loci combined into a genetic risk score; HLA region [20 haplotypes; shared epitope (SE)]; smoking; and alcohol consumption. The SE was tested for its association with radiological erosions. Logistic regression models were used, including ancestry-informative principal components, to control for admixture. European/Asian susceptibility loci were associated with RA in African ancestry individuals. The genetic risk score provided an odds ratio (OR) for RA of 1.53 (95% CI: 1.31, 1.79; P = 1.3 × 10 - 7 ). HLA haplotype ORs in European and African ancestry individuals were highly correlated ( r = 0.83, 95% CI: 0.56, 0.94; P = 1.1 × 10 - 4 ). Ever-smoking increased (OR = 2.36, 95% CI: 1.46, 3.82; P = 4.6 × 10 - 4 ) and drinking alcohol reduced (OR = 0.34, 95% CI: 0.20, 0.56; P = 2.7 × 10 - 5 ) RA risk in African ancestry individuals. The SE was associated with erosions (OR = 2.61, 95% CI: 1.36, 5.01; P = 3.9 × 10 - 3 ). Gene-environment RA risk factors identified in European/Asian ancestry populations are relevant in African ancestry individuals. As modern statistical methods facilitate analysing ancestrally diverse populations, future genetic studies should incorporate African ancestry individuals to ensure their implications for precision medicine are universally applicable. © The Author 2017. Published by Oxford University Press on behalf of the British Society for

  20. Genetic testing of canine degenerative myelopathy in the South African Boxer dog population

    Directory of Open Access Journals (Sweden)

    Gareth E. Zeiler

    2013-10-01

    Full Text Available Canine degenerative myelopathy (DM is a progressive disease process that is diagnosed late in life and mainly affects the pelvic limbs. Factors that make an ante-mortem definitive diagnosis of DM include: an insidious onset and clinical manifestation that mimics other disease processes of the pelvic limbs (hip dysplasia, cranial cruciate ligament rupture, etc. or there may even be concurrent disease processes, old-age onset and lack of reliable diagnostic methods. Until recently, South African dog owners had to submit samples to laboratories overseas for genetic testing in order to confirm an affected dog (homozygous A/A and to aid in the ante-mortem diagnosis of DM. Only affected dogs have been confirmed to manifest the clinical signs of DM. This study aimed to verify whether genetic testing by a local genetic laboratory was possible in order to detect a missense mutation of the superoxide dismutase gene (SOD1 that is implicated in causing the clinical signs of DM. The study also aimed to detect and map the inheritance of this disease process in a local Boxer dog population where the pedigree of the sampled population was known. Venous blood collected from Boxer dogs using a simple random sampling technique. The samples were genotyped for the SOD1:c.118G>A polymorphism. Carrier and affected Boxer dogs were detected. A pedigree that demonstrated the significance of inheriting a carrier or affected state in the population was mapped. The present study concludes that genotyping of the missense mutation in Boxer dogs is possible in South Africa. There are carrier and affected Boxer dogs in the local population, making DM a plausible diagnosis in aged dogs presenting with pelvic limb pathology.

  1. Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons.

    Science.gov (United States)

    Curto, M; Puppo, P; Kratschmer, S; Meimberg, H

    2017-08-22

    Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572-575, 2005; Saunders and Gibson, J Ecol 93: 649-652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168-173, 2004; Silvertown et al., J Ecol 93: 653-657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above. Genetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands. These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different

  2. The influence of acculturation and breast cancer-specific distress on perceived barriers to genetic testing for breast cancer among women of African descent.

    Science.gov (United States)

    Sussner, Katarina M; Thompson, Hayley S; Jandorf, Lina; Edwards, Tiffany A; Forman, Andrea; Brown, Karen; Kapil-Pair, Nidhi; Bovbjerg, Dana H; Schwartz, Marc D; Valdimarsdottir, Heiddis B

    2009-09-01

    Rising health disparities are increasingly evident in relation to use of genetic services (including genetic counseling and testing) for breast cancer risk, with women of African descent less likely to use genetic services compared with Whites. Meanwhile, little is known regarding potential within-group acculturation and psychological differences underlying perceived barriers to genetic testing among women of African descent. Hypothesized contributions of acculturation factors and breast cancer-specific distress to perceived barriers to genetic testing were examined with a statistical analysis of baseline data from 146 women of African descent (56% US born and 44% foreign born) meeting genetic breast cancer risk criteria and participating in a larger longitudinal study that included the opportunity for free genetic counseling and testing. Perceived barriers assessed included: (1) anticipation of negative emotional reactions, (2) stigma, (3) confidentiality concerns, (4) family-related worry, and (5) family-related guilt associated with genetic testing. In multivariate analyses, being foreign born was a significant predictor of anticipated negative emotional reactions about genetic testing (beta=0.26; SE=0.11; p=0.01). Breast cancer-specific distress scores (avoidance symptoms) were positively related to anticipated negative emotional reactions (beta=0.02; SE=0.005; p=barriers to genetic testing among women of African descent. The potential utility of culturally tailored genetic counseling services taking into account such influences and addressing emotional and psychological concerns of women considering genetic testing for breast cancer should be investigated.

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

    Science.gov (United States)

    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

  4. Mechanisms of population heterogeneity among molting common mergansers on Kodiak Island, Alaska: Implications for genetic assessments of migratory connectivity

    Science.gov (United States)

    Pearce, John M.; Zwiefelhofer, Denny; Maryanski, Nate

    2009-01-01

    Quantifying population genetic heterogeneity within nonbreeding aggregations can inform our understanding of patterns of site fidelity, migratory connectivity, and gene flow between breeding and nonbreeding areas. However, characterizing mechanisms that contribute to heterogeneity, such as migration and dispersal, is required before site fidelity and migratory connectivity can be assessed accurately. We studied nonbreeding groups of Common Mergansers (Mergus merganser) molting on Kodiak Island, Alaska, from 2005 to 2007, using banding data to assess rates of recapture, mitochondrial (mt) DNA to determine natal area, and nuclear microsatellite genotypes to assess dispersal. Using baseline information from differentiated mtDNA haplogroups across North America, we were able to assign individuals to natal regions and document population genetic heterogeneity within and among molting groups. Band-recovery and DNA data suggest that both migration from and dispersal among natal areas contribute to admixed groups of males molting on Kodiak Island. A lack of differentiation in the Common Merganser's nuclear, bi-parentally inherited DNA, observed across North America, implies that dispersal can mislead genetic assessments of migratory connectivity and assignments of nonbreeding individuals to breeding areas. Thus multiple and independent data types are required to account for such behaviors before accurate assessments of migratory connectivity can be made.

  5. Genetic variation in IL-16 miRNA target site and time to prostate cancer diagnosis in African American men

    Science.gov (United States)

    Hughes, Lucinda; Ruth, Karen; Rebbeck, Timothy R.; Giri, Veda N.

    2013-01-01

    Background Men with a family history of prostate cancer and African American men are at high risk for prostate cancer and in need of personalized risk estimates to inform screening decisions. This study evaluated genetic variants in genes encoding microRNA (miRNA) binding sites for informing of time to prostate cancer diagnosis among ethnically-diverse, high-risk men undergoing prostate cancer screening. Methods The Prostate Cancer Risk Assessment Program (PRAP) is a longitudinal screening program for high-risk men. Eligibility includes men ages 35-69 with a family history of prostate cancer or African descent. Participants with ≥ 1 follow-up visit were included in the analyses (n=477). Genetic variants in regions encoding miRNA binding sites in four target genes (ALOX15, IL-16, IL-18, and RAF1) previously implicated in prostate cancer development were evaluated. Genotyping methods included Taqman® SNP Genotyping Assay (Applied Biosystems) or pyrosequencing. Cox models were used to assess time to prostate cancer diagnosis by risk genotype. Results Among 256 African Americans with ≥ one follow-up visit, the TT genotype at rs1131445 in IL-16 was significantly associated with earlier time to prostate cancer diagnosis vs. the CC/CT genotypes (p=0.013), with a suggestive association after correction for false-discovery (p=0.065). Hazard ratio after controlling for age and PSA for TT vs. CC/CT among African Americans was 3.0 (95% CI 1.26-7.12). No association to time to diagnosis was detected among Caucasians by IL-16 genotype. No association to time to prostate cancer diagnosis was found for the other miRNA target genotypes. Conclusions Genetic variation in IL-16 encoding miRNA target site may be informative of time to prostate cancer diagnosis among African American men enrolled in prostate cancer risk assessment, which may inform individualized prostate cancer screening strategies in the future. PMID:24061634

  6. Genetic variation at the ApoB 3' HVR minisatellite locus in the Mbenzele Pygmies from the Central African Republic.

    Science.gov (United States)

    Destro-Bisol, Giovanni; Belledi, Michele; Capelli, Cristian; Maviglia, Riccardo; Spedini, Gabriella

    2000-09-01

    This study analyzes the polymorphic minisatellite ApoB 3' HVR in the Mbenzele Pygmies from the Central African Republic. A total of 14 alleles was observed, with frequencies ranging from 0.020 (19, 21, 27, and 45 repeat unit alleles) to 0.210 (37 repeat unit allele). Departure from Hardy-Weinberg equilibrium was not statistically significant. The estimated heterozygosity was 0.874 +/- 0.016. Taking data from the literature into consideration, the results support the hypothesis that the Africans are different from non-Africans due to greater ApoB 3' HVR genetic diversity and a unimodal profile of ApoB 3' HVR allele frequency distribution. Interpopulational relationships were also analyzed using an F(ST) based genetic distance. The results highlight the similarity between the Mbenzele Pygmies and Bantu-speaking groups (Ewondo and Zulu), and the divergence between the Mbenzele and San, the two groups which are often considered to be the most direct descendants of proto-Africans. Am. J. Hum. Biol. 12:588-592, 2000. Copyright 2000 Wiley-Liss, Inc.

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

    Science.gov (United States)

    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. © 2015 Wiley Periodicals, Inc.

  8. STRESS, RELATIONSHIP SATISFACTION, AND HEALTH AMONG AFRICAN AMERICAN WOMEN: GENETIC MODERATION OF EFFECTS

    Science.gov (United States)

    Lei, Man-Kit; Beach, Steven R. H.; Simons, Ronald L.; Barr, Ashley B.; Cutrona, Carolyn E.; Philibert, Robert A.

    2015-01-01

    We examined whether romantic relationship satisfaction would serve as a link between early and later stressors which in turn would influence the Thyroid Function Index (TFI), an indicator of physiological stress response. Using the framework of genetic susceptibility theory combined with hypotheses derived from the vulnerability-stress-adaptation and stress-generation models, we tested whether the hypothesized mediational model would be conditioned by 5-HTTLPR genotype, with greater effects and stronger evidence of mediation among carriers of the “s” allele. In a sample of African American women in romantic relationships (n = 270), we found that 5-HTTLPR moderated each stage of the hypothesized mediational model in a “for better or for worse” manner. That is genetic polymorphisms function to exacerbate not only the detrimental impact of negative environments (i.e. “for worse effects”) but also the beneficial impact of positive environments (i.e. “for better effects”). The effect of early stress on relationship satisfaction was greater among carriers of the “short” allele than among those who did not carry the short allele, and was significantly different in both the “for better” and “for worse” direction. Likewise, the effect of relationship satisfaction on later stressors was moderated in a “for better” or “for worse” manner. Finally, impact on physiological stress, indexed using TFI level, indicated that the impact of later stressors on TFI level was greater in the presence of the short allele, and also followed a “for better” or “for worse” pattern. As expected, the proposed mediational model provided a better fit for “s” allele carriers. PMID:26376424

  9. Pleistocene aridification cycles shaped the contemporary genetic architecture of Southern African baboons.

    Directory of Open Access Journals (Sweden)

    Riashna Sithaldeen

    Full Text Available Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa's faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons (Papio spp. supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes, are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Nef through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region's biodiversity.

  10. The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii).

    Science.gov (United States)

    Kurita, Kazuki; Toda, Mamoru

    2017-04-01

    We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history. In this study, analysis of mtDNA sequences and microsatellite polymorphism demonstrate contrasting patterns of phylogeography and population structure: P. kishinouyei exhibits a lower genetic variability and lower genetic differentiation among islands than P. stimpsonii, consistent with recent population expansion. However, historical demographic analyses indicate that the relatively high genetic uniformity in P. kishinouyei is not attributable to recent expansion. We detected significant isolation-by-distance patterns among P. kishinouyei populations on the land bridge islands, but not among P. stimpsonii populations occurring on those same islands. Our results suggest that P. kishinouyei populations have maintained gene flows across islands until recently, probably via ephemeral Quaternary land bridges. The lower genetic variability in P. kishinouyei may also indicate smaller effective population sizes on average than that of P. stimpsonii. We interpret these differences as a consequence of ecological divergence between the two species, primarily in trophic level and habitat preference.

  11. Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies.

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    Joseph P Jarvis

    Full Text Available African Pygmy groups show a distinctive pattern of phenotypic variation, including short stature, which is thought to reflect past adaptation to a tropical environment. Here, we analyze Illumina 1M SNP array data in three Western Pygmy populations from Cameroon and three neighboring Bantu-speaking agricultural populations with whom they have admixed. We infer genome-wide ancestry, scan for signals of positive selection, and perform targeted genetic association with measured height variation. We identify multiple regions throughout the genome that may have played a role in adaptive evolution, many of which contain loci with roles in growth hormone, insulin, and insulin-like growth factor signaling pathways, as well as immunity and neuroendocrine signaling involved in reproduction and metabolism. The most striking results are found on chromosome 3, which harbors a cluster of selection and association signals between approximately 45 and 60 Mb. This region also includes the positional candidate genes DOCK3, which is known to be associated with height variation in Europeans, and CISH, a negative regulator of cytokine signaling known to inhibit growth hormone-stimulated STAT5 signaling. Finally, pathway analysis for genes near the strongest signals of association with height indicates enrichment for loci involved in insulin and insulin-like growth factor signaling.

  12. Genetic and morphological characterisation of the Ankole Longhorn cattle in the African Great Lakes region

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    Okeyo Mwai A

    2008-09-01

    Full Text Available Abstract The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size, genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were genotyped using 15 DNA microsatellites. Femoral length, horn length, horn circumference, rump height, body length and fore-limb circumference showed the largest differences between regions. An overall FST index indicated that 2.7% of the total genetic variation was present among sub-populations. The least differentiation was observed between the two sub-populations of Mbarara south and Luwero in Uganda, while the highest level of differentiation was observed between the Mugamba in Burundi and Malagarasi in Tanzania. An estimated membership of four for the inferred clusters from a model-based Bayesian approach was obtained. Both analyses on distance-based and model-based methods consistently isolated the Mugamba sub-population in Burundi from the others.

  13. Evolutionary forces shaping genomic islands of population differentiation in humans

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    Hofer Tamara

    2012-03-01

    Full Text Available Abstract Background Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. Methods Individual SNPs of the Human Genome Diversity Panel (HGDP showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM. A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. Results Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. Conclusions Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i as much as 20% of islands are in non-genic regions ii these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii most loci are

  14. Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan

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    Nobushima Fuyuo

    2006-10-01

    Full Text Available Abstract Background Morus boninensis, is an endemic plant of the Bonin (Ogasawara Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Results Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. Conclusion The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a

  15. Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.

    Science.gov (United States)

    Tani, Naoki; Yoshimaru, Hiroshi; Kawahara, Takayuki; Hoshi, Yoshio; Nobushima, Fuyuo; Yasui, Takaya

    2006-10-11

    Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.

  16. Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis)

    Czech Academy of Sciences Publication Activity Database

    Phalen, D. N.; Hall, J.; Ganesh, G.; Hartigan, Ashlie; Smith, C.; De Jong, C.; Field, H.; Rose, K.

    2017-01-01

    Roč. 98, č. 2 (2017), s. 428-437 ISSN 0022-2372 Institutional support: RVO:60077344 Keywords : diversity * flying fox * mitochondrial DNA * phylogeny * Pteropus melanotus natalis Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 1.630, year: 2016

  17. Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae detect gene flow between island populations and genetic diversity loss

    Directory of Open Access Journals (Sweden)

    Sammler Svenja

    2012-10-01

    Full Text Available Abstract Background The Visayan Tarictic Hornbill (Penelopides panini and the Walden’s Hornbill (Aceros waldeni are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp of the mitochondrial control region I and at 12–19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay, and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant sister taxa, the Luzon Tarictic Hornbill (P. manillae from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Results Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. Conclusions We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A

  18. Genetic diversity and connectivity in the East African giant mud crab Scylla serrata: Implications for fisheries management.

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    Cyrus Rumisha

    Full Text Available The giant mud crab Scylla serrata provides an important source of income and food to coastal communities in East Africa. However, increasing demand and exploitation due to the growing coastal population, export trade, and tourism industry are threatening the sustainability of the wild stock of this species. Because effective management requires a clear understanding of the connectivity among populations, this study was conducted to assess the genetic diversity and connectivity in the East African mangrove crab S. serrata. A section of 535 base pairs of the cytochrome oxidase subunit I (COI gene and eight microsatellite loci were analysed from 230 tissue samples of giant mud crabs collected from Kenya, Tanzania, Mozambique, Madagascar, and South Africa. Microsatellite genetic diversity (He ranged between 0.56 and 0.6. The COI sequences showed 57 different haplotypes associated with low nucleotide diversity (current nucleotide diversity = 0.29%. In addition, the current nucleotide diversity was lower than the historical nucleotide diversity, indicating overexploitation or historical bottlenecks in the recent history of the studied population. Considering that the coastal population is growing rapidly, East African countries should promote sustainable fishing practices and sustainable use of mangrove resources to protect mud crabs and other marine fauna from the increasing pressure of exploitation. While microsatellite loci did not show significant genetic differentiation (p > 0.05, COI sequences revealed significant genetic divergence between sites on the East coast of Madagascar (ECM and sites on the West coast of Madagascar, mainland East Africa, as well as the Seychelles. Since East African countries agreed to achieve the Convention on Biological Diversity (CBD target to protect over 10% of their marine areas by 2020, the observed pattern of connectivity and the measured genetic diversity can serve to provide useful information for designing

  19. Genetic variants demonstrating flip-flop phenomenon and breast cancer risk prediction among women of African ancestry.

    Science.gov (United States)

    Wang, Shengfeng; Qian, Frank; Zheng, Yonglan; Ogundiran, Temidayo; Ojengbede, Oladosu; Zheng, Wei; Blot, William; Nathanson, Katherine L; Hennis, Anselm; Nemesure, Barbara; Ambs, Stefan; Olopade, Olufunmilayo I; Huo, Dezheng

    2018-04-01

    Few studies have evaluated the performance of existing breast cancer risk prediction models among women of African ancestry. In replication studies of genetic variants, a change in direction of the risk association is a common phenomenon. Termed flip-flop, it means that a variant is risk factor in one population but protective in another, affecting the performance of risk prediction models. We used data from the genome-wide association study (GWAS) of breast cancer in the African diaspora (The Root consortium), which included 3686 participants of African ancestry from Nigeria, USA, and Barbados. Polygenic risk scores (PRSs) were constructed from the published odds ratios (ORs) of four sets of susceptibility loci for breast cancer. Discrimination capacity was measured using the area under the receiver operating characteristic curve (AUC). Flip-flop phenomenon was observed among 30~40% of variants across studies. Using the 34 variants with consistent directionality among previous studies, we constructed a PRS with AUC of 0.531 (95% confidence interval [CI]: 0.512-0.550), which is similar to the PRS using 93 variants and ORs from European ancestry populations (AUC = 0.525, 95% CI: 0.506-0.544). Additionally, we found the 34-variant PRS has good discriminative accuracy in women with family history of breast cancer (AUC = 0.586, 95% CI: 0.532-0.640). We found that PRS based on variants identified from prior GWASs conducted in women of European and Asian ancestries did not provide a comparable degree of risk stratification for women of African ancestry. Further large-scale fine-mapping studies in African ancestry populations are desirable to discover population-specific genetic risk variants.

  20. Genetic polymorphisms in prehistoric Pacific islanders determined by analysis of ancient bone DNA.

    Science.gov (United States)

    Hagelberg, E; Clegg, J B

    1993-05-22

    A previously characterized Asian-specific mitochondrial DNA (mtDNA) length mutation has been detected in DNA isolated from prehistoric human bones from Polynesia, including Hawaii, Chatham Islands and Society Islands. In contrast, the Asian mutation was absent in skeletal samples from the Melanesian archipelagos of New Britain and Vanuatu and in the oldest samples from Fiji, Tonga and Samoa in the central Pacific (2700-1600 years BP) although it was present in a more recent prehistoric sample from Tonga. These results, augmented by informative DNA sequence data from the hypervariable region of mtDNA, fail to support current views that the central Pacific was settled directly by voyagers from island Southeast Asia, the putative ancestors of modern Polynesians. An earlier occupation by peoples from the neighbouring Melanesian archipelagos seems more likely.

  1. Complex patterns of genetic and phenotypic divergence in an island bird and the consequences for delimiting conservation units.

    Science.gov (United States)

    Phillimore, A B; Owens, I P F; Black, R A; Chittock, J; Burke, T; Clegg, S M

    2008-06-01

    Substantial phenotypic and genetic variation is often found below the species level and this may be useful in quantifying biodiversity and predicting future diversification. However, relatively few studies have tested whether different aspects of intraspecific variation show congruent patterns across populations. Here, we quantify several aspects of divergence between 13 insular populations of an island endemic bird, the Vanuatu white-eye (Zosterops flavifrons). The components of divergence studied are mitochondrial DNA (mtDNA), nuclear DNA microsatellites and morphology. These different aspects of divergence present subtly different scenarios. For instance, an mtDNA phylogenetic tree reveals a potential cryptic species on the most southerly island in Vanuatu and considerable divergence between at least two other major phylogroups. Microsatellite loci suggest that population genetic divergence between insular populations, both between and within phylogroups, is substantial, a result that is consistent with a low level of interisland gene flow. Finally, most populations were found to be strongly morphologically divergent, but no single population was morphologically diagnosable from all others. Taken together, our results show that, although many measures of divergence are concordant in this system, the number of divergent units identified varies widely depending on the characters considered and approach used. A continuum of divergence and a degree of discordance between different characters are both to be expected under simple models of evolution, but they present problems in terms of delimiting conservation units.

  2. Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

    Directory of Open Access Journals (Sweden)

    Stephanie G Schuttler

    Full Text Available Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana and Asian (Elephas maximus species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and

  3. Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

    Science.gov (United States)

    Schuttler, Stephanie G; Philbrick, Jessica A; Jeffery, Kathryn J; Eggert, Lori S

    2014-01-01

    Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r) tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r) tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines

  4. Genetic variability of Rickettsia spp. in Ixodes persulcatus ticks from continental and island areas of the Russian Far East.

    Science.gov (United States)

    Igolkina, Y; Bondarenko, E; Rar, V; Epikhina, T; Vysochina, N; Pukhovskaya, N; Tikunov, A; Ivanov, L; Golovljova, I; Ivanov, М; Tikunova, N

    2016-10-01

    Rickettsia spp. are intracellular Gram-negative bacteria transmitted by arthropods. Two potentially pathogenic rickettsiae, Candidatus Rickettsia tarasevichiae and Rickettsia helvetica, have been found in unfed adult Ixodes persulcatus ticks. The aim of this study was to assess the prevalence and genetic variability of Rickettsia spp. in I. persulcatus ticks collected from different locations in the Russian Far East. In total, 604 adult I. persulcatus ticks collected from four sites in the Khabarovsk Territory (continental area) and one site in Sakhalin Island were examined for the presence of Rickettsia spp. by real-time PCR. Nested PCR with species-specific primers and sequencing were used for genotyping of revealed rickettsiae. The overall prevalence of Rickettsia spp. in ticks collected in different sites varied from 67.9 to 90.7%. However, the proportion of different Rickettsia species observed in ticks from Sakhalin Island significantly differed from that in ticks from the Khabarovsk Territory. In Sakhalin Island, R. helvetica prevailed in examined ticks, while Candidatus R. tarasevichiae was predominant in the Khabarovsk Territory. For gltA and ompB gene fragments, the sequences obtained for Candidatus R. tarasevichiae from all studied sites were identical to each other and to the known sequences of this species. According to sequence analysis of gltA, оmpB and sca4 genes, R. helvetica isolates from Sakhalin Island and the Khabarovsk Territory were identical to each other, but they differed from R. helvetica from other regions and from those found in other tick species. For the first time, DNA of pathogenic Rickettsia heilongjiangensis was detected in I. persulcatus ticks in two sites from the Khabarovsk Territory. The gltA, ompA and оmpB gene sequences of R. heilongjiangensis were identical to or had solitary mismatches with the corresponding sequences of R. heilongjiangensis found in other tick species. Copyright © 2016 Elsevier GmbH. All rights

  5. Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae in Western Mediterranean: out of the Iberian Peninsula and into the islands

    Directory of Open Access Journals (Sweden)

    Valeriia Shiposha

    2016-09-01

    Full Text Available Annual Mediterranean species of the genus Brachypodium are promising model plants for energy crops since their selfing nature and short-life cycles are an advantage in breeding programs. The false brome, B. distachyon, has already been sequenced and new genomic initiatives have triggered the de-novo genome sequencing of its close relatives such as B. stacei, a species that was until recently mistaken for B. distachyon. However, the success of these initiatives hinges on detailed knowledge about the distribution of genetic variation within and among populations for the effective use of germplasm in a breeding program. Understanding population genetic diversity and genetic structure is also an important prerequisite for designing effective experimental populations for genomic wide studies. However, population genetic data are still limited in B. stacei. We therefore selected and amplified 10 nuclear microsatellite markers to depict patterns of population structure and genetic variation among 181 individuals from 19 populations of B. stacei occurring in its predominant range, the western Mediterranean area: mainland Iberian Peninsula, continental Balearic Islands and oceanic Canary Islands. Our genetic results support the occurrence of a predominant selfing system with extremely high levels of homozygosity across the analyzed populations. Despite the low level of genetic variation found, two different genetic clusters were retrieved, one clustering all SE Iberian mainland populations and the island of Minorca and another one grouping all S Iberian mainland populations, the Canary Islands and all Majorcan populations except one that clustered with the former group. These results, together with a high sharing of alleles (89% suggest different colonization routes from the mainland Iberian Peninsula into the islands. A recent colonization scenario could explain the relatively low levels of genetic diversity and low number of alleles found in the Canary

  6. Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands.

    Science.gov (United States)

    Shiposha, Valeriia; Catalán, Pilar; Olonova, Marina; Marques, Isabel

    2016-01-01

    Annual Mediterranean species of the genus Brachypodium are promising model plants for energy crops since their selfing nature and short-life cycles are an advantage in breeding programs. The false brome, B. distachyon, has already been sequenced and new genomic initiatives have triggered the de-novo genome sequencing of its close relatives such as B. stacei, a species that was until recently mistaken for B. distachyon. However, the success of these initiatives hinges on detailed knowledge about the distribution of genetic variation within and among populations for the effective use of germplasm in a breeding program. Understanding population genetic diversity and genetic structure is also an important prerequisite for designing effective experimental populations for genomic wide studies. However, population genetic data are still limited in B. stacei. We therefore selected and amplified 10 nuclear microsatellite markers to depict patterns of population structure and genetic variation among 181 individuals from 19 populations of B. stacei occurring in its predominant range, the western Mediterranean area: mainland Iberian Peninsula, continental Balearic Islands and oceanic Canary Islands. Our genetic results support the occurrence of a predominant selfing system with extremely high levels of homozygosity across the analyzed populations. Despite the low level of genetic variation found, two different genetic clusters were retrieved, one clustering all SE Iberian mainland populations and the island of Minorca and another one grouping all S Iberian mainland populations, the Canary Islands and all Majorcan populations except one that clustered with the former group. These results, together with a high sharing of alleles (89%) suggest different colonization routes from the mainland Iberian Peninsula into the islands. A recent colonization scenario could explain the relatively low levels of genetic diversity and low number of alleles found in the Canary Islands

  7. Beck Depression Inventory-II: Factor Analyses with Three Groups of Midlife Women of African Descent in the Midwest, the South, and the U.S. Virgin Islands.

    Science.gov (United States)

    Gary, Faye A; Yarandi, Hossein; Evans, Edris; Still, Carolyn; Mickels, Prince; Hassan, Mona; Campbell, Doris; Conic, Ruzica

    2018-03-01

    This research encompasses a factor analysis of the Beck Depression Inventory-II (BDI-II), which involves three groups of midlife women of African descent who reside in the Midwest, the South, and the U.S. Virgin Islands. The purpose of the study was to determine the factor structure of the BDI-II when administered to a sample of women aged 40-65 of African descent who reside in the three distinct geographical regions of the United States. A correlational, descriptive design was used, and 536 women of African descent were invited to participate in face-to-face interviews that transpired in community settings. Results of the factor analysis revealed a two-factor explanation. Factor one included symptoms such as punishment feelings and pessimism (cognitive), and the second factor included symptoms such as tiredness and loss of energy (somatic-affective). The application of the Beck Depression Inventory-II among the three groups of women generated specific information about each group and common findings across the groups. Knowledge gained from the research could help to guide specific intervention programs for the three groups of women, and explicate the common approaches that could be used for the three groups.

  8. Using Hadoop MapReduce for Parallel Genetic Algorithms: A Comparison of the Global, Grid and Island Models.

    Science.gov (United States)

    Ferrucci, Filomena; Salza, Pasquale; Sarro, Federica

    2017-06-29

    The need to improve the scalability of Genetic Algorithms (GAs) has motivated the research on Parallel Genetic Algorithms (PGAs), and different technologies and approaches have been used. Hadoop MapReduce represents one of the most mature technologies to develop parallel algorithms. Based on the fact that parallel algorithms introduce communication overhead, the aim of the present work is to understand if, and possibly when, the parallel GAs solutions using Hadoop MapReduce show better performance than sequential versions in terms of execution time. Moreover, we are interested in understanding which PGA model can be most effective among the global, grid, and island models. We empirically assessed the performance of these three parallel models with respect to a sequential GA on a software engineering problem, evaluating the execution time and the achieved speedup. We also analysed the behaviour of the parallel models in relation to the overhead produced by the use of Hadoop MapReduce and the GAs' computational effort, which gives a more machine-independent measure of these algorithms. We exploited three problem instances to differentiate the computation load and three cluster configurations based on 2, 4, and 8 parallel nodes. Moreover, we estimated the costs of the execution of the experimentation on a potential cloud infrastructure, based on the pricing of the major commercial cloud providers. The empirical study revealed that the use of PGA based on the island model outperforms the other parallel models and the sequential GA for all the considered instances and clusters. Using 2, 4, and 8 nodes, the island model achieves an average speedup over the three datasets of 1.8, 3.4, and 7.0 times, respectively. Hadoop MapReduce has a set of different constraints that need to be considered during the design and the implementation of parallel algorithms. The overhead of data store (i.e., HDFS) accesses, communication, and latency requires solutions that reduce data store

  9. Analysis of genetic diversity of Piper spp. in Hainan Island (China ...

    African Journals Online (AJOL)

    Inter-simple sequence repeat (ISSR) analysis was used to evaluate the genetic variation of Piper spp. from Hainan, China. 247 polymorphic bands out of a total of 248 (99.60%) were generated from 74 individual plants of Piper spp. The overall level of genetic diversity among Piper spp. in Hainan was high, with the mean ...

  10. Parallel island genetic algorithm applied to a nuclear power plant auxiliary feedwater system surveillance tests policy optimization

    International Nuclear Information System (INIS)

    Pereira, Claudio M.N.A.; Lapa, Celso M.F.

    2003-01-01

    In this work, we focus the application of an Island Genetic Algorithm (IGA), a coarse-grained parallel genetic algorithm (PGA) model, to a Nuclear Power Plant (NPP) Auxiliary Feedwater System (AFWS) surveillance tests policy optimization. Here, the main objective is to outline, by means of comparisons, the advantages of the IGA over the simple (non-parallel) genetic algorithm (GA), which has been successfully applied in the solution of such kind of problem. The goal of the optimization is to maximize the system's average availability for a given period of time, considering realistic features such as: i) aging effects on standby components during the tests; ii) revealing failures in the tests implies on corrective maintenance, increasing outage times; iii) components have distinct test parameters (outage time, aging factors, etc.) and iv) tests are not necessarily periodic. In our experiments, which were made in a cluster comprised by 8 1-GHz personal computers, we could clearly observe gains not only in the computational time, which reduced linearly with the number of computers, but in the optimization outcome

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

    Science.gov (United States)

    Archie, Elizabeth A; Moss, Cynthia J; Alberts, Susan C

    2006-03-07

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

  12. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline; Ho, Shwen; Pires, Inê s S.; Tester, Mark A.; Negrã o, Só nia; Schmö cke, Sandra M.

    2017-01-01

    with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through

  13. Comparison of deterministically predicted genetic gains with those realised in a South African Eucalyptus grandis breeding program

    CSIR Research Space (South Africa)

    Verryn, SD

    2009-06-01

    Full Text Available breeding endeavours, are essential for modelling and predicting the economic impact of further genetic improvement. Materials and Methods The “South African Population” (plantation origin) breeding lines with the F1 generation (‘SSO’-series), F2 (‘A... trials SSO1 and SSO4, as representatives of the improvement. It was assumed that selective thinning of the ‘male families’ took place at 50%. (Male families are trees which contribute towards the pollen cloud. These families may be selectively thinned...

  14. Genetic polymorphism of CSN1S2 in South African dairy goat ...

    African Journals Online (AJOL)

    Rulien

    2016-12-24

    Dec 24, 2016 ... variation for αs2-casein in the South African goat populations ... of Pretoria's experimental farm (Saanens) and commercial goat farms in the provinces of Gauteng. (Toggenburg), North West (British Alpine and Toggenburg), ...

  15. Evidence of stable genetic structure across a remote island archipelago through self-recruitment in a widely dispersed coral reef fish

    KAUST Repository

    Priest, Mark

    2012-11-19

    We used microsatellite markers to assess the population genetic structure of the scribbled rabbitfish Siganus spinus in the western Pacific. This species is a culturally important food fish in the Mariana Archipelago and subject to high fishing pressure. Our primary hypothesis was to test whether the individuals resident in the southern Mariana Island chain were genetically distinct and hence should be managed as discrete stocks. In addition to spatial sampling of adults, newly-settled individuals were sampled on Guam over four recruitment events to assess the temporal stability of the observed spatial patterns, and evidence of self-recruitment. We found significant genetic structure in S. spinus across the western Pacific, with Bayesian analyses revealing three genetically distinct clusters: the southernMariana Islands, east Micronesia, and the west Pacific; with the southern Mariana Islands beingmore strongly differentiated fromthe rest of the region. Analyses of temporal samples from Guam indicated the southern Mariana cluster was stable over time, with no genetic differentiation between adults versus recruits, or between samples collected across four separate recruitment events spanning 11 months. Subsequent assignment tests indicated seven recruits had self-recruited from within the Southern Mariana Islands population. Our results confirm the relative isolation of the southern Mariana Islands population and highlight how local processes can act to isolate populations that, by virtue of their broad-scale distribution, have been subject to traditionally high gene flows. Our results add to a growing consensus that self-recruitment is a highly significant influence on the population dynamics of tropical reef fish. 2012 The Authors. Ecology and Evolution published by Blackwell Publishing Ltd.

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

    Directory of Open Access Journals (Sweden)

    Nuha Elhassan

    Full Text Available 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.

  17. Experiences of discrimination and their impact on the mental health among African American, Asian and Pacific Islander, and Latino men who have sex with men.

    Science.gov (United States)

    Choi, Kyung-Hee; Paul, Jay; Ayala, George; Boylan, Ross; Gregorich, Steven E

    2013-05-01

    We examined the associations between specific types and sources of discrimination and mental health outcomes among US racial/ethnic minority men who have sex with men (MSM) and how these associations varied by race/ethnicity. A chain-referral sample of 403 African American, 393 Asian and Pacific Islander (API), and 400 Latino MSM recruited in Los Angeles County, California completed a standardized questionnaire. Data were obtained from the Ethnic Minority Men's Health Study from May 2008 to October 2009. Past-year experiences of racism within the general community and perceived homophobia among heterosexual friends were positively associated with depression and anxiety. Past-year homophobia experienced within the general community was also positively associated with anxiety. These statistically significant associations did not vary across racial/ethnic groups. The positive association of perceived racism within the gay community with anxiety differed by race/ethnicity, and was statistically significant only for APIs. Perceived homophobia within the family was not associated with either depression or anxiety. Higher levels of experiences of discrimination were associated with psychological distress among MSM of color. However, specific types and sources of discrimination were differentially linked to negative mental health outcomes among African American, API, and Latino MSM.

  18. Race and Beta-Blocker Survival Benefit in Patients With Heart Failure: An Investigation of Self-Reported Race and Proportion of African Genetic Ancestry.

    Science.gov (United States)

    Luzum, Jasmine A; Peterson, Edward; Li, Jia; She, Ruicong; Gui, Hongsheng; Liu, Bin; Spertus, John A; Pinto, Yigal M; Williams, L Keoki; Sabbah, Hani N; Lanfear, David E

    2018-05-08

    It remains unclear whether beta-blockade is similarly effective in black patients with heart failure and reduced ejection fraction as in white patients, but self-reported race is a complex social construct with both biological and environmental components. The objective of this study was to compare the reduction in mortality associated with beta-blocker exposure in heart failure and reduced ejection fraction patients by both self-reported race and by proportion African genetic ancestry. Insured patients with heart failure and reduced ejection fraction (n=1122) were included in a prospective registry at Henry Ford Health System. This included 575 self-reported blacks (129 deaths, 22%) and 547 self-reported whites (126 deaths, 23%) followed for a median 3.0 years. Beta-blocker exposure (BBexp) was calculated from pharmacy claims, and the proportion of African genetic ancestry was determined from genome-wide array data. Time-dependent Cox proportional hazards regression was used to separately test the association of BBexp with all-cause mortality by self-reported race or by proportion of African genetic ancestry. Both sets of models were evaluated unadjusted and then adjusted for baseline risk factors and beta-blocker propensity score. BBexp effect estimates were protective and of similar magnitude both by self-reported race and by African genetic ancestry (adjusted hazard ratio=0.56 in blacks and adjusted hazard ratio=0.48 in whites). The tests for interactions with BBexp for both self-reported race and for African genetic ancestry were not statistically significant in any model ( P >0.1 for all). Among black and white patients with heart failure and reduced ejection fraction, reduction in all-cause mortality associated with BBexp was similar, regardless of self-reported race or proportion African genetic ancestry. © 2018 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

  19. Human leptospirosis: seroreactivity and genetic susceptibility in the population of São Miguel Island (Azores, Portugal.

    Directory of Open Access Journals (Sweden)

    Lisa M Esteves

    Full Text Available Leptospirosis is a worldwide zoonotic and recognized neglected infectious disease. It has been observed that only a proportion of individuals exposed to pathogenic species of Leptospira become infected and develop clinically evident disease. Moreover, little information is available in subsequent reinfections. In the present study, we determine if a first infection with leptospirosis protects against subsequent reinfection, and investigate which of the host genetic factors are involved in the susceptibility and resistance to leptospirosis.We conducted, in 2011, a retrospective hospital-based case-control study in the São Miguel Island population (Azores archipelago. In order to determine the seropositivity against pathogenic Leptospira after the first episode of leptospirosis, we performed a serological evaluation in 97 unrelated participants diagnosed with leptospirosis between 1992 and 2011. The results revealed that 46.4% of the 97 participants have circulating anti-Leptospira antibodies, and from these participants 35.6% maintained the seroprevalence for the same serogroup. Moreover, three of them were reinfected with unrelated Leptospira serovars. The genetic study was carried out by adding a control group composed of 470 unrelated healthy blood donors, also from São Miguel Island. Twenty five SNPs among twelve innate immune genes - IL1α, IL1β, IL6, IL10, IL12RB1, TLR2, TLR4, TLR9, CD14, CISH, LTA and TNF - were genotyped, as well as HLA class I (-A and -B genes. Association analysis indicates that genotypes -511GG (OR=1.6, 95%CI 1.01-2.56, p=0.04 in IL1β, +1196CG (OR=2.0, 95%CI 1.26-3.27, p=0.003 in IL12RB1, -292TA (OR=1.8, 95% CI 1.06-2.1, p=0.03 and +3415CG (OR=1.8, 95% CI 1.08-3.08, p=0.02, both in CISH confer susceptibility to pathogenic Leptospira.The present study suggests some degree of long-term protection against leptospires with an attenuation of symptoms in case of reinfection. Moreover, our data supports the genetic

  20. Genetic evidence of African slavery at the beginning of the trans-Atlantic slave trade.

    Science.gov (United States)

    Martiniano, Rui; Coelho, Catarina; Ferreira, Maria Teresa; Neves, Maria João; Pinhasi, Ron; Bradley, Daniel G

    2014-08-08

    An archaeological excavation in Valle da Gafaria (Lagos, Portugal), revealed two contiguous burial places outside the medieval city walls, dating from the 15(th)-17(th) centuries AD: one was interpreted as a Leprosarium cemetery and the second as an urban discard deposit, where signs of violent, unceremonious burials suggested that these remains may belong to slaves captured in Africa by the Portuguese. We obtained random short autosomal sequence reads from seven individuals: two from the latter site and five from the Leprosarium and used these to call SNP identities and estimate ancestral affinities with modern reference data. The Leprosarium site samples were less preserved but gave some probability of both African and European ancestry. The two discard deposit burials each gave African affinity signals, which were further refined toward modern West African or Bantu genotyped samples. These data from distressed burials illustrate an African contribution to a low status stratum of Lagos society at a time when this port became a hub of the European trade in African slaves which formed a precursor to the transatlantic transfer of millions.

  1. Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species, the African forest elephant (Loxodonta cyclotis).

    Science.gov (United States)

    Ishida, Yasuko; Gugala, Natalie A; Georgiadis, Nicholas J; Roca, Alfred L

    2018-05-01

    The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants ( Loxodonta cyclotis ) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male-mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male-mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.

  2. Sex and genetic effects on upper and lower body fat and associations with diabetes in multigenerational families of African heritage.

    Science.gov (United States)

    Miljkovic-Gacic, Iva; Wang, Xiaojing; Kammerer, Candace M; Bunker, Clareann H; Patrick, Alan L; Wheeler, Victor W; Kuller, Lewis H; Evans, Rhobert W; Zmuda, Joseph M

    2008-06-01

    Very few studies have comprehensively defined the genetic and environmental influences on body fat storage in the arms and legs and their association with diabetes, especially in families of African heritage. We analyzed body fat distribution by dual-energy x-ray absorptiometry (percentage total fat, percentage trunk fat, percentage arm fat, and percentage leg fat) and fasting serum glucose in 471 individuals (mean age, 43 years) from 8 multigenerational Afro-Caribbean families (mean family size = 51; 3535 relative pairs). Diabetes was inversely associated with percentage leg fat (P = .009) and, to some extent, positively associated with percentage arm fat independent of age, sex, and body size (P = .08), but not with anthropometric or dual-energy x-ray absorptiometric measures of total and central adiposity. Furthermore, percentage leg fat was inversely, whereas percentage arm fat was positively, associated with body mass index, waist circumference, and serum glucose (P Genetic correlation (rho(G)) between arm and leg fat was -0.61 (P genetic influences. This study provides new evidence for a strong genetic and sex contribution to upper and lower body fat, with relatively little covariation between these traits due to shared genes. Our findings also suggest that, in this population, leg fat is associated with diabetes independent of overall adiposity.

  3. Genetic ancestry, self-reported race and ethnicity in African Americans and European Americans in the PCaP cohort.

    Directory of Open Access Journals (Sweden)

    Lara E Sucheston

    Full Text Available Family history and African-American race are important risk factors for both prostate cancer (CaP incidence and aggressiveness. When studying complex diseases such as CaP that have a heritable component, chances of finding true disease susceptibility alleles can be increased by accounting for genetic ancestry within the population investigated. Race, ethnicity and ancestry were studied in a geographically diverse cohort of men with newly diagnosed CaP.Individual ancestry (IA was estimated in the population-based North Carolina and Louisiana Prostate Cancer Project (PCaP, a cohort of 2,106 incident CaP cases (2063 with complete ethnicity information comprising roughly equal numbers of research subjects reporting as Black/African American (AA or European American/Caucasian/Caucasian American/White (EA from North Carolina or Louisiana. Mean genome wide individual ancestry estimates of percent African, European and Asian were obtained and tested for differences by state and ethnicity (Cajun and/or Creole and Hispanic/Latino using multivariate analysis of variance models. Principal components (PC were compared to assess differences in genetic composition by self-reported race and ethnicity between and within states.Mean individual ancestries differed by state for self-reporting AA (p = 0.03 and EA (p = 0.001. This geographic difference attenuated for AAs who answered "no" to all ethnicity membership questions (non-ethnic research subjects; p = 0.78 but not EA research subjects, p = 0.002. Mean ancestry estimates of self-identified AA Louisiana research subjects for each ethnic group; Cajun only, Creole only and both Cajun and Creole differed significantly from self-identified non-ethnic AA Louisiana research subjects. These ethnicity differences were not seen in those who self-identified as EA.Mean IA differed by race between states, elucidating a potential contributing factor to these differences in AA research participants: self-reported ethnicity

  4. Molecular genetic studies of natives on Easter Island: evidence of an early European and Amerindian contribution to the Polynesian gene pool.

    Science.gov (United States)

    Lie, B A; Dupuy, B M; Spurkland, A; Fernández-Viña, M A; Hagelberg, E; Thorsby, E

    2007-01-01

    Most archaeological and linguistic evidence suggest a Polynesian origin of the population of Easter Island (Rapanui), and this view has been supported by the identification of Polynesian mitochondrial DNA (mtDNA) polymorphisms in prehistoric skeletal remains. However, some evidence of an early South American contact also exists (the sweet potato, bottle gourd etc.), but genetic studies have so far failed to show an early Amerindian contribution to the gene pool on Easter Island. To address this issue, we analyzed mtDNA and Y chromosome markers and performed high-resolution human leukocyte antigen (HLA) genotyping of DNA harvested from previously collected sera of 48 reputedly nonadmixed native Easter Islanders. All individuals carried mtDNA types and HLA alleles previously found in Polynesia, and most men carried Y chromosome markers of Polynesian origin, providing further evidence of a Polynesian origin of the population of Easter Island. A few individuals carried HLA alleles and/or Y chromosome markers of European origin. More interestingly, some individuals carried the HLA alleles A*0212 and B*3905, which are of typical Amerindian origin. The genealogy of some of the individuals carrying these non-Polynesian HLA alleles and their haplotypic backgrounds suggest an introduction into Easter Island in the early 1800s, or earlier. Thus, there may have been an early European and Amerindian contribution to the Polynesian gene pool of Easter Island.

  5. African Journals Online (AJOL)

    African Journals Online (AJOL)

    It has also been difficult for African researchers to access the work of other African academics. In partnership with hundreds of journals from all over the continent, AJOL works to change this, so that African-origin research output is available to Africans and to the rest of the ... Egyptian Journal of Medical Human Genetics.

  6. Ferroan dolomites in Miocene sediments of the Xisha Islands and their genetic model

    Science.gov (United States)

    Xu, Hong; Zhang, Weiwei; Wei, Kai; He, Qingkun; Jiang, Yunshui; Xu, Tingting; Jiang, Xuejun; Yan, Guijing; Song, Hongying; Wang, Jianghai

    2018-01-01

    Carbonate rocks are important reservoirs for global petroleum exploration. The largest oilfield in the South China Sea, Liuhua 11-1, is distributed in the massive carbonate reef area of the Zhujiang (Pearl) River Mouth Basin. Previous studies showed that one 802.17-m-long core from well Xichen-1 in the South China Sea mainly consisted of white and light gray-white organic reefs. Recently, a Miocene whole core (161.9 m long) of well Xiyong-2, near well Xichen-1, was found to contain six layers of yellowish brown, light yellowish gray, iron black, or light yellowish gray-white organic reefs. Scanning electron microscope images of these layers reveal a typical ferroan dolomite rich in Fe (up to 29%), with the high concentrations of Mn, Cu, W, Zn, Cr, Ni, and Co. Systematic X-ray powder diffraction analysis yields a 1.9-6.1 match in phase ratio with ankerite, 5.4-26.9 with dolomite, and zero with calcite, which indicate that the samples can be classified as ferroan dolomite. The iron and heavy metals are inferred to be originated from multiple volcanic eruptions of Gaojianshi Island in the Dongdao Atoll during the middle-late Miocene. These elements were dissolved in seawater, likely as a sol, and carried to Yongxing Island in the Xuande Atoll by sea currents and tides enhanced by prevailing winds, and deposited as a part of the sedimentation process in the study area. The ferroan dolomite has Sr content of (125-285)×10-6, which is lower than the accepted Sr boundary value of dolomite. This finding suggests that dolomitization occurred during large-scale global glacial regression in the late Miocene. The isolated Xisha carbonate platform, exposed to air, underwent freshwater leaching and dolomitization induced by mixed water, and caused the extensive Fe-Mg exchange along the organic reef profile to form ankerite and ferroan dolomite. These results may help to understand paleoceanographic environmental changes in the South China Sea during the Miocene.

  7. Genetics of coronary artery calcification among African Americans, a meta-analysis

    NARCIS (Netherlands)

    M.K. Wojczynski (Mary ); M. Li (Mingyao); L.F. Bielak (Lawrence F.); K.F. Kerr (Kathleen); A. Reiner (Alexander); N.D. Wong (Nathan); L.R. Yanek (Lisa); L. Qu (Liming); C.C. White (Charles); L.A. Lange (Leslie); J.F. Ferguson (Jane); J. He (Jing); T. Young (Taylor); T.H. Mosley (Thomas); J.A. Smith (Jennifer A); B.G. Kral (Brian); X. Guo (Xiuqing); Q. Wong (Quenna); S.K. Ganesh (Santhi); S.R. Heckbert (Susan); M.D. Griswold (Michael); D.H. O'Leary (Daniel H.); M.J. Budoff (Matthew); J. Carr (Jeffrey); H.A. Taylor (Herman); D.A. Bluemke (David); S. Demissie (Serkalem); S.-J. Hwang (Shih-Jen); D.N. Paltoo (Dina); J.F. Polak (Joseph F.); B.M. Psaty (Bruce); D.M. Becker (Diane); M.A. Province (Mike); W.S. Post (Wendy S.); C.J. O'Donnell (Christopher); J.G. Wilson (James); T.B. Harris (Tamara); M. Kavousi (Maryam); L.A. Cupples (Adrienne); J.I. Rotter (Jerome); M. Fornage (Myriam); L.C. Becker (Lewis); P.A. Peyser (Patricia A.); I.B. Borecki (Ingrid); M.P. Reilly (Muredach)

    2013-01-01

    textabstractBackground: Coronary heart disease (CHD) is the major cause of death in the United States. Coronary artery calcification (CAC) scores are independent predictors of CHD. African Americans (AA) have higher rates of CHD but are less well-studied in genomic studies. We assembled the largest

  8. The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus

    Directory of Open Access Journals (Sweden)

    Thébaud Christophe

    2010-05-01

    Full Text Available Abstract Background Oceanic islands provide unique scenarios for studying the roles of geography and ecology in driving population divergence and speciation. Assessing the relative importance of selective and neutral factors in driving population divergence is central to understanding how such divergence may lead to speciation in small oceanic islands, where opportunities for gene flow and population mixing are potentially high. Here we report a case of genetic and morphological structure in the Mascarene grey white-eye (Zosterops borbonicus a species that shows a striking, geographically structured plumage polymorphism on the topographically and ecologically complex island of Réunion, yet is monotypic on the relatively uniform neighbouring island of Mauritius. Results Analysis of 276 AFLP loci in 197 individuals revealed prolonged independent evolution of Réunion and Mauritius populations, which is congruent with previous mtDNA assessments. Furthermore, populations on Réunion showed significant differentiation into three main genetic groups separating lowland from highland areas despite the small geographic distances involved. Genetic differentiation along the altitudinal gradient is consistent with morphometric analysis of fitness-related traits. Birds in the highlands were larger, yet had relatively smaller beaks than in the lowlands, suggesting the role of selection in shaping morphology and restricting gene flow along the gradient. No genetic differentiation between plumage morphs was detected in neutral markers, suggesting that plumage differences are of recent origin. Conclusions Our results suggest a dual role of vicariance and natural selection in differentiating populations of a passerine bird in an oceanic island at very small spatial scales. We propose a combination of past microallopatry driven by volcanic activity and selection-constrained dispersal along steep ecological gradients to explain the striking levels of population

  9. History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico

    Science.gov (United States)

    Via, Marc; Gignoux, Christopher R.; Roth, Lindsey A.; Fejerman, Laura; Galanter, Joshua; Choudhry, Shweta; Toro-Labrador, Gladys; Viera-Vera, Jorge; Oleksyk, Taras K.; Beckman, Kenneth; Ziv, Elad; Risch, Neil

    2011-01-01

    Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations. PMID:21304981

  10. Genetic analysis of body weight in South African Angora kids and ...

    African Journals Online (AJOL)

    Variance and covariance components and ratios pertaining to direct additive genetic variation, maternal additive genetic variation, maternal permanent environmental variation, and the relationship between direct and maternal effects for birth weight (BW; kg), weaning weight (WW; kg) and body weight at 8, 12 and 16 ...

  11. BRCA Genetic Screening in Middle Eastern and North African: Mutational Spectrum and Founder BRCA1 Mutation (c.798_799delTT in North African

    Directory of Open Access Journals (Sweden)

    Abdelilah Laraqui

    2015-01-01

    Full Text Available Background. The contribution of BRCA1 mutations to both hereditary and sporadic breast and ovarian cancer (HBOC has not yet been thoroughly investigated in MENA. Methods. To establish the knowledge about BRCA1 mutations and their correlation with the clinical aspect in diagnosed cases of HBOC in MENA populations. A systematic review of studies examining BRCA1 in BC women in Cyprus, Jordan, Egypt, Lebanon, Morocco, Algeria, and Tunisia was conducted. Results. Thirteen relevant references were identified, including ten studies which performed DNA sequencing of all BRCA1 exons. For the latter, 31 mutations were detected in 57 of the 547 patients ascertained. Familial history of BC was present in 388 (71% patients, of whom 50 were mutation carriers. c.798_799delTT was identified in 11 North African families, accounting for 22% of total identified BRCA1 mutations, suggesting a founder allele. A broad spectrum of other mutations including c.68_69delAG, c.181T>G, c.5095C>T, and c.5266dupC, as well as sequence of unclassified variants and polymorphisms, was also detected. Conclusion. The knowledge of genetic structure of BRCA1 in MENA should contribute to the assessment of the necessity of preventive programs for mutation carriers and clinical management. The high prevalence of BC and the presence of frequent mutations of the BRCA1 gene emphasize the need for improving screening programs and individual testing/counseling.

  12. Will Climate Change, Genetic and Demographic Variation or Rat Predation Pose the Greatest Risk for Persistence of an Altitudinally Distributed Island Endemic?

    Directory of Open Access Journals (Sweden)

    Alison Shapcott

    2012-11-01

    Full Text Available Species endemic to mountains on oceanic islands are subject to a number of existing threats (in particular, invasive species along with the impacts of a rapidly changing climate. The Lord Howe Island endemic palm Hedyscepe canterburyana is restricted to two mountains above 300 m altitude. Predation by the introduced Black Rat (Rattus rattus is known to significantly reduce seedling recruitment. We examined the variation in Hedyscepe in terms of genetic variation, morphology, reproductive output and demographic structure, across an altitudinal gradient. We used demographic data to model population persistence under climate change predictions of upward range contraction incorporating long-term climatic records for Lord Howe Island. We also accounted for alternative levels of rat predation into the model to reflect management options for control. We found that Lord Howe Island is getting warmer and drier and quantified the degree of temperature change with altitude (0.9 °C per 100 m. For H. canterburyana, differences in development rates, population structure, reproductive output and population growth rate were identified between altitudes. In contrast, genetic variation was high and did not vary with altitude. There is no evidence of an upward range contraction as was predicted and recruitment was greatest at lower altitudes. Our models predicted slow population decline in the species and that the highest altitude populations are under greatest threat of extinction. Removal of rat predation would significantly enhance future persistence of this species.

  13. Genetic polymorphisms and asthma: findings from a case-control study in the Madeira island population.

    Science.gov (United States)

    Berenguer, Anabela Gonçalves; Fernandes, Ana Teresa; Oliveira, Susana; Rodrigues, Mariana; Ornelas, Pedro; Romeira, Diogo; Serrão, Tânia; Rosa, Alexandra; Câmara, Rita

    2014-09-04

    Asthma is a complex disease influenced by multiple genetic and environmental factors. While Madeira has the highest prevalence of asthma in Portugal (14.6%), the effect of both genetic and environmental factors in this population has never been assessed. We categorized 98 asthma patients according to the Global Initiative for Asthma (GINA) guidelines, established their sensitization profile, and measured their forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) indexes. Selected single nucleotide polymorphisms (SNPs) were analysed as potential markers for asthma susceptibility and severity in the interleukin 4 (IL4), interleukin 13 (IL13), beta-2-adrenergic receptor (ADRB2), a disintegrin and metalloprotease 33 (ADAM33), gasdermin-like (GSDML) and the signal transducer and activator of transcription 6 (STAT6) genes comparatively to a population reference set. Although mites are the major source of allergic sensitization, no significant difference was found amongst asthma severity categories. IL4-590*CT/TT and IL4-RP2*253183/183183 were found to predict the risk (2-fold) and severity (3 to 4-fold) of asthma and were associated with a lower FEV1 index. ADRB2-c.16*AG is a risk factor (3.5-fold), while genotype GSDML-236*TT was protective (4-fold) for moderate-severe asthma. ADAM33-V4*C was associated to asthma and mild asthma by the transmission disequilibrium test (TDT). Finally, ADAM33-V4*CC and STAT6-21*TT were associated with higher sensitization (mean wheal size ≥10 mm) to house dust (1.4-fold) and storage mite (7.8-fold). In Madeira, IL4-590C/T, IL4-RP2 253/183, GSDML-236C/T and ADAM33-V4C/G SNPs are important risk factors for asthma susceptibility and severity, with implications for asthma healthcare management.

  14. Association of ABCB1 genetic variants with renal function in Africans and in Caucasians

    Directory of Open Access Journals (Sweden)

    Elston Robert C

    2008-06-01

    Full Text Available Abstract Background The P-glycoprotein, encoded by the ABCB1 gene, is expressed in human endothelial and mesangial cells, which contribute to control renal plasma flow and glomerular filtration rate. We investigated the association of ABCB1 variants with renal function in African and Caucasian subjects. Methods In Africans (290 subjects from 62 pedigrees, we genotyped the 2677G>T and 3435 C>T ABCB1 polymorphisms. Glomerular filtration rate (GFR was measured using inulin clearance and effective renal plasma flow (ERPF using para-aminohippurate clearance. In Caucasians (5382 unrelated subjects, we analyzed 30 SNPs located within and around ABCB1, using data from the Affymetrix 500 K chip. GFR was estimated using the simplified Modification of the Diet in Renal Disease (MDRD and Cockcroft-Gault equations. Results In Africans, compared to the reference genotype (GG or CC, each copy of the 2677T and 3435T allele was associated, respectively, with: GFR higher by 10.6 ± 2.9 (P P = 0.06 mL/min; ERPF higher by 47.5 ± 11.6 (P P = 0.007 mL/min; and renal resistances lower by 0.016 ± 0.004 (P P = 0.004 mm Hg/mL/min. In Caucasians, we identified 3 polymorphisms in the ABCB1 gene that were strongly associated with all estimates of GFR (smallest P value = 0.0006, overall P = 0.014 after multiple testing correction. Conclusion Variants of the ABCB1 gene were associated with renal function in both Africans and Caucasians and may therefore confer susceptibility to nephropathy in humans. If confirmed in other studies, these results point toward a new candidate gene for nephropathy in humans.

  15. Genetic Structure of Pastoral and Farmer Populations in the African Sahel

    Czech Academy of Sciences Publication Activity Database

    Černý, Viktor; Pereira, L.; Musilová, E.; Kujanová, M.; Vašíková, A.; Blasi, P.; Garofalo, L.; Soares, P.; Diallo, I.; Brdička, R.; Novelletto, A.

    2011-01-01

    Roč. 28, č. 9 (2011), s. 2491-2500 ISSN 0737-4038 R&D Projects: GA ČR GA206/08/1587 Institutional research plan: CEZ:AV0Z80020508 Keywords : African Sahel * pastoralism * archaeogenetics Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 5.550, year: 2011 http://mbe.oxfordjournals.org/content/28/9/2491

  16. Genetic diversity of the causative agent of ice-ice disease of the seaweed Kappaphycus alvarezii from Karimunjawa island, Indonesia

    Science.gov (United States)

    Syafitri, E.; Prayitno, S. B.; Ma'ruf, W. F.; Radjasa, O. K.

    2017-02-01

    An essential step in investigating the bacterial role in the occurrence of diseases in Kappaphycus alvarezii is the characterization of bacteria associated with this seaweed. A molecular characterization was conducted on the genetic diversity of the causative agents of ice-ice disease associated with K. alvarezii widely known as the main source of kappa carrageenan. K. alvrezii infected with ice-ice were collected from the Karimunjawa island, North Java Sea, Indonesia. Using Zobell 2216E marine agar medium, nine bacterial species were isolated from the infected seaweed. The molecular characterizations revealed that the isolated bacteria causing ice-ice disease were closely related to the genera of Alteromonas, Bacillus, Pseudomonas, Pseudoalteromonas, Glaciecola, Aurantimonas, and Rhodococcus. In order to identify the symptoms causative organisms, the isolated bacterial species were cultured and were evaluated for their pathogenity. Out of 9 species, only 3 isolates were able to cause the ice-ice symptoms and consisted of Alteromonas macleodii, Pseudoalteromonas issachenkonii and Aurantimonas coralicida. A. macleodii showed the highest pathogenity.

  17. Population genetic analyses are consistent with the introduction of Ceramium secundatum (Ceramiaceae, Rhodophyta) to Narragansett Bay, Rhode Island, USA.

    Science.gov (United States)

    Bruce, Meghann R; Saunders, Gary W

    2015-11-01

    During ongoing DNA barcode (COI-5P) surveys of the macroalgal flora along the northwest Atlantic coast, we discovered a population of Ceramium secundatum in Narragansett Bay, Rhode Island, USA. This species is regarded as common and widespread in the northeast Atlantic, ranging from Norway to Morocco, but until now has not been reported from the western Atlantic. Several lines of evidence suggest that C. secundatum may be introduced to Narragansett Bay: (1) despite extensive collecting, specimens have only been obtained from a limited geographic range in the northwest Atlantic; (2) three other nonindigenous seaweed species are reportedly introduced in this region, which is thought to be a consequence of shipping; and (3) this species is introduced to South Africa and New Zealand. To investigate this suspected introduction, we applied population genetic analyses (using the cox2-3 spacer) to compare the Narragansett Bay C. secundatum population to native populations in the Republic of Ireland and the United Kingdom. Collectively, analyses of biogeographical and molecular data indicate that C. secundatum is likely introduced to Narragansett Bay. The implications of this discovery are discussed.

  18. Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia.

    Science.gov (United States)

    Brandão, Andreia; Eng, Ken Khong; Rito, Teresa; Cavadas, Bruno; Bulbeck, David; Gandini, Francesca; Pala, Maria; Mormina, Maru; Hudson, Bob; White, Joyce; Ko, Tsang-Ming; Saidin, Mokhtar; Zafarina, Zainuddin; Oppenheimer, Stephen; Richards, Martin B; Pereira, Luísa; Soares, Pedro

    2016-04-01

    There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20% of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.

  19. Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus).

    Science.gov (United States)

    Campana, Michael G; Parker, Lillian D; Hawkins, Melissa T R; Young, Hillary S; Helgen, Kristofer M; Szykman Gunther, Micaela; Woodroffe, Rosie; Maldonado, Jesús E; Fleischer, Robert C

    2016-12-09

    The African wild dog (Lycaon pictus) is an endangered African canid threatened by severe habitat fragmentation, human-wildlife conflict, and infectious disease. A highly specialized carnivore, it is distinguished by its social structure, dental morphology, absence of dewclaws, and colorful pelage. We sequenced the genomes of two individuals from populations representing two distinct ecological histories (Laikipia County, Kenya and KwaZulu-Natal Province, South Africa). We reconstructed population demographic histories for the two individuals and scanned the genomes for evidence of selection. We show that the African wild dog has undergone at least two effective population size reductions in the last 1,000,000 years. We found evidence of Lycaon individual-specific regions of low diversity, suggestive of inbreeding or population-specific selection. Further research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole. We documented positive selection on the Lycaon mitochondrial genome. Finally, we identified several candidate genes (ASIP, MITF, MLPH, PMEL) that may play a role in the characteristic Lycaon pelage.

  20. Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae).

    Science.gov (United States)

    Jaros, Ursula; Tribsch, Andreas; Comes, Hans Peter

    2018-02-12

    Disentangling the relative roles of past fragmentation (vicariance), colonization (dispersal) and post-divergence gene flow in the genetic divergence of continental island organisms remains a formidable challenge. Amplified fragment length polymorphisms (AFLPs) were used to (1) gain further insights into the biogeographical processes underlying the Pleistocene diversification of the Aegean Nigella arvensis complex; (2) evaluate the role of potential key factors driving patterns of population genetic variability (mating system, geographical isolation and historical contingencies); and (3) test the robustness of conclusions previously drawn from chloroplast (cp) DNA. Genetic diversity was analysed for 235 AFLP markers from 48 populations (497 individuals) representing 11 taxa of the complex using population genetic methods and Bayesian assignment tests. Most designated taxa are identifiable as genetically distinct units. Both fragmentation and dispersal-driven diversification processes occurred at different geological time scales, from Early to Late Pleistocene, specifically (1) sea barrier-induced vicariant speciation in the Cyclades, the Western Cretan Strait and Ikaria; and (2) bi-regional colonizations of the 'Southern Aegean Island Arc' from the Western vs. Eastern Aegean mainland, followed by allopatric divergences in Crete vs. Rhodos and Karpathos/Kasos. Outcrossing island taxa experienced drift-related demographic processes that are magnified in the two insular selfing species. Population genetic differentiation on the mainland seems largely driven by dispersal limitation, while in the Central Aegean it may still be influenced by historical events (island fragmentation and sporadic long-distance colonization). The biogeographical history of Aegean Nigella is more complex than expected for a strictly allopatric vicariant model of divergence. Nonetheless, the major phylogeographical boundaries of this radiation are largely congruent with the geography and

  1. Proportionally more deleterious genetic variation in European than in African populations

    DEFF Research Database (Denmark)

    Lohmueller, Kirk E; Indap, Amit R; Schmidt, Steffen

    2008-01-01

    of functional SNPs considered, including synonymous, non-synonymous, predicted 'benign', predicted 'possibly damaging' and predicted 'probably damaging' SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans. EA...... individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at 'probably damaging' SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs...

  2. Bimodal volcanism in northeast Puerto Rico and the Virgin Islands (Greater Antilles Island Arc): Genetic links with Cretaceous subduction of the mid-Atlantic ridge Caribbean spur

    Science.gov (United States)

    Jolly, Wayne T.; Lidiak, Edward G.; Dickin, Alan P.

    2008-07-01

    Bimodal extrusive volcanic rocks in the northeast Greater Antilles Arc consist of two interlayered suites, including (1) a predominantly basaltic suite, dominated by island arc basalts with small proportions of andesite, and (2) a silicic suite, similar in composition to small volume intrusive veins of oceanic plagiogranite commonly recognized in oceanic crustal sequences. The basaltic suite is geochemically characterized by variable enrichment in the more incompatible elements and negative chondrite-normalized HFSE anomalies. Trace element melting and mixing models indicate the magnitude of the subducted sediment component in Antilles arc basalts is highly variable and decreases dramatically from east to west along the arc. In the Virgin Islands, the sediment component ranges between 4% during the Cenomanian-Campanian interval. The silicic suite, consisting predominantly of rhyolites, is characterized by depleted Al 2O 3 (average Virgin Islands on the east, rhyolites comprise up to 80% of Lower Albian strata (112 to 105 Ma), and about 20% in post-Albian strata (105 to 100 Ma). Farther west, in Puerto Rico, more limited proportions (Atlantic Ridge, which was located approximately midway between North and South America until Campanian times. Within this hypothetical setting the centrally positioned Virgin Islands terrain remained approximately fixed above the subducting ridge as the Antilles arc platform swept northeastward into the slot between the Americas. Accordingly, heat flow in the Virgin Islands was elevated throughout the Cretaceous, giving rise to widespread crustal melting, whereas the subducted sediment flux was limited. Conversely, toward the west in central Puerto Rico, which was consistently more remote from the subducting ridge, heat flow was relatively low and produced limited crustal melting, while the sediment flux was comparatively elevated.

  3. Stress and Coping with Racism and Their Role on Sexual Risk for HIV among African American, Asian/Pacific Islander, and Latino Men Who Have Sex With Men

    Science.gov (United States)

    Han, Chong-suk; Ayala, George; Paul, Jay; Boylan, Ross; Gregorich, Steven E.; Choi, Kyung-Hee

    2014-01-01

    The deleterious effects of racism on a wide range of health outcomes, including HIV risk, is well documented among racial/ethnic minority groups in the United States. However, little is known about how men of color who have sex with men (MSM) cope with stress from racism and whether the coping strategies they employ buffer against the impact of racism on sexual risk for HIV transmission. We examined associations of stress and coping with racism with unprotected anal intercourse (UAI) in a sample of African American (n = 403), Asian/Pacific Islander (n = 393), and Latino (n = 400) MSM recruited in Los Angeles County, CA during 2008–2009. Almost two-thirds (65%) of the sample reported being stressed as a consequence of racism experienced within the gay community. Overall, 51% of the sample reported having UAI in the prior six months. After controlling for race/ethnicity, age, nativity, marital status, sexual orientation, education, HIV serostatus, and lifetime history of incarceration, the multivariate analysis found statistically significant main effects of stress from racism and avoidance coping on UAI; no statistically significant main effects of dismissal, education/confrontation, and social-support seeking were observed. None of the interactions of stress with the four coping measures were statistically significant. Although stress from racism within the gay community increased the likelihood of engaging in UAI among MSM of color, we found little evidence that coping responses to racism buffered stress from racism. Instead, avoidance coping appears to suggest an increase in UAI. PMID:25060122

  4. Genetic structure analysis of a highly inbred captive population of the African antelope Addax nasomaculatus. Conservation and management implications.

    Science.gov (United States)

    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. © 2010 Wiley-Liss, Inc.

  5. Genetic and Molecular Differences in Prostate Carcinogenesis between African American and Caucasian American Men

    Directory of Open Access Journals (Sweden)

    Shiv Srivastava

    2013-07-01

    Full Text Available Prostate cancer is the most common non-skin cancer and the second leading cause of cancer-related death for men in the United States. Prostate cancer incidence and associated mortality are highest in African American men in comparison to other races. The observed differences in incidence and disease aggressiveness at presentation support a potential role for different pathways of prostate carcinogenesis between African American and Caucasian men. This review focuses on some of the recent molecular biology discoveries, which have been investigated in prostate carcinogenesis and their likely contribution to the known discrepancies across race and ethnicity. Key discussion points include the androgen receptor gene structure and function, genome-wide association studies and epigenetics. The new observations of the ethnic differences of the ERG oncogene, the most common prostate cancer gene, are providing new insights into ERG based stratification of prostate cancers in the context of ethnically diverse patient populations. This rapidly advancing knowledge has the likely potential to benefit clinical practice. Current and future work will improve the ability to sub-type prostate cancers by molecular alterations and lead to targeted therapy against this common malignancy.

  6. HLA similarities indicate shared genetic risk in 21-hydroxylase autoantibody positive South African and United States Addison's disease.

    Science.gov (United States)

    Ross, I L; Babu, S; Armstrong, T; Zhang, L; Schatz, D; Pugliese, A; Eisenbarth, G; Baker Ii, P

    2014-10-01

    Genetic similarities between patients from the United States and South African (SA) Addison's Disease (AD) strengthen evidence for genetic association. SA-AD (n = 73), SA healthy controls (N = 78), and US-AD patients (N = 83) were genotyped for DQA1, DQB1, DRB1, and HLA-B alleles. Serum was tested for the quantity of 21OH-AA and IFNα-AA at the Barbara Davis Center. Although not as profound as in US-AD, in SA-AD 21OH-AA + subjects the predominantly associated risk haplotypes were DRB1*0301-DQB1*0201 (DR3), DRB1*04xx-DQB1*0302 (DR4), and the combined DR3/4 genotype. DQB1*0302 associated DRB1*04xx haplotypes conferred higher risk than those DRB1*04xx haplotypes associated with other DQB1 alleles. We found negative association in 21OH-AA + SA-AD for DQA1*0201-DQB1*0202 and DQA1*0101-DQB1*0501 vs SA controls, and positive association for DQA1*0401-DQB1*0402 vs US-AD. Apart from the class II DR3 haplotype, HLA-B8 did not have an independent effect; however together DR3 and HLA-B8 conferred the highest risk vs 21OH-AA negative SA-AD and SA-controls. HLA-B7 (often with DR4) conferred novel risk in 21OH-AA + SA-AD vs controls. This study represents the first comparison between South African and United States AD populations utilizing genotyping and serology performed at the same center. SA-AD and US-AD 21OH-AA + patients share common HLA risk haplotypes including DR4 (with HLA-B7) and DR3 (with HLA-B8), strengthening previously described HLA associations and implicating similar genetic etiology. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. Emergence of quinolone resistance among extended-spectrum beta-lactamase-producing Enterobacteriaceae in the Central African Republic: genetic characterization

    Directory of Open Access Journals (Sweden)

    Frank Thierry

    2011-08-01

    Full Text Available Abstract Background Cross-resistance to quinolones and beta-lactams is frequent in Enterobacteriaceae, due to the wide use of these antibiotics clinically and in the food industry. Prescription of one of these categories of antibiotic may consequently select for bacteria resistant to both categories. Genetic mechanisms of resistance may be secondary to a chromosomal mutation located in quinolone resistance determining region of DNA gyrase or topoisomerase IV or to a plasmid acquisition. The insertion sequence ISCR1 is often associated with qnr and may favour its dissemination in Gram-negative bacteria. The aim of this study was to determine the genetic mechanism of quinolone resistance among extended-spectrum beta-lactamase-producing Enterobacteriaceae strains in the Central African Republic. Findings Among seventeen ESBL-producing Enterobacteriaceae isolated from urine, pus or stool between January 2003 and October 2005 in the Central African Republic, nine were resistant to ciprofloxacin (seven from community patients and two from hospitalized patients. The ESBL were previously characterized as CTX-M-15 and SHV-12. Susceptibility to nalidixic acid, norfloxacin and ciprofloxacin, and the minimal inhibitory concentrations of these drugs were determined by disc diffusion and agar dilution methods, respectively. The presence of plasmid-borne ISCR1-qnrA region was determined by PCR and amplicons, if any, were sent for sequencing. Quinolone resistance determining region of DNA gyrase gyrA gene was amplified by PCR and then sequenced for mutation characterization. We found that all CTX-M-producing strains were resistant to the tested quinolones. All the isolates had the same nucleotide mutation at codon 83 of gyrA. Two Escherichia coli strains with the highest MICs were shown to harbour an ISCR1-qnrA1 sequence. This genetic association might favour dissemination of resistance to quinolone and perhaps other antibiotics among Enterobacteriaceae

  8. Genetic diversity in South African maize ( Zea mays L.) genotypes as ...

    African Journals Online (AJOL)

    One thousand and forty three (1043) maize genotypes including white and yellow maize inbred lines as well as hybrids from the public germplasm collection were characterized with 80 microsatellite markers distributed throughout the genome. A total of 1874 alleles were amplified and used in the genetic diversity analysis.

  9. Analysis of the genetic diversity of selected East African sweet potato

    African Journals Online (AJOL)

    The genetic relationship of the germplasm was evaluated using the Jaccard's coefficient for dissimilarity analysis, unweighted pair group method with arithmetic means (UPGMA) tree and principal component analysis (PCoA) on DARwin software, while summary statistics was done using PowerMarker and Popgene ...

  10. Non-genetic factors affecting fertility traits in South African Holstein ...

    African Journals Online (AJOL)

    referee1

    2014-03-08

    Mar 8, 2014 ... non-genetic factors affect the fertility of dairy cows. ... (2002) found conception rates of 64% in open heifers and 39% in .... the number of days from calving date to first service date for Holstein cows in the USA increased from.

  11. Non-genetic factors affecting fertility traits in South African Holstein ...

    African Journals Online (AJOL)

    Profitable milk production and genetic improvement in dairy herds depend largely on fertile cows calving annually to initiate a new lactation period. Over the last 30 years, several studies have indicated a decline in the reproductive performance of dairy cows. From the perspectives of many farmers and veterinarians, the ...

  12. Low genetic variation in the MHC class II DRB gene and MHC-linked microsatellites in endangered island populations of the leopard cat (Prionailurus bengalensis) in Japan.

    Science.gov (United States)

    Saka, Toshinori; Nishita, Yoshinori; Masuda, Ryuichi

    2018-02-01

    Isolated populations of the leopard cat (Prionailurus bengalensis) on Tsushima and Iriomote islands in Japan are classified as subspecies P. b. euptilurus and P. b. iriomotensis, respectively. Because both populations have decreased to roughly 100, an understanding of their genetic diversity is essential for conservation. We genotyped MHC class II DRB exon 2 and MHC-linked microsatellite loci to evaluate the diversity of MHC genes in the Tsushima and Iriomote cat populations. We detected ten and four DRB alleles in these populations, respectively. A phylogenetic analysis showed DRB alleles from both populations to be closely related to those in other felid DRB lineages, indicating trans-species polymorphism. The MHC-linked microsatellites were more polymorphic in the Tsushima than in the Iriomote population. The MHC diversity of both leopard cat populations is much lower than in the domestic cat populations on these islands, probably due to inbreeding associated with founder effects, geographical isolation, or genetic drift. Our results predict low resistance of the two endangered populations to new pathogens introduced to the islands.

  13. Genetic variations in vitamin D-related pathways and breast cancer risk in African American women in the AMBER consortium

    Science.gov (United States)

    Yao, Song; Haddad, Stephen A.; Hu, Qiang; Liu, Song; Lunetta, Kathryn L.; Ruiz-Narvaez, Edward A.; Hong, Chi-Chen; Zhu, Qianqian; Sucheston-Campbell, Lara; Cheng, Ting-Yuan David; Bensen, Jeannette T.; Johnson, Candace S.; Trump, Donald L.; Haiman, Christopher A.; Olshan, Andrew F.; Palmer, Julie R.; Ambrosone, Christine B.

    2016-01-01

    Studies of genetic variations in vitamin D-related pathways and breast cancer risk have been conducted mostly in populations of European ancestry, and only sparsely in African Americans (AA), who are known for a high prevalence of vitamin D deficiency. We analyzed 24,445 germline variants in 63 genes from vitamin D-related pathways in the African American Breast Cancer Epidemiology and Risk (AMBER) consortium, including 3,663 breast cancer cases and 4,687 controls. Odds ratios (OR) were derived from logistic regression models for overall breast cancer, by estrogen receptor (ER) status (1,983 ER positive and 1,098 ER negative), and for case-only analyses of ER status. None of the three vitamin D-related pathways were associated with breast cancer risk overall or by ER status. Gene-level analyses identified associations with risk for several genes at a nominal p ≤ 0.05, particularly for ER− breast cancer, including rs4647707 in DDB2. In case-only analyses, vitamin D metabolism and signaling pathways were associated with ER− cancer (pathway-level p = 0.02), driven by a single gene CASR (gene-level p = 0.001). The top SNP in CASR was rs112594756 (p = 7 × 10−5, gene-wide corrected p = 0.01), followed by a second signal from a nearby SNP rs6799828 (p = 1 × 10−4, corrected p = 0.03). In summary, several variants in vitamin D pathways were associated with breast cancer risk in AA women. In addition, CASR may be related to tumor ER status, supporting a role of vitamin D or calcium in modifying breast cancer phenotypes. PMID:26650177

  14. Genetic divergence and diversity in the Mona and Virgin Islands Boas, Chilabothrus monensis (Epicrates monensis) (Serpentes: Boidae), West Indian snakes of special conservation concern.

    Science.gov (United States)

    Rodríguez-Robles, Javier A; Jezkova, Tereza; Fujita, Matthew K; Tolson, Peter J; García, Miguel A

    2015-07-01

    Habitat fragmentation reduces the extent and connectivity of suitable habitats, and can lead to changes in population genetic structure. Limited gene flow among isolated demes can result in increased genetic divergence among populations, and decreased genetic diversity within demes. We assessed patterns of genetic variation in the Caribbean boa Chilabothrus monensis (Epicrates monensis) using two mitochondrial and seven nuclear markers, and relying on the largest number of specimens of these snakes examined to date. Two disjunct subspecies of C. monensis are recognized: the threatened C. m. monensis, endemic to Mona Island, and the rare and endangered C. m. granti, which occurs on various islands of the Puerto Rican Bank. Mitochondrial and nuclear markers revealed unambiguous genetic differences between the taxa, and coalescent species delimitation methods indicated that these snakes likely are different evolutionary lineages, which we recognize at the species level, C. monensis and C. granti. All examined loci in C. monensis (sensu stricto) are monomorphic, which may indicate a recent bottleneck event. Each population of C. granti exclusively contains private mtDNA haplotypes, but five of the seven nuclear genes assayed are monomorphic, and nucleotide diversity is low in the two remaining markers. The faster pace of evolution of mtDNA possibly reflects the present-day isolation of populations of C. granti, whereas the slower substitution rate of nuDNA may instead mirror the relatively recent episodes of connectivity among the populations facilitated by the lower sea level during the Pleistocene. The small degree of overall genetic variation in C. granti suggests that demes of this snake could be managed as a single unit, a practice that would significantly increase their effective population size. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. A Tale of Two Aggregations: Kinship and Population Genetics of Whale Sharks (Rhincodon typus) at Shib Habil, Saudi Arabia, and Mafia Island, Tanzania.

    KAUST Repository

    Hardenstine, Royale

    2015-12-01

    In a recent global study of whale shark population genetics, aggregations were found to belong to either the Indo-Pacific or Atlantic population. This overview included an aggregation found within the Red Sea near Al Lith, Saudi Arabia, however the Mafia Island, Tanzania, aggregation was not part of the study. Both aggregations have unique aspects with the Saudi Arabian individuals showing sexual parity with no segregation, while recent acoustic results have revealed cryptic residency at Mafia Island. Genetic analysis using 11 microsatellite markers was performed on whale sharks from both locations. A combination of primers sourced from previous studies and newly designed primers were used to compare both aggregations and the individuals within. Samples were collected in the Red Sea for 5 seasons spanning 6 years, and for 2 seasons in Tanzania. Analysis with STRUCTURE showed a lack of significant genetic differences between the two aggregations, confirming that whale sharks in Tanzania are part of the Indo-Pacific population. Kinship analysis using COLONY found two potential pairs of full siblings in Tanzania. One pair had a high probability (.993) of being a full sibling dyad while the other had a lower probability (.357). There were no sibling pairs identified from the Red Sea aggregation. Genetic diversity was investigated using allelic richness over the 6 seasons at Al Lith, with values showing no significant change. This is in contrast to results that showed a decline in genetic diversity at Western Australia’s Ningaloo reef. These differences, however, only highlight the need for genetic diversity studies over longer time periods and at other aggregations within the Indo-Pacific.

  16. Genome-wide association study of a nicotine metabolism biomarker in African American smokers: impact of chromosome 19 genetic influences.

    Science.gov (United States)

    Chenoweth, Meghan J; Ware, Jennifer J; Zhu, Andy Z X; Cole, Christopher B; Cox, Lisa Sanderson; Nollen, Nikki; Ahluwalia, Jasjit S; Benowitz, Neal L; Schnoll, Robert A; Hawk, Larry W; Cinciripini, Paul M; George, Tony P; Lerman, Caryn; Knight, Joanne; Tyndale, Rachel F

    2018-03-01

    The activity of CYP2A6, the major nicotine-inactivating enzyme, is measurable in smokers using the nicotine metabolite ratio (NMR; 3'hydroxycotinine/cotinine). Due to its role in nicotine clearance, the NMR is associated with smoking behaviours and response to pharmacotherapies. The NMR is highly heritable (~80%), and on average lower in African Americans (AA) versus whites. We previously identified several reduce and loss-of-function CYP2A6 variants common in individuals of African descent. Our current aim was to identify novel genetic influences on the NMR in AA smokers using genome-wide approaches. Genome-wide association study (GWAS). Multiple sites within Canada and the United States. AA smokers from two clinical trials: Pharmacogenetics of Nicotine Addiction Treatment (PNAT)-2 (NCT01314001; n = 504) and Kick-it-at-Swope (KIS)-3 (NCT00666978; n = 450). Genome-wide SNP genotyping, the NMR (phenotype) and population substructure and NMR covariates. Meta-analysis revealed three independent chromosome 19 signals (rs12459249, rs111645190 and rs185430475) associated with the NMR. The top overall hit, rs12459249 (P = 1.47e-39; beta = 0.59 per C (versus T) allele, SE = 0.045), located ~9.5 kb 3' of CYP2A6, remained genome-wide significant after controlling for the common (~10% in AA) non-functional CYP2A6*17 allele. In contrast, rs111645190 and rs185430475 were not genome-wide significant when controlling for CYP2A6*17. In total, 96 signals associated with the NMR were identified; many were not found in prior NMR GWASs in individuals of European descent. The top hits were also associated with the NMR in a third cohort of AA (KIS2; n = 480). None of the hits were in UGT or OCT2 genes. Three independent chromosome 19 signals account for ~20% of the variability in the nicotine metabolite ratio in African American smokers. The hits identified may contribute to inter-ethnic variability in nicotine metabolism, smoking behaviours and tobacco-related disease risk

  17. Meta-analysis of genome-wide association studies in African Americans provides insights into the genetic architecture of type 2 diabetes

    DEFF Research Database (Denmark)

    Ng, Maggie C Y; Shriner, Daniel; Chen, Brian H

    2014-01-01

    . In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs......) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications...... for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies....

  18. Comprehensive Genetic Characterization of Intraprostatic Chronic Inflammation and Prostate Cancer in African American Men

    Science.gov (United States)

    2017-09-01

    Response and Eradication of Androgen Receptor Amplification with High-dose Testosterone in Prostate Cancer ." Eur Urol 71(6): 997-998. Case Report...34 Prostate -specific Antigen Response and Eradication of Androgen Receptor Amplification with High-dose Testosterone in Prostate Cancer ." Eur Urol 71...AWARD NUMBER: W81XWH-15-1-0379 TITLE: Comprehensive genetic characterization of intraprostatic chronic inflammation and prostate cancer in

  19. Towards A Genetic Business Code For Growth in the South African Transport Industry

    Directory of Open Access Journals (Sweden)

    J.H. Vermeulen

    2003-11-01

    Full Text Available As with each living organism, it is proposed that an organisation possesses a genetic code. In the fast-changing business environment it would be invaluable to know what constitutes organisational growth and success in terms of such a code. To identify this genetic code a quantitative methodological framework, supplemented by a qualitative approach, was used and the views of top management in the Transport Industry were solicited. The Repertory Grid was used as the primary data-collection method. Through a phased data-analysis process an integrated profile of first- and second-order constructs, and opposite poles, was compiled. By utilising deductive and inductive strategies three strands of a Genetic Business Growth Code were identified, namely a Leadership Strand, Organisational Architecture Strand and Internal Orientation Strand. The study confirmed the value of a Genetic Business Code for growth in the Transport Industry. Opsomming Daar word voorgestel dat ’n organisasie, soos elke lewende organisme, oor ’n genetiese kode beskik. In die snelveranderende sake-omgewing sal dit onskatbaar wees om te weet wat organisasiegroei en –sukses veroorsaak. ’n Kwantitatiewe metodologie-raamwerk, aangevul deur ’n kwalitatiewe benadering is gebruik om hierdie genetiese kode te identifiseer, en die menings van topbestuur in die Vervoerbedryf is ingewin met behulp van die “Repertory Grid" as die vernaamste metode van data-insameling. ’n Geïntegreerde profiel van eerste- en tweedeordekonstrukte, met hulle teenoorgestelde pole, is opgestel. Drie stringe van ’n Genetiese Sakegroeikode, nl. ’n Leierskapstring, die Organisasieargitektuur-string en die Innerlike-ingesteldheidstring is geïdentifiseer deur deduktiewe en induktiewe strategieë te gebruik. Die studie bevestig die waarde van ’n Genetiese Sakekode vir groei in die Vervoerbedryf.

  20. Possibilities and pitfalls for modern biotechnology in the development of African genetic toxicology

    International Nuclear Information System (INIS)

    Anwar, Wagida A.

    2005-01-01

    Developing countries are currently going through a transitional phase facing the new challenges of globalization and its potential negative impact. Research policy should highlight the need to mobilize resources for human resource development, networking, improved research culture, information sharing, and pragmatic use of research findings. Advancement in molecular genetics whether at the educational or research level should greatly progress in developing countries so as to improve diagnosis, treatment, understanding of disease risk factors, and prevention. Currently, there is a growing interest to genetic toxicology research, the use of different biomarkers, and genetic susceptibility testing, which can contribute effectively in risk assessment. Africa has unique environmental exposures and public health circumstances, which make it ideal for environmental mutagenicity and carcinogenicity research. There are exposures to chemical genotoxicants (e.g., automobile exhaust, pesticides, metals, and cytotoxic drugs) and to lifestyle factors (e.g., consumption of tobacco products) that have been linked to the expression of biological effects and to increased risk for cancer. Infections can be associated with cancer development when the environmental factors interact with the infection and lead to the enhancement of the carcinogenic process. The high prevalence of viral pathogens and the improper use of pesticides may endanger biological functions beyond those for which they originally manufactured. Biomarkers are used to detect the effects of pesticides before adverse clinical health occurs. The scientific community plays a crucial role in understanding the environmental causes of human health problems and through its collaboration with communities, industries, and government agencies can help in resolving health problems

  1. Possibilities and pitfalls for modern biotechnology in the development of African genetic toxicology.

    Science.gov (United States)

    Anwar, Wagida A

    2005-09-01

    Developing countries are currently going through a transitional phase facing the new challenges of globalization and its potential negative impact. Research policy should highlight the need to mobilize resources for human resource development, networking, improved research culture, information sharing, and pragmatic use of research findings. Advancement in molecular genetics whether at the educational or research level should greatly progress in developing countries so as to improve diagnosis, treatment, understanding of disease risk factors, and prevention. Currently, there is a growing interest to genetic toxicology research, the use of different biomarkers, and genetic susceptibility testing, which can contribute effectively in risk assessment. Africa has unique environmental exposures and public health circumstances, which make it ideal for environmental mutagenicity and carcinogenicity research. There are exposures to chemical genotoxicants (e.g., automobile exhaust, pesticides, metals, and cytotoxic drugs) and to lifestyle factors (e.g., consumption of tobacco products) that have been linked to the expression of biological effects and to increased risk for cancer. Infections can be associated with cancer development when the environmental factors interact with the infection and lead to the enhancement of the carcinogenic process. The high prevalence of viral pathogens and the improper use of pesticides may endanger biological functions beyond those for which they originally manufactured. Biomarkers are used to detect the effects of pesticides before adverse clinical health occurs. The scientific community plays a crucial role in understanding the environmental causes of human health problems and through its collaboration with communities, industries, and government agencies can help in resolving health problems.

  2. Meta-analysis of genome-wide association studies in African Americans provides insights into the genetic architecture of type 2 diabetes.

    Directory of Open Access Journals (Sweden)

    Maggie C Y Ng

    2014-08-01

    Full Text Available Type 2 diabetes (T2D is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1 and two novel loci (HLA-B and INS-IGF2 at genome-wide significance (4.15 × 10(-94African Americans. Overall, this study identified two novel susceptibility loci for T2D in African Americans. A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies.

  3. Genetic diversity of the Japanese wood pigeon, Columba janthina, endemic to islands of East Asia, estimated by newly developed microsatellite markers.

    Science.gov (United States)

    Ando, Haruko; Kaneko, Shingo; Suzuki, Hajime; Horikoshi, Kazuo; Takano, Hajime; Ogawa, Hiroko; Isagi, Yuji

    2011-12-01

    The Japanese wood pigeon Columba janthina is endemic to islands of East Asia and is listed as Near Threatened by the International Union for Conservation of Nature (IUCN). One subspecies, C. janthina nitens, in particular, is at the greatest risk of extinction due to its small population size. To reduce the extinction risk of C. janthina, it is important to understand the species' present genetic status and to develop an appropriate conservation plan based on genetic data. We developed seven new microsatellite markers for two subspecies of C. janthina: C. janthina janthina and C. janthina nitens. We also confirmed the cross-use of one microsatellite marker developed for Columba livia var. domestica. Seven loci were polymorphic in C. janthina janthina, while two loci were polymorphic in C. janthina nitens. Using the markers, we performed preliminary analysis of genetic diversity and genetic structure within each subspecies. The expected heterozygosity ranged from 0.00 to 0.64 in C. janthina janthina and from 0.00 to 0.08 in C. janthina nitens. Each subspecies and each population within C. janthina janthina had different allele frequencies. C. janthina nitens exhibited far lower genetic diversity than C. janthina janthina. Furthermore, C. janthina nitens appears to have experienced strong genetic drift from a common ancestral population, inferred by STRUCTURE analysis. The markers described here may be useful for investigating genetic diversity and genetic structure of C. janthina populations, and could be used to estimate appropriate evolutionary significant unit and to guide development of a captive breeding program based on genetic information.

  4. African genetic ancestry interacts with body mass index to modify risk for uterine fibroids.

    Science.gov (United States)

    Giri, Ayush; Edwards, Todd L; Hartmann, Katherine E; Torstenson, Eric S; Wellons, Melissa; Schreiner, Pamela J; Velez Edwards, Digna R

    2017-07-01

    Race, specifically African ancestry, and obesity are important risk factors for uterine fibroids, and likely interact to provide the right conditions for fibroid growth. However, existing studies largely focus on the main-effects rather than their interaction. Here, we firstly provide evidence for interaction between categories of body mass index (BMI) and reported-race in relation to uterine fibroids. We then investigate whether the association between inferred local European ancestry and fibroid risk is modified by BMI in African American (AA) women in the Vanderbilt University Medical Center bio-repository (BioVU) (539 cases and 794 controls) and the Coronary Artery Risk Development in Young Adults study (CARDIA, 264 cases and 173 controls). We used multiple logistic regression to evaluate interactions between local European ancestry and BMI in relation to fibroid risk, then performed fixed effects meta-analysis. Statistical significance threshold for local-ancestry and BMI interactions was empirically estimated with 10,000 permutations (p-value = 1.18x10-4). Admixture mapping detected an association between European ancestry and fibroid risk which was modified by BMI (continuous-interaction p-value = 3.75x10-5) around ADTRP (chromosome 6p24); the strongest association was found in the obese category (ancestry odds ratio (AOR) = 0.51, p-value = 2.23x10-5). Evaluation of interaction between genotyped/imputed variants and BMI in this targeted region suggested race-specific interaction, present in AAs only; strongest evidence was found for insertion/deletion variant (6:11946435), again in the obese category (OR = 1.66, p-value = 1.72x10-6). We found nominal evidence for interaction between local ancestry and BMI at a previously reported region in chromosome 2q31-32, which includes COL5A2, and TFPI, an immediate downstream target of ADTRP. Interactions between BMI and SNPs (single nucleotide polymorphisms) found in this region in AA women were also detected in an

  5. Giant Galápagos tortoises; molecular genetic analyses identify a trans-island hybrid in a repatriation program of an endangered taxon

    Directory of Open Access Journals (Sweden)

    Caccone Adalgisa

    2007-02-01

    Full Text Available Abstract Background Giant Galápagos tortoises on the island of Española have been the focus of an intensive captive breeding-repatriation programme for over 35 years that saved the taxon from extinction. However, analysis of 118 samples from released individuals indicated that the bias sex ratio and large variance in reproductive success among the 15 breeders has severely reduced the effective population size (Ne. Results We report here that an analysis of an additional 473 captive-bred tortoises released back to the island reveals an individual (E1465 that exhibits nuclear microsatellite alleles not found in any of the 15 breeders. Statistical analyses incorporating genotypes of 304 field-sampled individuals from all populations on the major islands indicate that E1465 is most probably a hybrid between an Española female tortoise and a male from the island of Pinzón, likely present on Española due to human transport. Conclusion Removal of E1465 as well as its father and possible (half-siblings is warranted to prevent further contamination within this taxon of particular conservation significance. Despite this detected single contamination, it is highly noteworthy to emphasize the success of this repatriation program conducted over nearly 40 years and involving release of over 2000 captive-bred tortoises that now reproduce in situ. The incorporation of molecular genetic analysis of the program is providing guidance that will aid in monitoring the genetic integrity of this ambitious effort to restore a unique linage of a spectacular animal.

  6. Antigenic and genetic characterization of a divergent African virus, Ikoma lyssavirus.

    Science.gov (United States)

    Horton, Daniel L; Banyard, Ashley C; Marston, Denise A; Wise, Emma; Selden, David; Nunez, Alejandro; Hicks, Daniel; Lembo, Tiziana; Cleaveland, Sarah; Peel, Alison J; Kuzmin, Ivan V; Rupprecht, Charles E; Fooks, Anthony R

    2014-05-01

    In 2009, a novel lyssavirus (subsequently named Ikoma lyssavirus, IKOV) was detected in the brain of an African civet (Civettictis civetta) with clinical rabies in the Serengeti National Park of Tanzania. The degree of nucleotide divergence between the genome of IKOV and those of other lyssaviruses predicted antigenic distinction from, and lack of protection provided by, available rabies vaccines. In addition, the index case was considered likely to be an incidental spillover event, and therefore the true reservoir of IKOV remained to be identified. The advent of sensitive molecular techniques has led to a rapid increase in the discovery of novel viruses. Detecting viral sequence alone, however, only allows for prediction of phenotypic characteristics and not their measurement. In the present study we describe the in vitro and in vivo characterization of IKOV, demonstrating that it is (1) pathogenic by peripheral inoculation in an animal model, (2) antigenically distinct from current rabies vaccine strains and (3) poorly neutralized by sera from humans and animals immunized against rabies. In a laboratory mouse model, no protection was elicited by a licensed rabies vaccine. We also investigated the role of bats as reservoirs of IKOV. We found no evidence for infection among 483 individuals of at least 13 bat species sampled across sites in the Serengeti and Southern Kenya.

  7. A study of genetic markers in the South African Blesbok (Damaliscus Dorcas Phillipsi

    Directory of Open Access Journals (Sweden)

    D. R Osterhoff

    1972-12-01

    Full Text Available During culling operations on blesbok from the Rietvlei Nature Reserve, 198 blood samples were obtained for study of genetic markers including haemoglobins, transferrins, amylases, albumins and carbonic anhydrases. All animals exhibited the same pattern. Blood typing was performed by using goat reagents. These reagents could possibly be used to establish the relationship between the blesbok and the bontebok. Immunoelectrophoresis was used to detect any immunological differences; 123 blesbok samples were tested against antibovine serum prepared in rabbits. The animals could be grouped into four distinguishable types according to the shape and presence of the alpha-2-macroglobulin and the "horizontal55 band.

  8. Concentrations of Semivolatile Organic Compounds Associated with African Dust Air Masses in Mali, Cape Verde, Trinidad and Tobago, and the U.S. Virgin Islands, 2001-2008

    Science.gov (United States)

    Garrison, Virginia H.; Foreman, William T.; Genualdi, Susan A.; Majewski, Michael S.; Mohammed, Azad; Simonich, Staci Massey

    2011-01-01

    Every year, billions of tons of fine particles are eroded from the surface of the Sahara Desert and the Sahel of West Africa, lifted into the atmosphere by convective storms, and transported thousands of kilometers downwind. Most of the dust is carried west to the Americas and the Caribbean in the Saharan Air Layer (SAL). Dust air masses predominately impact northern South America during the Northern Hemisphere winter and the Caribbean and Southeastern United States in summer. Dust concentrations vary considerably temporally and spatially. In a dust source region (Mali), concentrations range from background levels of 575 micrograms per cubic meter (mu/u g per m3) to 13,000 mu/u g per m3 when visibility degrades to a few meters (Gillies and others, 1996). In the Caribbean, concentrations of 200 to 600 mu/u g per m3 in the mid-Atlantic and Barbados (Prospero and others, 1981; Talbot and others, 1986), 3 to 20 mu/u g per m3 in the Caribbean (Prospero and Nees, 1986; Perry and others, 1997); and >100 mu/u g per m3 in the Virgin Islands (this dataset) have been reported during African dust conditions. Mean dust particle size decreases as the SAL traverses from West Africa to the Caribbean and Americas as a result of gravitational settling. Mean particle size reaching the Caribbean is <1 micrometer (mu/u m) (Perry and others, 1997), and even finer particles are carried into Central America, the Southeastern United States, and maritime Canada. Particles less than 2.5 mu/u m diameter (termed PM2.5) can be inhaled deeply into human lungs. A large body of literature has shown that increased PM2.5 concentrations are linked to increased cardiovascular/respiratory morbidity and mortality (for example, Dockery and others, 1993; Penn and others, 2005).

  9. Stress and coping with racism and their role in sexual risk for HIV among African American, Asian/Pacific Islander, and Latino men who have sex with men.

    Science.gov (United States)

    Han, Chong-suk; Ayala, George; Paul, Jay P; Boylan, Ross; Gregorich, Steven E; Choi, Kyung-Hee

    2015-02-01

    The deleterious effects of racism on a wide range of health outcomes, including HIV risk, are well documented among racial/ethnic minority groups in the United States. However, little is known about how men of color who have sex with men (MSM) cope with stress from racism and whether the coping strategies they employ buffer against the impact of racism on sexual risk for HIV transmission. We examined associations of stress and coping with racism with unprotected anal intercourse (UAI) in a sample of African American (N = 403), Asian/Pacific Islander (N = 393), and Latino (N = 400) MSM recruited in Los Angeles County, CA during 2008-2009. Almost two-thirds (65 %) of the sample reported being stressed as a consequence of racism experienced within the gay community. Overall, 51 % of the sample reported having UAI in the prior 6 months. After controlling for race/ethnicity, age, nativity, marital status, sexual orientation, education, HIV serostatus, and lifetime history of incarceration, the multivariate analysis found statistically significant main effects of stress from racism and avoidance coping on UAI; no statistically significant main effects of dismissal, education/confrontation, and social-support seeking were observed. None of the interactions of stress with the four coping measures were statistically significant. Although stress from racism within the gay community increased the likelihood of engaging in UAI among MSM of color, we found little evidence that coping responses to racism buffered stress from racism. Instead, avoidance coping appears to suggest an increase in UAI.

  10. Increased Y-chromosome resolution of haplogroup O suggests genetic ties between the Ami aborigines of Taiwan and the Polynesian Islands of Samoa and Tonga.

    Science.gov (United States)

    Mirabal, Sheyla; Herrera, Kristian J; Gayden, Tenzin; Regueiro, Maria; Underhill, Peter A; Garcia-Bertrand, Ralph L; Herrera, Rene J

    2012-01-25

    The Austronesian expansion has left its fingerprint throughout two thirds of the circumference of the globe reaching the island of Madagascar in East Africa to the west and Easter Island, off the coast of Chile, to the east. To date, several theories exist to explain the current genetic distribution of Austronesian populations, with the "slow boat" model being the most widely accepted, though other conjectures (i.e., the "express train" and "entangled bank" hypotheses) have also been widely discussed. In the current study, 158 Y chromosomes from the Polynesian archipelagos of Samoa and Tonga were typed using high resolution binary markers and compared to populations across Mainland East Asia, Taiwan, Island Southeast Asia, Melanesia and Polynesia in order to establish their patrilineal genetic relationships. Y-STR haplotypes on the C2 (M38), C2a (M208), O1a (M119), O3 (M122) and O3a2 (P201) backgrounds were utilized in an attempt to identify the differing sources of the current Y-chromosomal haplogroups present throughout Polynesia (of Melanesian and/or Asian descent). We find that, while haplogroups C2a, S and K3-P79 suggest a Melanesian component in 23%-42% of the Samoan and Tongan Y chromosomes, the majority of the paternal Polynesian gene pool exhibits ties to East Asia. In particular, the prominence of sub-haplogroup O3a2c* (P164), which has previously been observed at only minimal levels in Mainland East Asians (2.0-4.5%), in both Polynesians (ranging from 19% in Manua to 54% in Tonga) and Ami aborigines from Taiwan (37%) provides, for the first time, evidence for a genetic connection between the Polynesian populations and the Ami. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Participants' perceptions of research benefits in an African genetic epidemiology study.

    Science.gov (United States)

    Appiah-Poku, John; Newton, Sam; Kass, Nancy

    2011-12-01

      Both the Council for International Organization of Medical Sciences and the Helsinki Declaration emphasize that the potential benefits of research should outweigh potential harms; consequently, some work has been conducted on participants' perception of benefits in therapeutic research. However, there appears to be very little work conducted with participants who have joined non-therapeutic research. This work was done to evaluate participants' perception of benefits in a genetic epidemiological study by examining their perception of the potential benefits of enrollment.   In-depth interviews lasting between 45 and 60 minutes were conducted with a convenient sample of 25 ill patients and 25 healthy accompanying relatives enrolled in a genetic epidemiological study of tuberculosis. Recorded interviews were transcribed and analyzed using content analysis.   Participants perceived that research was beneficial and some of the benefits included the generation of new knowledge, finding the cause of diseases, as well as the control, eradication and prevention of disease. Some thought that research was risky whilst others thought that the benefits outweighed the risks.   Participants perceived research to be beneficial and most of them thought that, though it was risky, the benefits outweighed the risks. It is our view that researchers need to give serious consideration to participant's perception of benefits in designing their consent forms, to see to the fulfillment of achievable goals. © 2011 Blackwell Publishing Ltd.

  12. Genetic signatures for enhanced olfaction in the African mole-rats.

    Directory of Open Access Journals (Sweden)

    Sofia Stathopoulos

    Full Text Available The Olfactory Receptor (OR superfamily, the largest in the vertebrate genome, is responsible for vertebrate olfaction and is traditionally subdivided into 17 OR families. Recent studies characterising whole-OR subgenomes revealed a 'birth and death' model of evolution for a range of species, however little is known about fine-scale evolutionary dynamics within single-OR families. This study reports the first assessment of fine-scale OR evolution and variation in African mole-rats (Bathyergidae, a family of subterranean rodents endemic to sub-Saharan Africa. Because of the selective pressures of life underground, enhanced olfaction is proposed to be fundamental to the evolutionary success of the Bathyergidae, resulting in a highly diversified OR gene-repertoire. Using a PCR-sequencing approach, we analysed variation in the OR7 family across 14 extant bathyergid species, which revealed enhanced levels of functional polymorphisms concentrated across the receptors' ligand-binding region. We propose that mole-rats are able to recognise a broad range of odorants and that this diversity is reflected throughout their OR7 gene repertoire. Using both classic tests and tree-based methods to test for signals of selection, we investigate evolutionary forces across the mole-rat OR7 gene tree. Four well-supported clades emerged in the OR phylogeny, with varying signals of selection; from neutrality to positive and purifying selection. Bathyergid life-history traits and environmental niche-specialisation are explored as possible drivers of adaptive OR evolution, emerging as non-exclusive contributors to the positive selection observed at OR7 genes. Our results reveal unexpected complexity of evolutionary mechanisms acting within a single OR family, providing insightful perspectives into OR evolutionary dynamics.

  13. Population genetic structure of gray wolves (Canis lupus) in a marine archipelago suggests island-mainland differentiation consistent with dietary niche

    DEFF Research Database (Denmark)

    Stronen, Astrid Vik; Navid, Erin L; Quinn, Michael S

    2014-01-01

    Background Emerging evidence suggests that ecological heterogeneity across space can influence the genetic structure of populations, including that of long-distance dispersers such as large carnivores. On the central coast of British Columbia, Canada, wolf (Canis lupus L., 1758) dietary niche...... mainland and island wolves. This pattern occurs despite field observations that individuals easily traverse the 30 km wide study area and swim up to 13 km among landmasses in the region. Conclusions Natal habitat-biased dispersal (i.e., the preference for dispersal into familiar ecological environments...

  14. Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus and the role of selection within primates

    Directory of Open Access Journals (Sweden)

    Willem G. Coetzer

    2018-06-01

    Full Text Available Vervet monkeys (Chlorocebus pygerythrus are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like receptor (TLR gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7 and a reproductively linked gene, acrosin (ACR, across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11–21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys, with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR. TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR coding regions also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly

  15. al mena: a comprehensive resource of human genetic variants integrating genomes and exomes from Arab, Middle Eastern and North African populations.

    Science.gov (United States)

    Koshy, Remya; Ranawat, Anop; Scaria, Vinod

    2017-10-01

    Middle East and North Africa (MENA) encompass very unique populations, with a rich history and encompasses characteristic ethnic, linguistic and genetic diversity. The genetic diversity of MENA region has been largely unknown. The recent availability of whole-exome and whole-genome sequences from the region has made it possible to collect population-specific allele frequencies. The integration of data sets from this region would provide insights into the landscape of genetic variants in this region. We integrated genetic variants from multiple data sets systematically, available from this region to create a compendium of over 26 million genetic variations. The variants were systematically annotated and their allele frequencies in the data sets were computed and available as a web interface which enables quick query. As a proof of principle for application of the compendium for genetic epidemiology, we analyzed the allele frequencies for variants in transglutaminase 1 (TGM1) gene, associated with autosomal recessive lamellar ichthyosis. Our analysis revealed that the carrier frequency of selected variants differed widely with significant interethnic differences. To the best of our knowledge, al mena is the first and most comprehensive repertoire of genetic variations from the Arab, Middle Eastern and North African region. We hope al mena would accelerate Precision Medicine in the region.

  16. Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study

    OpenAIRE

    Perera, Minoli A; Cavallari, Larisa H; Limdi, Nita A; Gamazon, Eric R; Konkashbaev, Anuar; Daneshjou, Roxana; Pluzhnikov, Anna; Crawford, Dana C; Wang, Jelai; Liu, Nianjun; Tatonetti, Nicholas; Bourgeois, Stephane; Takahashi, Harumi; Bradford, Yukiko; Burkley, Benjamin M

    2013-01-01

    Summary BackgroundVKORC1 and CYP2C9 are important contributors to warfarin dose variability, but explain less variability for individuals of African descent than for those of European or Asian descent. We aimed to identify additional variants contributing to warfarin dose requirements in African Americans. MethodsWe did a genome-wide association study of discovery and replication cohorts. Samples from African-American adults (aged ≥18 years) who were taking a stable maintenance dose of warfar...

  17. The genetic and developmental basis of an exaggerated craniofacial trait in East African cichlids.

    Science.gov (United States)

    Concannon, Moira R; Albertson, R Craig

    2015-12-01

    The evolution of an exaggerated trait can lead to a novel morphology that allows organisms to exploit new niches. The molecular bases of such phenotypes can reveal insights into the evolution of unique traits. Here, we investigate a rare morphological innovation in modern haplochromine cichlids, a flap of fibrous tissue that causes a pronounced projection of the snout, which is limited to a single genus (Labeotropheus) of Lake Malawi cichlids. We compare flap size in our focal species L. fuelleborni (LF) to homologous landmarks in other closely related cichlid species that show a range of ecological overlap with LF, and demonstrate that variation in flap size is discontinuous among Malawi cichlid species. We demonstrate further that flap development in LF begins at early juvenile stages, and scales allometrically with body size. We then used an F2 hybrid mapping population, derived via crossing LF to a close ecological competitor that lacks this trait, Tropheops "red cheek" (TRC), to identify quantitative trait loci (QTL) that underlie flap development. In all, we identified four loci associated with variation in flap size, and for each the LF allele contributed to a larger flap. We next cross-referenced our QTL map with population genomic data, comparing natural populations of LF and TRC, to identify divergent polymorphisms within each QTL interval. Candidate genes for flap development are discussed. Together, these data indicate a relatively simple and tractable genetic basis for this morphological innovation, which is consistent with its apparently sudden and saltatory evolutionary history. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 662-670, 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  18. A small cohort of Island Southeast Asian women founded Madagascar.

    Science.gov (United States)

    Cox, Murray P; Nelson, Michael G; Tumonggor, Meryanne K; Ricaut, François-X; Sudoyo, Herawati

    2012-07-22

    The settlement of Madagascar is one of the most unusual, and least understood, episodes in human prehistory. Madagascar was one of the last landmasses to be reached by people, and despite the island's location just off the east coast of Africa, evidence from genetics, language and culture all attests that it was settled jointly by Africans, and more surprisingly, Indonesians. Nevertheless, extremely little is known about the settlement process itself. Here, we report broad geographical screening of Malagasy and Indonesian genetic variation, from which we infer a statistically robust coalescent model of the island's initial settlement. Maximum-likelihood estimates favour a scenario in which Madagascar was settled approximately 1200 years ago by a very small group of women (approx. 30), most of Indonesian descent (approx. 93%). This highly restricted founding population raises the possibility that Madagascar was settled not as a large-scale planned colonization event from Indonesia, but rather through a small, perhaps even unintended, transoceanic crossing.

  19. Phylogeography of a successful aerial disperser: the golden orb spider Nephila on Indian Ocean islands

    Directory of Open Access Journals (Sweden)

    Kuntner Matjaž

    2011-05-01

    Full Text Available Abstract Background The origin and diversification patterns of lineages across the Indian Ocean islands are varied due to the interplay of the complex geographic and geologic island histories, the varying dispersal abilities of biotas, and the proximity to major continental landmasses. Our aim was to reconstruct phylogeographic history of the giant orbweaving spider (Nephila on western Indian Ocean islands (Madagascar, Mayotte, Réunion, Mauritius, Rodrigues, to test its origin and route of dispersal, and to examine the consequences of good dispersal abilities for colonization and diversification, in comparison with related spiders (Nephilengys inhabiting the same islands, and with other organisms known for over water dispersal. We used mitochondrial (COI and nuclear (ITS2 markers to examine phylogenetic and population genetic patterns in Nephila populations and species. We employed Bayesian and parsimony methods to reconstruct phylogenies and haplotype networks, respectively, and calculated genetic distances, fixation indices, and estimated clade ages under a relaxed clock model. Results Our results suggest an African origin of Madagascar Nephila inaurata populations via Cenozoic dispersal, and the colonization of the Mascarene islands from Madagascar. We find evidence of gene flow across Madagascar and Comoros. The Mascarene islands share a common 'ancestral' COI haplotype closely related to those found on Madagascar, but itself absent, or as yet unsampled, from Madagascar. Each island has one or more unique haplotypes related to the ancestral Mascarene haplotype. The Indian Ocean N. inaurata are genetically distinct from the African populations. Conclusions Nephila spiders colonized Madagascar from Africa about 2.5 (0.6-5.3 Ma. Our results are consistent with subsequent, recent and rapid, colonization of all three Mascarene islands. On each island, however, we detected unique haplotypes, consistent with a limited gene flow among the islands

  20. The combined effects of genetic risk and perceived discrimination on blood pressure among African Americans in the Jackson Heart Study.

    Science.gov (United States)

    Taylor, Jacquelyn Y; Sun, Yan V; Barcelona de Mendoza, Veronica; Ifatunji, Mosi; Rafferty, Jane; Fox, Ervin R; Musani, Solomon K; Sims, Mario; Jackson, James S

    2017-10-01

    Both genomics and environmental stressors play a significant role in increases in blood pressure (BP). In an attempt to further explain the hypertension (HTN) disparity among African Americans (AA), both genetic underpinnings (selected candidate genes) and stress due to perceived racial discrimination (as reported in the literature) have independently been linked to increased BP among AAs. Although Gene x Environment interactions on BP have been examined, the environmental component of these investigations has focused more on lifestyle behaviors such as smoking, diet, and physical activity, and less on psychosocial stressors such as perceived discrimination.The present study uses candidate gene analyses to identify the relationship between Everyday Discrimination (ED) and Major Life Discrimination (MLD) with increases in systolic BP (SBP) and diastolic BP (DBP) among AA in the Jackson Heart Study. Multiple linear regression models reveal no association between discrimination and BP after adjusting for age, sex, body mass index (BMI), antihypertensive medication use, and current smoking status.Subsequent candidate gene analysis identified 5 SNPs (rs7602215, rs3771724, rs1006502, rs1791926, and rs2258119) that interacted with perceived discrimination and SBP, and 3 SNPs (rs2034454, rs7602215, and rs3771724) that interacted with perceived discrimination and DBP. Most notably, there was a significant SNP × discrimination interaction for 2 SNPs on the SLC4A5 gene: rs3771724 (MLD: SBP P = .034, DBP P = .031; ED: DBP: P = .016) and rs1006502 (MLD: SBP P = .034, DBP P = .030; ED: DBP P = .015).This study supports the idea that SNP × discrimination interactions combine to influence clinically relevant traits such as BP. Replication with similar epidemiological samples is required to ascertain the role of genes and psychosocial stressors in the development and expression of high BP in this understudied population.

  1. Heat Islands

    Science.gov (United States)

    EPA's Heat Island Effect Site provides information on heat islands, their impacts, mitigation strategies, related research, a directory of heat island reduction initiatives in U.S. communities, and EPA's Heat Island Reduction Program.

  2. Island biogeography

    DEFF Research Database (Denmark)

    Whittaker, Robert James; Fernández-Palacios, José María; Matthews, Thomas J.

    2017-01-01

    Islands provide classic model biological systems. We review how growing appreciation of geoenvironmental dynamics of marine islands has led to advances in island biogeographic theory accommodating both evolutionary and ecological phenomena. Recognition of distinct island geodynamics permits gener...

  3. Blue Tigers, Black Tapirs, & the Pied Raven of the Faroe Islands: Teaching Genetic Drift Using Real-Life Animal Examples

    Science.gov (United States)

    Robischon, Marcel

    2015-01-01

    Genetic drift is a concept of population genetics that is central to understanding evolutionary processes and aspects of conservation biology. It is frequently taught using rather abstract representations. I introduce three real-life zoological examples, based on historical and recent color morphs of tigers, tapirs, and ravens, that can complement…

  4. Genetic, household and spatial clustering of leprosy on an island in Indonesia: a population-based study

    NARCIS (Netherlands)

    Bakker, Mirjam I.; May, Linda; Hatta, Mochammad; Kwenang, Agnes; Klatser, Paul R.; Oskam, Linda; Houwing-Duistermaat, Jeanine J.

    2005-01-01

    ABSTRACT : BACKGROUND : It is generally accepted that genetic factors play a role in susceptibility to both leprosy per se and leprosy type, but only few studies have tempted to quantify this. Estimating the contribution of genetic factors to clustering of leprosy within families is difficult since

  5. Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression.

    Science.gov (United States)

    Murray, Gemma G R; Woolhouse, Mark E J; Tapio, Miika; Mbole-Kariuki, Mary N; Sonstegard, Tad S; Thumbi, Samuel M; Jennings, Amy E; van Wyk, Ilana Conradie; Chase-Topping, Margo; Kiara, Henry; Toye, Phil; Coetzer, Koos; deC Bronsvoort, Barend M; Hanotte, Olivier

    2013-11-09

    Positive multi-locus heterozygosity-fitness correlations have been observed in a number of natural populations. They have been explained by the correlation between heterozygosity and inbreeding, and the negative effect of inbreeding on fitness (inbreeding depression). Exotic introgression in a locally adapted population has also been found to reduce fitness (outbreeding depression) through the breaking-up of co-adapted genes, or the introduction of non-locally adapted gene variants. In this study we examined the inter-relationships between genome-wide heterozygosity, introgression, and death or illness as a result of infectious disease in a sample of calves from an indigenous population of East African Shorthorn Zebu (crossbred Bos taurus x Bos indicus) in western Kenya. These calves were observed from birth to one year of age as part of the Infectious Disease in East African Livestock (IDEAL) project. Some of the calves were found to be genetic hybrids, resulting from the recent introgression of European cattle breed(s) into the indigenous population. European cattle are known to be less well adapted to the infectious diseases present in East Africa. If death and illness as a result of infectious disease have a genetic basis within the population, we would expect both a negative association of these outcomes with introgression and a positive association with heterozygosity. In this indigenous livestock population we observed negative associations between heterozygosity and both death and illness as a result of infectious disease and a positive association between European taurine introgression and episodes of clinical illness. We observe the effects of both inbreeding and outbreeding depression in the East African Shorthorn Zebu, and therefore find evidence of a genetic component to vulnerability to infectious disease. These results indicate that the significant burden of infectious disease in this population could, in principle, be reduced by altered breeding

  6. How does mother-to-child transmission of HIV differ among African populations? Lessons from MBL2 genetic variation in Zimbabweans.

    Science.gov (United States)

    Mhandire, Kudakwashe; Pharo, Gavin; Kandawasvika, Gwendolene Q; Duri, Kerina; Swart, Marelize; Stray-Pedersen, Babill; Dandara, Collet

    2014-07-01

    Mannose binding lectin (MBL) is a pathogen pattern recognition protein involved in antimicrobial activities. Variation in MBL2 gene has been extensively implicated in differential outcomes of infectious diseases in studies conducted outside Africa, but virtually very little is known on the role of this candidate gene in the African continent. We investigated human genetic variations in MBL2 in a Zimbabwean pediatric population and their putative associations with HIV infection in perinatally exposed children. One hundred and four children aged 7 to 9 years comprising 68 perinatally exposed to HIV (32 who were born infected and 36 who were uninfected) and 36 unexposed controls were recruited. DNA samples were genotyped for MBL2 polymorphisms using PCR-RFLP and sequencing. HIV infected children had markedly variable and significantly lower mean height (p=0.03) and weight (p=0.005) when compared to the uninfected children. Using all samples, frequencies for MBL2 genetic variants for the Zimbabwean population were calculated. Twelve single nucleotide polymorphisms were observed and minor alleles occurred with the following frequencies: -550C>G (G: 0.02), -435G>A (A: 0.08), -428A>C (C: 0.39), -394A>G (A: 0.39), -328AGAGAA ins/del (AGAGAA ins: 0.44), -245G>A (A: 0.05), -221C>G (C: 0.12), -111A>T (T: 0.10), -70C>T (C: 0.46), +4C>T (C: 0.45), novel -595G>A (A: 0.02), and 170G>A (0.24). We found that the MBL2 +4T variant displayed a trend for association with reduced risk of HIV transmission from mother-to-child but the remaining vast majority of the genetic markers did not show a significant association. We conclude (1) the MBL2 gene is highly polymorphic in the Zimbabwean population, and (2) MBL2 genetic variation does not appear to play a major role in influencing the risk of mother-to-child HIV transmission in our study sample. These observations contest the hitherto significant role of this candidate gene for HIV transmission from mother-to-child in non-African

  7. The Escherichia coli argW-dsdCXA genetic island is highly variable, and E. coli K1 strains commonly possess two copies of dsdCXA.

    Science.gov (United States)

    Moritz, Rebecca L; Welch, Rodney A

    2006-11-01

    The genome sequences of Escherichia coli pathotypes reveal extensive genetic variability in the argW-dsdCXA island. Interestingly, the archetype E. coli K1 neonatal meningitis strain, strain RS218, has two copies of the dsdCXA genes for d-serine utilization at the argW and leuX islands. Because the human brain contains d-serine, an epidemiological study emphasizing K1 isolates surveyed the dsdCXA copy number and function. Forty of 41 (97.5%) independent E. coli K1 isolates could utilize d-serine. Southern blot hybridization revealed physical variability within the argW-dsdC region, even among 22 E. coli O18:K1:H7 isolates. In addition, 30 of 41 K1 strains, including 21 of 22 O18:K1:H7 isolates, had two dsdCXA loci. Mutational analysis indicated that each of the dsdA genes is functional in a rifampin-resistant mutant of RS218, mutant E44. The high percentage of K1 strains that can use d-serine is in striking contrast to our previous observation that only 4 of 74 (5%) isolates in the diarrheagenic E. coli (DEC) collection have this activity. The genome sequence of diarrheagenic E. coli isolates indicates that the csrRAKB genes for sucrose utilization are often substituted for dsdC and a portion of dsdX present at the argW-dsdCXA island of extraintestinal isolates. Among DEC isolates there is a reciprocal pattern of sucrose fermentation versus d-serine utilization. The ability to use d-serine is a trait strongly selected for among E. coli K1 strains, which have the ability to infect a wide range of extraintestinal sites. Conversely, diarrheagenic E. coli pathotypes appear to have substituted sucrose for d-serine as a potential nutrient.

  8. Genetic variants of methyl metabolizing enzymes and epigenetic regulators: Associations with promoter CpG island hypermethylation in colorectal cancer

    NARCIS (Netherlands)

    Vogel, S. de; Wouters, K.A.D.; Gottschalk, R.W.H.; Schooten, F.J. van; Goeij, A.F.P.M. de; Bruïne, A.P. de; Goldbohm, R.A.; Brandt, P.A. van den; Weijenberg, M.P.; Engeland, M. van

    2009-01-01

    Aberrant DNA methylation affects carcinogenesis of colorectal cancer. Folate metabolizing enzymes may influence the bioavailability of methyl groups, whereas DNA and histone methyltransferases are involved in epigenetic regulation of gene expression. We studied associations of genetic variants of

  9. Genetic polymorphisms in one-carbon metabolism: associations with CpG island methylator phenotype (CIMP) in colon cancer and the modifying effects of diet.

    Science.gov (United States)

    Curtin, Karen; Slattery, Martha L; Ulrich, Cornelia M; Bigler, Jeannette; Levin, Theodore R; Wolff, Roger K; Albertsen, Hans; Potter, John D; Samowitz, Wade S

    2007-08-01

    This study investigated associations between CpG island methylator phenotype (CIMP) colon cancer and genetic polymorphisms relevant to one-carbon metabolism and thus, potentially the provision of methyl groups and risk of colon cancer. Data from a large, population-based case-control study (916 incident colon cancer cases and 1,972 matched controls) were used. Candidate polymorphisms in methylenetetrahydrofolate reductase (MTHFR), thymidylate synthase (TS), transcobalamin II (TCNII), methionine synthase (MTR), reduced folate carrier (RFC), methylenetetrahydrofolate dehydrogenase 1 (MTHFD1), dihydrofolate reductase (DHFR) and alcohol dehydrogenase 3 (ADH3) were evaluated. CIMP- or CIMP+ phenotype was based on five CpG island markers: MINT1, MINT2, MINT31, p16 and MLH1. The influence of specific dietary factors (folate, methionine, vitamin B(12) and alcohol) on these associations was also analyzed. We hypothesized that polymorphisms involved in the provision of methyl groups would be associated with CIMP+ tumors (two or more of five markers methylated), potentially modified by diet. Few associations specific to CIMP+ tumors were observed overall, which does not support the hypothesis that the provision of methyl groups is important in defining a methylator phenotype. However, our data suggest that genetic polymorphisms in MTHFR 1,298A > C, interacting with diet, may be involved in the development of highly CpG-methylated colon cancers. AC and CC genotypes in conjunction with a high-risk dietary pattern (low folate and methionine intake and high alcohol use) were associated with CIMP+ (OR = 2.1, 95% CI = 1.3-3.4 versus AA/high risk; P-interaction = 0.03). These results provide only limited support for a role of polymorphisms in one-carbon metabolism in the etiology of CIMP colon cancer.

  10. Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia

    OpenAIRE

    Brand?o, Andreia; Eng, Ken Khong; Rito, Teresa; Cavadas, Bruno; Bulbeck, David; Gandini, Francesca; Pala, Maria; Mormina, Maru; Hudson, Bob; White, Joyce; Ko, Tsang-Ming; Saidin, Mokhtar; Zafarina, Zainuddin; Oppenheimer, Stephen; Richards, Martin B.

    2016-01-01

    There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a ...

  11. High genetic differentiation between an African and a non-African strain of Drosophila simulans revealed by segregation distortion and reduced crossover frequency.

    Science.gov (United States)

    Tatsuta, Haruki; Takano-Shimizu, Toshiyuki

    2009-11-01

    Drosophila simulans strains originating from Madagascar and nearby islands in the Indian Ocean often differ from those elsewhere in the number of sex comb teeth and the degree of morphological anomaly in hybrids with D. melanogaster. Here, we report a strong segregation distortion in the F1 intercross between two D. simulans strains originating from Madagascar and the US, possibly at both the gametic and zygotic levels. Strong bias against alleles of the Madagascar strain was observed for all ten marker loci distributed over the entire second chromosome in the F1 intercross, but only a few showed a weak distortion in the isogenic backgrounds of either strains. Significant deviations of genotype frequencies from Hardy-Weinberg proportions were consistently observed for the second chromosome. By contrast, the X and third chromosomes did not show any strong segregation distortion. Crossover frequency on the second chromosome was uniformly reduced in isogenic backgrounds whereas the map lengths in the F1 intercross were comparable to or larger than that of the standard D. melanogaster map. We discuss these findings in relation to previous studies on other traits and interspecific differences between D. mauritiana, which is endemic to Mauritius Island, and D. simulans.

  12. Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity

    Science.gov (United States)

    Nougairède, Antoine; Joffret, Marie-Line; Deshpande, Jagadish M.; Dubot-Pérès, Audrey; Héraud, Jean-Michel

    2014-01-01

    Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied. PMID:24598878

  13. Genetic variation in N- and C-terminal regions of bovine DNAJA1 heat shock protein gene in African, Asian and American cattle

    Science.gov (United States)

    Ajayi, Oyeyemi O.; Peters, Sunday O.; De Donato, Marcos; Mujibi, F. Denis; Khan, Waqas A.; Hussain, Tanveer; Babar, Masroor E.; Imumorin, Ikhide G.; Thomas, Bolaji N.

    2018-01-01

    DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak. In-silico functional analysis with PANTHER predicted putative deleterious functional impact of c.161 T>A; p. V54Q while alignment of bovine and human NTR-J domains revealed that p.Q19H, p.E20Q and p. E21X mutations occurred in helix 2 and p.V54Q missense mutation occurred in helix 3 respectively. The 124 bp insertion found in the yak DNAJA1 ortholog may have significant functional relevance warranting further investigation. Our results suggest that these genetic differences may be concomitant with population genetic history and possible functional consequences for climate adaptation in bovidae. PMID:29290829

  14. Chemokine Ligand 5 (CCL5 and chemokine receptor (CCR5 genetic variants and prostate cancer risk among men of African Descent: a case-control study

    Directory of Open Access Journals (Sweden)

    Kidd LaCreis R

    2012-11-01

    Full Text Available Abstract Background Chemokine and chemokine receptors play an essential role in tumorigenesis. Although chemokine-associated single nucleotide polymorphisms (SNPs are associated with various cancers, their impact on prostate cancer (PCA among men of African descent is unknown. Consequently, this study evaluated 43 chemokine-associated SNPs in relation to PCA risk. We hypothesized inheritance of variant chemokine-associated alleles may lead to alterations in PCA susceptibility, presumably due to variations in antitumor immune responses. Methods Sequence variants were evaluated in germ-line DNA samples from 814 African-American and Jamaican men (279 PCA cases and 535 controls using Illumina’s Goldengate genotyping system. Results Inheritance of CCL5 rs2107538 (AA, GA+AA and rs3817655 (AA, AG, AG+AA genotypes were linked with a 34-48% reduction in PCA risk. Additionally, the recessive and dominant models for CCR5 rs1799988 and CCR7 rs3136685 were associated with a 1.52-1.73 fold increase in PCA risk. Upon stratification, only CCL5 rs3817655 and CCR7 rs3136685 remained significant for the Jamaican and U.S. subgroups, respectively. Conclusions In summary, CCL5 (rs2107538, rs3817655 and CCR5 (rs1799988 sequence variants significantly modified PCA susceptibility among men of African descent, even after adjusting for age and multiple comparisons. Our findings are only suggestive and require further evaluation and validation in relation to prostate cancer risk and ultimately disease progression, biochemical/disease recurrence and mortality in larger high-risk subgroups. Such efforts will help to identify genetic markers capable of explaining disproportionately high prostate cancer incidence, mortality, and morbidity rates among men of African descent.

  15. The genetic structure of populations from Haiti and Jamaica reflect divergent demographic histories.

    Science.gov (United States)

    Simms, Tanya M; Rodriguez, Carol E; Rodriguez, Rosa; Herrera, Rene J

    2010-05-01

    The West Indies represent an amalgamation of African, European and in some cases, East Asian sources, but the contributions from each ethnic group remain relatively unexplored from a genetic perspective. In the present study, we report, for the first time, allelic frequency data across the complete set of 15 autosomal STR loci for general collections from Haiti and Jamaica, which were subsequently used to examine the genetic diversity present in each island population. Our results indicate that although both Haiti and Jamaica display genetic affinities with the continental African collections, a stronger African signal is detected in Haiti than in Jamaica. Although only minimal contributions from non-African sources were observed in Haiti, Jamaica displays genetic input from both European and East Asian sources, an admixture profile similar to other New World collections of African descent analyzed in this report. The divergent genetic signatures present in these populations allude to the different migratory events of Africans, Europeans, and East Asians into the New World.

  16. Multiple Paternity and Preliminary Population Genetics of Giant Pacific Octopuses, Enteroctopus dofleini, in Oregon, Washington and the Southeast Coast of Vancouver Island, BC

    Directory of Open Access Journals (Sweden)

    Shawn Larson

    2015-06-01

    Full Text Available A total of 77 giant Pacific octopus, Enteroctopus dofleini, tissue samples were collected from the Oregon Coast (OR, Neah Bay Washington (NB, Puget Sound Washington (PS and the southeast coast of Vancouver Island, British Columbia, Canada (BC for genetic analyses. A suite of eight variable microsatellite markers developed from giant Pacific octopuses were amplified in these samples to determine population diversity, structure, relatedness and paternity. The majority of loci met Hardy-Weinberg equilibrium expectations within each population. We found moderate genetic diversity (average observed heterozygosity = 0.445, range = 0.307–0.515 and average expected heterozygosity = 0.567, range = 0.506–0.696 and moderate population structuring with distinct separation of groups (FST values ranged from 0.101 between BC and PS to 0.237 between BC and NB. Several egg strings from the BC population were collected from three female octopus dens for relatedness and paternity analyses. Results suggest strong support for multiple paternity within one egg clutch with progeny sired by between two to four males.

  17. A comparison of genetic connectivity in two deep sea corals to examine whether seamounts are isolated islands or stepping stones for dispersal

    Science.gov (United States)

    Miller, Karen J.; Gunasekera, Rasanthi M.

    2017-04-01

    Ecological processes in the deep sea are poorly understood due to the logistical constraints of sampling thousands of metres below the ocean’s surface and remote from most land masses. Under such circumstances, genetic data provides unparalleled insight into biological and ecological relationships. We use microsatellite DNA to compare the population structure, reproductive mode and dispersal capacity in two deep sea corals from seamounts in the Southern Ocean. The solitary coral Desmophyllum dianthus has widespread dispersal consistent with its global distribution and resilience to disturbance. In contrast, for the matrix-forming colonial coral Solenosmilia variabilis asexual reproduction is important and the dispersal of sexually produced larvae is negligible, resulting in isolated populations. Interestingly, despite the recognised impacts of fishing on seamount communities, genetic diversity on fished and unfished seamounts was similar for both species, suggesting that evolutionary resilience remains despite reductions in biomass. Our results provide empirical evidence that a group of seamounts can function either as isolated islands or stepping stones for dispersal for different taxa. Furthermore different strategies will be required to protect the two sympatric corals and consequently the recently declared marine reserves in this region may function as a network for D. dianthus, but not for S. variabilis.

  18. Comparison of historical bottleneck effects and genetic consequences of re-introduction in a critically endangered island passerine.

    Science.gov (United States)

    Bristol, Rachel M; Tucker, Rachel; Dawson, Deborah A; Horsburgh, Gavin; Prys-Jones, Robert P; Frantz, Alain C; Krupa, Andy; Shah, Nirmal J; Burke, Terry; Groombridge, Jim J

    2013-09-01

    Re-introduction is an important tool for recovering endangered species; however, the magnitude of genetic consequences for re-introduced populations remains largely unknown, in particular the relative impacts of historical population bottlenecks compared to those induced by conservation management. We characterize 14 microsatellite loci developed for the Seychelles paradise flycatcher and use them to quantify temporal and spatial measures of genetic variation across a 134-year time frame encompassing a historical bottleneck that reduced the species to ~28 individuals in the 1960s, through the initial stages of recovery and across a second contemporary conservation-introduction-induced bottleneck. We then evaluate the relative impacts of the two bottlenecks, and finally apply our findings to inform broader re-introduction strategy. We find a temporal trend of significant decrease in standard measures of genetic diversity across the historical bottleneck, but only a nonsignificant downward trend in number of alleles across the contemporary bottleneck. However, accounting for the different timescales of the two bottlenecks (~40 historical generations versus introduction. In some cases, the loss of genetic diversity per generation can, initially at least, be greater across re-introduction-induced bottlenecks. © 2013 John Wiley & Sons Ltd.

  19. Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands.

    Science.gov (United States)

    Gama, Luis T; Martínez, Amparo M; Carolino, Inês; Landi, Vincenzo; Delgado, Juan V; Vicente, Antonio A; Vega-Pla, José L; Cortés, Oscar; Sousa, Conceição O

    2013-06-14

    Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies. A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results. Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and

  20. Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers

    Science.gov (United States)

    Aziz Ebrahimi; Abdolkarim Zarei; Shaneka Lawson; Keith E. Woeste; M. J. M. Smulders

    2016-01-01

    Persian walnut (Juglans regia L.) is the world's most widely grown nut crop, but large-scale assessments and comparisons of the genetic diversity of the crop are notably lacking. To guide the conservation and utilization of Persian walnut genetic resources, genotypes (n = 189) from 25 different regions in 14 countries on...

  1. The value of small habitat islands for the conservation of genetic variability in a steppe grass species

    Science.gov (United States)

    Wódkiewicz, Maciej; Dembicz, Iwona; Moysiyenko, Ivan I.

    2016-10-01

    The habitat loss and fragmentation due to agricultural land-conversion affected the steppe throughout its range. In Ukraine, 95% of steppe was destroyed in the last two centuries. Remaining populations are confined to few refuges, like nature reserves, loess ravines, and kurgans (small burial mounds), the latter being often subject to destruction by archeological excavations. Stipa capillata L. is a typical grass species of Eurasian steppes and extrazonal dry grasslands, that was previously used as a model species in studies on steppe ecology. The aim of our research was to assess genetic diversity of S. capillata populations within different types of steppe refuges (loess ravines, biosphere reserve, kurgan) and to evaluate the value of the latter group for the preservation of genetic diversity in the study species. We assessed genetic diversity of 266 individuals from 15 populations (nine from kurgans, three from loess ravines and three from Askania-Nova Biosphere Reserve) with eight Universal Rice Primers (URPs). Studied populations showed high intra-population variability (I: 0.262-0.419, PPB: 52.08-82.64%). Populations from kurgans showed higher genetic differentiation (ΦST = 0.247) than those from loess ravines (ΦST = 0.120) and the biosphere reserve (ΦST = 0.142). Although the diversity metrics were to a small extent lower for populations from kurgans than from larger refugia we conclude that all studied populations of the species still preserve high genetic variability and are valuable for protection. To what extent this pattern holds true under continuous fragmentation in the future must be carefully monitored.

  2. Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests.

    Science.gov (United States)

    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.

  3. Genome-Wide Association Meta-Analyses to Identify Common Genetic Variants Associated with Hallux Valgus in Caucasian and African Americans

    Science.gov (United States)

    Hsu, Yi-Hsiang; Liu, Youfang; Hannan, Marian T.; Maixner, William; Smith, Shad B.; Diatchenko, Luda; Golightly, Yvonne M.; Menz, Hylton B.; Kraus, Virginia B.; Doherty, Michael; Wilson, A.G.; Jordan, Joanne M.

    2016-01-01

    Objective Hallux valgus (HV) affects ~36% of Caucasian adults. Although considered highly heritable, the underlying genetic determinants are unclear. We conducted the first genome-wide association study (GWAS) aimed to identify genetic variants associated with HV. Methods HV was assessed in 3 Caucasian cohorts (n=2,263, n=915, and n=1,231 participants, respectively). In each cohort, a GWAS was conducted using 2.5M imputed single nucleotide polymorphisms (SNPs). Mixed-effect regression with the additive genetic model adjusted for age, sex, weight and within-family correlations was used for both sex-specific and combined analyses. To combine GWAS results across cohorts, fixed-effect inverse-variance meta-analyses were used. Following meta-analyses, top-associated findings were also examined in an African American cohort (n=327). Results The proportion of HV variance explained by genome-wide genotyped SNPs was 50% in men and 48% in women. A higher proportion of genetic determinants of HV was sex-specific. The most significantly associated SNP in men was rs9675316 located on chr17q23-a24 near the AXIN2 gene (p=5.46×10−7); the most significantly associated SNP in women was rs7996797 located on chr13q14.1-q14.2 near the ESD gene (p=7.21×10−7). Genome-wide significant SNP-by-sex interaction was found for SNP rs1563374 located on chr11p15.1 near the MRGPRX3 gene (interaction p-value =4.1×10−9). The association signals diminished when combining men and women. Conclusion Findings suggest that the potential pathophysiological mechanisms of HV are complex and strongly underlined by sex-specific interactions. The identified genetic variants imply contribution of biological pathways observed in osteoarthritis as well as new pathways, influencing skeletal development and inflammation. PMID:26337638

  4. Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests

    Science.gov (United States)

    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

  5. African Journals Online: Portugal

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  6. African Journals Online: Tuvalu

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  7. African Journals Online: Romania

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  8. African Journals Online: Austria

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  9. African Journals Online: Palau

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  10. African Journals Online: Comoros

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  11. African Journals Online: Myanmar

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  12. African Journals Online: Lesotho

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  13. African Journals Online: Latvia

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  14. African Journals Online: Bhutan

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  15. Demographic history of Canary Islands male gene-pool: replacement of native lineages by European

    Directory of Open Access Journals (Sweden)

    Amorim António

    2009-08-01

    Full Text Available Abstract Background The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th–18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times. Results Autochthonous (E-M81 and prominent (E-M78 and J-M267 Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th–18th centuries than today. Conclusion The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.

  16. Genetic Alterations in Prostate Cancers among African American Men and Comparisons with Cancers from European and Asian Patients

    Science.gov (United States)

    2016-10-01

    ERG (T_E) that creates the fusion of these two genes. Preliminary result analysis suggests that the tumor genome of African American PCa may harbor a...Table 1) that creates the fusion of these two genes, as this fusion is one of the most common somatically acquired changes of genomic structure in...based molecular markers for predication of cancer progression. To evaluate the feasibility of using DNA from FFPE samples, we performed exploratory

  17. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  18. Genetic diversity and differentiation among insular honey bee populations in the southwest Indian Ocean likely reflect old geographical isolation and modern introductions.

    Science.gov (United States)

    Techer, Maéva Angélique; Clémencet, Johanna; Simiand, Christophe; Turpin, Patrick; Garnery, Lionel; Reynaud, Bernard; Delatte, Hélène

    2017-01-01

    With globalization the Western honey bee has become a nearly cosmopolitan species, but it was originally restricted to the Old World. This renowned model of biodiversity has diverged into five evolutionary lineages and several geographic "subspecies." If Apis mellifera unicolor is indubitably an African subspecies endemic to Madagascar, its relationship with honey bees from three archipelagos in the southwest Indian Ocean (SWIO) hotspot of biodiversity is misunderstood. We compared recent mtDNA diversity data to an original characterization of the nuclear diversity from honey bees in the Mascarenes and Comoros archipelagos, using 14 microsatellites, but also additional mtDNA tRNALeu-cox2 analysis. Our sampling offers the most comprehensive dataset for the SWIO populations with a total of 3,270 colonies from 10 islands compared with 855 samples from Madagascar, 113 from Africa, and 138 from Europe. Comprehensive mitochondrial screening confirmed that honey bees from La Réunion, Mauritius, and Comoros archipelagos are mainly of African origin (88.1% out of 2,746 colonies) and that coexistence with European lineages occurs only in the Mascarenes. PCA, Bayesian, and genetic differentiation analysis showed that African colonies are not significantly distinct on each island, but have diversified among islands and archipelagos. FST levels progressively decreased in significance from European and African continental populations, to SWIO insular and continental populations, and finally among islands from the same archipelago. Among African populations, Madagascar shared a nuclear background with and was most closely related to SWIO island populations (except Rodrigues). Only Mauritius Island presented clear cytoplasmic disequilibrium and genetic structure characteristic of an admixed population undergoing hybridization, in this case, between A. m. unicolor and A. m. ligustica, A. m. carnica and A. m. mellifera-like individuals. Finally, global genetic clustering analysis

  19. Genetic diversity and differentiation among insular honey bee populations in the southwest Indian Ocean likely reflect old geographical isolation and modern introductions.

    Directory of Open Access Journals (Sweden)

    Maéva Angélique Techer

    Full Text Available With globalization the Western honey bee has become a nearly cosmopolitan species, but it was originally restricted to the Old World. This renowned model of biodiversity has diverged into five evolutionary lineages and several geographic "subspecies." If Apis mellifera unicolor is indubitably an African subspecies endemic to Madagascar, its relationship with honey bees from three archipelagos in the southwest Indian Ocean (SWIO hotspot of biodiversity is misunderstood. We compared recent mtDNA diversity data to an original characterization of the nuclear diversity from honey bees in the Mascarenes and Comoros archipelagos, using 14 microsatellites, but also additional mtDNA tRNALeu-cox2 analysis. Our sampling offers the most comprehensive dataset for the SWIO populations with a total of 3,270 colonies from 10 islands compared with 855 samples from Madagascar, 113 from Africa, and 138 from Europe. Comprehensive mitochondrial screening confirmed that honey bees from La Réunion, Mauritius, and Comoros archipelagos are mainly of African origin (88.1% out of 2,746 colonies and that coexistence with European lineages occurs only in the Mascarenes. PCA, Bayesian, and genetic differentiation analysis showed that African colonies are not significantly distinct on each island, but have diversified among islands and archipelagos. FST levels progressively decreased in significance from European and African continental populations, to SWIO insular and continental populations, and finally among islands from the same archipelago. Among African populations, Madagascar shared a nuclear background with and was most closely related to SWIO island populations (except Rodrigues. Only Mauritius Island presented clear cytoplasmic disequilibrium and genetic structure characteristic of an admixed population undergoing hybridization, in this case, between A. m. unicolor and A. m. ligustica, A. m. carnica and A. m. mellifera-like individuals. Finally, global genetic

  20. Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

    Science.gov (United States)

    Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

    2012-09-01

    Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  1. Genetic variation in the vitamin D related pathway and breast cancer risk in women of African ancestry in the root consortium.

    Science.gov (United States)

    Wang, Shengfeng; Huo, Dezheng; Kupfer, Sonia; Alleyne, Dereck; Ogundiran, Temidayo O; Ojengbede, Oladosu; Zheng, Wei; Nathanson, Katherine L; Nemesure, Barbara; Ambs, Stefan; Olopade, Olufunmilayo I; Zheng, Yonglan

    2018-01-01

    The vitamin D related pathway has been evaluated in carcinogenesis but its genetic contribution remains poorly understood. We examined single-nucleotide polymorphisms (SNPs) in the vitamin D related pathway genes using data from a genome-wide association study (GWAS) of breast cancer in the African Diaspora that included 3,686 participants (1,657 cases). Pathway- and gene-level analyses were conducted using the adaptive rank truncated product test. Odds ratios (OR) and 95% confidence intervals (CI) were estimated at SNP-level. After stringent Bonferroni corrections, we observed no significant association between variants in the vitamin D pathway and breast cancer risk at the pathway-, gene-, or SNP-level. In addition, no association was found for either the reported signals from GWASs of vitamin D related traits, or the SNPs within vitamin D receptor (VDR) binding regions. Furthermore, a decrease in genetically predicted 25(OH)D levels by Mendelian randomization was not associated with breast cancer (p = 0.23). However, an association for breast cancer with the pigment synthesis/metabolism pathway almost approached significance (pathway-level p = 0.08), driven primarily by a nonsense SNP rs41302073 in TYRP1, with an OR of 1.54 (95% CI = 1.24-1.91, p adj  = 0.007). In conclusion, we found no evidence to support an association between vitamin D status and breast cancer risk in women of African ancestry, suggesting that vitamin D is unlikely to have significant effect on breast carcinogenesis. Interestingly, TYRP1 might be related to breast cancer through a non-vitamin D relevant mechanism but further studies are needed. © 2017 UICC.

  2. The elimination of the onchocerciasis vector from the island of Bioko as a result of larviciding by the WHO African Programme for Onchocerciasis Control.

    Science.gov (United States)

    Traoré, S; Wilson, M D; Sima, A; Barro, T; Diallo, A; Aké, A; Coulibaly, S; Cheke, R A; Meyer, R R F; Mas, J; McCall, P J; Post, R J; Zouré, H; Noma, M; Yaméogo, L; Sékétéli, A V; Amazigo, U V

    2009-09-01

    The island of Bioko is part of the Republic of Equatorial Guinea and is the only island in the World to have endemic onchocerciasis. The disease is hyperendemic and shows a forest-type epidemiology with low levels of blindness and high levels of skin disease, and the whole population of 68,000 is estimated to be at risk. Control of onchocerciasis began in 1990 using ivermectin and this yielded significant clinical benefits but transmission was not interrupted. Feasibility and preparatory studies carried out between 1995 and 2002 confirmed the probable isolation of the vector on the island, the high vectorial efficiency of the Bioko form of Simulium yahense, the seasonality of river flow, blackfly breeding and biting densities, and the distribution of the vector breeding sites. It was proposed that larviciding should be carried out from January to April, when most of the island's rivers were dry or too low to support Simulium damnosum s.l., and that most rivers would not need to be treated above 500 m altitude because they were too small to support the breeding of S. damnosum s.l. Larviciding (with temephos) would need to be carried out by helicopter (because of problems of access by land), supplemented by ground-based delivery. Insecticide susceptibility trials showed that the Bioko form was highly susceptible to temephos, and insecticide carry was tested in the rivers by assessing the length of river in which S. damnosum s.l. larvae were killed below a temephos dosing point. Regular fly catching points were established in 1999 to provide pre-control biting densities, and to act as monitoring points for control efforts. An environmental impact assessment concluded that the proposed control programme could be expected to do little damage, and a large-scale larviciding trial using ground-based applications of temephos (Abate 20EC) throughout the northern (accessible) part of the island was carried out for five weeks from 12 February 2001. Following this, a first

  3. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  4. Genetic Diversity and Population Structure of a Threatened African Tree Species, Milicia excelsa, Using Nuclear Micro satellites DNA Markers

    International Nuclear Information System (INIS)

    Ouinsavi, Ch.; Sokpon, N.; Ouinsavi, Ch.; Khasa, D.P.

    2009-01-01

    To accurately estimate the genetic diversity and population structure for improved conservation planning of Milicia excelsa tree, 212 individuals from twelve population samples covering the species' range in Benin were surveyed at seven specific micro satellite DNA loci. All loci were variable, with the mean number of alleles per locus ranging from 5.86 to 7.69. Considerable genetic variability was detected for all populations at the seven loci (AR=4.60; HE=0.811). Moderate but statistically significant genetic differentiation was found among populations considering both FST (0.112) and RST (0.342). All of the populations showed heterozygosity deficits in test of Hardy-Weinberg Equilibrium and significantly positive FIS values due to inbreeding occurring in the species. Pairwise FST values were positively and significantly correlated with geographical distances (r=0.432; P=.007, Mantel's test) indicating that populations are differentiated by isolation by distance. Bayesian analysis of population structure showed division of the genetic variation into four clusters revealing the existence of heterogeneity in population genetic structure. Altogether, these results indicate that genetic variation in Milicia excelsa is geographically structured. Information gained from this study also emphasized the need for in situ conservation of the relict populations and establishment of gene flow corridors through agroforestry systems for interconnecting these remnant populations.

  5. Canary Islands

    Science.gov (United States)

    1992-01-01

    This easterly looking view shows the seven major volcanic islands of the Canary Island chain (28.0N, 16.5W) and offers a unique view of the islands that have become a frequent vacation spot for Europeans. The northwest coastline of Africa, (Morocco and Western Sahara), is visible in the background. Frequently, these islands create an impact on local weather (cloud formations) and ocean currents (island wakes) as seen in this photo.

  6. Escaping Devil's Island: Confronting Racism, Learning History

    Science.gov (United States)

    Grant, Carl A.

    2011-01-01

    This article argues that African Americans, especially males living in urban areas, are physically and mentally trapped on a Devil's Island. The penal colony on the coast of French Guiana is a metaphor for the boundaries and constraints that close off opportunities and constrain African American historical knowledge. The article argues that…

  7. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea.

    Science.gov (United States)

    Chen, Jing; Xie, Bingbing; Yang, Yaran; Yang, Meng; Liu, Chao; Lv, Yuexin; Chen, Chuguang; Liu, Xu; Fang, Xiangdong; Wu, Huijuan; Yan, Jiangwei

    2017-08-01

    Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10 -38 . The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.

  8. Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study

    Science.gov (United States)

    Perera, Minoli A; Cavallari, Larisa H; Limdi, Nita A; Gamazon, Eric R; Konkashbaev, Anuar; Daneshjou, Roxana; Pluzhnikov, Anna; Crawford, Dana C; Wang, Jelai; Liu, Nianjun; Tatonetti, Nicholas; Bourgeois, Stephane; Takahashi, Harumi; Bradford, Yukiko; Burkley, Benjamin M; Desnick, Robert J; Halperin, Jonathan L; Khalifa, Sherief I; Langaee, Taimour Y; Lubitz, Steven A; Nutescu, Edith A; Oetjens, Matthew; Shahin, Mohamed H; Patel, Shitalben R; Sagreiya, Hersh; Tector, Matthew; Weck, Karen E; Rieder, Mark J; Scott, Stuart A; Wu, Alan HB; Burmester, James K; Wadelius, Mia; Deloukas, Panos; Wagner, Michael J; Mushiroda, Taisei; Kubo, Michiaki; Roden, Dan M; Cox, Nancy J; Altman, Russ B; Klein, Teri E; Nakamura, Yusuke; Johnson, Julie A

    2013-01-01

    Summary Background VKORC1 and CYP2C9 are important contributors to warfarin dose variability, but explain less variability for individuals of African descent than for those of European or Asian descent. We aimed to identify additional variants contributing to warfarin dose requirements in African Americans. Methods We did a genome-wide association study of discovery and replication cohorts. Samples from African-American adults (aged ≥18 years) who were taking a stable maintenance dose of warfarin were obtained at International Warfarin Pharmacogenetics Consortium (IWPC) sites and the University of Alabama at Birmingham (Birmingham, AL, USA). Patients enrolled at IWPC sites but who were not used for discovery made up the independent replication cohort. All participants were genotyped. We did a stepwise conditional analysis, conditioning first for VKORC1 −1639G→A, followed by the composite genotype of CYP2C9*2 and CYP2C9*3. We prespecified a genome-wide significance threshold of p<5×10−8 in the discovery cohort and p<0·0038 in the replication cohort. Findings The discovery cohort contained 533 participants and the replication cohort 432 participants. After the prespecified conditioning in the discovery cohort, we identified an association between a novel single nucleotide polymorphism in the CYP2C cluster on chromosome 10 (rs12777823) and warfarin dose requirement that reached genome-wide significance (p=1·51×10−8). This association was confirmed in the replication cohort (p=5·04×10−5); analysis of the two cohorts together produced a p value of 4·5×10−12. Individuals heterozygous for the rs12777823 A allele need a dose reduction of 6·92 mg/week and those homozygous 9·34 mg/week. Regression analysis showed that the inclusion of rs12777823 significantly improves warfarin dose variability explained by the IWPC dosing algorithm (21% relative improvement). Interpretation A novel CYP2C single nucleotide polymorphism exerts a clinically relevant

  9. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  10. The population structure of Glossina palpalis gambiensis from island and continental locations in Coastal Guinea.

    Directory of Open Access Journals (Sweden)

    Philippe Solano

    Full Text Available We undertook a population genetics analysis of the tsetse fly Glossina palpalis gambiensis, a major vector of sleeping sickness in West Africa, using microsatellite and mitochondrial DNA markers. Our aims were to estimate effective population size and the degree of isolation between coastal sites on the mainland of Guinea and Loos Islands. The sampling locations encompassed Dubréka, the area with the highest Human African Trypanosomosis (HAT prevalence in West Africa, mangrove and savannah sites on the mainland, and two islands, Fotoba and Kassa, within the Loos archipelago. These data are discussed with respect to the feasibility and sustainability of control strategies in those sites currently experiencing, or at risk of, sleeping sickness.We found very low migration rates between sites except between those sampled around the Dubréka area that seems to contain a widely dispersed and panmictic population. In the Kassa island samples, various effective population size estimates all converged on surprisingly small values (10island samples in marked contrast to the large diffuse deme in Dubréka zones. We discuss how these genetic results suggest that different tsetse control strategies should be applied on the mainland and islands.

  11. Genetic variations, reproductive aging, and breast cancer risk in African American and European American women: The Women's Circle of Health Study.

    Science.gov (United States)

    Coignet, Marie V; Zirpoli, Gary Robert; Roberts, Michelle R; Khoury, Thaer; Bandera, Elisa V; Zhu, Qianqian; Yao, Song

    2017-01-01

    Reproductive aging phenotypes, including age at menarche (AM) and age at natural menopause (ANM), are well-established risk factors for breast cancer. In recent years, many genetic variants have been identified in association with AM and ANM in genome-wide association studies among European populations. Using data from the Women's Circle of Health Study (WCHS) of 1,307 European-American (EA) and 1,365 African-American (AA) breast cancer cases and controls, we aimed to replicate 53 earlier GWAS variants for AM and ANM in AA and EA groups and to perform analyses on total and net reproductive lifespan (TRLS; NRLS). Breast cancer risk was also examined in relation to a polygenic risk score (PRS) for each of the reproductive aging phenotypes. We replicated a number of variants in EA women, including rs7759938 in LIN28B for AM and rs16991615 in MCM8 for ANM; whereas in the AA group, only one SNP (rs2947411 in TMEM18) for AM was directionally consistent and nominally significant. In analysis of TRLS and NRLS, several SNPs were significant, including rs466639 in RXRG that was associated with both phenotypes in both AA and EA groups. None of the PRS was associated with breast cancer risk. Given the paucity of data available among AA populations, our study contributes to the literature of genetics of reproductive aging in AA women and highlights the importance of cross population replication of GWAS variants.

  12. Genetic mapping and legume synteny of aphid resistance in African cowpea (Vigna unguiculata L. Walp.) grown in California.

    Science.gov (United States)

    Huynh, Bao-Lam; Ehlers, Jeffrey D; Ndeve, Arsenio; Wanamaker, Steve; Lucas, Mitchell R; Close, Timothy J; Roberts, Philip A

    The cowpea aphid Aphis craccivora Koch (CPA) is a destructive insect pest of cowpea, a staple legume crop in Sub-Saharan Africa and other semiarid warm tropics and subtropics. In California, CPA causes damage on all local cultivars from early vegetative to pod development growth stages. Sources of CPA resistance are available in African cowpea germplasm. However, their utilization in breeding is limited by the lack of information on inheritance, genomic location and marker linkage associations of the resistance determinants. In the research reported here, a recombinant inbred line (RIL) population derived from a cross between a susceptible California blackeye cultivar (CB27) and a resistant African breeding line (IT97K-556-6) was genotyped with 1,536 SNP markers. The RILs and parents were phenotyped for CPA resistance using field-based screenings during two main crop seasons in a 'hotspot' location for this pest within the primary growing region of the Central Valley of California. One minor and one major quantitative trait locus (QTL) were consistently mapped on linkage groups 1 and 7, respectively, both with favorable alleles contributed from IT97K-556-6. The major QTL appeared dominant based on a validation test in a related F2 population. SNP markers flanking each QTL were positioned in physical contigs carrying genes involved in plant defense based on synteny with related legumes. These markers could be used to introgress resistance alleles from IT97K-556-6 into susceptible local blackeye varieties by backcrossing.

  13. Genetic diversity of the Mycobacterium tuberculosis East African–Indian family in three tropical Asian countries

    Directory of Open Access Journals (Sweden)

    Yih-Yuan Chen

    2017-12-01

    Full Text Available Background: The Beijing lineage of Mycobacterium tuberculosis (MTB is the most predominant MTB strain in Asian countries and is spreading worldwide, however, the East African–Indian (EAI lineage is also particularly prevalent in many tropical Asian countries. The evolutionary relationships among MTB EAI isolates from Taiwan and those of tropical Asian countries remain unknown. Methods: The EAI strains collected from patients in Taiwan were analyzed using spacer oligonucleotide typing and mycobacterial interspersed repetitive unit–variable number of tandem repeats (MIRU-VNTR typing, and compared with published profiles from Cambodia and Singapore to investigate potential epidemiological linkages. Results: Among the three countries, the EAI lineage was most prevalent in Cambodia (60%; Singapore, 25.62%; and Taiwan, 21.85%, having also the highest rates of multidrug resistance and lowest rates of clustering of MTB isolates. We describe a convenient method using seven selected MIRU-VNTR loci for first-line typing to discriminate Beijing and EAI lineages. A potential epidemiological linkage in these tropical Asian countries is also discussed based on a minimum-spanning tree constructed using 24 MIRU-VNTR loci of MTB EAI strains. Conclusion: This study identified evolutionary relationships among MTB EAI isolates from Taiwan and those of two other tropical Asian countries, Cambodia and Singapore. Keywords: East African–Indian family, Mycobacterium tuberculosis, tropical Asian countries

  14. Ethnic, racial and cultural identity and perceived benefits and barriers related to genetic testing for breast cancer among at-risk women of African descent in New York City.

    Science.gov (United States)

    Sussner, K M; Edwards, T A; Thompson, H S; Jandorf, L; Kwate, N O; Forman, A; Brown, K; Kapil-Pair, N; Bovbjerg, D H; Schwartz, M D; Valdimarsdottir, H B

    2011-01-01

    Due to disparities in the use of genetic services, there has been growing interest in examining beliefs and attitudes related to genetic testing for breast and/or ovarian cancer risk among women of African descent. However, to date, few studies have addressed critical cultural variations among this minority group and their influence on such beliefs and attitudes. We assessed ethnic, racial and cultural identity and examined their relationships with perceived benefits and barriers related to genetic testing for cancer risk in a sample of 160 women of African descent (49% self-identified African American, 39% Black-West Indian/Caribbean, 12% Black-Other) who met genetic risk criteria and were participating in a larger longitudinal study including the opportunity for free genetic counseling and testing in New York City. All participants completed the following previously validated measures: (a) the multi-group ethnic identity measure (including ethnic search and affirmation subscales) and other-group orientation for ethnic identity, (b) centrality to assess racial identity, and (c) Africentrism to measure cultural identity. Perceived benefits and barriers related to genetic testing included: (1) pros/advantages (including family-related pros), (2) cons/disadvantages (including family-related cons, stigma and confidentiality concerns), and (3) concerns about abuses of genetic testing. In multivariate analyses, several ethnic identity elements showed significant, largely positive relationships to perceived benefits about genetic testing for breast and/or ovarian cancer risk, the exception being ethnic search, which was positively associated with cons/disadvantages, in general, and family-related cons/disadvantages. Racial identity (centrality) showed a significant association with confidentiality concerns. Cultural identity (Africentrism) was not related to perceived benefits and/or barriers. Ethnic and racial identity may influence perceived benefits and barriers

  15. Interleukin-10 (IL-10) pathway: genetic variants and outcomes of HIV-1 infection in African American adolescents.

    Science.gov (United States)

    Shrestha, Sadeep; Wiener, Howard W; Aissani, Brahim; Song, Wei; Shendre, Aditi; Wilson, Craig M; Kaslow, Richard A; Tang, Jianming

    2010-10-14

    Immunological and clinical outcomes can vary considerably at the individual and population levels during both treated and untreated HIV-1 infection. Cytokines encoded by the interleukin-10 gene (IL10) family have broad immunomodulatory function in viral persistence, and several SNPs in the IL10 promoter sequence have been reported to influence pathogenesis or acquisition of HIV-1 infection. We examined 104 informative SNPs in IL10, IL19, IL20, IL24, IL10RA and IL10RB among 250 HIV-1 seropositive and 106 high-risk seronegative African American adolescents in the REACH cohort. In subsequent evaluation of five different immunological and virological outcomes related to HIV-1 infection, 25 SNPs were associated with a single outcome and three were associated with two different outcomes. One SNP, rs2243191 in the IL19 open reading frame (Ser to Phe substitution) was associated with CD4(+) T-cell increase during treatment. Another SNP rs2244305 in IL10RB (in strong linkage disequilibrium with rs443498) was associated with an initial decrease in CD4(+) T-cell by 23 ± 9% and 29 ± 9% every 3 months (for AA and AG genotypes, respectively, compared with GG) during ART-free period. These associations were reversed during treatment, as CD4(+) T-cell increased by 31 ± 0.9% and 17 ± 8% every 3 months for AA and AG genotype, respectively. In African Americans, variants in IL10 and related genes might influence multiple outcomes of HIV-1 infection, especially immunological response to HAART. Fine mapping coupled with analysis of gene expression and function should help reveal the immunological importance of the IL10 gene family to HIV-1/AIDS.

  16. Genetic moderation of child maltreatment effects on depression and internalizing symptoms by 5-HTTLPR, BDNF, NET, and CRHR1 genes in African-American children

    Science.gov (United States)

    Cicchetti, Dante; Rogosch, Fred A.

    2014-01-01

    Genetic moderation of the effects of child maltreatment on depression and internalizing symptoms was investigated in a sample of low-income maltreated and nonmaltreated African-American children (N = 1,096). Lifetime child maltreatment experiences were independently coded from Child Protective Services records and maternal report. Child depression and internalizing problems were assessed in the context of a summer research camp by self-report (Children’s Depression Inventory, CDI) and adult counselor-report (Teacher Report Form, TRF). DNA was obtained from buccal cell or saliva samples and genotyped for polymorphisms of the following genes: 5-HTTLPR, BDNF, NET, and CRHR1. ANCOVAs with age and gender as covariates were conducted, with maltreatment status and respective polymorphism as main effects and their GxE interactions. Maltreatment consistently was associated with higher CDI and TRF symptoms. Results for child self-report symptoms indicated a GxE interaction for BDNF and maltreatment. Additionally, BDNF and tri-allelic 5-HTTLPR interacted with child maltreatment in a GxGxE interaction. Analyses for counselor-report of child anxiety/depression symptoms on the TRF indicated moderation of child maltreatment effects by tri-allelic 5-HTTLPR. These effects were elaborated based on variation in developmental timing of maltreatment experiences. NET was found to further moderate the GxE interaction of 5-HTTLPR and maltreatment status revealing a GxGxE interaction. This GxGxE was extended by consideration of variation in maltreatment subtype experiences. Finally, GxGxE effects were observed for the co-action of BDNF and the CRHR1 haplotype. The findings illustrate the variable influence of specific genotypes in GxE interactions based on variation in maltreatment experiences and the importance of a multi-genic approach for understanding influences on depression and internalizing symptoms among African-American children. PMID:25422957

  17. Genetic analysis of environmental strains of the plant pathogen Phytophthora capsici reveals heterogeneous repertoire of effectors and possible effector evolution via genomic island.

    Science.gov (United States)

    Iribarren, María Josefina; Pascuan, Cecilia; Soto, Gabriela; Ayub, Nicolás Daniel

    2015-11-01

    Phytophthora capsici is a virulent oomycete pathogen of many vegetable crops. Recently, it has been demonstrated that the recognition of the RXLR effector AVR3a1 of P. capsici (PcAVR3a1) triggers a hypersensitive response and plays a critical role in mediating non-host resistance. Here, we analyzed the occurrence of PcAVR3a1 in 57 isolates of P. capsici derived from globe squash, eggplant, tomato and bell pepper cocultivated in a small geographical area. The occurrence of PcAVR3a1 in environmental strains of P. capsici was confirmed by PCR in only 21 of these pathogen isolates. To understand the presence-absence pattern of PcAVR3a1 in environmental strains, the flanking region of this gene was sequenced. PcAVR3a1 was found within a genetic element that we named PcAVR3a1-GI (PcAVR3a1 genomic island). PcAVR3a1-GI was flanked by a 22-bp direct repeat, which is related to its site-specific recombination site. In addition to the PcAVR3a1 gene, PcAVR3a1-GI also encoded a phage integrase probably associated with the excision and integration of this mobile element. Exposure to plant induced the presence of an episomal circular intermediate of PcAVR3a1-GI, indicating that this mobile element is functional. Collectively, these findings provide evidence of PcAVR3a1 evolution via mobile elements in environmental strains of Phytophthora. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. An X chromosome association scan of the Norfolk Island genetic isolate provides evidence for a novel migraine susceptibility locus at Xq12.

    Directory of Open Access Journals (Sweden)

    Bridget H Maher

    Full Text Available Migraine is a common and debilitating neurovascular disorder with a complex envirogenomic aetiology. Numerous studies have demonstrated a preponderance of women affected with migraine and previous pedigree linkage studies in our laboratory have identified susceptibility loci on chromosome Xq24-Xq28. In this study we have used the genetic isolate of Norfolk Island to further analyse the X chromosome for migraine susceptibility loci.An association approach was employed to analyse 14,124 SNPs spanning the entire X chromosome. Genotype data from 288 individuals comprising a large core-pedigree, of which 76 were affected with migraine, were analysed. Although no SNP reached chromosome-wide significance (empirical α = 1 × 10(-5 ranking by P-value revealed two primary clusters of SNPs in the top 25. A 10 SNP cluster represents a novel migraine susceptibility locus at Xq12 whilst a 11 SNP cluster represents a previously identified migraine susceptibility locus at Xq27. The strongest association at Xq12 was seen for rs599958 (OR = 1.75, P = 8.92 × 10(-4, whilst at Xq27 the strongest association was for rs6525667 (OR = 1.53, P = 1.65 × 10(-4. Further analysis of SNPs at these loci was performed in 5,122 migraineurs from the Women's Genome Health Study and provided additional evidence for association at the novel Xq12 locus (P<0.05.Overall, this study provides evidence for a novel migraine susceptibility locus on Xq12. The strongest effect SNP (rs102834, joint P = 1.63 × 10(-5 is located within the 5'UTR of the HEPH gene, which is involved in iron homeostasis in the brain and may represent a novel pathway for involvement in migraine pathogenesis.

  19. Typing late prehistoric cows and bulls--osteology and genetics of cattle at the Eketorp ringfort on the Öland island in Sweden.

    Directory of Open Access Journals (Sweden)

    Ylva Telldahl

    Full Text Available Human management of livestock and the presence of different breeds have been discussed in archaeozoology and animal breeding. Traditionally osteometrics has been the main tool in addressing these questions. We combine osteometrics with molecular sex identifications of 104 of 340 morphometrically analysed bones in order to investigate the use of cattle at the Eketorp ringfort on the Öland island in Sweden. The fort is dated to 300-1220/50 A.D., revealing three different building phases. In order to investigate specific patterns and shifts through time in the use of cattle the genetic data is evaluated in relation to osteometric patterns and occurrence of pathologies on cattle metapodia. Males were genotyped for a Y-chromosomal SNP in UTY19 that separates the two major haplogroups, Y1 and Y2, in taurine cattle. A subset of the samples were also genotyped for one SNP involved in coat coloration (MC1R, one SNP putatively involved in resistance to cattle plague (TLR4, and one SNP in intron 5 of the IGF-1 gene that has been associated to size and reproduction.The results of the molecular analyses confirm that the skeletal assemblage from Eketorp is dominated by skeletal elements from females, which implies that dairying was important. Pathological lesions on the metapodia were classified into two groups; those associated with the use as draught animals and those lesions without a similar aetiology. The results show that while bulls both exhibit draught related lesions and other types of lesions, cows exhibit other types of lesions. Interestingly, a few elements from females exhibit draught related lesions. We conclude that this reflects the different use of adult female and male cattle.Although we note some variation in the use of cattle at Eketorp between Iron Age and Medieval time we have found little evidence for the use of different types of animals for specific purposes. The use of specific (genetic breeds seems to be a phenomenon that developed

  20. Typing late prehistoric cows and bulls--osteology and genetics of cattle at the Eketorp ringfort on the Öland island in Sweden.

    Science.gov (United States)

    Telldahl, Ylva; Svensson, Emma; Götherström, Anders; Storå, Jan

    2011-01-01

    Human management of livestock and the presence of different breeds have been discussed in archaeozoology and animal breeding. Traditionally osteometrics has been the main tool in addressing these questions. We combine osteometrics with molecular sex identifications of 104 of 340 morphometrically analysed bones in order to investigate the use of cattle at the Eketorp ringfort on the Öland island in Sweden. The fort is dated to 300-1220/50 A.D., revealing three different building phases. In order to investigate specific patterns and shifts through time in the use of cattle the genetic data is evaluated in relation to osteometric patterns and occurrence of pathologies on cattle metapodia. Males were genotyped for a Y-chromosomal SNP in UTY19 that separates the two major haplogroups, Y1 and Y2, in taurine cattle. A subset of the samples were also genotyped for one SNP involved in coat coloration (MC1R), one SNP putatively involved in resistance to cattle plague (TLR4), and one SNP in intron 5 of the IGF-1 gene that has been associated to size and reproduction.The results of the molecular analyses confirm that the skeletal assemblage from Eketorp is dominated by skeletal elements from females, which implies that dairying was important. Pathological lesions on the metapodia were classified into two groups; those associated with the use as draught animals and those lesions without a similar aetiology. The results show that while bulls both exhibit draught related lesions and other types of lesions, cows exhibit other types of lesions. Interestingly, a few elements from females exhibit draught related lesions. We conclude that this reflects the different use of adult female and male cattle.Although we note some variation in the use of cattle at Eketorp between Iron Age and Medieval time we have found little evidence for the use of different types of animals for specific purposes. The use of specific (genetic) breeds seems to be a phenomenon that developed later than the

  1. Typing Late Prehistoric Cows and Bulls—Osteology and Genetics of Cattle at the Eketorp Ringfort on the Öland Island in Sweden

    Science.gov (United States)

    Telldahl, Ylva; Svensson, Emma; Götherström, Anders; Storå, Jan

    2011-01-01

    Human management of livestock and the presence of different breeds have been discussed in archaeozoology and animal breeding. Traditionally osteometrics has been the main tool in addressing these questions. We combine osteometrics with molecular sex identifications of 104 of 340 morphometrically analysed bones in order to investigate the use of cattle at the Eketorp ringfort on the Öland island in Sweden. The fort is dated to 300–1220/50 A.D., revealing three different building phases. In order to investigate specific patterns and shifts through time in the use of cattle the genetic data is evaluated in relation to osteometric patterns and occurrence of pathologies on cattle metapodia. Males were genotyped for a Y-chromosomal SNP in UTY19 that separates the two major haplogroups, Y1 and Y2, in taurine cattle. A subset of the samples were also genotyped for one SNP involved in coat coloration (MC1R), one SNP putatively involved in resistance to cattle plague (TLR4), and one SNP in intron 5 of the IGF-1 gene that has been associated to size and reproduction. The results of the molecular analyses confirm that the skeletal assemblage from Eketorp is dominated by skeletal elements from females, which implies that dairying was important. Pathological lesions on the metapodia were classified into two groups; those associated with the use as draught animals and those lesions without a similar aetiology. The results show that while bulls both exhibit draught related lesions and other types of lesions, cows exhibit other types of lesions. Interestingly, a few elements from females exhibit draught related lesions. We conclude that this reflects the different use of adult female and male cattle. Although we note some variation in the use of cattle at Eketorp between Iron Age and Medieval time we have found little evidence for the use of different types of animals for specific purposes. The use of specific (genetic) breeds seems to be a phenomenon that developed later than

  2. South African southern ocean research programme

    CSIR Research Space (South Africa)

    SASCAR

    1987-01-01

    Full Text Available This document describes the South African National Antarctic Research Programme's (SANARP) physical, chemical and biological Southern Ocean research programme. The programme has three main components: ecological studies of the Prince Edward Islands...

  3. Genetic adaptation of giant lobelias (Lobelia aberdarica and Lobelia telekii to different altitudes in East African mountains

    Directory of Open Access Journals (Sweden)

    Shu-Ying eZhao

    2016-04-01

    Full Text Available The giant lobelias in East African mountains are good models for studying molecular mechanisms of adaptation to different altitudes. In this study, we generated RNA-seq data of a middle-altitude species Lobelia aberdarica and a high-altitude species L. telekii, followed by selective pressure estimation of their orthologous genes. Our aim was to explore the important genes potentially involved in adaptation to different altitudes. About 9.3 Gb of clean nucleotides, 167,929 – 170,534 unigenes with total lengths of 159,762,099 – 171,138,936 bp for each of the two species were generated. OrthoMCL method identified 3,049 1:1 orthologous genes (each species was represented by one ortholog. Estimations of non-synonymous to synonymous rate were performed using an approximate method and a maximum likelihood method in PAML. 85 orthologous genes were under positive selection. At least 8 of these genes are possibly involved in DNA repair, response to DNA damage and temperature stimulus, and regulation of gene expression, which hints on how giant lobelias adapt to high altitudinal environment that characterised by cold, low oxygen and strong ultraviolet radiation. The negatively selected genes are over-represented in Gene ontology terms of hydrolase, macromolecular complex assembly among others. This study sheds light on understanding the molecular mechanism of adaptation to different altitudes, and provides genomic resources for further studies of giant lobelias.

  4. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda.

    Science.gov (United States)

    Gaieski, Jill B; Owings, Amanda C; Vilar, Miguel G; Dulik, Matthew C; Gaieski, David F; Gittelman, Rachel M; Lindo, John; Gau, Lydia; Schurr, Theodore G

    2011-11-01

    Discovered in the early 16th century by European colonists, Bermuda is an isolated set of islands located in the mid-Atlantic. Shortly after its discovery, Bermuda became the first English colony to forcibly import its labor by trafficking in enslaved Africans, white ethnic minorities, and indigenous Americans. Oral traditions circulating today among contemporary tribes from the northeastern United States recount these same events, while, in Bermuda, St. David's Islanders consider their histories to be linked to a complex Native American, European, and African past. To investigate the influence of historical events on biological ancestry and native cultural identity, we analyzed genetic variation in 111 members of Bermuda's self-proclaimed St. David's Island Native Community. Our results reveal that the majority of mitochondrial DNA (mtDNA) and Y-chromosome haplotypes are of African and West Eurasian origin. However, unlike other English-speaking New World colonies, most African mtDNA haplotypes appear to derive from central and southeast Africa, reflecting the extent of maritime activities in the region. In light of genealogical and oral historical data from the St. David's community, the low frequency of Native American mtDNA and NRY lineages may reflect the influence of genetic drift, the demographic impact of European colonization, and historical admixture with persons of non-native backgrounds, which began with the settlement of the islands. By comparing the genetic data with genealogical and historical information, we are able to reconstruct the complex history of this Bermudian community, which is unique among New World populations. Copyright © 2011 Wiley-Liss, Inc.

  5. Canary Islands (Spain): Their Importance in NATO’s Strategy.

    Science.gov (United States)

    1987-04-22

    considered to be divided into two groups of * islands. One is the eastern islands, made up of Gran Canaria, Lanzarote and Fuerteventura and the other...feet (1,370 to 2,130 meters) and Lanzarote and Fuerteventura, the islands closest to the African coast, do not exceed 2,400 feet (730 meters) in...heights. Each island, except Lanzarote and Fuerteventura, is divided into two faces, one to the north, exposed to the humid winds, full of vegetation

  6. Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations.

    Science.gov (United States)

    Badro, Danielle A; Douaihy, Bouchra; Haber, Marc; Youhanna, Sonia C; Salloum, Angélique; Ghassibe-Sabbagh, Michella; Johnsrud, Brian; Khazen, Georges; Matisoo-Smith, Elizabeth; Soria-Hernanz, David F; Wells, R Spencer; Tyler-Smith, Chris; Platt, Daniel E; Zalloua, Pierre A

    2013-01-01

    The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of F(ST)'s, R(ST)'s, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

  7. Genetic Diversity of the Hepatitis B Virus Strains in Cuba: Absence of West-African Genotypes despite the Transatlantic Slave Trade

    Science.gov (United States)

    Rodríguez Lay, Licel A.; Corredor, Marité B.; Villalba, Maria C.; Frómeta, Susel S.; Wong, Meilin S.; Valdes, Lidunka; Samada, Marcia; Sausy, Aurélie; Hübschen, Judith M.; Muller, Claude P.

    2015-01-01

    Cuba is an HBsAg low-prevalence country with a high coverage of anti-hepatitis B vaccine. Its population is essentially the result of the population mix of Spanish descendants and former African slaves. Information about genetic characteristics of hepatitis B virus (HBV) strains circulating in the country is scarce. The HBV genotypes/subgenotypes, serotypes, mixed infections, and S gene mutations of 172 Cuban HBsAg and HBV-DNA positive patients were determined by direct sequencing and phylogenetic analysis. Phylogenetic analysis of HBV S gene sequences showed a predominance of genotype A (92.4%), subgenotype A2 (84.9%) and A1 (7.6%). Genotype D (7.0%) and subgenotype C1 (0.6%) were also detected but typical (sub)genotypes of contemporary West-Africa (E, A3) were conspicuously absent. All genotype A, D, and C strains exhibited sequence characteristics of the adw2, ayw2, and adrq serotypes, respectively. Thirty-three (19.1%) patients showed single, double, or multiple point mutations inside the Major Hydrophilic domain associated with vaccine escape; eighteen (10.5%) patients had mutations in the T-cell epitope (amino acids 28-51), and there were another 111 point mutations downstream of the S gene. One patient had an HBV A1/A2 mixed infection. This first genetic study of Cuban HBV viruses revealed only strains that were interspersed with strains from particularly Europe, America, and Asia. The absence of genotype E supports previous hypotheses about an only recent introduction of this genotype into the general population in Africa. The presence of well-known vaccine escape (3.5%) and viral resistance mutants (2.9%) warrants strain surveillance to guide vaccination and treatment strategies. PMID:25978398

  8. Genetically Distinct Glossina fuscipes fuscipes Populations in the Lake Kyoga Region of Uganda and Its Relevance for Human African Trypanosomiasis

    Directory of Open Access Journals (Sweden)

    Richard Echodu

    2013-01-01

    Full Text Available Tsetse flies (Glossina spp. are the sole vectors of Trypanosoma brucei—the agent of human (HAT and animal (AAT trypanosomiasis. Glossina fuscipes fuscipes (Gff is the main vector species in Uganda—the only country where the two forms of HAT disease (rhodesiense and gambiense occur, with gambiense limited to the northwest. Gff populations cluster in three genetically distinct groups in northern, southern, and western Uganda, respectively, with a contact zone present in central Uganda. Understanding the dynamics of this contact zone is epidemiologically important as the merger of the two diseases is a major health concern. We used mitochondrial and microsatellite DNA data from Gff samples in the contact zone to understand its spatial extent and temporal stability. We show that this zone is relatively narrow, extending through central Uganda along major rivers with south to north introgression but displaying no sex-biased dispersal. Lack of obvious vicariant barriers suggests that either environmental conditions or reciprocal competitive exclusion could explain the patterns of genetic differentiation observed. Lack of admixture between northern and southern populations may prevent the sympatry of the two forms of HAT disease, although continued control efforts are needed to prevent the recolonization of tsetse-free regions by neighboring populations.

  9. Bivariate analysis of the genetic variability among some accessions of African Yam Bean (Sphenostylis stenocarpa (Hochst ex A. RichHarms

    Directory of Open Access Journals (Sweden)

    Solomon Tayo AKINYOSOYE

    2017-12-01

    Full Text Available Variability is an important factor to consider in crop improvement programmes. This study was conducted in two years to assess genetic variability and determine relationship between seed yield, its components and tuber production characters among twelve accessions of African yam bean. Data collected were subjected to combined analysis of variance (ANOVA, Principal Component Analysis (PCA, hierarchical and K-means clustering analyses. Results obtained revealed that genotype by year (G × Y interaction had significant effects on some of variables measured (days to first flowering, days to 50 % flowering, number of pod per plant, pod length, seed yield and tuber yield per plant in this study.The first five principal components (PC with Eigen values greater than 1.0 accounted for about 66.70 % of the total variation, where PC1 and PC 2 accounted for 39.48 % of variation and were associated with seed and tuber yield variables. Three heterotic groups were clearly delineated among genotypes with accessions AY03 and AY10 identified for high seed yield and tuber yield respectively. Non-significant relationship that existed between tuber and seed yield per plant of these accessions was recommended for further test in various agro-ecologies for their suitability, adaptability and possible exploitation of heterosis to further improve the accessions.

  10. Using genetic profiles of African forest elephants to infer population structure, movements, and habitat use in a conservation and development landscape in Gabon.

    Science.gov (United States)

    Eggert, L S; Buij, R; Lee, M E; Campbell, P; Dallmeier, F; Fleischer, R C; Alonso, A; Maldonado, J E

    2014-02-01

    Conservation of wide-ranging species, such as the African forest elephant (Loxodonta cyclotis), depends on fully protected areas and multiple-use areas (MUA) that provide habitat connectivity. In the Gamba Complex of Protected Areas in Gabon, which includes 2 national parks separated by a MUA containing energy and forestry concessions, we studied forest elephants to evaluate the importance of the MUA to wide-ranging species. We extracted DNA from elephant dung samples and used genetic information to identify over 500 individuals in the MUA and the parks. We then examined patterns of nuclear microsatellites and mitochondrial control-region sequences to infer population structure, movement patterns, and habitat use by age and sex. Population structure was weak but significant, and differentiation was more pronounced during the wet season. Within the MUA, males were more strongly associated with open habitats, such as wetlands and savannas, than females during the dry season. Many of the movements detected within and between seasons involved the wetlands and bordering lagoons. Our results suggest that the MUA provides year-round habitat for some elephants and additional habitat for others whose primary range is in the parks. With the continuing loss of roadless wilderness areas in Central Africa, well-managed MUAs will likely be important to the conservation of wide-ranging species. © 2013 Society for Conservation Biology.

  11. Breeding phenology of African Black Oystercatchers Haematopus ...

    African Journals Online (AJOL)

    The timing of the start and duration of breeding and the effect of these on breeding productivity were analysed for African Black Oystercatchers Haematopus moquini on Robben Island, South Africa, over three breeding seasons from 2001 to 2004. African Black Oystercatchers have a long breeding season, from November ...

  12. A Tale of Two Aggregations: Kinship and Population Genetics of Whale Sharks (Rhincodon typus) at Shib Habil, Saudi Arabia, and Mafia Island, Tanzania.

    KAUST Repository

    Hardenstine, Royale

    2015-01-01

    the Mafia Island, Tanzania, aggregation was not part of the study. Both aggregations have unique aspects with the Saudi Arabian individuals showing sexual parity with no segregation, while recent acoustic results have revealed cryptic residency at Mafia

  13. Origin, evolution, and population genetics of the selfish Segregation Distorter gene duplication in European and African populations of Drosophila melanogaster.

    Science.gov (United States)

    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. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  14. Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas

    Directory of Open Access Journals (Sweden)

    Kevin C. Deitz

    2016-09-01

    Full Text Available Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression.

  15. Taino and African maternal heritage in the Greater Antilles.

    Science.gov (United States)

    Bukhari, Areej; Luis, Javier Rodriguez; Alfonso-Sanchez, Miguel A; Garcia-Bertrand, Ralph; Herrera, Rene J

    2017-12-30

    Notwithstanding the general interest and the geopolitical importance of the island countries in the Greater Antilles, little is known about the specific ancestral Native American and African populations that settled them. In an effort to alleviate this lacuna of information on the genetic constituents of the Greater Antilles, we comprehensively compared the mtDNA compositions of Cuba, Dominican Republic, Haiti, Jamaica and Puerto Rico. To accomplish this, the mtDNA HVRI and HVRII regions, as well as coding diagnostic sites, were assessed in the Haitian general population and compared to data from reference populations. The Taino maternal DNA is prominent in the ex-Spanish colonies (61.3%-22.0%) while it is basically non-existent in the ex-French and ex-English colonies of Haiti (0.0%) and Jamaica (0.5%), respectively. The most abundant Native American mtDNA haplogroups in the Greater Antilles are A2, B2 and C1. The African mtDNA component is almost fixed in Haiti (98.2%) and Jamaica (98.5%), and the frequencies of specific African haplogroups vary considerably among the five island nations. The strong persistence of Taino mtDNA in the ex-Spanish colonies (and especially in Puerto Rico), and its absence in the French and English excolonies is likely the result of different social norms regarding mixed marriages with Taino women during the early years after the first contact with Europeans. In addition, this article reports on the results of an integrative approach based on mtDNA analysis and demographic data that tests the hypothesis of a southward shift in raiding zones along the African west coast during the period encompassing the Transatlantic Slave Trade. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. African Journals Online: El Salvador

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  17. African Journals Online: Costa Rica

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  18. African Journals Online: Saint Bartelemey

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  19. Marshall Islands

    OpenAIRE

    World Bank

    2015-01-01

    This note aims to build understanding of the existing disaster risk financing and insurance (DRFI) tools in use in The Marshall Islands and to identify gaps where potential engagement could further develop financial resilience. The likelihood that a hazardous event will have a significant impact on the Marshall Islands has risen with the increasing levels of population and assets in the urban ...

  20. Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.

    Science.gov (United States)

    Karan, M; Evans, D S; Reilly, D; Schulte, K; Wright, C; Innes, D; Holton, T A; Nikles, D G; Dickinson, G R

    2012-03-01

    Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93,943 sequences with an average read length of 234 bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa. © 2011 Blackwell Publishing Ltd.

  1. Green turtles (Chelonia mydas foraging at Arvoredo Island in Southern Brazil: genetic characterization and mixed stock analysis through mtDNA control region haplotypes

    Directory of Open Access Journals (Sweden)

    Maíra Carneiro Proietti

    2009-01-01

    Full Text Available We analyzed mtDNA control region sequences of green turtles (Chelonia mydas from Arvoredo Island, a foraging ground in southern Brazil, and identified eight haplotypes. Of these, CM-A8 (64% and CM-A5 (22% were dominant, the remainder presenting low frequencies ( 0.05. Mixed Stock Analysis, incorporating eleven Atlantic and one Mediterranean rookery as possible sources of individuals, indicated Ascension and Aves islands as the main contributing stocks to the Arvoredo aggregation (68.01% and 22.96%, respectively. These results demonstrate the extensive relationships between Arvoredo Island and other Atlantic foraging and breeding areas. Such an understanding provides a framework for establishing adequate management and conservation strategies for this endangered species.

  2. Spatio-temporal patterns of coral recruitment at Vamizi Island ...

    African Journals Online (AJOL)

    Spatio-temporal patterns of coral recruitment at Vamizi Island, Quirimbas Archipelago, Mozambique. ... Spatial and temporal patterns of recruitment of reef corals were assessed for the first time in Mozambique ... AJOL African Journals Online.

  3. Marine dispersal determines the genetic population structure of migratory stream fauna of Puerto Rico: evidence for island-scale population recovery processes

    Science.gov (United States)

    Benjamin D. Cook; Sofie Bernays; Catherine M. Pringle; Jane M. Hughes

    2009-01-01

    Various components of island stream faunas, including caridean shrimps, fish, and gastropods, undertake obligate amphidromous migration, whereby larvae are released in upstream freshwater reaches, drift downstream to estuaries or marine waters, then migrate upstream as postlarvae to freshwater adult habitats. Longitudinal migration from estuaries to headwaters is well...

  4. Shifting migration patterns without genetic erosion: evidence from the Zamia pumila complex (Cycadales: Zamiaceae) at the northern of the Caribbean island biodiversity hotspot

    Science.gov (United States)

    The Bahamas archipelago is the northernmost land area of the Caribbean island biodiversity hotspot (CIBH). It is defined by several banks composed of quaternary carbonates that are tectonically stable. Such stability has provided direct geological evidence of global ice-volume changes that is valuab...

  5. Large-scale pattern of genetic differentiation within African rainforest trees: insights on the roles of ecological gradients and past climate changes on the evolution of Erythrophleum spp (Fabaceae).

    Science.gov (United States)

    Duminil, Jerome; Brown, Richard P; Ewédjè, Eben-Ezer B K; Mardulyn, Patrick; Doucet, Jean-Louis; Hardy, Olivier J

    2013-09-12

    The evolutionary events that have shaped biodiversity patterns in the African rainforests are still poorly documented. Past forest fragmentation and ecological gradients have been advocated as important drivers of genetic differentiation but their respective roles remain unclear. Using nuclear microsatellites (nSSRs) and chloroplast non-coding sequences (pDNA), we characterised the spatial genetic structure of Erythrophleum (Fabaceae) forest trees in West and Central Africa (Guinea Region, GR). This widespread genus displays a wide ecological amplitude and taxonomists recognize two forest tree species, E. ivorense and E. suaveolens, which are difficult to distinguish in the field and often confused. Bayesian-clustering applied on nSSRs of a blind sample of 648 specimens identified three major gene pools showing no or very limited introgression. They present parapatric distributions correlated to rainfall gradients and forest types. One gene pool is restricted to coastal evergreen forests and corresponds to E. ivorense; a second one is found in gallery forests from the dry forest zone of West Africa and North-West Cameroon and corresponds to West-African E. suaveolens; the third gene pool occurs in semi-evergreen forests and corresponds to Central African E. suaveolens. These gene pools have mostly unique pDNA haplotypes but they do not form reciprocally monophyletic clades. Nevertheless, pDNA molecular dating indicates that the divergence between E. ivorense and Central African E. suaveolens predates the Pleistocene. Further Bayesian-clustering applied within each major gene pool identified diffuse genetic discontinuities (minor gene pools displaying substantial introgression) at a latitude between 0 and 2°N in Central Africa for both species, and at a longitude between 5° and 8°E for E. ivorense. Moreover, we detected evidence of past population declines which are consistent with historical habitat fragmentation induced by Pleistocene climate changes. Overall

  6. Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010.

    Directory of Open Access Journals (Sweden)

    Alessandra Falchi

    Full Text Available BACKGROUND: The aim of this study was to analyse the genetic patterns of Hemagglutinin (HA genes of influenza A strains circulating on Corsica Island during the 2006-2009 epidemic seasons and the 2009-2010 pandemic season. METHODS: Nasopharyngeal samples from 371 patients with influenza-like illness (ILI were collected by General Practitioners (GPs of the Sentinelles Network through a randomised selection routine. RESULTS: Phylogenetic analysis of HA revealed that A/H3N2 strains circulating on Corsica were closely related to the WHO recommended vaccine strains in each analyzed season (2006-2007 to 2008-2009. Seasonal Corsican influenza A/H1N1 isolated during the 2007-2008 season had drifted towards the A/Brisbane/59/2007 lineage, the A/H1N1 vaccine strain for the 2008-2009 season. The A/H1N1 2009 (A/H1N1pdm strains isolated on Corsica Island were characterized by the S220T mutation specific to clade 7 isolates. It should be noted that Corsican isolates formed a separate sub-clade of clade 7 as a consequence of the presence of the fixed substitution D222E. The percentages of the perfect match vaccine efficacy, estimated by using the p(epitope model, against influenza viruses circulating on Corsica Island varied substantially across the four seasons analyzed, and tend to be highest for A/H1N1 compared with A/H3N2 vaccines, suggesting that cross-immunity seems to be stronger for the H1 HA gene. CONCLUSION: The molecular analysis of the HA gene of influenza viruses that circulated on Corsica Island between 2006-2010 showed for each season the presence of a dominant lineage characterized by at least one fixed mutation. The A/H3N2 and A/H1N1pdm isolates were characterized by multiples fixation at antigenic sites. The fixation of specific mutations at each outbreak could be explained by the combination of a neutral phenomenon and a founder effect, favoring the presence of a dominant lineage in a closed environment such as Corsica Island.

  7. Art Music by Caribbean Composers: U.S. Virgin Islands

    Directory of Open Access Journals (Sweden)

    Gangelhoff, Christine

    2011-10-01

    Full Text Available Virgin Island music is syncretic, reflecting both African and European heritage. While older traditions including cariso and bamboula are virtually extinct, quelbe is popular throughout the islands, with bands such as Stanley and The Ten Sleepless Nights performing frequently.

  8. Bone island and leprosy

    Energy Technology Data Exchange (ETDEWEB)

    Carpintero, P.; Garcia-Frasquet, A. [Department of Orthopaedic Surgery, Cordoba University, Medical School, Reina Sofia University Hospital, Cordoba (Spain); Tarradas, E. [Department of Imaging, Cordoba University, Medical School, Cordoba (Spain); Logrono, C. [Department of Dermatology, Reina Sofia University Hospital, Cordoba (Spain); Carrascal, A. [Department of Radiology, Infanta Elena Hospital, Huelva (Spain); Carreto, A. [Department of Radiology, Reina Sofia University Hospital, Cordoba (Spain)

    1998-06-01

    Objective. To determine the incidence of bone islands in leprosy patients. Design. X-rays of feet and hands of patients with Hansen`s disease (leprosy) were reviewed retrospectively. A second group of related age- and sex-matched patients who did not have Hansen`s disease was used for control purposes. Controls had undergone hand or foot X-rays during diagnosis of other pathologies. The patients with Hansen`s disease were compared with the control group, and were also analyzed as subgroups with different types of leprosy. The results were subjected to statistical analysis. Patients. Ninety patients with Hansen`s disease were randomly selected for this study. Patients who had had ulcers on hands or feet were excluded from the study. Results and conclusions. Bone islands were demonstrated in 20 patients with Hansen`s disease; no bone islands were observed in the controls. This was statistically significant (P<0.01). Bone islands were only seen in patients with lepromatous leprosy and borderline types but were not demonstrated in patients with tuberculoid leprosy. There was also a statistically significant relationship for a disease duration of 15 years or more. The cause of this raised incidence of enostosis in leprosy patients is not clear, but there may be a genetic predisposition in patients with leprosy, or it may be a side effect of leprosy, especially the lepromatous form. (orig.) With 4 figs., 2 tabs., 9 refs.

  9. Bone island and leprosy

    International Nuclear Information System (INIS)

    Carpintero, P.; Garcia-Frasquet, A.; Tarradas, E.; Logrono, C.; Carrascal, A.; Carreto, A.

    1998-01-01

    Objective. To determine the incidence of bone islands in leprosy patients. Design. X-rays of feet and hands of patients with Hansen's disease (leprosy) were reviewed retrospectively. A second group of related age- and sex-matched patients who did not have Hansen's disease was used for control purposes. Controls had undergone hand or foot X-rays during diagnosis of other pathologies. The patients with Hansen's disease were compared with the control group, and were also analyzed as subgroups with different types of leprosy. The results were subjected to statistical analysis. Patients. Ninety patients with Hansen's disease were randomly selected for this study. Patients who had had ulcers on hands or feet were excluded from the study. Results and conclusions. Bone islands were demonstrated in 20 patients with Hansen's disease; no bone islands were observed in the controls. This was statistically significant (P<0.01). Bone islands were only seen in patients with lepromatous leprosy and borderline types but were not demonstrated in patients with tuberculoid leprosy. There was also a statistically significant relationship for a disease duration of 15 years or more. The cause of this raised incidence of enostosis in leprosy patients is not clear, but there may be a genetic predisposition in patients with leprosy, or it may be a side effect of leprosy, especially the lepromatous form. (orig.)

  10. Development and Use of Genetic Methods for Assessing Aquatic Environmental Condition and Recruitment Dynamics of Native Stream Fishes on Pacific Islands

    Science.gov (United States)

    2014-04-01

    likely differences among individuals within and between populations ( Radtke and Kinzie 1996, Benson and Fitzsimmons 2002). In addition, estimates of...larval life duration from otolith rings have shown differences among islands that may reflect differences in currents ( Radtke et al. 2001... Radtke et al. 1988). In combination with length or mass data, ring counts allow precise estimation of growth rates of individuals as well as

  11. African Anthropologist

    African Journals Online (AJOL)

    PROMOTING ACCESS TO AFRICAN RESEARCH ... It provides a forum for African and Africanist anthropologists to publish research reports, articles, book ... A Qualitative Exploration · EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

  12. HLA genes in Madeira Island (Portugal) inferred from sequence-based typing: footprints from different origins.

    Science.gov (United States)

    Spínola, Hélder; Bruges-Armas, Jácome; Mora, Marian Gantes; Middleton, Derek; Brehm, António

    2006-04-01

    Human leukocyte antigen (HLA)-A, HLA-B, and HLA-DRB1 polymorphisms were examined in Madeira Island populations. The data was obtained at high-resolution level, using sequence-based typing (SBT). The most frequent alleles at each loci were: A*020101 (24.6%), B*5101 (9.7%), B*440201 (9.2%), and DRB1*070101 (15.7%). The predominant three-loci haplotypes in Madeira were A*020101-B*510101-DRB1*130101 (2.7%) and A*010101-B*0801-DRB1*030101 (2.4%), previously found in north and central Portugal. The present study corroborates historical sources and other genetic studies that say Madeira were populated not only by Europeans, mostly Portuguese, but also sub-Saharan Africans due to slave trade. Comparison with other populations shows that Madeira experienced a stronger African influence due to slave trade than Portugal mainland and even the Azores archipelago. Despite this African genetic input, haplotype and allele frequencies were predominantly from European origin, mostly common to mainland Portugal.

  13. Evidence of stable genetic structure across a remote island archipelago through self-recruitment in a widely dispersed coral reef fish

    KAUST Repository

    Priest, Mark; Halford, Andrew R; McIlwain, Jennifer L

    2012-01-01

    We used microsatellite markers to assess the population genetic structure of the scribbled rabbitfish Siganus spinus in the western Pacific. This species is a culturally important food fish in the Mariana Archipelago and subject to high fishing

  14. Movement and Dance on the Sea Islands.

    Science.gov (United States)

    Twining, Mary Arnold

    1985-01-01

    Describes the role of movement and dance in the lives of Blacks living on the Sea Islands off the coasts of South Carolina and Georgia. Claims that the isolation of this area helps preserve its Africanicity and culture. Focuses particularly on the uses of rhythmic chanting in worship and in children's games. (KH)

  15. Island biology and morphological divergence of the Skyros wall lizard Podarcis gaigeae: a combined role for local selection and genetic drift on color morph frequency divergence?

    Directory of Open Access Journals (Sweden)

    Runemark Anna

    2010-09-01

    Full Text Available Abstract Background Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet- and mainland populations. Results Geographically close islet- and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (Ne:s ST for throat color morph frequencies fell within the neutral FST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that

  16. African Journals Online: African Studies

    African Journals Online (AJOL)

    Items 51 - 56 of 56 ... Research Review of the Institute of African Studies. Please note: As of 2013 the Research Review of the Institute of African Studies is now publishing under the title Contemporary Journal of African Studies. You can view the CJAS pages on AJOL here: http://www.ajol.info/index.php/contjas/index.

  17. Genome Island: A Virtual Science Environment in Second Life

    Science.gov (United States)

    Clark, Mary Anne

    2009-01-01

    Mary Anne CLark describes the organization and uses of Genome Island, a virtual laboratory complex constructed in Second Life. Genome Island was created for teaching genetics to university undergraduates but also provides a public space where anyone interested in genetics can spend a few minutes, or a few hours, interacting with genetic…

  18. Genetic Diversification and Dispersal of Taro (Colocasia esculenta (L. Schott.

    Directory of Open Access Journals (Sweden)

    H Chaïr

    Full Text Available Taro (Colocasia esculenta (L. Schott is widely distributed in tropical and sub-tropical areas. However, its origin, diversification and dispersal remain unclear. While taro genetic diversity has been documented at the country and regional levels in Asia and the Pacific, few reports are available from Americas and Africa where it has been introduced through human migrations. We used eleven microsatellite markers to investigate the diversity and diversification of taro accessions from nineteen countries in Asia, the Pacific, Africa and America. The highest genetic diversity and number of private alleles were observed in Asian accessions, mainly from India. While taro has been diversified in Asia and the Pacific mostly via sexual reproduction, clonal reproduction with mutation appeared predominant in African and American countries investigated. Bayesian clustering revealed a first genetic group of diploids from the Asia-Pacific region and to a second diploid-triploid group mainly from India. Admixed cultivars between the two genetic pools were also found. In West Africa, most cultivars were found to have originated from India. Only one multi-locus lineage was assigned to the Asian pool, while cultivars in Madagascar originated from India and Indonesia. The South African cultivars shared lineages with Japan. The Caribbean Islands cultivars were found to have originated from the Pacific, while in Costa Rica they were from India or admixed between Indian and Asian groups. Taro dispersal in the different areas of Africa and America is thus discussed in the light of available records of voyages and settlements.

  19. Class renormalization: islands around islands

    International Nuclear Information System (INIS)

    Meiss, J.D.

    1986-01-01

    An orbit of 'class' is one that rotates about a periodic orbit of one lower class with definite frequency. This contrasts to the 'level' of a periodic orbit which is the number of elements in its continued fraction expansion. Level renormalization is conventionally used to study the structure of quasi-periodic orbits. The scaling structure of periodic orbits encircling other periodic orbits in area preserving maps is discussed here. Fixed points corresponding to the accumulation of p/q bifurcations are found and scaling exponents determined. Fixed points for q > 2 correspond to self-similar islands around islands. Frequencies of the island boundary circles at the fixed points are obtained. Importance of this scaling for the motion of particles in stochastic regions is emphasized. (author)

  20. Prostate cancer disparities in Black men of African descent: a comparative literature review of prostate cancer burden among Black men in the United States, Caribbean, United Kingdom, and West Africa

    Directory of Open Access Journals (Sweden)

    Reams R Renee

    2009-02-01

    Full Text Available Abstract Background African American men have the highest prostate cancer morbidity and mortality rates than any other racial or ethnic group in the US. Although the overall incidence of and mortality from prostate cancer has been declining in White men since 1991, the decline in African American men lags behind White men. Of particular concern is the growing literature on the disproportionate burden of prostate cancer among other Black men of West African ancestry in the Caribbean Islands, United Kingdom and West Africa. This higher incidence of prostate cancer observed in populations of African descent may be attributed to the fact that these populations share ancestral genetic factors. To better understand the burden of prostate cancer among men of West African Ancestry, we conducted a review of the literature on prostate cancer incidence, prevalence, and mortality in the countries connected by the Transatlantic Slave Trade. Results Several published studies indicate high prostate cancer burden in Nigeria and Ghana. There was no published literature for the countries Benin, Gambia and Senegal that met our review criteria. Prostate cancer morbidity and/or mortality data from the Caribbean Islands and the United Kingdom also provided comparable or worse prostate cancer burden to that of US Blacks. Conclusion The growing literature on the disproportionate burden of prostate cancer among other Black men of West African ancestry follows the path of the Transatlantic Slave Trade. To better understand and address the global prostate cancer disparities seen in Black men of West African ancestry, future studies should explore the genetic and environmental risk factors for prostate cancer among this group.

  1. The Impact of Stress on the Life History Strategies of African American Adolescents: Cognitions, Genetic Moderation, and the Role of Discrimination

    Science.gov (United States)

    Gibbons, Frederick X.; Roberts, Megan E.; Gerrard, Meg; Li, Zhigang; Beach, Steven R. H.; Simons, Ronald L.; Weng, Chih-Yuan; Philibert, Robert A.

    2012-01-01

    The impact of 3 different sources of stress--environmental, familial (e.g., low parental investment), and interpersonal (i.e., racial discrimination)--on the life history strategies (LHS) and associated cognitions of African American adolescents were examined over an 11-year period (5 waves, from age 10.5 to 21.5). Analyses indicated that each one…

  2. Nutritional Genetics: The Case of Alcohol and the MTHFR C677T Polymorphism in relation to homocysteine in a Black South African Population

    NARCIS (Netherlands)

    Nienaber-Rousseau, C.; Pisa, P.T.; Venster, C.S.; Ellis, S.M.; Kruger, A.; Moss, S.; Boonstra, A.; Towers, G.W.

    2013-01-01

    Background/Aims: It is unknown whether the effect of alcohol consumption on homocysteine (Hcy) is modulated by the methylenetetrahydrofolate reductase (MTHFR) C677T. We explored this hypothesized effect by analyzing cross-sectional data of 1,827 black South Africans. Methods: Total Hcy

  3. Using genetic profiles of African forest elephants to infer population structure, movements, and habitat use in a conservation and development landscape in Gabon

    NARCIS (Netherlands)

    Eggert, L. S.; Buij, R.; Lee, M. E.; Campbell, P.; Dallmeier, F.; Fleischer, R. C.; Alonso, A.; Maldonado, J. E.

    Conservation of wide-ranging species, such as the African forest elephant (Loxodonta cyclotis), depends on fully protected areas and multiple-use areas (MUA) that provide habitat connectivity. In the Gamba Complex of Protected Areas in Gabon, which includes 2 national parks separated by a MUA

  4. using genetic profiles of african forest elephants to infer population structure, movements, and habitat use in a conservation and development landscape in gabon

    NARCIS (Netherlands)

    Eggert, L.S.; Buij, R.; Lee, M.E.; Campbell, P.; Dallmeier, F.; Fleischer, R.C.; Alonso, A.; Maldonado, J.

    2014-01-01

    Conservation of wide-ranging species, such as the African forest elephant (Loxodonta cyclotis), depends on fully protected areas and multiple-use areas (MUA) that provide habitat connectivity. In the Gamba Complex of Protected Areas in Gabon, which includes 2 national parks separated by a MUA

  5. Genetic diversity and difference within and between bitter and sweet African bush mango trees (Irvingia spp., Irvingiaceae) in West and Central Africa

    NARCIS (Netherlands)

    Vihotogbé, R.; Berg, van den R.G.; Missinhoun, A.A.; Sinsin, B.; Sosef, M.S.M.

    2015-01-01

    Economically important food tree species in sub-Saharan Africa should be domesticated to enhance their production within agro forestry systems. The African bush mango trees (Irvingia species) are highly preserved and integrated in agro forestry systems in tropical Africa. However, the taxonomic

  6. Composition and Genetic Diversity of Mosquitoes (Diptera: Culicidae) on Islands and Mainland Shores of Kenya’s Lakes Victoria and Baringo

    Science.gov (United States)

    Ajamma, Yvonne Ukamaka; Villinger, Jandouwe; Omondi, David; Salifu, Daisy; Onchuru, Thomas Ogao; Njoroge, Laban; Muigai, Anne W. T.; Masiga, Daniel K.

    2016-01-01

    The Lake Baringo and Lake Victoria regions of Kenya are associated with high seroprevalence of mosquito-transmitted arboviruses. However, molecular identification of potential mosquito vector species, including morphologically identified ones, remains scarce. To estimate the diversity, abundance, and distribution of mosquito vectors on the mainland shores and adjacent inhabited islands in these regions, we collected and morphologically identified adult and immature mosquitoes and obtained the corresponding sequence variation at cytochrome c oxidase 1 (COI) and internal transcribed spacer region 2 (ITS2) gene regions. A total of 63 species (including five subspecies) were collected from both study areas, 47 of which have previously been implicated as disease vectors. Fourteen species were found only on island sites, which are rarely included in mosquito diversity surveys. We collected more mosquitoes, yet with lower species composition, at Lake Baringo (40,229 mosquitoes, 32 species) than at Lake Victoria (22,393 mosquitoes, 54 species). Phylogenetic analysis of COI gene sequences revealed Culex perexiguus and Cx. tenagius that could not be distinguished morphologically. Most Culex species clustered into a heterogeneous clade with closely related sequences, while Culex pipiens clustered into two distinct COI and ITS2 clades. These data suggest limitations in current morphological identification keys. This is the first DNA barcode report of Kenyan mosquitoes. To improve mosquito species identification, morphological identifications should be supported by their molecular data, while diversity surveys should target both adults and immatures. The diversity of native mosquito disease vectors identified in this study impacts disease transmission risks to humans and livestock. PMID:27402888

  7. Emerging rabbit haemorrhagic disease virus 2 (RHDV2) at the gates of the African continent.

    Science.gov (United States)

    Martin-Alonso, Aarón; Martin-Carrillo, Natalia; Garcia-Livia, Katherine; Valladares, Basilio; Foronda, Pilar

    2016-10-01

    Until the beginning of this decade, the genetic characterization of rabbit haemorrhagic disease virus (RHDV) from Iberian Peninsula had revealed the existence of two genogroups, G1 and sporadically G6. In 2010, the new emerging rabbit haemorrhagic disease variant, RHDV2 or RHDVb, was described in France, from where it has rapidly spread throughout Europe, including Iberian Peninsula countries. Nevertheless, although cases of rabbit haemorrhagic disease (RHD) have been reported in the Canary Islands, a Spanish archipelago located 100km off the coast of Morocco, no genetic characterization of RHDV had been carried out. Consequently, in order to identify the circulating RHDV strains in this archipelago, liver samples of six farm rabbits and fifteen wild rabbits were collected from several areas of the largest island, Tenerife, and analyzed for the presence of RHDV by antigen capture double antibody sandwich ELISA. In case of positive ELISA result, we amplified and sequenced two fragments of the vp60 gene, which were concatenated for phylogenetic purposes. The sequences analysis revealed the presence of RHDV2 in both farm and wild rabbits from several areas of Tenerife. This result constitutes the first finding of RHDV2 in the Canary Islands. These RHDV2 strains found in Tenerife shared two exclusive SNPs that have not been observed in the rest of RHDV2 strains. The identification of RHDV2 and the absence of classic RHDV strains in this study suggest that RHDV2 may be replacing classic strains in Tenerife, as has been also proposed in Iberian Peninsula, France and Azores. Given the proximity of the Canary Islands to the African continent, this result should raise awareness about a possible dispersal of RHDV2 from the Canary Islands to the North of Africa. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans)

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Sanchez Sanchez, Juan Jose; Barbaro, Anna

    2008-01-01

    BACKGROUND: Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached...

  9. African Journals Online: Biology & Life Sciences

    African Journals Online (AJOL)

    Items 51 - 71 of 71 ... The journal publishes original articles in the broad discipline of basic genetics ... review articles, issues and opinions, special communications, letters to ... Ostrich: Journal of African Ornithology is a scientific journal published ...

  10. A new species of iguana Brachylophus Cuvier 1829 (Sauria: Iguania: Iguanidae) from Gau Island, Fiji Islands.

    Science.gov (United States)

    Fisher, Robert N; Niukula, Jone; Watling, Dick; Harlow, Peter S

    2017-06-06

    The south Pacific iguanas (Brachylophus) currently have three recognized living species in Fiji.  Recent surveys have uncovered more specific variation (morphological and genetic) within the genus and have better defined the geographic ranges of the named species.  One of these recent discoveries is a strikingly different iguana from all other island populations in Fiji which is restricted to Gau Island of the Lomaiviti Province.  Gau is the fifth largest island in Fiji and maintains excellent upland forests in the higher elevations.  We describe this population from Gau Island as a new species, Brachylophus gau sp. nov., in recognition of its type locality.

  11. African Zoology

    African Journals Online (AJOL)

    African Zoology, a peer-reviewed research journal, publishes original scientific contributions and critical reviews that focus principally on African fauna in terrestrial, freshwater, and marine ecosystems. Research from other regions that advances practical and theoretical aspects of zoology will be considered. Rigorous ...

  12. Indigenous chicken genetic resources in South Africa

    African Journals Online (AJOL)

    User

    A comparison of genetic diversity between South African conserved and field ... economic loss for human populations, especially in developing countries. .... for Development of National Management of Farm Animal Genetic Resources.

  13. Genetics Home Reference: complement component 8 deficiency

    Science.gov (United States)

    ... in people with Hispanic, Japanese, or African Caribbean heritage, whereas type II primarily occurs in people of Northern European descent. Related Information What information about a genetic condition can statistics provide? Why are some genetic ...

  14. Exploration of the Hypothalamic-Pituitary-Adrenal Axis to Improve Animal Welfare by Means of Genetic Selection: Lessons from the South African Merino

    Directory of Open Access Journals (Sweden)

    Schalk Cloete

    2013-05-01

    Full Text Available It is a difficult task to improve animal production by means of genetic selection, if the environment does not allow full expression of the animal’s genetic potential. This concept may well be the future for animal welfare, because it highlights the need to incorporate traits related to production and robustness, simultaneously, to reach sustainable breeding goals. This review explores the identification of potential genetic markers for robustness within the hypothalamic-pituitary-adrenal axis (HPAA, since this axis plays a vital role in the stress response. If genetic selection for superior HPAA responses to stress is possible, then it ought to be possible to breed robust and easily managed genotypes that might be able to adapt to a wide range of environmental conditions whilst expressing a high production potential. This approach is explored in this review by means of lessons learnt from research on Merino sheep, which were divergently selected for their multiple rearing ability. These two selection lines have shown marked differences in reproduction, production and welfare, which makes this breeding programme ideal to investigate potential genetic markers of robustness. The HPAA function is explored in detail to elucidate where such genetic markers are likely to be found.

  15. African Journals Online: Syrian Arab Republic

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  16. African Journals Online: Curaçao

    African Journals Online (AJOL)

    ... Cambodia, Cameroon, Canada, Cayman Islands, Central African Republic, Chad, Chile, China, Colombia, Comoros, Congo, Democratic Republic, Congo, Republic, Costa Rica, Côte d'Ivoire, Croatia, Cuba, Curaçao, Cyprus, Czech Republic, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, Arab Rep.

  17. South African red data book – Birds

    CSIR Research Space (South Africa)

    Brooke, RK

    1984-12-01

    Full Text Available Antarctic Tern Kerguelen Tern. All are included because of feral cat Felis catus predation on Marion Island. Only the Common Diving Petrel and the Kerguelen Tern do not visit South African coastal waters. It is also instructive to examine the 102...

  18. Strengthening African Union for African Integration: An African ...

    African Journals Online (AJOL)

    Log in or Register to get access to full text downloads. ... in the international state system and seek for African initiative in solving African problems. ... of the African Union by examining the efforts of African Leaders towards African integration, ...

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

    Science.gov (United States)

    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. Published by Elsevier Ltd.

  20. Genetic heritage of Croatians in the Southeastern European gene pool-Y chromosome analysis of the Croatian continental and Island population.

    Science.gov (United States)

    Šarac, Jelena; Šarić, Tena; Havaš Auguštin, Dubravka; Novokmet, Natalija; Vekarić, Nenad; Mustać, Mate; Grahovac, Blaženka; Kapović, Miljenko; Nevajda, Branimir; Glasnović, Anton; Missoni, Saša; Rootsi, Siiri; Rudan, Pavao

    2016-11-01

    The research objective of this study is to enlarge and deepen the Y chromosome research on the Croatian population and enable additional insights into the population diversity and historic events that shaped the current genetic landscape of Croatia and Southeastern Europe (SEE). A high-resolution phylogenetic and phylogeographic analysis of 66 biallelic (SNPs) and 17 microsatellite (STRs) markers of the Y chromosome was performed using 720 Croatian samples. The obtained results were placed in a wider European context by comparison with ∼4450 samples from a number of other European populations. A high diversity of haplogroups was observed in the overall Croatian sample, and all typical European Y chromosome haplogroups with corresponding clinal patterns were observed. Three distinct genetic signals were identifiable in the Croatian paternal gene pool - I2a1b-M423, R1a1a1b1a*-M558, and E1b1b1a1b1a-V13 haplogroups. The analyses of the dominant and autochthonous I2a1b-M423 lineage (>30%) suggest that SEE had a significant role in the Upper Paleolithic, the R1a1a1b1a*-M558 lineage (19%) represents a signal from present day Slavic populations of Central Europe in the Croatian population, and the phylogeography of the E1b1b1a1b1a-V13 clade (around 9%) implies cultural diffusion of agriculture into Europe via the Balkan Peninsula. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:837-845, 2016. © 2016Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  1. The Impact of Stress on the Life History Strategies of African American Adolescents: Cognitions, Genetic Moderation, and the Role of Discrimination

    OpenAIRE

    Gibbons, Frederick X.; Roberts, Megan E.; Gerrard, Meg; Li, Zhigang; Beach, Steven R. H.; Simons, Ronald L.; Weng, Chih-Yuan; Philibert, Robert A.

    2012-01-01

    The impact of three different sources of stress—environmental, familial (e.g., low parental investment), and interpersonal (i.e., racial discrimination)—on the life history strategies (LHS) and associated cognitions of African American adolescents were examined over an 11-year period (five waves, from age 10.5 to 21.5). Analyses indicated that each one of the sources of stress was associated with faster LHS cognitions (e.g., tolerance of deviance, willingness to engage in risky sex), which, i...

  2. Pollination, biogeography and phylogeny of oceanic island bellflowers (Campanulaceae)

    DEFF Research Database (Denmark)

    Olesen, Jens Mogens; Alarcón, M.; Ehlers, Bodil

    2012-01-01

    . These examples of vertebrate pollination evolved independently on each island or archipelago. We discuss if these pollination systems have an island or mainland origin and when they may have evolved, and finally, we attempt to reconstruct the pollinator-interaction history of each species.......We studied the pollination biology of nine island Campanulaceae species: Azorina vidalii, Musschia aurea, M. wollastonii, Canarina canariensis, Campanula jacobaea, Nesocodon mauritianus, and three species of Heterochaenia. In addition, we compared C. canariensis to its two African mainland...... relatives C. eminii and C. abyssinica. We asked to what extent related species converge in their floral biology and pollination in related habitats, i.e. oceanic islands. Study islands were the Azores, Madeira, Canary Islands, Cape Verde, Mauritius, and Réunion. Information about phylogenetic relationships...

  3. Africanization in the United States: replacement of feral European honeybees (Apis mellifera L.) by an African hybrid swarm.

    Science.gov (United States)

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

    2005-08-01

    The expansion of Africanized honeybees from South America to the southwestern United States in feral population from the southern United States undergoing Africanization. Our microsatellite data showed that (1) the process of Africanization involved both maternal and paternal bidirectional gene flow between European and Africanized honeybees and (2) the panmitic European population was replaced by panmitic mixtures of A. m. scutellata and European genes within 5 years after Africanization. The post-Africanization gene pool (1998-2001) was composed of a diverse array of recombinant classes with a substantial European genetic contribution (mean 25-37%). Therefore, the resulting feral honeybee population of south Texas was best viewed as a hybrid swarm.

  4. Tenarife Island, Canary Island Archipelago, Atlantic Ocean

    Science.gov (United States)

    1991-01-01

    Tenarife Island is one of the most volcanically active of the Canary Island archipelago, Atlantic Ocean, just off the NW coast of Africa, (28.5N, 16.5W). The old central caldera, nearly filled in by successive volcanic activity culminating in two stratocones. From those two peaks, a line of smaller cinder cones extend to the point of the island. Extensive gullies dissect the west side of the island and some forests still remain on the east side.

  5. Genomic island excisions in Bordetella petrii

    Directory of Open Access Journals (Sweden)

    Levillain Erwan

    2009-07-01

    Full Text Available Abstract Background Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B. petrii from the other sequenced Bordetellae is the presence of a large number of mobile genetic elements including several large genomic regions with typical characteristics of genomic islands collectively known as integrative and conjugative elements (ICEs. These elements mainly encode accessory metabolic factors enabling this bacterium to grow on a large repertoire of aromatic compounds. Results During in vitro culture of Bordetella petrii colony variants appear frequently. We show that this variability can be attributed to the presence of a large number of metastable mobile genetic elements on its chromosome. In fact, the genome sequence of B. petrii revealed the presence of at least seven large genomic islands mostly encoding accessory metabolic functions involved in the degradation of aromatic compounds and detoxification of heavy metals. Four of these islands (termed GI1 to GI3 and GI6 are highly related to ICEclc of Pseudomonas knackmussii sp. strain B13. Here we present first data about the molecular characterization of these islands. We defined the exact borders of each island and we show that during standard culture of the bacteria these islands get excised from the chromosome. For all but one of these islands (GI5 we could detect circular intermediates. For the clc-like elements GI1 to GI3 of B. petrii we provide evidence that tandem insertion of these islands which all encode highly related integrases and attachment sites may also lead to incorporation of genomic DNA which originally was not part of the island and to the formation of huge composite islands. By integration of a tetracycline resistance cassette into GI3 we found this island to be rather unstable and to be lost from

  6. The origin of platyrrhines: An evaluation of the Antarctic scenario and the floating island model.

    Science.gov (United States)

    Houle, A

    1999-08-01

    This paper evaluates whether 1) protoplatyrrhines could have migrated to South America via Antarctica, and 2) the floating island model is a plausible transoceanic mode of dispersal for land vertebrates like protoplatyrrhines. Results show that Eocene Antarctica and Australia supported large and dense forests, and that the Antarctic fauna was comprised of many species of vertebrates, including placental and marsupial land mammals. However, no primate remains have ever been reported from these continents. Antarctica and South America were connected until the Middle Eocene (i.e., after the oldest Asian anthropoids), but two major water barriers existed between Antarctica and Asia since the Early Eocene. The Eocene and Oligocene water gap separating Africa and Antarctica was excessively large. Thus, all scenarios involving an Antarctic route have been rejected. The African scenario is difficult to falsify because only one water barrier existed, both paleowinds and paleocurrents were favorable, and Paleogene African anthropoids show phylogenetic affinities to platyrrhines. I tested whether a journey on a hypothetical floating island over the Paleogene Atlantic Ocean exceeds the survival limit of a genetically viable group of animals such as protoplatyrrhines. Studies of water deprivation suggest that they could have been able, with a body weight averaging 1 kg, to survive without water for at least 13 days. I have used the present Atlantic Ocean as a model for the velocity of Paleogene paleowinds and paleocurrents. Considering winds as the key accelerating force of floating islands, the Paleogene Atlantic water barrier could have been crossed, in the most conservative scenario, in 8 days at 50 Mya, 11 days at 40 Mya, and 15 days at 30 Mya. In order to survive a transoceanic journey, however, protoplatyrrhines had to be preadapted to strong seasonal variations in water availability in their original (African) environment. Once on the sea, their brains would have

  7. Phylogenetic and phylogeographic evidence for a Pleistocene disjunction between Campanula jacobaea (Cape Verde Islands) and C. balfourii (Socotra).

    Science.gov (United States)

    Alarcón, Marisa; Roquet, Cristina; García-Fernández, Alfredo; Vargas, Pablo; Aldasoro, Juan José

    2013-12-01

    Our understanding of processes that led to biogeographic disjunct patterns of plant lineages in Macaronesia, North Africa and Socotra remains poor. Here, we study a group of Campanula species distributed across these areas integrating morphological and reproductive traits with phylogenetic and phylogeographic data based on the obtention of sequences for 4 highly variable cpDNA regions and AFLP data. The phylogeny obtained shows a sister relationship between Campanula jacobaea (endemic to Cape Verde Islands) and C. balfourii (endemic to Socotra), thus revealing a striking disjunct pattern (8300 km). These species diverged around 1.0 Mya; AFLP and haplotype data suggest that no genetic interchange has occurred since then. Their closest taxon, C. hypocrateriformis, is endemic to SW Morocco. The archipelagos of Macaronesia and Socotra have probably acted as refugia for North-African species, leading to speciation through isolation. Although C. balfourii has a restricted distribution, its genetic variability suggests that its populations have suffered no bottlenecks. C. jacobaea is also genetically rich and its distribution across Cape Verde Islands seems to have been influenced by the NE-SW trade winds, which may also have favoured the admixture found among the populations of the three southern islands. Floral features of the morphologically hypervariable C. jacobaea were also measured to assess whether the taxon C. bravensis, described for some of the southeast populations of C. jacobaea, corresponds to a different evolutionary entity. We show that morphological variation in C. jacobaea does not correspond to any genetic or geographic group. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. African Journals Online (AJOL)

    African Journals Online (AJOL)

    African Journals OnLine (AJOL) is the world's largest online library of ... AJOL works to change this, so that African-origin research output is available to Africans ... South African Medical Journal ... Global Journal of Pure and Applied Sciences.

  9. Immunizations and African Americans

    Science.gov (United States)

    ... Data > Minority Population Profiles > Black/African American > Immunizations Immunizations and African Americans African American adults are less ... 19 to 35 months had comparable rates of immunization. African American women are as likely to have ...

  10. Multiple independent colonization of the Canary Islands by the winged grasshopper genus Sphingonotus Fieber, 1852.

    Science.gov (United States)

    Husemann, Martin; Deppermann, Jana; Hochkirch, Axel

    2014-12-01

    Volcanic archipelagos represent ideal systems to study processes of colonization, differentiation and speciation. The Canary Islands are one of the best studied archipelagos, being composed of seven main islands with a well-known geological history. Most taxa have colonized these islands stepwise from the African or Iberian mainland from east to west, following their geological origin as well as the predominating wind direction and ocean currents. Furthermore, within-island radiations have been reported for several taxa. The grasshopper genus Sphingonotus is species-rich and occurs with nine fully winged species on the Canary Islands, seven of which are endemic to single or few islands. We inferred a phylogeny of these species and their North African and Iberian relatives based upon sequences of three mitochondrial genes and one nuclear gene of 136 specimens. Surprisingly, our results suggest that almost all Sphingonotus species colonized the archipelago independently from the mainland and nearly no inter-island colonization occurred. Despite their strong flight capabilities, only one pair of endemic species are closely related (S. sublaevis from Gran Canary and S. pachecoi from Lanzarote). Moreover, no within-island speciation events were detected. We hypothesize that passive wind dispersal from the African mainland was the main driver of the colonization process and that most Sphingonotus species are not able to cover inter-island distances by active flight. This, together with strong intrageneric niche overlap might explain the lack of within-island speciation in this taxon. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Detection of dengue virus type 4 in Easter Island, Chile.

    Science.gov (United States)

    Fernández, J; Vera, L; Tognarelli, J; Fasce, R; Araya, P; Villagra, E; Roos, O; Mora, J

    2011-10-01

    We report the detection of dengue virus type 4 (DENV-4) for the first time in Easter Island, Chile. The virus was detected in serum samples of two patients treated at the Hospital in Easter Island. The two samples were IgM positive, and the infection was confirmed by RT-PCR and genetic sequencing; viral isolation was possible with one of them. The Easter Island isolates were most closely related to genotype II of dengue type 4.

  12. Short communication Evaluation of genetic trends for traits of ...

    African Journals Online (AJOL)

    RamatsomaN

    2014-03-27

    Mar 27, 2014 ... Genetic evaluation for the South African dairy industry has kept pace ... for first lactation milk yield in South African Ayrshire cattle using an ... Genetic improvement in clinical mastitis is feasible as demonstrated in a study by Heringstad et al. ... Genetic parameters and trends of milk, fat, days open, and body.

  13. Genetic variations in multiple myeloma I

    DEFF Research Database (Denmark)

    Vangsted, A.; Klausen, T.W.; Vogel, Ulla Birgitte

    2012-01-01

    Few risk factors have been established for the plasma cell disorder multiple myeloma, but some of these like African American ethnicity and a family history of B-cell lymphoproliferative diseases suggest a genetic component for the disease. Genetic variation represents the genetic basis of variab......Few risk factors have been established for the plasma cell disorder multiple myeloma, but some of these like African American ethnicity and a family history of B-cell lymphoproliferative diseases suggest a genetic component for the disease. Genetic variation represents the genetic basis...

  14. The impact of stress on the life history strategies of African American adolescents: cognitions, genetic moderation, and the role of discrimination.

    Science.gov (United States)

    Gibbons, Frederick X; Roberts, Megan E; Gerrard, Meg; Li, Zhigang; Beach, Steven R H; Simons, Ronald L; Weng, Chih-Yuan; Philibert, Robert A

    2012-05-01

    The impact of 3 different sources of stress--environmental, familial (e.g., low parental investment), and interpersonal (i.e., racial discrimination)--on the life history strategies (LHS) and associated cognitions of African American adolescents were examined over an 11-year period (5 waves, from age 10.5 to 21.5). Analyses indicated that each one of the sources of stress was associated with faster LHS cognitions (e.g., tolerance of deviance, willingness to engage in risky sex), which, in turn, predicted faster LHS behaviors (e.g., frequent sexual behavior). LHS, then, negatively predicted outcome (resilience) at age 21.5 (i.e., faster LHS → less resilience). In addition, presence of the risk ("sensitivity") alleles of 2 monoamine-regulating genes, the serotonin transporter gene (5HTTLPR) and the dopamine D4 receptor gene (DRD4), moderated the impact of perceived racial discrimination on LHS cognitions: Participants with more risk alleles (higher "sensitivity") reported faster LHS cognitions at age 18 and less resilience at age 21 if they had experienced higher amounts of discrimination and slower LHS and more resilience if they had experienced smaller amounts of discrimination. Implications for LHS theories are discussed.

  15. Genetic Diversity and Phylogenetic Relationships of Coevolving Symbiont-Harboring Insect Trypanosomatids, and Their Neotropical Dispersal by Invader African Blowflies (Calliphoridae

    Directory of Open Access Journals (Sweden)

    Tarcilla C. Borghesan

    2018-02-01

    Full Text Available This study is about the inter- and intra-specific genetic diversity of trypanosomatids of the genus Angomonas, and their association with Calliphoridae (blowflies in Neotropical and Afrotropical regions. Microscopic examination of 3,900 flies of various families, mostly Calliphoridae, revealed that 31% of them harbored trypanosomatids. Small subunit rRNA (SSU rRNA barcoding showed that Angomonas predominated (46% over the other common trypanosomatids of blowflies of genera Herpetomonas and Wallacemonas. Among Angomonas spp., A. deanei was much more common than the two-other species, A. desouzai and A. ambiguus. Phylogenetic analyses based on SSU rRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH and internal transcribed spacer rDNA (ITS rDNA sequences revealed a marked genetic diversity within A. deanei, which comprised four infraspecific genotypes (Dea1–Dea4, and four corresponding symbiont genotypes (Kcr1–Kcr4. Host and symbiont phylogenies were highly congruent corroborating their co-divergence, consistent with host-symbiont interdependent metabolism and symbiont reduced genomes shaped by a long coevolutionary history. We compared the diversity of Angomonas/symbionts from three genera of blowflies, Lucilia, Chrysomya and Cochliomyia. A. deanei, A. desouzai, and A. ambiguus were found in the three genera of blowflies in South America. In Africa, A. deanei and A. ambiguus were identified in Chrysomya. The absence of A. desouzai in Africa and its presence in Neotropical Cochliomyia and Lucilia suggests parasite spillback of A. desouzai into Chrysomya, which was most likely introduced four decades ago from Africa into the Neotropic. The absence of correlation between parasite diversity and geographic and genetic distances, with identical genotypes of A. deanei found in the Neotropic and Afrotropic, is consistent with disjunct distribution due to the recent human-mediated transoceanic dispersal of Angomonas by Chrysomya. This

  16. Bibliography of sandy beaches and sandy beach organisms on the African continent

    CSIR Research Space (South Africa)

    Bally, R

    1986-01-01

    Full Text Available This bibliography covers the literature relating to sandy beaches on the African continent and outlying islands. The bibliography lists biological, chemical, geographical and geological references and covers shallow marine sediments, surf zones off...

  17. African Environment

    African Journals Online (AJOL)

    Environmental Studies and Regional Planning Bulletin African Environment is published in French and English, and for some issues, in Arabic. (only the issue below has been received by AJOL). Vol 10, No 3 (1999). DOWNLOAD FULL TEXT Open Access DOWNLOAD FULL TEXT Subscription or Fee Access. Table of ...

  18. African Journals Online: Central African Republic

    African Journals Online (AJOL)

    African Journals Online: Central African Republic. Home > African Journals Online: Central African Republic. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register · Browse By Category · Browse Alphabetically · Browse By Country · List All Titles · Free to read Titles This ...

  19. Researching Pacific island livelihoods:

    DEFF Research Database (Denmark)

    Egelund Christensen, Andreas; Mertz, Ole

    2010-01-01

    on contemporary theories of nissology and conceptual analytical frameworks for island research. Through a review of selected case-study-based island literature on changing livelihoods coming out of the South Pacific, we wish to illustrate and discuss advantages of finding common grounds for small island studies....... The focus is on two dimensions of island livelihood, migration and natural resource management, both of which are significant contributors in making island livelihoods and shaping Pacific seascapes. We argue that there is still a substantial lack of studies targeting small island dynamics that are empirical...

  20. A novel MERTK deletion is a common founder mutation in the Faroe Islands and is responsible for a high proportion of retinitis pigmentosa cases

    DEFF Research Database (Denmark)

    Ostergaard, Elsebet; Duno, Morten; Batbayli, Mustafa

    2011-01-01

    The aim of the study was to elucidate the genetic background of retinitis pigmentosa (RP) in a Faroe Islands population, a genetic isolate in the North Atlantic Ocean.......The aim of the study was to elucidate the genetic background of retinitis pigmentosa (RP) in a Faroe Islands population, a genetic isolate in the North Atlantic Ocean....

  1. Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa.

    Science.gov (United States)

    van Hooft, Pim; Keet, Dewald F; Brebner, Diana K; Bastos, Armanda D S

    2018-04-03

    Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, we investigate dispersal in lions sampled from the northern and southern extremes of Kruger National Park, a bush-like ecosystem in South Africa where bovine tuberculosis prevalence ranges from low to high across a north-south gradient. A total of 109 individuals sampled from 1998 to 2004 were typed using 11 microsatellite markers, and mitochondrial RS-3 gene sequences were generated for 28 of these individuals. Considerable north-south genetic differentiation was observed in both datasets. Dispersal was male-biased and generally further than 25 km, with long-distance male gene flow (75-200 km, detected for two individuals) confirming that male lions can travel large distances, even in bush-like ecosystems. In contrast, females generally did not disperse further than 20 km, with two distinctive RS-3 gene clusters for northern and southern females indicating no or rare long-distance female dispersal. However, dispersal rate for the predominantly non-territorial females from southern Kruger (fraction dispersers ≥0.68) was higher than previously reported. Of relevance was the below-average body condition of dispersers and their low presence in prides, suggesting low fitness. Large genetic differences between the two sampling localities, and low relatedness among males and high dispersal rates among females in the south, suggestive of unstable territory structure and high pride turnover, have potential implications for spread of diseases and the management of the Kruger lion population.

  2. Holocene sedimentology and coastal geomorphology of Zakynthos Island, Ionian Sea : A history of a divided Mediterranean island

    NARCIS (Netherlands)

    Avramidis, P.; Iliopoulos, G.; Nikolaou, K; Kontopoulos, N.; Koutsodendris, A.; van Wijngaarden, G.J.

    2017-01-01

    The island of Zakynthos is one of the most seismically active areas in the Mediterranean region because it is located very close to the convergent boundary between the African and Eurasian plates. Its evolution during the Holocene has been influenced by tectonic activity, catastrophic events and

  3. African Journals Online: African Studies

    African Journals Online (AJOL)

    Items 1 - 50 of 56 ... Africa Development is the quarterly bilingual journal of CODESRIA. .... relationship in the family, workplace, schools and organisations. .... activities, and personalities driving the democracy and development agenda in the region; 4. Conflict .... with preference for the results of African and Africanist studies.

  4. Co-evolution of human leukocyte antigen (HLA class I ligands with killer-cell immunoglobulin-like receptors (KIR in a genetically diverse population of sub-Saharan Africans.

    Directory of Open Access Journals (Sweden)

    Paul J Norman

    2013-10-01

    Full Text Available Interactions between HLA class I molecules and killer-cell immunoglobulin-like receptors (KIR control natural killer cell (NK functions in immunity and reproduction. Encoded by genes on different chromosomes, these polymorphic ligands and receptors correlate highly with disease resistance and susceptibility. Although studied at low-resolution in many populations, high-resolution analysis of combinatorial diversity of HLA class I and KIR is limited to Asian and Amerindian populations with low genetic diversity. At the other end of the spectrum is the West African population investigated here: we studied 235 individuals, including 104 mother-child pairs, from the Ga-Adangbe of Ghana. This population has a rich diversity of 175 KIR variants forming 208 KIR haplotypes, and 81 HLA-A, -B and -C variants forming 190 HLA class I haplotypes. Each individual we studied has a unique compound genotype of HLA class I and KIR, forming 1-14 functional ligand-receptor interactions. Maintaining this exceptionally high polymorphism is balancing selection. The centromeric region of the KIR locus, encoding HLA-C receptors, is highly diverse whereas the telomeric region encoding Bw4-specific KIR3DL1, lacks diversity in Africans. Present in the Ga-Adangbe are high frequencies of Bw4-bearing HLA-B*53:01 and Bw4-lacking HLA-B*35:01, which otherwise are identical. Balancing selection at key residues maintains numerous HLA-B allotypes having and lacking Bw4, and also those of stronger and weaker interaction with LILRB1, a KIR-related receptor. Correspondingly, there is a balance at key residues of KIR3DL1 that modulate its level of cell-surface expression. Thus, capacity to interact with NK cells synergizes with peptide binding diversity to drive HLA-B allele frequency distribution. These features of KIR and HLA are consistent with ongoing co-evolution and selection imposed by a pathogen endemic to West Africa. Because of the prevalence of malaria in the Ga-Adangbe and

  5. African Journals Online (AJOL)

    African Journals Online (AJOL)

    It has also been difficult for African researchers to access the work of other African academics. In partnership with hundreds of journals from all over the continent, AJOL works to change this, so that African-origin research output is available to Africans and to the rest of the world. AJOL is ... African Journal of AIDS Research.

  6. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations.

    Science.gov (United States)

    van de Loosdrecht, Marieke; Bouzouggar, Abdeljalil; Humphrey, Louise; Posth, Cosimo; Barton, Nick; Aximu-Petri, Ayinuer; Nickel, Birgit; Nagel, Sarah; Talbi, El Hassan; El Hajraoui, Mohammed Abdeljalil; Amzazi, Saaïd; Hublin, Jean-Jacques; Pääbo, Svante; Schiffels, Stephan; Meyer, Matthias; Haak, Wolfgang; Jeong, Choongwon; Krause, Johannes

    2018-05-04

    North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans, attributed to the Iberomaurusian culture, from Morocco. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans to Late Pleistocene North Africans. The Taforalt individuals derive one-third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  7. Diomede Islands, Bering Straight

    Science.gov (United States)

    2008-01-01

    The Diomede Islands consisting of the western island Big Diomede (also known as Imaqliq, Nunarbuk or Ratmanov Island), and the eastern island Little Diomede (also known as Krusenstern Island or Inaliq), are two rocky islands located in the middle of the Bering Strait between Russia and Alaska. The islands are separated by an international border and the International Date Line which is approximately 1.5 km from each island; you can look from Alaska into tomorrow in Russia. At the closest land approach between the United States, which controls Little Diomede, and Russia, which controls Big Diomede, they are 3 km apart. Little Diomede Island constitutes the Alaskan City of Diomede, while Big Diomede Island is Russia's easternmost point. The first European to reach the islands was the Russian explorer Semyon Dezhnev in 1648. The text of the 1867 treaty finalizing the sale of Alaska uses the islands to designate the border between the two nations. The image was acquired July 8, 2000, covers an area of 13.5 x 10.8 km, and is located at 65.8 degrees north latitude, 169 degrees west longitude. The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

  8. Tales of island tails

    NARCIS (Netherlands)

    Groot, de Alma V.; Oost, Albert P.; Veeneklaas, Roos M.; Lammerts, Evert Jan; Duin, van Willem E.; Wesenbeeck, van Bregje K.

    2016-01-01

    The Frisian islands (Southern North Sea) have extensive island tails, i.e. the entire downdrift side of an island consisting of salt marshes, dunes, beaches and beach plains, and green beaches. Currently, large parts of these tails are ageing and losing dynamics, partly due to human influence.

  9. Rhode Island unemployment

    OpenAIRE

    Leonard Lardaro

    2010-01-01

    How can a state like Rhode Island have such a high unemployment rate? This question has been asked often over the past year, especially since at one point, Rhode Island found itself with the dubious distinction of having the highest unemployment rate in the United States. Following that extreme, Rhode Island seemed to settle into a niche where its rank was third nationally.

  10. Geodetic Volcano Monitoring Research in Canary Islands: Recent Results

    Science.gov (United States)

    Fernandez, J.; Gonzalez, P. J.; Arjona, A.; Camacho, A. G.; Prieto, J. F.; Seco, A.; Tizzani, P.; Manzo, M. R.; Lanari, R.; Blanco, P.; Mallorqui, J. J.

    2009-05-01

    The Canarian Archipelago is an oceanic island volcanic chain with a long-standing history of volcanic activity (> 40 Ma). It is located off the NW coast of the African continent, lying over a transitional crust of the Atlantic African passive margin. At least 12 eruptions have been occurred on the islands of Lanzarote, Tenerife and La Palma in the last 500 years. Volcanism manifest predominantly as basaltic strombolian monogenetic activity (whole archipelago) and central felsic volcanism (active only in Tenerife Island). We concentrate our studies in the two most active islands, Tenerife and La Palma. In these islands, we tested different methodologies of geodetic monitoring systems. We use a combination of ground- and space-based techniques. At Tenerife Island, a differential interferometric study was performed to detect areas of deformation. DInSAR detected two clear areas of deformation, using this results a survey-based GPS network was designed and optimized to control those deformations and the rest of the island. Finally, using SBAS DInSAR results weak spatial long- wavelength subsidence signals has been detected. At La Palma, the first DInSAR analysis have not shown any clear deformation, so a first time series analysis was performed detecting a clear subsidence signal at Teneguia volcano, as for Tenerife a GPS network was designed and optimized taking into account stable and deforming areas. After several years of activities, geodetic results served to study ground deformations caused by a wide variety of sources, such as changes in groundwater levels, volcanic activity, volcano-tectonics, gravitational loading, etc. These results proof that a combination of ground-based and space-based techniques is suitable tool for geodetic volcano monitoring in Canary Islands. Finally, we would like to strength that those results could have serious implications on the continuous geodetic monitoring system design and implementation for the Canary Islands which is under

  11. Level of awareness of genetic counselling in Lagos, Nigeria: its ...

    African Journals Online (AJOL)

    Level of awareness of genetic counselling in Lagos, Nigeria: its advocacy on the inheritance of sickle cell disease. ... and the level of awareness about genetic counseling in 30 hospitals were carried out. ... AJOL African Journals Online.

  12. Molecular characterization of genetic diversity in some durum wheat ...

    African Journals Online (AJOL)

    Molecular characterization of genetic diversity in some durum wheat ... African Journal of Biotechnology ... Thus, RAPD offer a potentially simple, rapid and reliable method to evaluate genetic variation and relatedness among ten wheat ...

  13. The effect of selection on genetic parameter estimates

    African Journals Online (AJOL)

    Unknown

    The South African Journal of Animal Science is available online at ... A simulation study was carried out to investigate the effect of selection on the estimation of genetic ... The model contained a fixed effect, random genetic and random.

  14. Obesity and African Americans

    Science.gov (United States)

    ... Data > Minority Population Profiles > Black/African American > Obesity Obesity and African Americans African American women have the ... youthonline . [Accessed 08/18/2017] HEALTH IMPACT OF OBESITY People who are overweight are more likely to ...

  15. African Journals Online: Kenya

    African Journals Online (AJOL)

    Items 1 - 29 of 29 ... African Journal of Food, Agriculture, Nutrition and Development ... African and international non-governmental organizations (NGOs); African and .... for scholars and practitioners in all spheres of biological sciences to publish ...

  16. Retraction | Simon | African Zoology

    African Journals Online (AJOL)

    Panthera leo) ina. West African national park”. African Zoology is publishing an Editorial Expression of Concern regarding the following article: “New records of a threatened lion population (Panthera leo) in a West African national park” by ...

  17. Phylogenomic Analysis Reveals an Asian Origin for African Burkholderia pseudomallei and Further Supports Melioidosis Endemicity in Africa.

    Science.gov (United States)

    Sarovich, Derek S; Garin, Benoit; De Smet, Birgit; Kaestli, Mirjam; Mayo, Mark; Vandamme, Peter; Jacobs, Jan; Lompo, Palpouguini; Tahita, Marc C; Tinto, Halidou; Djaomalaza, Innocente; Currie, Bart J; Price, Erin P

    2016-01-01

    Burkholderia pseudomallei, an environmental bacterium that causes the deadly disease melioidosis, is endemic in northern Australia and Southeast Asia. An increasing number of melioidosis cases are being reported in other tropical regions, including Africa and the Indian Ocean islands. B. pseudomallei first emerged in Australia, with subsequent rare dissemination event(s) to Southeast Asia; however, its dispersal to other regions is not yet well understood. We used large-scale comparative genomics to investigate the origins of three B. pseudomallei isolates from Madagascar and two from Burkina Faso. Phylogenomic reconstruction demonstrates that these African B. pseudomallei isolates group into a single novel clade that resides within the more ancestral Asian clade. Intriguingly, South American strains reside within the African clade, suggesting more recent dissemination from West Africa to the Americas. Anthropogenic factors likely assisted in B. pseudomallei dissemination to Africa, possibly during migration of the Austronesian peoples from Indonesian Borneo to Madagascar ~2,000 years ago, with subsequent genetic diversity driven by mutation and recombination. Our study provides new insights into global patterns of B. pseudomallei dissemination and adds to the growing body of evidence of melioidosis endemicity in Africa. Our findings have important implications for melioidosis diagnosis and management in Africa. IMPORTANCE Sporadic melioidosis cases have been reported in the African mainland and Indian Ocean islands, but until recently, these regions were not considered areas where B. pseudomallei is endemic. Given the high mortality rate of melioidosis, it is crucial that this disease be recognized and suspected in all regions of endemicity. Previous work has shown that B. pseudomallei originated in Australia, with subsequent introduction into Asia; however, the precise origin of B. pseudomallei in other tropical regions remains poorly understood. Using

  18. African Journal of Biotechnology - Vol 12, No 39 (2013)

    African Journals Online (AJOL)

    African Journal of Biotechnology. ... Transgenic Bacillus thuringiensis (Bt) chickpea: India's most wanted genetically modified (GM) pulse crop ... from unpollinated ovary cultures of Ethiopian wheat (Triticum turgidum and Triticum aestivum) ...

  19. African Journal of Biotechnology - Vol 11, No 72 (2012)

    African Journals Online (AJOL)

    African Journal of Biotechnology. ... Microsatellite based investigation of genetic diversity in 24 synthetic wheat cultivars ... The influence of protective properties of packaging materials and application of modified atmosphere on packed dried ...

  20. African Journal of Biotechnology - Vol 9, No 21 (2010)

    African Journals Online (AJOL)

    African Journal of Biotechnology. ... Genotype x Environment interaction for quality traits in durum wheat cultivars adapted to different ... Effects of genetically modified herbicide-tolerant (GMHT) rice on biodiversity of weed in paddy fields ...

  1. A new species of iguana Brachylophus Cuvier 1829 (Sauria: Iguania: Iguanidae) from Gau Island, Fiji Islands

    Science.gov (United States)

    Fisher, Robert N.; Niukula, Jone; Watling, Dick; Harlow, Peter S.

    2017-01-01

    The south Pacific iguanas (Brachylophus) currently have three recognized living species in Fiji.  Recent surveys have uncovered more specific variation (morphological and genetic) within the genus and have better defined the geographic ranges of the named species.  One of these recent discoveries is a strikingly different iguana from all other island populations in Fiji which is restricted to Gau Island of the Lomaiviti Province.  Gau is the fifth largest island in Fiji and maintains excellent upland forests in the higher elevations.  We describe this population from Gau Island as a new species, Brachylophus gau sp. nov., in recognition of its type locality.

  2. Paradise Islands? Island States and Environmental Performance

    Directory of Open Access Journals (Sweden)

    Sverker C. Jagers

    2016-03-01

    Full Text Available Island states have been shown to outperform continental states on a number of large-scale coordination-related outcomes, such as levels of democracy and institutional quality. The argument developed and tested in this article contends that the same kind of logic may apply to islands’ environmental performance, too. However, the empirical analysis shows mixed results. Among the 105 environmental outcomes that we analyzed, being an island only has a positive impact on 20 of them. For example, island states tend to outcompete continental states with respect to several indicators related to water quality but not in aspects related to biodiversity, protected areas, or environmental regulations. In addition, the causal factors previously suggested to make islands outperform continental states in terms of coordination have weak explanatory power in predicting islands’ environmental performance. We conclude the paper by discussing how these interesting findings can be further explored.

  3. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome.

    Science.gov (United States)

    Mathias, Rasika Ann; Taub, Margaret A; Gignoux, Christopher R; Fu, Wenqing; Musharoff, Shaila; O'Connor, Timothy D; Vergara, Candelaria; Torgerson, Dara G; Pino-Yanes, Maria; Shringarpure, Suyash S; Huang, Lili; Rafaels, Nicholas; Boorgula, Meher Preethi; Johnston, Henry Richard; Ortega, Victor E; Levin, Albert M; Song, Wei; Torres, Raul; Padhukasahasram, Badri; Eng, Celeste; Mejia-Mejia, Delmy-Aracely; Ferguson, Trevor; Qin, Zhaohui S; Scott, Alan F; Yazdanbakhsh, Maria; Wilson, James G; Marrugo, Javier; Lange, Leslie A; Kumar, Rajesh; Avila, Pedro C; Williams, L Keoki; Watson, Harold; Ware, Lorraine B; Olopade, Christopher; Olopade, Olufunmilayo; Oliveira, Ricardo; Ober, Carole; Nicolae, Dan L; Meyers, Deborah; Mayorga, Alvaro; Knight-Madden, Jennifer; Hartert, Tina; Hansel, Nadia N; Foreman, Marilyn G; Ford, Jean G; Faruque, Mezbah U; Dunston, Georgia M; Caraballo, Luis; Burchard, Esteban G; Bleecker, Eugene; Araujo, Maria Ilma; Herrera-Paz, Edwin Francisco; Gietzen, Kimberly; Grus, Wendy E; Bamshad, Michael; Bustamante, Carlos D; Kenny, Eimear E; Hernandez, Ryan D; Beaty, Terri H; Ruczinski, Ingo; Akey, Joshua; Barnes, Kathleen C

    2016-10-11

    The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry.

  4. Psychiatric genetics in South Africa: cutting a rough diamond ...

    African Journals Online (AJOL)

    Psychiatric disorders place a considerable healthcare burden on South African society. Incorporating genetic technologies into future treatment plans offers a potential mechanism to reduce this burden. This review focuses on psychiatric genetic research that has been performed in South African populations with regards to ...

  5. ORIGINAL ARTICLES Huntington's disease: Genetic heterogeneity ...

    African Journals Online (AJOL)

    2008-03-01

    Mar 1, 2008 ... African origin.5 HD is considered rare among South African blacks, with an ... functions, syphilis, HIV and other tests in selected patients. We .... The discovery of a second genetic locus, resulting in HDL2,7 suggests the need ...

  6. Palm yellows phytoplasmas and their genetic classification

    African Journals Online (AJOL)

    ntushk

    African Journal of Biotechnology. Review. Palm yellows phytoplasmas and their genetic ... lethal yellowing-type phytoplasma disease was recorded on a number of palm species of mainly ..... Immunodominant membrane protein (imp) Gene.

  7. Evidence of high genetic connectivity for the longnose spurdog Squalus blainville in the Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    V. KOUSTENI

    2015-04-01

    Full Text Available Squalus blainville is one of the least studied Mediterranean shark species. Despite being intensively fished in several locations, biological knowledge is limited and no genetic structure information is available. This is the first study to examine the genetic structure of S. blainville in the Mediterranean Sea. Considering the high dispersal potential inferred for other squalid sharks, the hypothesis of panmixia was tested based on a 585 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I gene from 107 individuals and six nuclear microsatellite loci from 577 individuals. Samples were collected across the Ionian, Aegean and Libyan Seas and off the Balearic Islands. Twenty three additional sequences of Mediterranean and South African origin were retrieved from GenBank and included in the mitochondrial DNA analysis. The overall haplotype diversity was high, in contrast to the low nucleotide diversity. Low and non-significant pairwise ΦST and FST values along with a Bayesian cluster analysis suggested high connectivity with subsequent genetic homogeneity among the populations studied, and thus a high dispersal potential for S. blainville similar to other squalids. The historical demography of the species was also assessed, revealing a pattern of population expansion since the middle Pleistocene. These findings could be considered in species-specific conservation plans, although sampling over a larger spatial scale and more genetic markers are required to fully elucidate the genetic structure and dispersal potential of S. blainville.

  8. South African Antarctic research programme 1978-1982

    CSIR Research Space (South Africa)

    SASCAR

    1978-12-01

    Full Text Available This document provides a comprehensive review of the planned South African scientific activities in Antarctica and on the sub-Antarctic islands in the five year period starting in 1978. The scientific programmes are classified under five headings...

  9. Breeding success of African penguins Spheniscus demersus at ...

    African Journals Online (AJOL)

    The reproductive success of African penguins Spheniscus demersus at Dassen Island from 1994 to 2000 was variable, but much higher than previously reported figures for the species. Breeding success was positively related to the abundance of anchovy Engraulis encrasicolus and sardine Sardinops sagax, and the high ...

  10. Restoration of oiled African penguins Spheniscus demersus a ...

    African Journals Online (AJOL)

    There was a negative relationship between breeding and subsequent survival and breeding, suggesting a cost of reproduction for de-oiled birds. Keywords: African penguin; Apollo Sea; breeding; capture-mark-recapture; Dassen Island; de-oiling; oiling; rehabilitation; restoration; South Africa; Spheniscus demersus

  11. African Solutions to African Problems?

    DEFF Research Database (Denmark)

    Emmanuel, Nikolas G.; Schwartz, Brendan

    2017-01-01

    . The emergence of Déby’s Chad depends both on its ability to accomplish sub-imperial tasks encouraged by these actors, while obfuscating undemocratic governance and human rights abuses at home. Nonetheless, Déby’s role in regional security has helped him achieve a certain degree of agency in his relationship...... and maintain control of the state. These range from “liberal” desires to help control the region’s trouble spots in places like Mali, to clearly illiberal medaling in the domestic affairs of neighbors like the Central African Republic, with the fight against Boko Haram somewhere in the middle. This paper seeks...

  12. Phylogeographic patterns of Hawaiian Megalagrion damselflies (Odonata: Coenagrionidae) correlate with Pleistocene island boundaries

    Science.gov (United States)

    Jordan, Stephen A.; Simon, C.; Foote, D.; Englund, R.A.

    2005-01-01

    The Pleistocene geological history of the Hawaiian Islands is becoming well understood. Numerous predictions about the influence of this history on the genetic diversity of Hawaiian organisms have been made, including the idea that changing sea levels would lead to the genetic differentiation of populations isolated on individual volcanoes during high sea stands. Here, we analyse DNA sequence data from two closely related, endemic Hawaiian damselfly species in order to test these predictions, and generate novel insights into the effects of Pleistocene glaciation and climate change on island organisms. Megalagrion xanthomelas and Megalagrion pacificum are currently restricted to five islands, including three islands of the Maui Nui super-island complex (Molokai, Lanai, and Maui) that were connected during periods of Pleistocene glaciation, and Hawaii island, which has never been subdivided. Maui Nui and Hawaii are effectively a controlled, natural experiment on the genetic effects of Pleistocene sea level change. We confirm well-defined morphological species boundaries using data from the nuclear EF-1?? gene and show that the species are reciprocally monophyletic. We perform phylogeographic analyses of 663 base pairs (bp) of cytochrome oxidase subunit II (COII) gene sequence data from 157 individuals representing 25 populations. Our results point to the importance of Pleistocene land bridges and historical island habitat availability in maintaining inter-island gene flow. We also propose that repeated bottlenecks on Maui Nui caused by sea level change and restricted habitat availability are likely responsible for low genetic diversity there. An island analogue to northern genetic purity and southern diversity is proposed, whereby islands with little suitable habitat exhibit genetic purity while islands with more exhibit genetic diversity. ?? 2005 Blackwell Publishing Ltd.

  13. African Journals Online (AJOL)

    African Journals Online (AJOL)

    African Journals OnLine (AJOL) is the world's largest and pre-eminent collection of peer-reviewed, African-published scholarly journals. Historically, scholarly information has flowed from North to South and from West to East. It has also been difficult for African researchers to access the work of other African academics.

  14. Trends in African philosophy

    African Journals Online (AJOL)

    JONATHAN

    In the contention of Oladipo (2006), the debate on the idea of. African philosophy which has been divided into trends or schools, dates back to the 1960's and 70's, which constitute the modern epoch of African philosophy, when some African thinkers began to question the perspective that traditional African beliefs and.

  15. African Journals Online (AJOL)

    African Journals Online (AJOL)

    It has also been difficult for African researchers to access the work of other African ... search for an article by title, author/s or keywords,; and find other information sources ... Southern African Business Review; The role played by the South African ... The Basis of Distinction Between Qualitative and Quantitative Research in ...

  16. African Journals Online (AJOL)

    African Journals Online (AJOL)

    It has also been difficult for African researchers to access the work of other African academics. In partnership with hundreds of journals from all over the continent, AJOL works to change this, so that African-origin research output is available to Africans and ... Featured Country: South Africa, Featured Journal: Ergonomics SA ...

  17. Mitochondrial genomes suggest rapid evolution of dwarf California Channel Islands foxes (Urocyon littoralis).

    Science.gov (United States)

    Hofman, Courtney A; Rick, Torben C; Hawkins, Melissa T R; Funk, W Chris; Ralls, Katherine; Boser, Christina L; Collins, Paul W; Coonan, Tim; King, Julie L; Morrison, Scott A; Newsome, Seth D; Sillett, T Scott; Fleischer, Robert C; Maldonado, Jesus E

    2015-01-01

    Island endemics are typically differentiated from their mainland progenitors in behavior, morphology, and genetics, often resulting from long-term evolutionary change. To examine mechanisms for the origins of island endemism, we present a phylogeographic analysis of whole mitochondrial genomes from the endangered island fox (Urocyon littoralis), endemic to California's Channel Islands, and mainland gray foxes (U. cinereoargenteus). Previous genetic studies suggested that foxes first appeared on the islands >16,000 years ago, before human arrival (~13,000 cal BP), while archaeological and paleontological data supported a colonization >7000 cal BP. Our results are consistent with initial fox colonization of the northern islands probably by rafting or human introduction ~9200-7100 years ago, followed quickly by human translocation of foxes from the northern to southern Channel Islands. Mitogenomes indicate that island foxes are monophyletic and most closely related to gray foxes from northern California that likely experienced a Holocene climate-induced range shift. Our data document rapid morphological evolution of island foxes (in ~2000 years or less). Despite evidence for bottlenecks, island foxes have generated and maintained multiple mitochondrial haplotypes. This study highlights the intertwined evolutionary history of island foxes and humans, and illustrates a new approach for investigating the evolutionary histories of other island endemics.

  18. Tanzania - Mafia Island Airport

    Data.gov (United States)

    Millennium Challenge Corporation — The evaluation design and subsequent data gathering activities will address the following key research questions: a) Has the Mafia Island Airport Upgrade Project...

  19. The ichthyoplankton assemblage of the Canaries-African Coastal Transition Zone: A review

    Science.gov (United States)

    Rodriguez, J. M.; Moyano, M.; Hernandez-Leon, S.

    2009-12-01

    In this paper we review information on the ichthyoplankton assemblage of the Canaries-African Coastal Transition Zone (C-ACTZ). This CTZ shows the singularity that the Canary Archipelago interrupts the main flow of the Canary Current and Trade Winds, introducing large mesoscale variability, in the form of island warm wakes and cyclonic and anticyclonic eddies downstream of the islands. Besides, upwelling filaments stretch towards the archipelago from the African coastal upwelling, transporting phytoplankton, zooplankton and fish larvae. They also interact with eddies shed from the islands to exchange water properties and biogenic material. All these mesoscale features influence the composition, structure, abundance and distribution of the larval fish community (LFC) of the region. The Canary Current (CC) and eddies shed from the islands drag larvae of island neritic fish species into the oceanic region and contribute, along warm wakes, to the horizontal distribution of fish larvae. Upwelling and upwelling filaments transport larvae of African neritic species into the oceanic region. These larvae dominate the LFC and account for the relatively high average larval fish abundance found in the C-ACTZ during the summer upwelling season. Filaments originated in the region of Cape Juby-Cape Bojador are entrained around a quasi-permanent cyclonic eddy, trapped between Gran Canaria Island and the African coast, forming a system through which most of the African neritic larvae may return to the African shelf. However, some larvae reach the eastern islands of the Canary archipelago and they may be spread all over the neritic region of the archipelago by eddies shed from the islands. Also in summer, the distribution of the LFC of the C-ACTZ is vertically stratified and fish larvae seem to carry out little or not diel vertical migration. Overall, this study highlights the strong relationship between mesoscale oceanographic processes and the LFC in the C-ACTZ.

  20. Genetic Variation and Adaptation in Africa: Implications for Human Evolution and Disease

    Science.gov (United States)

    Gomez, Felicia; Hirbo, Jibril; Tishkoff, Sarah A.

    2014-01-01

    Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent. PMID:24984772

  1. Prostate Cancer Genetics in African Americans

    Science.gov (United States)

    2013-09-01

    tions the ~search is trying to answer, the sWdY is important to .the comn;unity .<Uld. )llC~n State’s Institutional Review Boards ~cailse. men with...for providing a balanced educational experience, the University offers a rigorous academic agenda with a broad range of disciplines, providing... Wii new hospital rehab tool • CU alum. 107. still true blue • Uke http://www.omaha.com/article/20110823/LIVEWELLOinOS239936/1165 Share 8/24

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

    Directory of Open Access Journals (Sweden)

    John E Pool

    Full Text Available 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

  3. Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

    Science.gov (United States)

    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 FST were found to be enriched in genomic regions of locally elevated cosmopolitan

  4. Determining the correct identity of South African Marthasterias ...

    African Journals Online (AJOL)

    Although the allopatric distribution, high genetic divergence (more than 3% for the COI fragment) and morphological differences suggest that the South African form should be raised to species status under the name Marthasterias africana, further work must assess an independent genetic marker (nuclear) to support raising ...

  5. Genetic Evidence for Modifying Oceanic Boundaries Relative to Fiji.

    Science.gov (United States)

    Shipley, Gerhard P; Taylor, Diana A; N'Yeurt, Antoine D R; Tyagi, Anand; Tiwari, Geetanjali; Redd, Alan J

    2016-07-01

    We present the most comprehensive genetic characterization to date of five Fijian island populations: Viti Levu, Vanua Levu, Kadavu, the Lau Islands, and Rotuma, including nonrecombinant Y (NRY) chromosome and mitochondrial DNA (mtDNA) haplotypes and haplogroups. As a whole, Fijians are genetically intermediate between Melanesians and Polynesians, but the individual Fijian island populations exhibit significant genetic structure reflecting different settlement experiences in which the Rotumans and the Lau Islanders were more influenced by Polynesians, and the other Fijian island populations were more influenced by Melanesians. In particular, Rotuman and Lau Islander NRY chromosomal and mtDNA haplogroup frequencies and Rotuman mtDNA hypervariable segment 1 region haplotypes more closely resemble those of Polynesians, while genetic markers of the other populations more closely resemble those of the Near Oceanic Melanesians. Our findings provide genetic evidence supportive of modifying regional boundaries relative to Fiji, as has been suggested by others based on a variety of nongenetic evidence. Specifically, for the traditional Melanesia/Polynesia/Micronesia scheme, our findings support moving the Melanesia-Polynesia boundary to include Rotuma and the Lau Islands in Polynesia. For the newer Near/Remote Oceania scheme, our findings support keeping Rotuma and the Lau Islands in Remote Oceania and locating the other Fijian island populations in an intermediate or "Central Oceania" region to better reflect the great diversity of Oceania.

  6. Heart Disease and African Americans

    Science.gov (United States)

    ... Minority Population Profiles > Black/African American > Heart Disease Heart Disease and African Americans Although African American adults are ... were 30 percent more likely to die from heart disease than non-Hispanic whites. African American women are ...

  7. Systemic lupus erythematosus in an African Caribbean population: incidence, clinical manifestations, and survival in the Barbados National Lupus Registry.

    Science.gov (United States)

    Flower, Cindy; Hennis, Anselm J M; Hambleton, Ian R; Nicholson, George D; Liang, Matthew H

    2012-08-01

    To assess the epidemiology, clinical features, and outcomes of systemic lupus erythematosus (SLE) in the predominantly African Caribbean population of Barbados. A national registry of all patients diagnosed with SLE was established in 2007. Complete case ascertainment was facilitated by collaboration with the island's sole rheumatology service, medical practitioners, and the lupus advocacy group. Informed consent was required for inclusion. Between January 1, 2000 and December 31, 2009, there were 183 new cases of SLE (98% African Caribbean) affecting 172 women and 11 men for unadjusted annual incidence rates of 12.21 (95% confidence interval [95% CI] 10.46-14.18) and 0.84 (95% CI 0.42-1.51) per 100,000 person-years, respectively. Excluding pediatric cases (ages <18 years), the unadjusted incidence rate among women was 15.14 per 100,000 person-years. The principal presenting manifestations were arthritis (84%), nephritis (47%), pleuritis (41.5%), malar rash (36.4%), and discoid lesions (33.1%). Antinuclear antibody positivity was 95%. The overall 5-year survival rate was 79.9% (95% CI 69.6-87.1), decreasing to 68% in patients with nephritis. A total of 226 persons with SLE were alive at the end of the study for point prevalences of 152.6 (95% CI 132.8-174.5) and 10.1 (95% CI 5.4-17.2) per 100,000 among women and men, respectively. Rates of SLE in Barbadian women are among the highest reported to date, with clinical manifestations similar to African American women and high mortality. Further study of this population and similar populations of West African descent might assist our understanding of environmental, genetic, and health care issues underpinning disparities in SLE. Copyright © 2012 by the American College of Rheumatology.

  8. Signatures of selection for environmental adaptation and zebu × taurine hybrid fitness in East African shorthorn zebu

    Science.gov (United States)

    The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ sample...

  9. Vancouver Island gas supply

    International Nuclear Information System (INIS)

    Des Brisay, C.

    2005-01-01

    Terasen Gas is pursuing alternatives for the supply of additional natural gas capacity to Vancouver Island. Its subsidiary, Terasen Gas (Vancouver Island) Inc. (TGVI), is responding to the need for delivery of increased gas supply and, is supporting plans for new gas-fired power generation on Vancouver Island. TGVI's proposal for new natural gas capacity involves a combination of compression and pipeline loops as well as the addition of a storage facility for liquefied natural gas (LNG) at Mt. Hayes to help manage price volatility. This presentation outlined the objectives and components of the resource planning process, including demand forecast scenarios and the preferred infrastructure options. tabs., figs

  10. African Journals Online: Angola

    African Journals Online (AJOL)

    El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Faeroe Islands, Falkland Islands (Malvinas), Fiji, Finland, France, France, MEtropolitan, French Guiana, French Polynesia, French Southern Territories, Gabon, Gambia, The, Georgia, Germany, Ghana, Gibraltar, Greece, Greenland, Grenada, Guam, Guatemala ...

  11. African Journals Online: Netherlands

    African Journals Online (AJOL)

    El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Faeroe Islands, Falkland Islands (Malvinas), Fiji, Finland, France, France, MEtropolitan, French Guiana, French Polynesia, French Southern Territories, Gabon, Gambia, The, Georgia, Germany, Ghana, Gibraltar, Greece, Greenland, Grenada, Guam, Guatemala ...

  12. African Journals Online: Suriname

    African Journals Online (AJOL)

    El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Faeroe Islands, Falkland Islands (Malvinas), Fiji, Finland, France, France, MEtropolitan, French Guiana, French Polynesia, French Southern Territories, Gabon, Gambia, The, Georgia, Germany, Ghana, Gibraltar, Greece, Greenland, Grenada, Guam, Guatemala ...

  13. African Journals Online: Argentina

    African Journals Online (AJOL)

    El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Faeroe Islands, Falkland Islands (Malvinas), Fiji, Finland, France, France, MEtropolitan, French Guiana, French Polynesia, French Southern Territories, Gabon, Gambia, The, Georgia, Germany, Ghana, Gibraltar, Greece, Greenland, Grenada, Guam, Guatemala ...

  14. African Journals Online: Mongolia

    African Journals Online (AJOL)

    ... Faeroe Islands, Falkland Islands (Malvinas), Fiji, Finland, France, France, MEtropolitan, French Guiana, French Polynesia, French Southern Territories, Gabon, Gambia, The, Georgia, Germany, Ghana, Gibraltar, Greece, Greenland, Grenada, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Honduras ...

  15. African ancestry protects against Alzheimer's disease-related neuropathology.

    Science.gov (United States)

    Schlesinger, D; Grinberg, L T; Alba, J G; Naslavsky, M S; Licinio, L; Farfel, J M; Suemoto, C K; de Lucena Ferretti, R E; Leite, R E P; de Andrade, M P; dos Santos, A C F; Brentani, H; Pasqualucci, C A; Nitrini, R; Jacob-Filho, W; Zatz, M

    2013-01-01

    Previous studies in dementia epidemiology have reported higher Alzheimer's disease rates in African-Americans when compared with White Americans. To determine whether genetically determined African ancestry is associated with neuropathological changes commonly associated with dementia, we analyzed a population-based brain bank in the highly admixed city of São Paulo, Brazil. African ancestry was estimated through the use of previously described ancestry-informative markers. Risk of presence of neuritic plaques, neurofibrillary tangles, small vessel disease, brain infarcts and Lewy bodies in subjects with significant African ancestry versus those without was determined. Results were adjusted for multiple environmental risk factors, demographic variables and apolipoprotein E genotype. African ancestry was inversely correlated with neuritic plaques (P=0.03). Subjects with significant African ancestry (n=112, 55.4%) showed lower prevalence of neuritic plaques in the univariate analysis (odds ratio (OR) 0.72, 95% confidence interval (CI) 0.55-0.95, P=0.01) and when adjusted for age, sex, APOE genotype and environmental risk factors (OR 0.43, 95% CI 0.21-0.89, P=0.02). There were no significant differences for the presence of other neuropathological alterations. We show for the first time, using genetically determined ancestry, that African ancestry may be highly protective of Alzheimer's disease neuropathology, functioning through either genetic variants or unknown environmental factors. Epidemiological studies correlating African-American race/ethnicity with increased Alzheimer's disease rates should not be interpreted as surrogates of genetic ancestry or considered to represent African-derived populations from the developing nations such as Brazil.

  16. Immunological change in a parasite-impoverished environment: divergent signals from four island taxa.

    Directory of Open Access Journals (Sweden)

    Jon S Beadell

    2007-09-01

    Full Text Available Dramatic declines of native Hawaiian avifauna due to the human-mediated emergence of avian malaria and pox prompted an examination of whether island taxa share a common altered immunological signature, potentially driven by reduced genetic diversity and reduced exposure to parasites. We tested this hypothesis by characterizing parasite prevalence, genetic diversity and three measures of immune response in two recently-introduced species (Neochmia temporalis and Zosterops lateralis and two island endemics (Acrocephalus aequinoctialis and A. rimitarae and then comparing the results to those observed in closely-related mainland counterparts. The prevalence of blood parasites was significantly lower in 3 of 4 island taxa, due in part to the absence of certain parasite lineages represented in mainland populations. Indices of genetic diversity were unchanged in the island population of N. temporalis; however, allelic richness was significantly lower in the island population of Z. lateralis while both allelic richness and heterozygosity were significantly reduced in the two island-endemic species examined. Although parasite prevalence and genetic diversity generally conformed to expectations for an island system, we did not find evidence for a pattern of uniformly altered immune responses in island taxa, even amongst endemic taxa with the longest residence times. The island population of Z. lateralis exhibited a significantly reduced inflammatory cell-mediated response while levels of natural antibodies remained unchanged for this and the other recently introduced island taxon. In contrast, the island endemic A. rimitarae exhibited a significantly increased inflammatory response as well as higher levels of natural antibodies and complement. These measures were unchanged or lower in A. aequinoctialis. We suggest that small differences in the pathogenic landscape and the stochastic history of mutation and genetic drift are likely to be important in

  17. South African Medical Journal

    African Journals Online (AJOL)

    The South African Medical Journal is published by the South African Medical Association, which represents ... G Watermeyer, S Thomson, 399-402 ... Assessing the value of Western Cape Provincial Government health administrative data and ...

  18. African Crop Science Journal

    African Journals Online (AJOL)

    AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search · USING AJOL ... The African Crop Science Journal, a quarterly publication, publishes original ... interactions, information science, environmental science and soil science.

  19. African Journals Online (AJOL)

    African Journals Online (AJOL)

    Lwati: A Journal of Contemporary Research. Vol 14, No 3 (2017) ... Journal of Business and Administrative Studies. Vol 6, No 2 (2014) ... Vol 11 (2015): African Journal of Educational Studies in Mathematics and Sciences Vol. 11, 2015. African ...

  20. South African Music Studies

    African Journals Online (AJOL)

    SAMUS: South African Music Studies is the official organ for the South African ... Shifty Records in Apartheid South Africa: Innovations in Independent Record ... Experiences of Belonging and Exclusion in the Production and Reception of ...

  1. Liberalism and African Culture.

    Science.gov (United States)

    Sindima, Harvey

    1990-01-01

    Discusses the effect of liberalism on the African understanding of education, community, and religion. Describes ways in which the European intrusion, that is, colonial governments, schools, and churches, undermined traditional African life and thought. (DM)

  2. African Studies Monographs

    African Journals Online (AJOL)

    The African Studies Monographs is a serial that promotes research and scholarship on the African perspective worldwide. This includes matters of philosophy, history, literature, arts and culture, environment, gender, politics, administration crisis management, etc.

  3. Isolation and molecular characterization of Chikungunya virus from the Andaman and Nicobar archipelago, India: evidence of an East, Central, and South African genotype.

    Science.gov (United States)

    Muruganandam, N; Chaaithanya, I K; Senthil, G S; Shriram, A N; Bhattacharya, D; Jeevabharathi, G S; Sudeep, A B; Pradeepkumar, N; Vijayachari, P

    2011-12-01

    Chikungunya virus (CHIKV) is an Alphavirus belonging to the family Togaviridae. In 2006, CHIKV infection struck the Andaman and Nicobar archipelago, with an attack rate of 60%. There were more than 10 cases with acute flaccid paralysis simulating the Guillian Barre Syndrome. The majority of the patients presented severe joint pain. The cause for such an explosive nature of the outbreak with increased morbidity was not known. The isolation of CHIKV was attempted and succeeded from nine subjects presenting clinical symptoms of Chikungunya fever. The cDNA of all the isolates was sequenced for partial E1 and nsP1 genes. Sequences were aligned based on the double locus sequence typing concept. The phylogenetic analysis shows that sequences of Andaman isolates grouped with the East, Central, and South African genotype of virus isolates from India, Sri Lanka, and Réunion. The genetic distance between Andaman isolates and the Réunion isolates was very small. The phylogenetic analysis confirmed the origin of the isolates responsible for the first ever confirmed CHIKV outbreak in these islands to be the East, Central, and South African genotype. In this manuscript, we discuss the involvement of the East, Central, and South African strain with the Chikungunya fever outbreak in this archipelago and double locus sequence typing as a first time approach.

  4. Island formation without attractive interaction

    NARCIS (Netherlands)

    Jansen, A.P.J.

    2008-01-01

    We show that adsorbates on surfaces can form islands even if there are no attractive interactions. Instead, strong repulsion between adsorbates at short distances can lead to islands, because such islands increase the entropy of the adsorbates that are not part of the islands. We suggest that this

  5. Continental Island Formation and the Archaeology of Defaunation on Zanzibar, Eastern Africa.

    Directory of Open Access Journals (Sweden)

    Mary E Prendergast

    Full Text Available With rising sea levels at the end of the Pleistocene, land-bridge or continental islands were formed around the world. Many of these islands have been extensively studied from a biogeographical perspective, particularly in terms of impacts of island creation on terrestrial vertebrates. However, a majority of studies rely on contemporary faunal distributions rather than fossil data. Here, we present archaeological findings from the island of Zanzibar (also known as Unguja off the eastern African coast, to provide a temporal perspective on island biogeography. The site of Kuumbi Cave, excavated by multiple teams since 2005, has revealed the longest cultural and faunal record for any eastern African island. This record extends to the Late Pleistocene, when Zanzibar was part of the mainland, and attests to the extirpation of large mainland mammals in the millennia after the island became separated. We draw on modeling and sedimentary data to examine the process by which Zanzibar was most recently separated from the mainland, providing the first systematic insights into the nature and chronology of this process. We subsequently investigate the cultural and faunal record from Kuumbi Cave, which provides at least five key temporal windows into human activities and faunal presence: two at the end of the Last Glacial Maximum (LGM, one during the period of post-LGM rapid sea level rise and island formation, and two in the late Holocene (Middle Iron Age and Late Iron Age. This record demonstrates the presence of large mammals during the period of island formation, and their severe reduction or disappearance in the Kuumbi Cave sequence by the late Holocene. While various limitations, including discontinuity in the sequence, problematize attempts to clearly attribute defaunation to anthropogenic or island biogeographic processes, Kuumbi Cave offers an unprecedented opportunity to examine post-Pleistocene island formation and its long-term consequences for

  6. Continental Island Formation and the Archaeology of Defaunation on Zanzibar, Eastern Africa

    Science.gov (United States)

    Prendergast, Mary E.; Rouby, Hélène; Punnwong, Paramita; Marchant, Robert; Crowther, Alison; Kourampas, Nikos; Shipton, Ceri; Walsh, Martin; Lambeck, Kurt; Boivin, Nicole L.

    2016-01-01

    With rising sea levels at the end of the Pleistocene, land-bridge or continental islands were formed around the world. Many of these islands have been extensively studied from a biogeographical perspective, particularly in terms of impacts of island creation on terrestrial vertebrates. However, a majority of studies rely on contemporary faunal distributions rather than fossil data. Here, we present archaeological findings from the island of Zanzibar (also known as Unguja) off the eastern African coast, to provide a temporal perspective on island biogeography. The site of Kuumbi Cave, excavated by multiple teams since 2005, has revealed the longest cultural and faunal record for any eastern African island. This record extends to the Late Pleistocene, when Zanzibar was part of the mainland, and attests to the extirpation of large mainland mammals in the millennia after the island became separated. We draw on modeling and sedimentary data to examine the process by which Zanzibar was most recently separated from the mainland, providing the first systematic insights into the nature and chronology of this process. We subsequently investigate the cultural and faunal record from Kuumbi Cave, which provides at least five key temporal windows into human activities and faunal presence: two at the end of the Last Glacial Maximum (LGM), one during the period of post-LGM rapid sea level rise and island formation, and two in the late Holocene (Middle Iron Age and Late Iron Age). This record demonstrates the presence of large mammals during the period of island formation, and their severe reduction or disappearance in the Kuumbi Cave sequence by the late Holocene. While various limitations, including discontinuity in the sequence, problematize attempts to clearly attribute defaunation to anthropogenic or island biogeographic processes, Kuumbi Cave offers an unprecedented opportunity to examine post-Pleistocene island formation and its long-term consequences for human and animal

  7. Continental Island Formation and the Archaeology of Defaunation on Zanzibar, Eastern Africa.

    Science.gov (United States)

    Prendergast, Mary E; Rouby, Hélène; Punnwong, Paramita; Marchant, Robert; Crowther, Alison; Kourampas, Nikos; Shipton, Ceri; Walsh, Martin; Lambeck, Kurt; Boivin, Nicole L

    2016-01-01

    With rising sea levels at the end of the Pleistocene, land-bridge or continental islands were formed around the world. Many of these islands have been extensively studied from a biogeographical perspective, particularly in terms of impacts of island creation on terrestrial vertebrates. However, a majority of studies rely on contemporary faunal distributions rather than fossil data. Here, we present archaeological findings from the island of Zanzibar (also known as Unguja) off the eastern African coast, to provide a temporal perspective on island biogeography. The site of Kuumbi Cave, excavated by multiple teams since 2005, has revealed the longest cultural and faunal record for any eastern African island. This record extends to the Late Pleistocene, when Zanzibar was part of the mainland, and attests to the extirpation of large mainland mammals in the millennia after the island became separated. We draw on modeling and sedimentary data to examine the process by which Zanzibar was most recently separated from the mainland, providing the first systematic insights into the nature and chronology of this process. We subsequently investigate the cultural and faunal record from Kuumbi Cave, which provides at least five key temporal windows into human activities and faunal presence: two at the end of the Last Glacial Maximum (LGM), one during the period of post-LGM rapid sea level rise and island formation, and two in the late Holocene (Middle Iron Age and Late Iron Age). This record demonstrates the presence of large mammals during the period of island formation, and their severe reduction or disappearance in the Kuumbi Cave sequence by the late Holocene. While various limitations, including discontinuity in the sequence, problematize attempts to clearly attribute defaunation to anthropogenic or island biogeographic processes, Kuumbi Cave offers an unprecedented opportunity to examine post-Pleistocene island formation and its long-term consequences for human and animal

  8. African Anthropologist: Submissions

    African Journals Online (AJOL)

    Author Guidelines. The African Anthropologist is a biannual journal of the Pan African Anthropological Association. It provides a forum for African and Africanist anthropologists to publish articles, research reports, review articles, and book reviews. The views expressed in any published material are those of the authors and ...

  9. African Journals Online (AJOL)

    African Journals Online (AJOL)

    African Journals OnLine (AJOL) is the world's largest and pre-eminent collection of peer-reviewed, African-published scholarly journals. Historically ... African Research Review; The Roles of Information Communication Technologies in Education: Review Article with Emphasis to the Computer and Internet Ethiopian Journal ...

  10. African Journals Online (AJOL)

    African Journals Online (AJOL)

    reviewed, African-published scholarly journals. Historically, scholarly information has flowed from North to South and from West to East. It has also been difficult for African researchers to access the work of other African academics. In partnership with ...

  11. African Journals Online (AJOL)

    African Journals Online (AJOL)

    It has also been difficult for African researchers to access the work of other African academics. ... search for an article by title, author/s or keywords,; and find other information ... Southern African Business Review; Project Work by Students for First ... The Basis of Distinction Between Qualitative and Quantitative Research in ...

  12. African Journals Online (AJOL)

    African Journals Online (AJOL)

    It has also been difficult for African researchers to access the work of other African ... search for an article by title, author/s or keywords,; and find other information ... Southern African Business Review; Effect of Globalization on Sovereignty of States ... The Basis of Distinction Between Qualitative and Quantitative Research in ...

  13. African Journals Online (AJOL)

    African Journals Online (AJOL)

    It has also been difficult for African researchers to access the work of other African ... search for an article by title, author/s or keywords,; and find other information sources ... Southern African Business Review; Conflicts in Africa: Meaning, Causes, ... The Basis of Distinction Between Qualitative and Quantitative Research in ...

  14. African Journals Online: Health

    African Journals Online (AJOL)

    Items 1 - 50 of 167 ... African Journal of AIDS Research (AJAR) is a peer-reviewed ... The African Journal of Drug & Alcohol Studies is an international ... The Journal has been produced through the efforts of Kenya Medical Research Institute (KEMRI) and the African .... in basic and clinical medical sciences as well as dentistry.

  15. African Journals Online (AJOL)

    African Journals Online (AJOL)

    South African Journal for Research in Sport, Physical Education and Recreation. Vol 17, No 4 (2017). African Health Sciences. Vol 6, No 1 (2015). Nigeria Journal of Pure and Applied Physics. Vol 5, No 2 (2017). Journal of Student Affairs in Africa. Vol 14, No 1 (2017). Annals of African Surgery. Vol 63, No 7-9 (2018).

  16. African Journals Online (AJOL)

    African Journals Online (AJOL)

    reviewed, African-published scholarly journals. Historically ... It has also been difficult for African researchers to access the work of other African academics. In partnership with ... Vol 15, No 1 (2018). SAHARA-J: Journal of Social Aspects of HIV/AIDS.

  17. African Journals Online (AJOL)

    African Journals Online (AJOL)

    West African Journal of Applied Ecology. Vol 6, No 2 (2017). Filosofia Theoretica: Journal of African Philosophy, Culture and Religions. AJOL African Journals Online. HOW TO USE AJOL... for Researchers · for Librarians · for Authors · FAQ's · More about AJOL · AJOL's Partners · Terms and Conditions of Use · Contact AJOL ...

  18. African Journals Online (AJOL)

    African Journals Online (AJOL)

    In partnership with hundreds of journals from all over the continent, AJOL works to change this, so that African-origin research output is available to Africans and to ... African Journal of AIDS Research. Vol 35, No 2 (2017). Zimbabwe Veterinary Journal. Vol 34, No 1 (2018). Eastern Africa Social Science Research Review.

  19. Coalescence of magnetic islands

    International Nuclear Information System (INIS)

    Pellat, R.

    1982-01-01

    The paper gives the analytical theory of the coalescence instability and of a new, one island, instability. These instabilities are expected to be relevant for the disruptions observed in Tokamak experiments and astrophysical plasmas

  20. Heat Island Compendium

    Science.gov (United States)

    Heat islands can be mitigated through measures like planting trees and vegetation, installing green roofs and cool roofs, and using cool pavements. The compendium describes all of these strategies and shows how communities around the country are being used