WorldWideScience

Sample records for genetic origin admixture

  1. Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba

    Science.gov (United States)

    2008-01-01

    Background Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. Results The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. Conclusion While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times. PMID:18644108

  2. Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba

    Directory of Open Access Journals (Sweden)

    Martínez-Fuentes Antonio

    2008-07-01

    Full Text Available Abstract Background Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I and five single nucleotide polymorphisms (SNPs in the mitochondrial DNA (mtDNA coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. Results The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. Conclusion While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.

  3. Nonrandom patterns of genetic admixture expose the complex historical hybrid origin of unisexual leaf beetle species in the genus Calligrapha.

    Science.gov (United States)

    Montelongo, Tinguaro; Gómez-Zurita, Jesús

    2015-01-01

    Many unisexual animal lineages supposedly arose from hybridization. However, support for their putative hybrid origins mostly comes from indirect methodologies, which are rarely confirmatory. Here we provide compelling data indicating that tetraploid unisexual Calligrapha are true genetic mosaics obtained via analysis of mitochondrial DNA (mtDNA) and allelic variation and coalescence times for three single-copy nuclear genes (CPS, HARS, and Wg) in five of six unisexual Calligrapha and a representative sample of bisexual species. Nuclear allelic diversity in unisexuals consistently segregates in the gene pools of at least two but up to three divergent bisexual species, interpreted as putative parentals of interspecific hybridization crosses. Interestingly, their mtDNA diversity derives from an additional yet undiscovered older evolutionary lineage that is possibly the same for all independently originated unisexual species. One possibly extinct species transferred its mtDNA to several evolutionary lineages in a wave of hybridization events during the Pliocene, whereby descendant species retained a polymorphic mtDNA constitution. Recent hybridizations, in the Pleistocene and always involving females with the old introgressed mtDNA, seemingly occurred in the lineages leading to unisexual species, decoupling mtDNA introgression (and inferences derived from these data, such as timing and parentage) from subsequent acquisition of the new reproductive mode. These results illuminate an unexpected complexity in possible routes to animal unisexuality, with implications for the interpretation of ancient unisexuality. If the origin of unisexuality requires a mechanism where (1) hybridization is a necessary but insufficient condition and (2) multiple bouts of hybridization involving more than two divergent lineages are required, then the origins of several classical unisexual systems may have to be reassessed.

  4. Admixture in Mexico City: implications for admixture mapping of type 2 diabetes genetic risk factors.

    Science.gov (United States)

    Martinez-Marignac, Veronica L; Valladares, Adan; Cameron, Emily; Chan, Andrea; Perera, Arjuna; Globus-Goldberg, Rachel; Wacher, Niels; Kumate, Jesús; McKeigue, Paul; O'Donnell, David; Shriver, Mark D; Cruz, Miguel; Parra, Esteban J

    2007-02-01

    Admixture mapping is a recently developed method for identifying genetic risk factors involved in complex traits or diseases showing prevalence differences between major continental groups. Type 2 diabetes (T2D) is at least twice as prevalent in Native American populations as in populations of European ancestry, so admixture mapping is well suited to study the genetic basis of this complex disease. We have characterized the admixture proportions in a sample of 286 unrelated T2D patients and 275 controls from Mexico City and we discuss the implications of the results for admixture mapping studies. Admixture proportions were estimated using 69 autosomal ancestry-informative markers (AIMs). Maternal and paternal contributions were estimated from geographically informative mtDNA and Y-specific polymorphisms. The average proportions of Native American, European and, West African admixture were estimated as 65, 30, and 5%, respectively. The contributions of Native American ancestors to maternal and paternal lineages were estimated as 90 and 40%, respectively. In a logistic model with higher educational status as dependent variable, the odds ratio for higher educational status associated with an increase from 0 to 1 in European admixture proportions was 9.4 (95%, credible interval 3.8-22.6). This association of socioeconomic status with individual admixture proportion shows that genetic stratification in this population is paralleled, and possibly maintained, by socioeconomic stratification. The effective number of generations back to unadmixed ancestors was 6.7 (95% CI 5.7-8.0), from which we can estimate that genome-wide admixture mapping will require typing about 1,400 evenly distributed AIMs to localize genes underlying disease risk between populations of European and Native American ancestry. Sample sizes of about 2,000 cases will be required to detect any locus that contributes an ancestry risk ratio of at least 1.5.

  5. The Complex Admixture History and Recent Southern Origins of Siberian Populations.

    Science.gov (United States)

    Pugach, Irina; Matveev, Rostislav; Spitsyn, Viktor; Makarov, Sergey; Novgorodov, Innokentiy; Osakovsky, Vladimir; Stoneking, Mark; Pakendorf, Brigitte

    2016-07-01

    Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether it remained habitable during the extreme cold of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, because commonly used methods assume a tree-like population history and at most single admixture events. Here we analyze geogenetic maps and use other approaches to distinguish the effects of shared ancestry from prehistoric migrations and contact, and develop a new method based on the covariance of ancestry components, to investigate the potentially complex admixture history. We furthermore adapt a previously devised method of admixture dating for use with multiple events of gene flow, and apply these methods to whole-genome genotype data from over 500 individuals belonging to 20 different Siberian ethnolinguistic groups. The results of these analyses indicate that there have been multiple layers of admixture detectable in most of the Siberian populations, with considerable differences in the admixture histories of individual populations. Furthermore, most of the populations of Siberia included here, even those settled far to the north, appear to have a southern origin, with the northward expansions of different populations possibly being driven partly by the advent of pastoralism, especially reindeer domestication. These newly developed methods to analyze multiple admixture events should aid in the investigation of similarly complex population histories elsewhere.

  6. Heterogeneity in Genetic Admixture across Different Regions of Argentina

    Science.gov (United States)

    Avena, Sergio; Via, Marc; Ziv, Elad; Pérez-Stable, Eliseo J.; Gignoux, Christopher R.; Dejean, Cristina; Huntsman, Scott; Torres-Mejía, Gabriela; Dutil, Julie; Matta, Jaime L.; Beckman, Kenneth; Burchard, Esteban González; Parolin, María Laura; Goicoechea, Alicia; Acreche, Noemí; Boquet, Mariel; Ríos Part, María Del Carmen; Fernández, Vanesa; Rey, Jorge; Stern, Mariana C.; Carnese, Raúl F.; Fejerman, Laura

    2012-01-01

    The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs) was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63–68%), 31% Indigenous American (28–33%) and 4% African (3–4%). We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA) 76%, 95%CI: 73–79%; Northeast (NEA) 54%, 95%CI: 49–58%; Northwest (NWA) 33%, 95%CI: 21–41%; South 54%, 95%CI: 49–59%; p<0.0001] as well as between the capital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75–86%) versus 68% (95%CI: 58–77%), p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88–94%) compared to 54% (95%CI: 51–57%) among those with no European grandparents (p<0.001). Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population. PMID:22506044

  7. Learning with Admixture: Modeling, Optimization, and Applications in Population Genetics

    DEFF Research Database (Denmark)

    Cheng, Jade Yu

    2016-01-01

    Population genetics is a branch of applied mathematics. It is a translation of scientific observations into mathematical models and their manipulations in order to produce quantitative predictions about evolution. Combining knowledge from genetics, statistics, and computer science, population...... data. Ohana's admixture module is based on classical structure modeling but uses new optimization subroutines through quadratic programming, which outperform the current state-of-the-art software in both speed and accuracy. Ohana presents a new method for phylogenetic tree inference using Gaussian...... the foundation for both CoalHMM and Ohana. Optimization modeling has been the main theme throughout my PhD, and it will continue to shape my work for the years to come. The algorithms and software I developed to study historical admixture and population evolution fall into a larger family of machine learning...

  8. Sex-specific genetic admixture of Mestizos, Amerindian Kichwas, and Afro-Ecuadorans from Ecuador.

    Science.gov (United States)

    González-Andrade, Fabricio; Sánchez, Dora; González-Solórzano, Jorge; Gascón, Santiago; Martínez-Jarreta, Begoña

    2007-02-01

    Three main ethnic groups live in the South American country of Ecuador: Mestizos, Amerindian natives, and African-derived populations, or Afro-Ecuadorans. Mestizos and Afro-Ecuadorans can be considered trihybrid populations containing genes originating in the Americas, Europe, and Africa, as is the case with equivalent populations in other Latin American countries. The proportion and the dynamics of the admixture process remain unknown. However, a certain sex asymmetry of the admixture process can be expected for historical reasons. We typed 11 Y-chromosome short tandem repeats (STRs) in these three ethnic groups to provide adequate allele and haplotype frequencies for forensic genetic purposes and to quantify admixture proportions in male lineages. In addition, a data set of 15 autosomal STRs in the same samples were reanalyzed for the same purpose. Contributions to Mestizo Y chromosomes were estimated to be 70% European, 28% Amerindian, and 2% African, whereas in autosomes the contributions were 19%, 73%, and 8%, respectively, which underlines the sexual asymmetry in mating, with Europeans contributing mostly males. European Y-chromosome haplotypes in Mestizos were similar to those in Spain. Moreover, about 10% of European Y chromosomes were found in the Amerindian Kichwa. As for Afro-Ecuadorans, their contributions to the male line are 44% African, 31% European, and 15% Native American; the last value is the highest percentage reported so far for an African-derived American group. Autosomal admixture was estimated as 56% African, 16% European, and 28% Amerindian.

  9. Origins, admixture and founder lineages in European Roma

    NARCIS (Netherlands)

    Martinez-Cruz, B.; Mendizabal, I.; Harmant, C.; Pablo, R. de; Ioana, M.; Angelicheva, D.; Kouvatsi, A.; Makukh, H.; Netea, M.G.; Pamjav, H.; Zalan, A.; Tournev, I.; Marushiakova, E.; Popov, V.; Bertranpetit, J.; Kalaydjieva, L.; Quintana-Murci, L.; Comas, D.

    2016-01-01

    The Roma, also known as 'Gypsies', represent the largest and the most widespread ethnic minority of Europe. There is increasing evidence, based on linguistic, anthropological and genetic data, to suggest that they originated from the Indian subcontinent, with subsequent bottlenecks and undetermined

  10. How important is intraspecific genetic admixture to the success of colonising populations?

    Science.gov (United States)

    Genetic admixture of divergent lineages is increasingly suspected to play an important role in the success of colonizing populations. This has become a particularly prominent theme in the literature on biological invasions, where admixture is now commonly proposed as an important...

  11. Origins, admixture and founder lineages in European Roma.

    Science.gov (United States)

    Martínez-Cruz, Begoña; Mendizabal, Isabel; Harmant, Christine; de Pablo, Rosario; Ioana, Mihai; Angelicheva, Dora; Kouvatsi, Anastasia; Makukh, Halyna; Netea, Mihai G; Pamjav, Horolma; Zalán, Andrea; Tournev, Ivailo; Marushiakova, Elena; Popov, Vesselin; Bertranpetit, Jaume; Kalaydjieva, Luba; Quintana-Murci, Lluis; Comas, David

    2016-06-01

    The Roma, also known as 'Gypsies', represent the largest and the most widespread ethnic minority of Europe. There is increasing evidence, based on linguistic, anthropological and genetic data, to suggest that they originated from the Indian subcontinent, with subsequent bottlenecks and undetermined gene flow from/to hosting populations during their diaspora. Further support comes from the presence of Indian uniparentally inherited lineages, such as mitochondrial DNA M and Y-chromosome H haplogroups, in a significant number of Roma individuals. However, the limited resolution of most genetic studies so far, together with the restriction of the samples used, have prevented the detection of other non-Indian founder lineages that might have been present in the proto-Roma population. We performed a high-resolution study of the uniparental genomes of 753 Roma and 984 non-Roma hosting European individuals. Roma groups show lower genetic diversity and high heterogeneity compared with non-Roma samples as a result of lower effective population size and extensive drift, consistent with a series of bottlenecks during their diaspora. We found a set of founder lineages, present in the Roma and virtually absent in the non-Roma, for the maternal (H7, J1b3, J1c1, M18, M35b, M5a1, U3, and X2d) and paternal (I-P259, J-M92, and J-M67) genomes. This lineage classification allows us to identify extensive gene flow from non-Roma to Roma groups, whereas the opposite pattern, although not negligible, is substantially lower (up to 6.3%). Finally, the exact haplotype matching analysis of both uniparental lineages consistently points to a Northwestern origin of the proto-Roma population within the Indian subcontinent.

  12. Genetic structure and admixture between Bayash Roma from northwestern Croatia and general Croatian population: evidence from Bayesian clustering analysis.

    Science.gov (United States)

    Novokmet, Natalija; Galov, Ana; Marjanović, Damir; Škaro, Vedrana; Projić, Petar; Lauc, Gordan; Primorac, Dragan; Rudan, Pavao

    2015-01-01

    The European Roma represent a transnational mosaic of minority population groups with different migration histories and contrasting experiences in their interactions with majority populations across the European continent. Although historical genetic contributions of European lineages to the Roma pool were investigated before, the extent of contemporary genetic admixture between Bayash Roma and non-Romani majority population remains elusive. The aim of this study was to assess the genetic structure of the Bayash Roma population from northwestern Croatia and the general Croatian population and to investigate the extent of admixture between them. A set of genetic data from two original studies (100 Bayash Roma from northwestern Croatia and 195 individuals from the general Croatian population) was analyzed by Bayesian clustering implemented in STRUCTURE software. By re-analyzing published data we intended to focus for the first time on genetic differentiation and structure and in doing so we clearly pointed to the importance of considering social phenomena in understanding genetic structuring. Our results demonstrated that two population clusters best explain the genetic structure, which is consistent with social exclusion of Roma and the demographic history of Bayash Roma who have settled in NW Croatia only about 150 years ago and mostly applied rules of endogamy. The presence of admixture was revealed, while the percentage of non-Croatian individuals in general Croatian population was approximately twofold higher than the percentage of non-Romani individuals in Roma population corroborating the presence of ethnomimicry in Roma.

  13. Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES

    Directory of Open Access Journals (Sweden)

    Le Marchand Loic

    2009-11-01

    Full Text Available Abstract Background Population structure and admixture have strong confounding effects on genetic association studies. Discordant frequencies for age-related macular degeneration (AMD risk alleles and for AMD incidence and prevalence rates are reported across different ethnic groups. We examined the genomic ancestry characterizing 538 Latinos drawn from the Los Angeles Latino Eye Study [LALES] as part of an ongoing AMD-association study. To help assess the degree of Native American ancestry inherited by Latino populations we sampled 25 Mayans and 5 Mexican Indians collected through Coriell's Institute. Levels of European, Asian, and African descent in Latinos were inferred through the USC Multiethnic Panel (USC MEP, formed from a sample from the Multiethnic Cohort (MEC study, the Yoruba African samples from HapMap II, the Singapore Chinese Health Study, and a prospective cohort from Shanghai, China. A total of 233 ancestry informative markers were genotyped for 538 LALES Latinos, 30 Native Americans, and 355 USC MEP individuals (African Americans, Japanese, Chinese, European Americans, Latinos, and Native Hawaiians. Sensitivity of ancestry estimates to relative sample size was considered. Results We detected strong evidence for recent population admixture in LALES Latinos. Gradients of increasing Native American background and of correspondingly decreasing European ancestry were observed as a function of birth origin from North to South. The strongest excess of homozygosity, a reflection of recent population admixture, was observed in non-US born Latinos that recently populated the US. A set of 42 SNPs especially informative for distinguishing between Native Americans and Europeans were identified. Conclusion These findings reflect the historic migration patterns of Native Americans and suggest that while the 'Latino' label is used to categorize the entire population, there exists a strong degree of heterogeneity within that population, and that

  14. Tracing the origin of the east-west population admixture in the Altai region (Central Asia.

    Directory of Open Access Journals (Sweden)

    Mercedes González-Ruiz

    Full Text Available A recent discovery of Iron Age burials (Pazyryk culture in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1 whether it was a result of migratory events (eastward firstly, westward secondly, or 2 whether it was a result of a local demographic expansion in a 'contact zone' between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan. Thus, this people not only shared the same culture (Pazyryk, but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.

  15. The influence of admixture and consanguinity on population genetic diversity in Middle East.

    Science.gov (United States)

    Yang, Xiong; Al-Bustan, Suzanne; Feng, Qidi; Guo, Wei; Ma, Zhiming; Marafie, Makia; Jacob, Sindhu; Al-Mulla, Fahd; Xu, Shuhua

    2014-11-01

    The Middle East (ME) is an important crossroad where modern humans migrated 'out of Africa' and spread into Europe and Asia. After the initial peopling and long-term isolation leading to well-differentiated populations, the ME also had a crucial role in subsequent human migrations among Africa, Europe and Asia; thus, recent population admixture has been common in the ME. On the other hand, consanguinity, a well-known practice in the ME, often reduces genetic diversity and works in opposition to admixture. Here, we explored the degree to which admixture and consanguinity jointly affected genetic diversity in ME populations. Genome-wide single-nucleotide polymorphism data were generated in two representative ME populations (Arabian and Iranian), with comparisons made with populations worldwide. Our results revealed an overall higher genetic diversity in both ME populations relative to other non-African populations. We identified a much larger number of long runs of homozygosity in ME populations than in any other populations, which was most likely attributed to high levels of consanguineous marriages that significantly decreased both individual and population heterozygosity. Additionally, we were able to distinguish African, European and Asian ancestries in ME populations and quantify the impact of admixture and consanguinity with statistical approaches. Interestingly, genomic regions with significantly excessive ancestry from individual source populations are functionally enriched in olfactory pathways, which were suspected to be under natural selection. Our findings suggest that genetic admixture, consanguinity and natural selection have collectively shaped the genetic diversity of ME populations, which has important implications in both evolutionary studies and medical practices.

  16. Genetics, surnames, grandparents' nationalities, and ethnic admixture in Southern Brazil: Do the patterns of variation coincide?

    Directory of Open Access Journals (Sweden)

    C.L. Dornelles

    1999-06-01

    Full Text Available A total of 2,708 individuals from the European-derived population of Rio Grande do Sul, divided into seven mesoregions, and of 226 individuals of similar origin from Santa Catarina were studied. Seventeen protein genetic systems, as well as grandparents' nationalities, individuals' surnames, and interethnic admixture were investigated. The alleles which presented the highest and lowest differences were GLO1*2 (16% and PGD*A (2%, respectively, but in general no significant genetic differences were found among mesoregions. The values observed were generally those expected for individuals of European descent, with the largest difference being a lower prevalence (34-39% of P*1. Significant heterogeneity among mesoregions was observed for the other variables considered, and was consistent with historical records. The Amerindian contribution to the gene pool of European-derived subjects in Rio Grande do Sul was estimated to be as high as 11%. Based on the four data sets, the most general finding was a tendency for a northeast-southwest separation of the populations studied. Seven significant phenotype associations between systems were observed at the 5% level (three at the 0.1% level. Of the latter, the two most interesting (since they were also observed in other studies were MNSs/Duffy and Rh/ACP.

  17. Genetics, surnames, grandparents' nationalities, and ethnic admixture in Southern Brazil: Do the patterns of variation coincide?

    Directory of Open Access Journals (Sweden)

    Dornelles C.L.

    1999-01-01

    Full Text Available A total of 2,708 individuals from the European-derived population of Rio Grande do Sul, divided into seven mesoregions, and of 226 individuals of similar origin from Santa Catarina were studied. Seventeen protein genetic systems, as well as grandparents' nationalities, individuals' surnames, and interethnic admixture were investigated. The alleles which presented the highest and lowest differences were GLO1*2 (16% and PGD*A (2%, respectively, but in general no significant genetic differences were found among mesoregions. The values observed were generally those expected for individuals of European descent, with the largest difference being a lower prevalence (34-39% of P*1. Significant heterogeneity among mesoregions was observed for the other variables considered, and was consistent with historical records. The Amerindian contribution to the gene pool of European-derived subjects in Rio Grande do Sul was estimated to be as high as 11%. Based on the four data sets, the most general finding was a tendency for a northeast-southwest separation of the populations studied. Seven significant phenotype associations between systems were observed at the 5% level (three at the 0.1% level. Of the latter, the two most interesting (since they were also observed in other studies were MNSs/Duffy and Rh/ACP.

  18. Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed.

    Science.gov (United States)

    Berthouly-Salazar, Cécile; Thévenon, Sophie; Van, Thu Nhu; Nguyen, Binh Trong; Pham, Lan Doan; Chi, Cuong Vu; Maillard, Jean-Charles

    2012-05-01

    The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H'mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H'mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5-6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.

  19. Genetic admixture and risk of hypertensive disorders of pregnancy among Latinas in Los Angeles County.

    Science.gov (United States)

    Shahabi, Ahva; Wilson, Melissa L; Lewinger, Juan Pablo; Goodwin, T Murphy; Stern, Mariana C; Ingles, Sue A

    2013-03-01

    Latinos are a heterogeneous population in terms of demographics, culture, and genetic admixture from three racial groups (white, African, and Native American). This study examines the role of genetic ancestry and environmental risk factors in the risk of hypertensive disorder of pregnancy among Latinas in Los Angeles County. Gestational hypertension, preeclampsia, eclampsia, or hemolysis, elevated liver enzymes, and low platelets (HELLP) syndrome cases (n = 125), plus unaffected controls (n = 161), were recruited from Los Angeles County + University of Southern California Women's and Children's Hospital from 1999 through 2008. Diagnoses were confirmed with extensive chart review. Personal information, demographics, and biospecimens were collected from all participants. Ancestry informative markers were used to estimate genetic ancestry proportions. After adjusting for European ancestry and key risk factors, African ancestry was positively associated with hypertensive disorders of pregnancy risk for the highest vs. the lowest quartiles of African ancestry (odds ratio = 2.6 [95% confidence interval = 1.1-6.1]). This association was stronger among women born in Mexico with parents born in Mexico (4.3 [1.4-13]). The results from generalized additive models showed a positive association between joint European/African ancestry and hypertensive disorders of pregnancy risk and an inverse association between Native American ancestry and risk. These associations were stronger among women of Mexican origin. Our findings suggest that higher Native American ancestry among Latinas may protect against hypertensive disorders of pregnancy. Further studies are needed to determine whether this protective effect is driven by specific alleles present in this population or by other risk factors that correlate with Native American ancestry.

  20. Analysis of admixture and genetic structure of two Native American groups of Southern Argentinean Patagonia.

    Science.gov (United States)

    Sala, Andrea; Corach, Daniel

    2014-03-01

    Argentinean Patagonia is inhabited by people that live principally in urban areas and by small isolated groups of individuals that belong to indigenous aboriginal groups; this territory exhibits the lowest population density of the country. Mapuche and Tehuelche (Mapudungun linguistic branch), are the only extant Native American groups that inhabit the Argentinean Patagonian provinces of Río Negro and Chubut. Fifteen autosomal STRs, 17 Y-STRs, mtDNA full length control region sequence and two sets of Y and mtDNA-coding region SNPs were analyzed in a set of 434 unrelated individuals. The sample set included two aboriginal groups, a group of individuals whose family name included Native American linguistic root and urban samples from Chubut, Río Negro and Buenos Aires provinces of Argentina. Specific Y Amerindian haplogroup Q1 was found in 87.5% in Mapuche and 58.82% in Tehuelche, while the Amerindian mtDNA haplogroups were present in all the aboriginal sample contributors investigated. Admixture analysis performed by means of autosomal and Y-STRs showed the highest degree of admixture in individuals carrying Mapuche surnames, followed by urban populations, and finally by isolated Native American populations as less degree of admixture. The study provided novel genetic information about the Mapuche and Tehuelche people and allowed us to establish a genetic correlation among individuals with Mapudungun surnames that demonstrates not only a linguistic but also a genetic relationship to the isolated aboriginal communities, representing a suitable proxy indicator for assessing genealogical background.

  1. Cultivar origin and admixture detection in Turkish olive oils by SNP-based CAPS assays.

    Science.gov (United States)

    Uncu, Ali Tevfik; Frary, Anne; Doganlar, Sami

    2015-03-04

    The aim of this study was to establish a DNA-based identification key to ascertain the cultivar origin of Turkish monovarietal olive oils. To reach this aim, we sequenced short fragments from five olive genes for SNP (single nucleotide polymorphism) identification and developed CAPS (cleaved amplified polymorphic DNA) assays for SNPs that alter restriction enzyme recognition motifs. When applied on the oils of 17 olive cultivars, a maximum of five CAPS assays were necessary to discriminate the varietal origin of the samples. We also tested the efficiency and limit of our approach for detecting olive oil admixtures. As a result of the analysis, we were able to detect admixing down to a limit of 20%. The SNP-based CAPS assays developed in this work can be used for testing and verification of the authenticity of Turkish monovarietal olive oils, for olive tree certification, and in germplasm characterization and preservation studies.

  2. Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers

    Directory of Open Access Journals (Sweden)

    Geiger Dan

    2010-10-01

    Full Text Available Abstract Background The question of a genetic contribution to the higher prevalence and incidence of end stage kidney disease (ESKD among African Americans (AA remained unresolved, until recent findings using admixture mapping pointed to the association of a genomic locus on chromosome 22 with this disease phenotype. In the current study we utilize this example to demonstrate the utility of applying a multi-step admixture mapping approach. Methods A multi-step case only admixture mapping study, consisted of the following steps was designed: 1 Assembly of the sample dataset (ESKD AA; 2 Design of the estimated mutual information ancestry informative markers (n = 2016 screening panel 3; Genotyping the sample set whose size was determined by a power analysis (n = 576 appropriate for the initial screening panel; 4 Inference of local ancestry for each individual and identification of regions with increased AA ancestry using two different ancestry inference statistical approaches; 5 Enrichment of the initial screening panel; 6 Power analysis of the enriched panel 7 Genotyping of additional samples. 8 Re-analysis of the genotyping results to identify a genetic risk locus. Results The initial screening phase yielded a significant peak using the ADMIXMAP ancestry inference program applying case only statistics. Subgroup analysis of 299 ESKD patients with no history of diabetes yielded peaks using both the ANCESTRYMAP and ADMIXMAP ancestry inference programs. The significant peak was found on chromosome 22. Genotyping of additional ancestry informative markers on chromosome 22 that took into account linkage disequilibrium in the ancestral populations, and the addition of samples increased the statistical significance of the finding. Conclusions A multi-step admixture mapping analysis of AA ESKD patients replicated the finding of a candidate risk locus on chromosome 22, contributing to the heightened susceptibility of African Americans to develop non

  3. Genetic admixture, relatedness, and structure patterns among Mexican populations revealed by the Y-chromosome.

    Science.gov (United States)

    Rangel-Villalobos, H; Muñoz-Valle, J F; González-Martín, A; Gorostiza, A; Magaña, M T; Páez-Riberos, L A

    2008-04-01

    Y-linked markers are suitable loci to analyze genetic diversity of human populations, offering knowledge of medical, forensic, and anthropological interest. In a population sample of 206 Mestizo males from western Mexico, we analyzed two binary loci (M3 and YAP) and six Y-STRs, adding to the analysis data of Mexican Mestizos and Amerindians, and relevant worldwide populations. The paternal ancestry estimated in western Mexican-Mestizos was mainly European (60-64%), followed by Amerindian (25-21%), and African ( approximately 15%). Significant genetic heterogeneity was established between Mestizos from western (Jalisco State) and northern Mexico (Chihuahua State) compared with Mexicans from the center of the Mexican Republic (Mexico City), this attributable to higher European ancestry in western and northern than in central and southeast populations, where higher Amerindian ancestry was inferred. This genetic structure has important implications for medical and forensic purposes. Two different Pre-Hispanic evolutionary processes were evident. In Mesoamerican region, populations presented higher migration rate (N(m) = 24.76), promoting genetic homogeneity. Conversely, isolated groups from the mountains and canyons of the Western and Northern Sierra Madre (Huichols and Tarahumaras, respectively) presented a lower migration rate (N(m) = 10.27) and stronger genetic differentiation processes (founder effect and/or genetic drift), constituting a Pre-Hispanic population substructure. Additionally, Tarahumaras presented a higher frequency of Y-chromosomes without Q3 that was explained by paternal European admixture (15%) and, more interestingly, by a distinctive Native-American ancestry. In Purepechas, a special admixture process involving preferential integration of non-Purepecha women in their communities could explain contrary genetic evidences (autosomal vs. Y-chromosome) for this tribe.

  4. Socioeconomic Status and Lung Cancer: Unraveling the Contribution of Genetic Admixture

    Science.gov (United States)

    Selvin, Steve; Wrensch, Margaret R.; Sison, Jennette D.; Hansen, Helen M.; Quesenberry, Charles P.; Seldin, Michael F.; Barcellos, Lisa F.; Buffler, Patricia A.; Wiencke, John K.

    2013-01-01

    Objectives. We examined the relationship between genetic ancestry, socioeconomic status (SES), and lung cancer among African Americans and Latinos. Methods. We evaluated SES and genetic ancestry in a Northern California lung cancer case–control study (1998–2003) of African Americans and Latinos. Lung cancer case and control participants were frequency matched on age, gender, and race/ethnicity. We assessed case–control differences in individual admixture proportions using the 2-sample t test and analysis of covariance. Logistic regression models examined associations among genetic ancestry, socioeconomic characteristics, and lung cancer. Results. Decreased Amerindian ancestry was associated with higher education among Latino control participants and greater African ancestry was associated with decreased education among African lung cancer case participants. Education was associated with lung cancer among both Latinos and African Americans, independent of smoking, ancestry, age, and gender. Genetic ancestry was not associated with lung cancer among African Americans. Conclusions. Findings suggest that socioeconomic factors may have a greater impact than genetic ancestry on lung cancer among African Americans. The genetic heterogeneity and recent dynamic migration and acculturation of Latinos complicate recruitment; thus, epidemiological analyses and findings should be interpreted cautiously. PMID:23948011

  5. Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations.

    Science.gov (United States)

    Mendez, Fernando L; Watkins, Joseph C; Hammer, Michael F

    2012-06-01

    Recent analysis of DNA extracted from two Eurasian forms of archaic human shows that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. Although these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We resequenced a 7-kb region encompassing the OAS1 gene in 88 individuals from six Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5' region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 myr, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1,500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

  6. Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea.

    Science.gov (United States)

    De Groote, Annelies; Hauquier, Freija; Vanreusel, Ann; Derycke, Sofie

    2017-07-01

    There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

  7. Effects of birthplace and individual genetic admixture on lung volume and exercise phenotypes of Peruvian Quechua.

    Science.gov (United States)

    Brutsaert, Tom D; Parra, Esteban; Shriver, Mark; Gamboa, Alfredo; Palacios, Jose-Antonio; Rivera, Maria; Rodriguez, Ivette; León-Velarde, Fabiola

    2004-04-01

    Forced vital capacity (FVC) and maximal exercise response were measured in two populations of Peruvian males (age, 18-35 years) at 4,338 m who differed by the environment in which they were born and raised, i.e., high altitude (Cerro de Pasco, Peru, BHA, n = 39) and sea level (Lima, Peru, BSL, n = 32). BSL subjects were transported from sea level to 4,338 m, and were evaluated within 24 hr of exposure to hypobaric hypoxia. Individual admixture level (ADMIX, % Spanish ancestry) was estimated for each subject, using 22 ancestry-informative genetic markers and also by skin reflectance measurement (MEL). Birthplace accounted for the approximately 10% larger FVC (P < 0.001), approximately 15% higher maximal oxygen consumption (VO(2)max, ml.min(-1).kg(-1)) (P < 0.001), and approximately 5% higher arterial oxygen saturation during exercise (SpO(2)) (P < 0.001) of BHA subjects. ADMIX was low in both study groups, averaging 9.5 +/- 2.6% and 2.1 +/- 0.3% in BSL and BHA subjects, respectively. Mean underarm MEL was significantly higher in the BSL group (P < 0.001), despite higher ADMIX. ADMIX was not associated with any study phenotype, but study power was not sufficient to evaluate hypotheses of genetic adaptation via the ADMIX variable. MEL and FVC were positively correlated in the BHA (P = 0.035) but not BSL (P = 0.335) subjects. However, MEL and ADMIX were not correlated across the entire study sample (P = 0.282). In summary, results from this study emphasize the importance of developmental adaptation to high altitude. While the MEL-FVC correlation may reflect genetic adaptation to high altitude, study results suggest that alternate (environmental) explanations be considered.

  8. Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations.

    Science.gov (United States)

    Quach, Hélène; Rotival, Maxime; Pothlichet, Julien; Loh, Yong-Hwee Eddie; Dannemann, Michael; Zidane, Nora; Laval, Guillaume; Patin, Etienne; Harmant, Christine; Lopez, Marie; Deschamps, Matthieu; Naffakh, Nadia; Duffy, Darragh; Coen, Anja; Leroux-Roels, Geert; Clément, Frederic; Boland, Anne; Deleuze, Jean-François; Kelso, Janet; Albert, Matthew L; Quintana-Murci, Lluis

    2016-10-20

    Humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli-ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus-and mapped expression quantitative trait loci (eQTLs). We identify numerous cis-eQTLs that contribute to the marked differences in immune responses detected within and between populations and a strong trans-eQTL hotspot at TLR1 that decreases expression of pro-inflammatory genes in Europeans only. We find that immune-responsive regulatory variants are enriched in population-specific signals of natural selection and show that admixture with Neandertals introduced regulatory variants into European genomes, affecting preferentially responses to viral challenges. Together, our study uncovers evolutionarily important determinants of differences in host immune responsiveness between human populations.

  9. Body fat and racial genetic admixture are associated with aerobic fitness levels in a multiethnic pediatric population.

    Science.gov (United States)

    Willig, Amanda L; Hunter, Gary R; Casazza, Krista; Heimburger, Douglas C; Beasley, T Mark; Fernandez, Jose R

    2011-11-01

    Aerobic fitness and adiposity are each independently associated with health outcomes among children, although the relationship between these two variables is unclear. Our objectives were to evaluate (i) the association of adiposity with aerobic fitness using objectively measured levels of percent body fat, compared to BMI as a percentile proxy for adiposity while controlling for genetic admixture, and (ii) the congruence of BMI categories with high and low body fat categories of objectively measured percent body fat. Participants were 232 African-American (AA), European-American (EA), and Hispanic-American (HA) children aged 7-12 years (Tanner stage body fat group (body fat group based on their percent body fat; children were also categorized according to BMI percentile. Children in the low body fat group had significantly higher aerobic fitness (P BMI percentile classification. Higher African genetic admixture was associated with lower aerobic fitness (P body fat and genetic admixture irrespective of BMI classification, and such differences should be taken into account when evaluating outcomes of health interventions.

  10. Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L..

    Directory of Open Access Journals (Sweden)

    Brad L Smith

    Full Text Available Previous genetic studies of Atlantic swordfish (Xiphias gladius L. revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.

  11. Range expansion of house sparrows (Passer domesticus) in Kenya: evidence of genetic admixture and human-mediated dispersal.

    Science.gov (United States)

    Schrey, Aaron W; Liebl, Andrea L; Richards, Christina L; Martin, Lynn B

    2014-01-01

    Introduced species offer an opportunity to study the ecological process of range expansions. Recently, 3 mechanisms have been identified that may resolve the genetic paradox (the seemingly unlikely success of introduced species given the expected reduction in genetic diversity through bottlenecks or founder effects): multiple introductions, high propagule pressure, and epigenetics. These mechanisms are probably also important in range expansions (either natural or anthropogenic), yet this possibility remains untested in vertebrates. We used microsatellite variation (7 loci) in house sparrows (Passer domesticus), an introduced species that has been spreading across Kenya for ~60 years, to determine if patterns of variation could explain how this human commensal overcame the genetic paradox and expresses such considerable phenotypic differentiation across this new range. We note that in some cases, polygenic traits and epistasis among genes, for example, may not have negative effects on populations. House sparrows arrived in Kenya by a single introduction event (to Mombasa, ~1950) and have lower genetic diversity than native European and introduced North American populations. We used Bayesian clustering of individuals (n = 233) to detect that at least 2 types of range expansion occurred in Kenya: one with genetic admixture and one with little to no admixture. We also found that genetic diversity increased toward a range edge, and the range expansion was consistent with long-distance dispersal. Based on these data, we expect that the Kenyan range expansion was anthropogenically influenced, as the expansions of other introduced human commensals may also be.

  12. Multiple Origins and Admixture of Recently Expanding Japanese Wild Boar (Sus scrofa leucomystax) Populations in Toyama Prefecture of Japan.

    Science.gov (United States)

    Yamazaki, Yuji; Adachi, Fuminari; Sawamura, Akira

    2016-02-01

    Japanese wild boar (Sus scrofa leucomystax) populations have expanded drastically throughout the Japanese Archipelago in recent decades. To elucidate the dispersal patterns of Japanese wild boar in Toyama Prefecture in central Japan, we used a multi-locus microsatellite DNA analysis to determine its population structure and the degree of admixture. The deviation from Hardy-Weinberg equilibrium was detected in either total or separate regional wild boar samples from Toyama Prefecture. This result could be explained by the Wahlund effect resulting from the mixture of samples from different sources. Bayesian structure analysis, assignment test, and factorial correspondence analysis suggested that wild boars around Toyama Prefecture derive from at least two ancestral sources. The migration and possible mating of each individual may have occurred recently and continued in each geographically neighboring region. The present genetic results may be useful for prediction of future dispersal patterns of Japanese wild boar, as well as other animals in expansion.

  13. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America.

    Science.gov (United States)

    Kosoy, Roman; Nassir, Rami; Tian, Chao; White, Phoebe A; Butler, Lesley M; Silva, Gabriel; Kittles, Rick; Alarcon-Riquelme, Marta E; Gregersen, Peter K; Belmont, John W; De La Vega, Francisco M; Seldin, Michael F

    2009-01-01

    To provide a resource for assessing continental ancestry in a wide variety of genetic studies, we identified, validated, and characterized a set of 128 ancestry informative markers (AIMs). The markers were chosen for informativeness, genome-wide distribution, and genotype reproducibility on two platforms (TaqMan assays and Illumina arrays). We analyzed genotyping data from 825 subjects with diverse ancestry, including European, East Asian, Amerindian, African, South Asian, Mexican, and Puerto Rican. A comprehensive set of 128 AIMs and subsets as small as 24 AIMs are shown to be useful tools for ascertaining the origin of subjects from particular continents, and to correct for population stratification in admixed population sample sets. Our findings provide general guidelines for the application of specific AIM subsets as a resource for wide application. We conclude that investigators can use TaqMan assays for the selected AIMs as a simple and cost efficient tool to control for differences in continental ancestry when conducting association studies in ethnically diverse populations.

  14. Interactions between genetic admixture, ethnic identity, APOE genotype and dementia prevalence in an admixed Cuban sample; a cross-sectional population survey and nested case-control study

    Directory of Open Access Journals (Sweden)

    Hernandez Milagros

    2011-03-01

    Full Text Available Abstract Background The prevalence and incidence of dementia are low in Nigeria, but high among African-Americans. In these populations there is a high frequency of the risk-conferring APOE-e4 allele, but the risk ratio is less than in Europeans. In an admixed population of older Cubans we explored the effects of ethnic identity and genetic admixture on APOE genotype, its association with dementia, and dementia prevalence. Methods A cross-sectional catchment area survey of 2928 residents aged 65 and over, with a nested case-control study of individual admixture. Dementia diagnosis was established using 10/66 Dementia and DSM-IV criteria. APOE genotype was determined in 2520 participants, and genetic admixture in 235 dementia cases and 349 controls. Results Mean African admixture proportions were 5.8% for 'white', 28.6% for 'mixed' and 49.6% for 'black' ethnic identities. All three groups were substantially admixed with considerable overlap. African admixture was linearly related to number of APOE-e4 alleles. One or more APOE-e4 alleles was associated with dementia in 'white' and 'black' but not 'mixed' groups but neither this, nor the interaction between APOE-e4 and African admixture (PR 0.52, 95% CI 0.13-2.08 were statistically significant. Neither ethnic identity nor African admixture was associated with dementia prevalence when assessed separately. However, considering their joint effects African versus European admixture was independently associated with a higher prevalence, and 'mixed' or 'black' identity with a lower prevalence of dementia. Conclusions APOE genotype is strongly associated with ancestry. Larger studies are needed to confirm whether the concentration of the high-risk allele in those with African ancestry is offset by an attenuation of its effect. Counter to our hypothesis, African admixture may be associated with higher risk of dementia. Although strongly correlated, effects of admixture and ethnic identity should be

  15. The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia.

    Science.gov (United States)

    Deng, Lian; Hoh, Boon Peng; Lu, Dongsheng; Fu, Ruiqing; Phipps, Maude E; Li, Shilin; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Ismail, Endom; Mokhtar, Siti Shuhada; Jin, Li; Zilfalil, Bin Alwi; Marshall, Christian R; Scherer, Stephen W; Al-Mulla, Fahd; Xu, Shuhua

    2014-09-01

    Peninsular Malaysia is a strategic region which might have played an important role in the initial peopling and subsequent human migrations in Asia. However, the genetic diversity and history of human populations--especially indigenous populations--inhabiting this area remain poorly understood. Here, we conducted a genome-wide study using over 900,000 single nucleotide polymorphisms (SNPs) in four major Malaysian ethnic groups (MEGs; Malay, Proto-Malay, Senoi and Negrito), and made comparisons of 17 world-wide populations. Our data revealed that Peninsular Malaysia has greater genetic diversity corresponding to its role as a contact zone of both early and recent human migrations in Asia. However, each single Orang Asli (indigenous) group was less diverse with a smaller effective population size (N(e)) than a European or an East Asian population, indicating a substantial isolation of some duration for these groups. All four MEGs were genetically more similar to Asian populations than to other continental groups, and the divergence time between MEGs and East Asian populations (12,000--6,000 years ago) was also much shorter than that between East Asians and Europeans. Thus, Malaysian Orang Asli groups, despite their significantly different features, may share a common origin with the other Asian groups. Nevertheless, we identified traces of recent gene flow from non-Asians to MEGs. Finally, natural selection signatures were detected in a batch of genes associated with immune response, human height, skin pigmentation, hair and facial morphology and blood pressure in MEGs. Notable examples include SYN3 which is associated with human height in all Orang Asli groups, a height-related gene (PNPT1) and two blood pressure-related genes (CDH13 and PAX5) in Negritos. We conclude that a long isolation period, subsequent gene flow and local adaptations have jointly shaped the genetic architectures of MEGs, and this study provides insight into the peopling and human migration

  16. 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

  17. Genetic admixture and diversity estimations in the Mexican Mestizo population from Mexico City using 15 STR polymorphic markers.

    Science.gov (United States)

    Juárez-Cedillo, Teresa; Zuñiga, Joaquín; Acuña-Alonzo, Victor; Pérez-Hernández, Nonanzit; Rodríguez-Pérez, José Manuel; Barquera, Rodrigo; Gallardo, Guillermo J; Sánchez-Arenas, Rosalinda; García-Peña, Maria Del Carmen; Granados, Julio; Vargas-Alarcón, Gilberto

    2008-06-01

    The 15 AmpFlSTR Identifiler loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA were analyzed in a sample of 378 unrelated individuals from Mexico City, Mexico. Significant deviations from HW equilibrium in 14/15 STR loci alleles were not detected. The D18S51 locus had the highest power of discrimination (0.970). Genetic admixture estimations revealed a 69% of Amerindian, 26% of European and 5% of African contribution. Comparative analyses between Mexicans and other neighboring populations reveal significant differences in genetic diversity. Our results are important for future comparative genetic studies in different Latin American ethnic groups, particularly Mexican Mestizos and Amerindians. They should also be helpful in genetics, population evolution, forensic and paternity testing.

  18. Northern range expansion of European populations of the wasp spider Argiope bruennichi is associated with global warming-correlated genetic admixture and population-specific temperature adaptations.

    Science.gov (United States)

    Krehenwinkel, Henrik; Tautz, Diethard

    2013-04-01

    Poleward range expansions are observed for an increasing number of species, which may be an effect of global warming during the past decades. However, it is still not clear in how far these expansions reflect simple geographical shifts of species ranges, or whether new genetic adaptations play a role as well. Here, we analyse the expansion of the wasp spider Argiope bruennichi into Northern Europe during the last century. We have used a range-wide sampling of contemporary populations and historical specimens from museums to trace the phylogeography and genetic changes associated with the range shift. Based on the analysis of mitochondrial, microsatellite and SNP markers, we observe a higher level of genetic diversity in the expanding populations, apparently due to admixture of formerly isolated lineages. Using reciprocal transplant experiments for testing overwintering tolerance, as well as temperature preference and tolerance tests in the laboratory, we find that the invading spiders have possibly shifted their temperature niche. This may be a key adaptation for survival in Northern latitudes. The museum samples allow a reconstruction of the invasion's genetic history. A first, small-scale range shift started around 1930, in parallel with the onset of global warming. A more massive invasion of Northern Europe associated with genetic admixture and morphological changes occurred in later decades. We suggest that the latter range expansion into far Northern latitudes may be a consequence of the admixture that provided the genetic material for adaptations to new environmental regimes. Hence, global warming could have facilitated the initial admixture of populations and this resulted in genetic lineages with new habitat preferences.

  19. Genetic landscape of populations along the Silk Road: admixture and migration patterns

    OpenAIRE

    Mezzavilla, Massimo; Vozzi, Diego; Pirastu, Nicola; Girotto, Giorgia; D’Adamo, Pio; Gasparini, Paolo; Colonna, Vincenza

    2014-01-01

    Background The ancient Silk Road has been a trading route between Europe and Central Asia from the 2nd century BCE to the 15th century CE. While most populations on this route have been characterized, the genetic background of others remains poorly understood, and little is known about past migration patterns. The scientific expedition “Marco Polo” has recently collected genetic and phenotypic data in six regions (Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, Tajikistan) along the Sil...

  20. Admixture and genetic relationships of Mexican Mestizos regarding Latin American and Caribbean populations based on 13 CODIS-STRs.

    Science.gov (United States)

    Salazar-Flores, J; Zuñiga-Chiquette, F; Rubi-Castellanos, R; Álvarez-Miranda, J L; Zetina-Hérnandez, A; Martínez-Sevilla, V M; González-Andrade, F; Corach, D; Vullo, C; Álvarez, J C; Lorente, J A; Sánchez-Diz, P; Herrera, R J; Cerda-Flores, R M; Muñoz-Valle, J F; Rangel-Villalobos, H

    2015-02-01

    Short tandem repeats (STRs) of the combined DNA index system (CODIS) are probably the most employed markers for human identification purposes. STR databases generated to interpret DNA profiles are also helpful for anthropological purposes. In this work, we report admixture, population structure, and genetic relationships of Mexican Mestizos with respect to Latin American and Caribbean populations based on 13 CODIS-STRs. In addition, new STR population data were included from Tijuana, Baja California (Northwest, Mexico), which represents an interesting case of elevated genetic flow as a bordering city with the USA. Inter-population analyses included CODIS-STR data from 11 Mexican Mestizo, 12 Latin American and four Caribbean populations, in addition to European, Amerindian, and African genetic pools as ancestral references. We report allele frequencies and statistical parameters of forensic interest (PD, PE, Het, PIC, typical PI), for 15 STRs in Tijuana, Baja California. This Mexican border city was peculiar by the increase of African ancestry, and by presenting three STRs in Hardy-Weinberg disequilibrium, probably explained by recurrent gene flow. The Amerindian ancestry in Central and Southeast of Mexico was the greatest in Latin America (50.9-68.6%), only comparable with the North of Central America and Ecuador (48.8-56.4%), whereas the European ancestry was prevalent in South America (66.7-75%). The African ancestry in Mexico was the smallest (2.2-6.3%) in Latin America (≥ 2.6%), particularly regarding Brazil (21%), Honduras (62%), and the Caribbean (43.2-65.2%). CODIS-STRs allowed detecting significant population structure in Latin America based on greater presence of European, Amerindian, and African ancestries in Central/South America, Mexican Mestizos, and the Caribbean, respectively.

  1. Native American admixture in the Quebec founder population.

    Directory of Open Access Journals (Sweden)

    Claudia Moreau

    Full Text Available For years, studies of founder populations and genetic isolates represented the mainstream of genetic mapping in the effort to target genetic defects causing Mendelian disorders. The genetic homogeneity of such populations as well as relatively homogeneous environmental exposures were also seen as primary advantages in studies of genetic susceptibility loci that underlie complex diseases. European colonization of the St-Lawrence Valley by a small number of settlers, mainly from France, resulted in a founder effect reflected by the appearance of a number of population-specific disease-causing mutations in Quebec. The purported genetic homogeneity of this population was recently challenged by genealogical and genetic analyses. We studied one of the contributing factors to genetic heterogeneity, early Native American admixture that was never investigated in this population before. Consistent admixture estimates, in the order of one per cent, were obtained from genome-wide autosomal data using the ADMIXTURE and HAPMIX software, as well as with the fastIBD software evaluating the degree of the identity-by-descent between Quebec individuals and Native American populations. These genomic results correlated well with the genealogical estimates. Correlations are imperfect most likely because of incomplete records of Native founders' origin in genealogical data. Although the overall degree of admixture is modest, it contributed to the enrichment of the population diversity and to its demographic stratification. Because admixture greatly varies among regions of Quebec and among individuals, it could have significantly affected the homogeneity of the population, which is of importance in mapping studies, especially when rare genetic susceptibility variants are in play.

  2. Autosomal STRs provide genetic evidence for the hypothesis that Tai people originate from southern China.

    Directory of Open Access Journals (Sweden)

    Hao Sun

    Full Text Available Tai people are widely distributed in Thailand, Laos and southwestern China and are a large population of Southeast Asia. Although most anthropologists and historians agree that modern Tai people are from southwestern China and northern Thailand, the place from which they historically migrated remains controversial. Three popular hypotheses have been proposed: northern origin hypothesis, southern origin hypothesis or an indigenous origin. We compared the genetic relationships between the Tai in China and their "siblings" to test different hypotheses by analyzing 10 autosomal microsatellites. The genetic data of 916 samples from 19 populations were analyzed in this survey. The autosomal STR data from 15 of the 19 populations came from our previous study (Lin et al., 2010. 194 samples from four additional populations were genotyped in this study: Han (Yunnan, Dai (Dehong, Dai (Yuxi and Mongolian. The results of genetic distance comparisons, genetic structure analyses and admixture analyses all indicate that populations from northern origin hypothesis have large genetic distances and are clearly differentiated from the Tai. The simulation-based ABC analysis also indicates this. The posterior probability of the northern origin hypothesis is just 0.04 [95%CI: (0.01-0.06]. Conversely, genetic relationships were very close between the Tai and populations from southern origin or an indigenous origin hypothesis. Simulation-based ABC analyses were also used to distinguish the southern origin hypothesis from the indigenous origin hypothesis. The results indicate that the posterior probability of the southern origin hypothesis [0.640, 95%CI: (0.524-0.757] is greater than that of the indigenous origin hypothesis [0.324, 95%CI: (0.211-0.438]. Therefore, we propose that the genetic evidence does not support the hypothesis of northern origin. Our genetic data indicate that the southern origin hypothesis has higher probability than the other two hypotheses

  3. Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes.

    Science.gov (United States)

    Hvilsom, C; Frandsen, P; Børsting, C; Carlsen, F; Sallé, B; Simonsen, B T; Siegismund, H R

    2013-06-01

    Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies.

  4. Gender differences in ancestral contribution and admixture in Venezuelan populations.

    Science.gov (United States)

    Guerra, D Castro De; Pérez, C Figuera; Izaguirre, M H; Barahona, E Arroyo; Larralde, A Rodríguez; Lugo, M Vívenes De

    2011-06-01

    The origin of the contribution of uniparental heritage were analyzed in 615 samples of individuals proceeding from 13 towns classified according to historic differences in their emergence and development as African-derived, European-derived, and admixed/urban. Mitochondrial and Y-chromosome haplogroups were identified by PCR-restriction fragment length polymorphism. The results were compared with previous estimates of admixture made with autosomal markers and with historic aspects. The results show a predominantly indigenous genetic contribution through the female, being more prevalent in urban populations; the African contribution, although dispersed, presents a larger concentration in the African-derived towns, whereas the European contribution is limited to populations with this origin, reflecting isolation and the conservation of the distribution pattern of genes of the Colonial era. With regard to admixture through males, it is almost exclusively of European origin, whereas the African contribution is basically concentrated in the African-derived towns, and the Amerindian lineages are almost nonexistent. The genome of paternal heredity, as opposed to the autosomal and the mitochondrial, shows a homogeneous pattern of admixture that is independent of the origin of the population studied, suggesting that European genes have been introduced into the Venezuelan population through male immigrations, whereas the indigenous contribution has been preserved in the Venezuelan genetic pool through the women. These results provide evidence of the heterogeneity in the genetic origin of the Venezuelan population, which should be taken into account in forensic and epidemiologic genetic studies.

  5. Genetic evidence on the origins of Indian caste populations.

    Science.gov (United States)

    Bamshad, M; Kivisild, T; Watkins, W S; Dixon, M E; Ricker, C E; Rao, B B; Naidu, J M; Prasad, B V; Reddy, P G; Rasanayagam, A; Papiha, S S; Villems, R; Redd, A J; Hammer, M F; Nguyen, S V; Carroll, M L; Batzer, M A; Jorde, L B

    2001-06-01

    The origins and affinities of the approximately 1 billion people living on the subcontinent of India have long been contested. This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in approximately 265 males from eight castes of different rank to approximately 750 Africans, Asians, Europeans, and other Indians. For maternally inherited mtDNA, each caste is most similar to Asians. However, 20%-30% of Indian mtDNA haplotypes belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans, particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1 and 39 Alu elements

  6. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

    Science.gov (United States)

    Kidd, Jeffrey M; Gravel, Simon; Byrnes, Jake; Moreno-Estrada, Andres; Musharoff, Shaila; Bryc, Katarzyna; Degenhardt, Jeremiah D; Brisbin, Abra; Sheth, Vrunda; Chen, Rong; McLaughlin, Stephen F; Peckham, Heather E; Omberg, Larsson; Bormann Chung, Christina A; Stanley, Sarah; Pearlstein, Kevin; Levandowsky, Elizabeth; Acevedo-Acevedo, Suehelay; Auton, Adam; Keinan, Alon; Acuña-Alonzo, Victor; Barquera-Lozano, Rodrigo; Canizales-Quinteros, Samuel; Eng, Celeste; Burchard, Esteban G; Russell, Archie; Reynolds, Andy; Clark, Andrew G; Reese, Martin G; Lincoln, Stephen E; Butte, Atul J; De La Vega, Francisco M; Bustamante, Carlos D

    2012-10-05

    Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago.

  7. The population demography of Betula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing.

    Science.gov (United States)

    Tsuda, Y; Nakao, K; Ide, Y; Tsumura, Y

    2015-04-01

    Conservation of the local genetic variation and evolutionary integrity of economically and ecologically important trees is a key aspect of studies involving forest genetics, and a population demographic history of the target species provides valuable information for this purpose. Here, the genetic structure of 48 populations of Betula maximowicziana was assessed using 12 expressed sequence tag-simple sequence repeat (EST-SSR) markers. Genetic diversity was lower in northern populations than southern ones and structure analysis revealed three groups: northern and southern clusters and an admixed group. Eleven more genomic-SSR loci were added and the demographic history of these three groups was inferred by approximate Bayesian computation (ABC). The ABC revealed that a simple split scenario was much more likely than isolation with admixture, suggesting that the admixture-like structure detected in this species was due to ancestral polymorphisms. The ABC analysis suggested that the population growth and divergence of the three groups occurred 96 800 (95% CI, 20 500-599 000) and 28 300 (95% CI, 8700-98 400) years ago, respectively. We need to be aware of several sources of uncertainty in the inference such as assumptions about the generation time, overlapping of generations, confidence intervals of the estimated parameters and the assumed model in the ABC. However, the results of the ABC together with the model-based maps of reconstructed past species distribution and palaeoecological data suggested that the modern genetic structure of B. maximowicziana originated prior to the last glacial maximum (LGM) and that some populations survived in the northern range even during the LGM. © 2015 John Wiley & Sons Ltd.

  8. HLA class I variation controlled for genetic admixture in the Gila River Indian Community of Arizona: a model for the Paleo-Indians.

    Science.gov (United States)

    Williams, R C; McAuley, J E

    1992-01-01

    The genetic distribution of the HLA class I loci is presented for 619 "full blooded" Pima and Tohono O'odham Native Americans (Pimans) in the Gila River Indian Community. Variation in the Pimans is highly restricted. There are only three polymorphic alleles at the HLA-A locus, *A2, *A24, and *A31, and only 10 alleles with a frequency greater than 0.01 at HLA-B where *Bw48 (0.187), *B35 (0.173), and the new epitope *BN21 (0.143) have the highest frequencies. Two and three locus disequilibria values and haplotype frequencies are presented. Ten three-locus haplotypes account for more than 50% of the class I variation, with *A24 *BN21 *Cw3 (0.085) having the highest frequency. Gm allotypes demonstrate that little admixture from non-Indian populations has entered the Community since the 17th century when Europeans first came to this area. As a consequence many alleles commonly found in Europeans and European Americans are efficient markers for Caucasian admixture, while the "private" Indian alleles, *BN21 and *Bw48, can be used to measure Native American admixture in Caucasian populations. It is suggested that this distribution in "full blooded" Pimans approximates that of the Paleo-Indian migrants who first entered the Americas between 20,000 and 40,000 years ago.

  9. Human Population Admixture in Asia

    Directory of Open Access Journals (Sweden)

    Shuhua Xu

    2012-09-01

    Full Text Available Genetic admixture in human, the result of inter-marriage among people from different well-differentiated populations, has been extensively studied in the New World, where European colonization brought contact between peoples of Europe, Africa, and Asia and the Amerindian populations. In Asia, genetic admixing has been also prevalent among previously separated human populations. However, studies on admixed populations in Asia have been largely underrepresented in similar efforts in the New World. Here, I will provide an overview of population genomic studies that have been published to date on human admixture in Asia, focusing on population structure and population history.

  10. Reconstructing the Indian origin and dispersal of the European Roma: a maternal genetic perspective.

    Directory of Open Access Journals (Sweden)

    Isabel Mendizabal

    Full Text Available Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent. Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies.

  11. Reconstructing the Indian Origin and Dispersal of the European Roma: A Maternal Genetic Perspective

    Science.gov (United States)

    Mendizabal, Isabel; Valente, Cristina; Gusmão, Alfredo; Alves, Cíntia; Gomes, Verónica; Goios, Ana; Parson, Walther; Calafell, Francesc; Alvarez, Luis; Amorim, António; Gusmão, Leonor

    2011-01-01

    Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent. Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies. PMID:21264345

  12. Reconstructing the Indian origin and dispersal of the European Roma: a maternal genetic perspective.

    Science.gov (United States)

    Mendizabal, Isabel; Valente, Cristina; Gusmão, Alfredo; Alves, Cíntia; Gomes, Verónica; Goios, Ana; Parson, Walther; Calafell, Francesc; Alvarez, Luis; Amorim, António; Gusmão, Leonor; Comas, David; Prata, Maria João

    2011-01-10

    Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent. Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies.

  13. Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers.

    Science.gov (United States)

    Marcheco-Teruel, Beatriz; Parra, Esteban J; Fuentes-Smith, Evelyn; Salas, Antonio; Buttenschøn, Henriette N; Demontis, Ditte; Torres-Español, María; Marín-Padrón, Lilia C; Gómez-Cabezas, Enrique J; Alvarez-Iglesias, Vanesa; Mosquera-Miguel, Ana; Martínez-Fuentes, Antonio; Carracedo, Angel; Børglum, Anders D; Mors, Ole

    2014-07-01

    We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

  14. Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers.

    Directory of Open Access Journals (Sweden)

    Beatriz Marcheco-Teruel

    2014-07-01

    Full Text Available We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40% and Santiago de Cuba (39%, and the highest proportion of Native American ancestry in Granma (15%, Holguín (12% and Las Tunas (12%. We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

  15. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

    NARCIS (Netherlands)

    Upadhyay, M.R.; Chen, W.; Lenstra, J.A.; Goderie, C.R.J.; MacHugh, D.E.; Park, S.D.E.; Magee, D.A.; Matassino, D.; Ciani, F.; Megens, H.J.; Arendonk, van J.A.M.; Groenen, M.A.M.

    2017-01-01

    The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is

  16. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

    NARCIS (Netherlands)

    Upadhyay, M R; Chen, W|info:eu-repo/dai/nl/371747228; Lenstra, J A|info:eu-repo/dai/nl/067852335; Goderie, C R J; MacHugh, D E; Park, S D E; Magee, D A; Matassino, D; Ciani, F; Megens, H-J; van Arendonk, J A M; Groenen, M A M|info:eu-repo/dai/nl/412585650; Marsan, P A; Balteanu, V; Dunner, S; Garcia, J F; Ginja, C; Kantanen, J

    2017-01-01

    The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is

  17. Genetic and environmental origins of hypospadias

    DEFF Research Database (Denmark)

    Thorup, Jørgen Mogens; Nordenskjöld, Agneta; Hutson, John M

    2014-01-01

    PURPOSE OF REVIEW: The purpose of this study was to review and comment on recent original presentations dealing with genetic and environmental factors in the cause of hypospadias. RECENT FINDINGS: The heritability is definitely high and having an affected family member is the highest identified...... for hypospadias, especially in genetically predisposed individuals. So far, however, no environmental chemical pollutants or endocrine disruptor with a general common impact on the risk for hypospadias in most societies has been demonstrated. SUMMARY: A major point that should be considered regarding the action...... of environmental toxicants in inducing hypospadias is the cumulative effects of multiple low-dose exposures. Furthermore, interactions between genetic and environmental factors may help to explain nonreplication in genetic studies of hypospadias....

  18. The puzzling origin of the genetic code.

    Science.gov (United States)

    Cedergren, R; Miramontes, P

    1996-06-01

    Recent results add to the mystery of the origin of the genetic code. In spite of early doubts, RNA can discriminate between hydrophobic amino acids under certain contexts. Moreover, codon reassignment, which has taken place in several organisms and mitochondria, is not a random process. Finally, phylogenies of some aminoacyl-tRNA synthetases suggest that the entire code was not completely assigned at the time of the divergence of bacteria from nucleated cells.

  19. 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...... 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....

  20. Genetic admixture studies on four in situ evolved, two migrant and twenty-one ethnic populations of Tamil Nadu, south India

    Indian Academy of Sciences (India)

    G. Suhasini; E. Sonaa; S. Shila; C. R. Srikumari; G. Jayaraman; A. Ramesh

    2011-08-01

    We analysed the genetic structure of ∼1000 samples representing 27 ethnic groups settled in Tamil Nadu, south India, derived from two linguistic families (Dravidians and Indo–Europeans) representing four religious groups (Hinduism, Islam, Christianity and Jainism) using 11 mtDNA markers. Out of 27 ethnic groups, four are in situ populations (Anglo-Indian, Labbai Muslim, Nadar Christian and south Indian Jain) and two are migrants (Gypsy and north Indian Jain) from north India to Tamil Nadu, and 21 are native ethnic groups. Six of the markers we used were monomorphic (HaeIII663, HpaI3592, AluI5176, AluI7025, AluI13262, 9-bp deletion) and five markers were polymorphic (DdeI10394, AluI10397, HinfI12308, HincII13259 and HaeIII16517). Haplogroup frequencies, genetic affinities and admixture analysis are based on the genotype data of polymorphic markers observed in these populations. Haplogroup frequencies indicate that various ethnic groups entered Tamil Nadu during different time periods. Genetic affinities and admixture estimates revealed that the ethnic groups possessing advanced knowledge of farming cluster in a branch (C), and could be the late arrived settlers as agriculture, was introduced to this region at about 5 to 3 thousand years ago. In situ ethnic groups appear to have arisen at various times as a result of the prevailing dominant socio-cultural forces. Hierarchical Hindu caste system created many ethnic groups in the history of its existence; some of them became isolated for considerable period of time. Over all, among Tamil ethnic groups, in spite of caste systems’ rigidity, built in flexibility in the system in the form of hypergamy and hypogamy had allowed maternal gene flow between them.

  1. Genetic admixture studies on four in situ evolved, two migrant and twenty-one ethnic populations of Tamil Nadu, south India.

    Science.gov (United States)

    Suhasini, G; Sonaa, E; Shila, S; Srikumari, C R; Jayaraman, G; Ramesh, A

    2011-08-01

    We analysed the genetic structure of ≈ 1000 samples representing 27 ethnic groups settled in Tamil Nadu, south India, derived from two linguistic families (Dravidians and Indo-Europeans) representing four religious groups (Hinduism, Islam, Christianity and Jainism) using 11 mtDNA markers. Out of 27 ethnic groups, four are in situ populations (Anglo-Indian, Labbai Muslim, Nadar Christian and south Indian Jain) and two are migrants (Gypsy and north Indian Jain) from north India to Tamil Nadu, and 21 are native ethnic groups. Six of the markers we used were monomorphic (HaeIII663, HpaI3592, AluI5176, AluI7025, AluI13262, 9-bp deletion) and five markers were polymorphic (DdeI10394, AluI10397, HinfI12308, HincII13259 and HaeIII16517). Haplogroup frequencies, genetic affinities and admixture analysis are based on the genotype data of polymorphic markers observed in these populations. Haplogroup frequencies indicate that various ethnic groups entered Tamil Nadu during different time periods. Genetic affinities and admixture estimates revealed that the ethnic groups possessing advanced knowledge of farming cluster in a branch (C), and could be the late arrived settlers as agriculture, was introduced to this region at about 5 to 3 thousand years ago. In situ ethnic groups appear to have arisen at various times as a result of the prevailing dominant socio-cultural forces. Hierarchical Hindu caste system created many ethnic groups in the history of its existence; some of them became isolated for considerable period of time. Over all, among Tamil ethnic groups, in spite of caste systems' rigidity, built in flexibility in the system in the form of hypergamy and hypogamy had allowed maternal gene flow between them.

  2. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution

    Directory of Open Access Journals (Sweden)

    Piera Di Lorenzo

    2016-09-01

    Full Text Available Over the last 20 years, the two uniparentally inherited marker systems, namely mitochondrial DNA and Y chromosome have been widely employed to solve questions about origin and prehistorical range expansions, demographic processes, both in humans and domestic animals. The mtDNA and the Y chromosome, with their unique patterns of inheritance, continue to be extremely important source of information. These markers played significant roles in farm animals in the evaluation of the genetic variation within- and among-breed strains and lines and have widely applied in the fields of linkage mapping, paternity tests, prediction of breeding values in genome-assisted selection, analysis of genetic diversity within breeds detection of population admixture, assessment of inbreeding and relationships between breeds, and assignment of individuals to their breed of origin. This approach offers a unique opportunity to save genetic resources and achieving improved productivity. In the past years, significant progress was achieved in reconstructing detailed cattle phylogenies; many studies indicated multiple parental sources and several levels of phylogeographic structuring. More detailed researches are still in progress in order to provide a more comprehensive picture of such extant variability. This paper is focused on reviewing the use of the two uniparental markers as valuable tool for the characterization of cattle genetic diversity. Furthermore, their implications in animal breeding, management and genetic resources conservation are also reported.

  3. admixturegraph: an R package for admixture graph manipulation and fitting.

    Science.gov (United States)

    Leppälä, Kalle; Nielsen, Svend V; Mailund, Thomas

    2017-06-01

    Admixture graphs generalize phylogenetic trees by allowing genetic lineages to merge as well as split. In this paper we present the R package admixturegraph containing tools for building and visualizing admixture graphs, for fitting graph parameters to genetic data, for visualizing goodness of fit and for evaluating the relative goodness of fit between different graphs. GitHub: https://github.com/mailund/admixture_graph and CRAN: https://cran.r-project.org/web/packages/admixturegraph . mailund@birc.au.dk .

  4. Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers.

    Science.gov (United States)

    Hollard, Clémence; Keyser, Christine; Giscard, Pierre-Henri; Tsagaan, Turbat; Bayarkhuu, Noost; Bemmann, Jan; Crubézy, Eric; Ludes, Bertrand

    2014-09-01

    The Altai Mountains have been a long-term boundary zone between the Eurasian Steppe populations and South and East Asian populations. To disentangle some of the historical population movements in this area, 14 ancient human specimens excavated in the westernmost part of the Mongolian Altai were studied. Thirteen of them were dated from the Middle to the End of the Bronze Age and one of them to the Eneolithic period. The environmental conditions encountered in this region led to the good preservation of DNA in the human remains. Therefore, a multi-markers approach was adopted for the genetic analysis of identity, ancestry and phenotype markers. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages. To go further in the search of the origin of these ancient specimens, phenotypical characters (i.e. hair and eye color) were determined. For this purpose, we adapted the HIrisPlex assay recently described to MALDI-TOF mass spectrometry. In addition, some ancestry informative markers were analyzed with this assay. The results revealed mixed phenotypes among this group confirming the probable admixed ancestry of the studied Altaian population at the Middle Bronze Age. The good results obtained from ancient DNA samples suggest that this approach might be relevant for forensic casework too.

  5. Towards Understanding the Origin of Genetic Languages

    CERN Document Server

    Patel, Apoorva D

    2007-01-01

    Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from viruses and bacteria to human beings. Advances in genetics and experience in designing computers have taken us to a stage where we can understand the optimisation principles at the root of this system, from the availability of basic building blocks to the execution of tasks. The languages of DNA and proteins are argued to be the optimal solutions to the information processing tasks they carry out. The analysis also suggests simpler predecessors to these languages, and provides fascinating clues about their origin. Obviously, a comprehensive unraveling of the puzzle of life would have a lot to say about what we may design or convert ourselves into.

  6. A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín.

    Science.gov (United States)

    Conley, Andrew B; Rishishwar, Lavanya; Norris, Emily T; Valderrama-Aguirre, Augusto; Mariño-Ramírez, Leonardo; Medina-Rivas, Miguel A; Jordan, I King

    2017-09-06

    At least twenty percent of Colombians identify as having African ancestry, yielding the second largest population of Afro-descendants in Latin America. To date, there have been relatively few studies focused on the genetic ancestry of Afro-Latino populations. We report a comparative analysis of the genetic ancestry of Chocó, a state located on Colombia's Pacific coast with a population that is >80% Afro-Colombian. We compared genome-wide patterns of genetic ancestry and admixture for Chocó to six other admixed American populations, with an emphasis on a Mestizo population from the nearby Colombian city of Medellín. One hundred sample donors from Chocó were genotyped across 610,545 genomic sites and compared to 94 publicly available whole genome sequences from Medellín. At the continental level, Chocó shows mostly African genetic ancestry (76%) with a nearly even split between European (13%) and Native American (11%) fractions, whereas Medellín has primarily European ancestry (75%), followed by Native American (18%) and African (7%). Sample donors from Chocó self-identify as having more African ancestry, and conversely less European and Native American ancestry, than can be genetically inferred, as opposed to what we previously found for Medellín, where individuals tend to over-estimate levels of European ancestry. We developed a novel approach for subcontinental ancestry assignment, which allowed us to characterize subcontinental source populations for each of the three distinct continental ancestry fractions separately. Despite the clear differences between Chocó and Medellín at the level of continental ancestry, the two populations show overall patterns of subcontinental ancestry that are highly similar. Their African subcontinental ancestries are only slightly different, with Chocó showing more exclusive shared ancestry with the modern Yoruba (Nigerian) population and Medellín having relatively more shared ancestry with West African populations in

  7. Partitioning of Genetic Trends by Origin in Croatian Simmental Cattle

    Directory of Open Access Journals (Sweden)

    Marija Špehar

    2011-12-01

    Full Text Available The objective of this study was to partition genetic trend for milk (protein yield and meat (net daily gain traits by the origin of selection in Croatian Simmental cattle. In order to evaluate overall genetic trend, breeding values were averaged by the year of birth and origin. Origin was defined as a country where animal was initially registered. Overall genetic trend for protein yield was positive. The relative effect of three origins on the overall genetic trend for protein yield was 43.5% for Germany, 33.9% for Croatia, and 22.1% for Austria at the end of analysed period. Genetic trend for net daily gain was also positive. The Croatian and German partitions had large contribution to the overall genetic trend, while small partition was attributed to the Austrian origin. At the end of analysed period, the relative effect of these three origins on the overall genetic trend for net daily gain was 57.0% for Croatia, 38.5% for Germany, and 4.5% for Austria. Selection work originated from Austria, Croatia, and Germany had effect on genetic trend in Croatia. Other origins did not contribute notably to the overall genetic trend of both traits.

  8. Partitioning of Genetic Trends by Origin in Croatian Simmental Cattle

    Directory of Open Access Journals (Sweden)

    Marija Špehar

    2011-10-01

    Full Text Available The objective of this study was to partition genetic trend for milk (protein yield and meat (net daily gain traits by the origin of selection in Croatian Simmental cattle. In order to evaluate overall genetic trend, breeding values were averaged by the year of birth and origin. Origin was defined as a country where animal was initially registered. Overall genetic trend for protein yield was positive. The relative effect of three origins on the overall genetic trend for protein yield was 43.5% for Germany, 33.9% for Croatia, and 22.1% for Austria at the end of analysed period. Genetic trend for net daily gain was also positive. The Croatian and German partitions had large contribution to the overall genetic trend, while small partition was attributed to the Austrian origin. At the end of analysed period, the relative effect of these three origins on the overall genetic trend for net daily gain was 57.0% for Croatia, 38.5% for Germany, and 4.5% for Austria. Selection work originated from Austria, Croatia, and Germany had effect on genetic trend in Croatia. Other origins did not contribute notably to the overall genetic trend of both traits.

  9. Genetic structure in village dogs reveals a Central Asian domestication origin.

    Science.gov (United States)

    Shannon, Laura M; Boyko, Ryan H; Castelhano, Marta; Corey, Elizabeth; Hayward, Jessica J; McLean, Corin; White, Michelle E; Abi Said, Mounir; Anita, Baddley A; Bondjengo, Nono Ikombe; Calero, Jorge; Galov, Ana; Hedimbi, Marius; Imam, Bulu; Khalap, Rajashree; Lally, Douglas; Masta, Andrew; Oliveira, Kyle C; Pérez, Lucía; Randall, Julia; Tam, Nguyen Minh; Trujillo-Cornejo, Francisco J; Valeriano, Carlos; Sutter, Nathan B; Todhunter, Rory J; Bustamante, Carlos D; Boyko, Adam R

    2015-11-01

    Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups--a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations--including those of Vietnam, India, and Egypt-show minimal evidence of European admixture. These populations exhibit a clear gradient of short--range linkage disequilibrium consistent with a Central Asian domestication origin.

  10. An Ethnolinguistic and Genetic Perspective on the Origins of the Dravidian-Speaking Brahui in Pakistan.

    Science.gov (United States)

    Pagani, Luca; Colonna, Vincenza; Tyler-Smith, Chris; Ayub, Qasim

    2017-01-01

    Pakistan is a part of South Asia that modern humans encountered soon after they left Africa ~50 - 70,000 years ago. Approximately 9,000 years ago they began establishing cities that eventually expanded to represent the Harappan culture, rivalling the early city states of Mesopotamia. The modern state constitutes the north western land mass of the Indian sub-continent and is now the abode of almost 200 million humans representing many ethnicities and linguistic groups. Studies utilising autosomal, Y chromosomal and mitochondrial DNA markers in selected Pakistani populations revealed a mixture of Western Eurasian-, South- and East Asian-specific lineages, some of which were unequivocally associated with past migrations. Overall in Pakistan, genetic relationships are generally predicted more accurately by geographic proximity than linguistic origin. The Dravidian-speaking Brahui population are a prime example of this. They currently reside in south-western Pakistan, surrounded by Indo-Europeans speakers with whom they share a common genetic origin. In contrast, the Hazara share the highest affinity with East Asians, despite their Indo-European linguistic affiliation. In this report we reexamine the genetic origins of the Brahuis, and compare them with diverse populations from India, including several Dravidian-speaking groups, and present a genetic perspective on ethnolinguistic groups in present-day Pakistan. Given the high affinity of Brahui to the other Indo-European Pakistani populations and the absence of population admixture with any of the examined Indian Dravidian groups, we conclude that Brahui are an example of cultural (linguistic) retention following a major population replacement.

  11. The scale and nature of Viking settlement in Ireland from Y-chromosome admixture analysis.

    Science.gov (United States)

    McEvoy, Brian; Brady, Claire; Moore, Laoise T; Bradley, Daniel G

    2006-12-01

    The Vikings (or Norse) played a prominent role in Irish history but, despite this, their genetic legacy in Ireland, which may provide insights into the nature and scale of their immigration, is largely unexplored. Irish surnames, some of which are thought to have Norse roots, are paternally inherited in a similar manner to Y-chromosomes. The correspondence of Scandinavian patrilineal ancestry in a cohort of Irish men bearing surnames of putative Norse origin was examined using both slow mutating unique event polymorphisms and relatively rapidly changing short tandem repeat Y-chromosome markers. Irish and Scandinavian admixture proportions were explored for both systems using six different admixture estimators, allowing a parallel investigation of the impact of method and marker type in Y-chromosome admixture analysis. Admixture proportion estimates in the putative Norse surname group were highly consistent and detected little trace of Scandinavian ancestry. In addition, there is scant evidence of Scandinavian Y-chromosome introgression in a general Irish population sample. Although conclusions are largely dependent on the accurate identification of Norse surnames, the findings are consistent with a relatively small number of Norse settlers (and descendents) migrating to Ireland during the Viking period (ca. AD 800-1200) suggesting that Norse colonial settlements might have been largely composed of indigenous Irish. This observation adds to previous genetic studies that point to a flexible Viking settlement approach across North Atlantic Europe.

  12. Origin and evolutionary process of the genetic code.

    Science.gov (United States)

    Ikehara, Kenji; Niihara, Yuka

    2007-01-01

    The genetic code plots the relationship between a triplet base sequence on RNA and an amino acid that corresponds to a protein associated with a required function in organisms. Accurate knowledge about the genetic code, including its origin and evolutionary process, would be helpful for determining the causes of genetic disorders and discovering new medical treatments, as well as for understanding the origin of life. This review begins with discussion of several well-known theories on the origin of the genetic code. Then, a GNC-SNS primitive genetic code hypothesis, which we originally proposed, is explained in relation to the weak points of other theories. S and N denote G or C and any of the four bases, respectively. We also introduce our hypothesis of the GADV-protein world hypothesis on the origin of life, where GADV stands for the four amino acids, Gly[G], Ala[A], Asp[D] and Val[V]. Next, we discuss the reason why genetic disorders, which should be triggered by base replacements, are repressed at a low level under the universal genetic code. Finally, we explain the current difficulties we faced in treating genetic disorders, suggesting a prospect for a new type of treatments of these disorders.

  13. Principal components analysis of population admixture.

    Directory of Open Access Journals (Sweden)

    Jianzhong Ma

    Full Text Available With the availability of high-density genotype information, principal components analysis (PCA is now routinely used to detect and quantify the genetic structure of populations in both population genetics and genetic epidemiology. An important issue is how to make appropriate and correct inferences about population relationships from the results of PCA, especially when admixed individuals are included in the analysis. We extend our recently developed theoretical formulation of PCA to allow for admixed populations. Because the sampled individuals are treated as features, our generalized formulation of PCA directly relates the pattern of the scatter plot of the top eigenvectors to the admixture proportions and parameters reflecting the population relationships, and thus can provide valuable guidance on how to properly interpret the results of PCA in practice. Using our formulation, we theoretically justify the diagnostic of two-way admixture. More importantly, our theoretical investigations based on the proposed formulation yield a diagnostic of multi-way admixture. For instance, we found that admixed individuals with three parental populations are distributed inside the triangle formed by their parental populations and divide the triangle into three smaller triangles whose areas have the same proportions in the big triangle as the corresponding admixture proportions. We tested and illustrated these findings using simulated data and data from HapMap III and the Human Genome Diversity Project.

  14. Reverse genetics: Its origins and prospects

    Energy Technology Data Exchange (ETDEWEB)

    Berg, P. (Stanford Univ., CA (United States))

    1991-04-01

    The nucleotide sequence of a gene and its flanking segments alone will not tell us how its expression is regulated during development and differentiation, or in response to environmental changes. To comprehend the physiological significance of the molecular details requires biological analysis. Recombinant DNA techniques provide a powerful experimental approach. A strategy termed reverse genetics' utilizes the analysis of the activities of mutant and normal genes and experimentally constructed mutants to explore the relationship between gene structure and function thereby helping elucidate the relationship between genotype and phenotype.

  15. Hypermethioninemias of genetic and non-genetic origin: A review.

    Science.gov (United States)

    Mudd, S Harvey

    2011-02-15

    This review covers briefly the major conditions, genetic and non-genetic, sometimes leading to abnormally elevated methionine, with emphasis on recent developments. A major aim is to assist in the differential diagnosis of hypermethioninemia. The genetic conditions are: (1) Homocystinuria due to cystathionine β-synthase (CBS) deficiency. At least 150 different mutations in the CBS gene have been identified since this deficiency was established in 1964. Hypermethioninemia is due chiefly to remethylation of the accumulated homocysteine. (2) Deficient activity of methionine adenosyltransferases I and III (MAT I/III), the isoenzymes the catalytic subunit of which are encoded by MAT1A. Methionine accumulates because its conversion to S-adenosylmethionine (AdoMet) is impaired. (3) Glycine N-methyltrasferase (GNMT) deficiency. Disruption of a quantitatively major pathway for AdoMet disposal leads to AdoMet accumulation with secondary down-regulation of methionine flux into AdoMet. (4) S-adenosylhomocysteine (AdoHcy) hydrolase (AHCY) deficiency. Not being catabolized normally, AdoHcy accumulates and inhibits many AdoMet-dependent methyltransferases, producing accumulation of AdoMet and, thereby, hypermethioninemia. (5) Citrin deficiency, found chiefly in Asian countries. Lack of this mitochondrial aspartate-glutamate transporter may produce (usually transient) hypermethioninemia, the immediate cause of which remains uncertain. (6) Fumarylacetoacetate hydrolase (FAH) deficiency (tyrosinemia type I) may lead to hypermethioninemia secondary either to liver damage and/or to accumulation of fumarylacetoacetate, an inhibitor of the high K(m) MAT. Additional possible genetic causes of hypermethioninemia accompanied by elevations of plasma AdoMet include mitochondrial disorders (the specificity and frequency of which remain to be elucidated). Non-genetic conditions include: (a) Liver disease, which may cause hypermethioninemia, mild, or severe. (b) Low-birth-weight and

  16. Genetic evidence for the multiple origins of Pinghua Chinese

    Institute of Scientific and Technical Information of China (English)

    Yan LU; Shang-Ling PAN; Shu-Ming QIN; Zheng-Dong QIN; Chuan-Chao WANG; Rui-Jing GAN; Hui LI

    2013-01-01

    Linguistics and genetics always reach similar results in phylogenetic studies of human populations.A previous study found that populations speaking Han Chinese dialects have closer genetic relationships to each other than to neighboring ethnic groups.However,the Pinghua Chinese population from Guangxi is an exception.We have reported that northem Pinghua people are genetically related to populations speaking Daic languages.In this study,we further studied the southern Pinghua population.The Y chromosome and mitochondrial DNA haplogroup components and network analysis indicated that northern and southern Pinghua populations were genetically different.Therefore,we concluded that the Pinghua speakers may have various origins,even though Pinghua dialects are similar.Pinghua dialects might have originated when the Daic or Hmongic speakers from different regions learnt to speak the same Chinese dialect hundreds of years ago.Speakers of one language do not always have just one origin.

  17. Two perspectives on the origin of the standard genetic code.

    Science.gov (United States)

    Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

    2014-12-01

    The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

  18. [A study on origin of genetic ethics problem and countermeasure].

    Science.gov (United States)

    Cheng, Yan-Ping

    2008-03-01

    The genetic ethical problem is one of problems which are the most disputable or difficult to resolve perfectly in the fields of life science. In these years the research for the problems is being concentrated on the types of genetic ethical problem and the ways to resolve them. But the systematic research for origin of genetic ethical problem is rare to be known. Thus it seems to be short of theoretical support to bring forward corresponding countermeasure. In this paper we focus on the evolving germ of genetic ethical problem and its evolving rule from the twofold views of human biological evolution and cultural evolution. A human being is a double offspring with biological evolution and cultural evolution . And he is a species which has both biological and cultural attribute on the earth. Through comparing and studying human biological evolution , cultural evolution, and characteristics of both biological attribute and cultural attribute, we bring forward a viewpoint that all ethical problems originate from a conflict originating from interplay of human biological evolution and cultural evolution. We intend to seek for the gist of theory and practice in order to research for genetic ethical problem and put forward some corresponding countermeasures. At the same time we'll advance a series of corresponding countermeasures of genetic ethical problem. The final aim in the paper is that not only some of our opinions will be admitted, but also through learning and understanding genetic ethical problem and its origin, the decision-makers and investigators in genetics field will be promoted to have more sense of fate and responsibility , so that the average public are able to misunderstand less and understand more for studying and genetics applying. We all work hard for genetics career to make it in healthy and continuing development and give a lot of happiness to human beings.

  19. Admixture estimates for the population of Havana City.

    Science.gov (United States)

    Cintado, A; Companioni, O; Nazabal, M; Camacho, H; Ferrer, A; De Cossio, M E Fernandez; Marrero, A; Ale, M; Villarreal, A; Leal, L; Casalvilla, R; Benitez, J; Novoa, L; Diaz-Horta, O; Dueñas, M

    2009-01-01

    The Cuban population is essentially a result of the admixture between Spanish, West African and, to a lesser degree, Amerindian tribes that inhabited the island. The study analysed the genetic structure of the three principal ethnic groups from Havana City, and the contribution of parental populations to its genetic pool. According to genealogical information and anthropological traits, 206 subjects were classified as Mulatto, of Spanish decent or of African descent. Seventeen Ancestry Informative Markers, with high difference in frequency between parental populations, were selected to estimate individual and group admixture proportions. The statistical analyses were performed using the ADMIX, ADMIX95 and STRUCTURE 2.1 packages. The results demonstrate a high level of European and African admixture in Mulattos (57-59% European; 41-43% West African). The European contribution was higher in those of Spanish descent (85%) while in those of African descent, the West African contribution ranged between 74% and 76%. Genetic structure was only detected in Mulattos and those of African descent. An Amerindian contribution was not detectable in the studied sample. Our findings indicate the existence of admixture and genetic structure in the population of Havana City. This study represents one of the first steps towards understanding Cuban population admixture in order to produce successful experimental designs for admixture mapping.

  20. Indian Ocean Crossroads: Human Genetic Origin and Population Structure in the Maldives

    Science.gov (United States)

    Pijpe, Jeroen; Voogt, Alex; Oven, Mannis; Henneman, Peter; Gaag, Kristiaan J; Kayser, Manfred; Knijff, Peter

    2013-01-01

    The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago. Am J Phys Anthropol 151:58–67, 2013. © 2013 Wiley Periodicals, Inc. PMID:23526367

  1. Admixture mapping as a tool in gene discovery.

    Science.gov (United States)

    Seldin, Michael F

    2007-06-01

    Admixture mapping is a rapidly developing method to map susceptibility alleles in complex genetic disease associated with continental ancestry. Theoretically, when admixture between continental populations has occurred relatively recently, the chromosomal segments derived from the parental populations can be deduced from the differences in genotype allele frequencies. Progress in computational algorithms, in identification of ancestry informative single nucleotide polymorphisms, and in recent studies applying these tools suggests that this approach will complement other strategies for identifying the variation that underlies many complex diseases.

  2. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations.

    Science.gov (United States)

    Omberg, Larsson; Salit, Jacqueline; Hackett, Neil; Fuller, Jennifer; Matthew, Rebecca; Chouchane, Lotfi; Rodriguez-Flores, Juan L; Bustamante, Carlos; Crystal, Ronald G; Mezey, Jason G

    2012-06-26

    Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

  3. Admixture estimates for Caracas, Venezuela, based on autosomal, Y-chromosome, and mtDNA markers.

    Science.gov (United States)

    Martínez, Helios; Rodríguez-Larralde, Alvaro; Izaguirre, Mary Helen; De Guerra, Dinorah Castro

    2007-04-01

    The present Venezuelan population is the product of admixture of Amerindians, Europeans, and Africans, a process that was not homogeneous throughout the country. Blood groups, short tandem repeats (STRs), mtDNA, and Y-chromosome markers have been used successfully in admixture studies, but few such studies have been conducted in Venezuela. In this study we aim to estimate the admixture components of samples from two different socioeconomic levels from Caracas, Venezuela's capital city, compare their differences, and infer sexual asymmetry in the European Amerindian union patterns. Gene frequencies for blood groups ABO and Rh (CDE) and for the STRs VWA, F13A01, and FES/FPS and mtDNA and Y-chromosome haplogroups were studied in a sample of 60 individuals living in Caracas, taken from a private clinic (high socioeconomic level), and 50 individuals, also living in Caracas, drawn from a public maternity clinic (low socioeconomic level). The admixture analysis for the five autosomal markers gives a high European component (0.78) and an almost negligible African sub-Saharan component (0.06) for the high socioeconomic level, whereas for the low socioeconomic level the sub-Saharan, European, and Amerindian components were 0.21, 0.42, and 0.36, respectively. Estimates of admixture based on mtDNA and Y-chromosome markers reveal that the Amerindian contribution to these Caracas samples is almost entirely through females, because the Y-chromosome Amerindian and African sub-Saharan chromosomes found in this study were scarce. Our study reveals that the identification of the grandparents' geographic origin is an important methodological aspect to take into account in genetic studies related to the reconstruction of historical events.

  4. Geographic patterns of genome admixture in Latin American Mestizos.

    Science.gov (United States)

    Wang, Sijia; Ray, Nicolas; Rojas, Winston; Parra, Maria V; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Mazzotti, Guido; Hill, Kim; Hurtado, Ana M; Camrena, Beatriz; Nicolini, Humberto; Klitz, William; Barrantes, Ramiro; Molina, Julio A; Freimer, Nelson B; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, Maria L; Tsuneto, Luiza T; Dipierri, José E; Alfaro, Emma L; Bailliet, Graciela; Bianchi, Nestor O; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Ruiz-Linares, Andrés

    2008-03-21

    The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.

  5. Geographic patterns of genome admixture in Latin American Mestizos.

    Directory of Open Access Journals (Sweden)

    Sijia Wang

    2008-03-01

    Full Text Available The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.

  6. Geographic Patterns of Genome Admixture in Latin American Mestizos

    Science.gov (United States)

    Wang, Sijia; Ray, Nicolas; Rojas, Winston; Parra, Maria V.; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M.; Camrena, Beatriz; Nicolini, Humberto; Klitz, William; Barrantes, Ramiro; Molina, Julio A.; Freimer, Nelson B.; Bortolini, Maria Cátira; Salzano, Francisco M.; Petzl-Erler, Maria L.; Tsuneto, Luiza T.; Dipierri, José E.; Alfaro, Emma L.; Bailliet, Graciela; Bianchi, Nestor O.; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Ruiz-Linares, Andrés

    2008-01-01

    The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region. PMID:18369456

  7. Genetic diversity of Poa pratensis L. depending on geographical origin and compared with genetic markers

    Directory of Open Access Journals (Sweden)

    Magdalena Szenejko

    2016-09-01

    Full Text Available Background Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. Methods The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA. Results The low value of Dice’s coefficient (0.369 along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. Discussion The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability.

  8. Genetic Study on Jade as the Origin of Chinese Civilization

    Directory of Open Access Journals (Sweden)

    Juan Wu

    2016-05-01

    Full Text Available This paper, based on the recent scholarship by Chinese mythologists’ on jade ideology, introduces the theoretical and methodological innovation of Chinese mythology, explores the genetic mechanism of Jade-as-God model, exams the integrated function of jade in the material and spiritual resource possession and distribution, analyzes its relation with the Chinese cultural origin and demonstrates the necessity and capacity of inter-disciplinary interpretation.

  9. Admixture, Population Structure, and F-Statistics.

    Science.gov (United States)

    Peter, Benjamin M

    2016-04-01

    Many questions about human genetic history can be addressed by examining the patterns of shared genetic variation between sets of populations. A useful methodological framework for this purpose isF-statistics that measure shared genetic drift between sets of two, three, and four populations and can be used to test simple and complex hypotheses about admixture between populations. This article provides context from phylogenetic and population genetic theory. I review how F-statistics can be interpreted as branch lengths or paths and derive new interpretations, using coalescent theory. I further show that the admixture tests can be interpreted as testing general properties of phylogenies, allowing extension of some ideas applications to arbitrary phylogenetic trees. The new results are used to investigate the behavior of the statistics under different models of population structure and show how population substructure complicates inference. The results lead to simplified estimators in many cases, and I recommend to replace F3 with the average number of pairwise differences for estimating population divergence. Copyright © 2016 by the Genetics Society of America.

  10. Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia

    Science.gov (United States)

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages. PMID:24376692

  11. Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia.

    Science.gov (United States)

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.

  12. Genetic diversity and maternal origin of Bangladeshi chicken.

    Science.gov (United States)

    Bhuiyan, M S A; Chen, Shanyuan; Faruque, S; Bhuiyan, A K F H; Beja-Pereira, Albano

    2013-06-01

    Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (ΦST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of

  13. GENETIC DIVERSITY AND THE ORIGINS OF CULTURAL FRAGMENTATION

    Science.gov (United States)

    Ashraf, Quamrul; Galor, Oded

    2013-01-01

    Despite the importance attributed to the effects of diversity on the stability and prosperity of nations, the origins of the uneven distribution of ethnic and cultural fragmentation across countries have been underexplored. Building on the role of deeply-rooted biogeographical forces in comparative development, this research empirically demonstrates that genetic diversity, predominantly determined during the prehistoric “out of Africa” migration of humans, is an underlying cause of various existing manifestations of ethnolinguistic heterogeneity. Further exploration of this uncharted territory may revolutionize the understanding of the effects of deeply-rooted factors on economic development and the composition of human capital across the globe. PMID:25506084

  14. Analysis of Ethnic Admixture in Prostate Cancer

    Science.gov (United States)

    2007-12-01

    5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-06-1-0181 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Cathryn Bock, Ph.D. 5d. PROJECT NUMBER...Our project uses a novel approach to gene discovery with greater power to detect genetic effects, admixture mapping, to identify prostate cancer...available through HapMap . Because ParAllele was out of business when we were ready to genotype, we used a panel of 1536 ancestry informative SNPs

  15. Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

    Science.gov (United States)

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  16. Human Genetic Ancestral Composition Correlates with the Origin of Mycobacterium leprae Strains in a Leprosy Endemic Population

    Science.gov (United States)

    Cardona-Castro, Nora; Cortés, Edwin; Beltrán, Camilo; Romero, Marcela; Badel-Mogollón, Jaime E.; Bedoya, Gabriel

    2015-01-01

    Recent reports have suggested that leprosy originated in Africa, extended to Asia and Europe, and arrived in the Americas during European colonization and the African slave trade. Due to colonization, the contemporary Colombian population is an admixture of Native-American, European and African ancestries. Because microorganisms are known to accompany humans during migrations, patterns of human migration can be traced by examining genomic changes in associated microbes. The current study analyzed 118 leprosy cases and 116 unrelated controls from two Colombian regions endemic for leprosy (Atlantic and Andean) in order to determine possible associations of leprosy with patient ancestral background (determined using 36 ancestry informative markers), Mycobacterium leprae genotype and/or patient geographical origin. We found significant differences between ancestral genetic composition. European components were predominant in Andean populations. In contrast, African components were higher in the Atlantic region. M. leprae genotypes were then analyzed for cluster associations and compared with the ancestral composition of leprosy patients. Two M. leprae principal clusters were found: haplotypes C54 and T45. Haplotype C54 associated with African origin and was more frequent in patients from the Atlantic region with a high African component. In contrast, haplotype T45 associated with European origin and was more frequent in Andean patients with a higher European component. These results suggest that the human and M. leprae genomes have co-existed since the African and European origins of the disease, with leprosy ultimately arriving in Colombia during colonization. Distinct M. leprae strains followed European and African settlement in the country and can be detected in contemporary Colombian populations. PMID:26360617

  17. Human Genetic Ancestral Composition Correlates with the Origin of Mycobacterium leprae Strains in a Leprosy Endemic Population.

    Science.gov (United States)

    Cardona-Castro, Nora; Cortés, Edwin; Beltrán, Camilo; Romero, Marcela; Badel-Mogollón, Jaime E; Bedoya, Gabriel

    2015-01-01

    Recent reports have suggested that leprosy originated in Africa, extended to Asia and Europe, and arrived in the Americas during European colonization and the African slave trade. Due to colonization, the contemporary Colombian population is an admixture of Native-American, European and African ancestries. Because microorganisms are known to accompany humans during migrations, patterns of human migration can be traced by examining genomic changes in associated microbes. The current study analyzed 118 leprosy cases and 116 unrelated controls from two Colombian regions endemic for leprosy (Atlantic and Andean) in order to determine possible associations of leprosy with patient ancestral background (determined using 36 ancestry informative markers), Mycobacterium leprae genotype and/or patient geographical origin. We found significant differences between ancestral genetic composition. European components were predominant in Andean populations. In contrast, African components were higher in the Atlantic region. M. leprae genotypes were then analyzed for cluster associations and compared with the ancestral composition of leprosy patients. Two M. leprae principal clusters were found: haplotypes C54 and T45. Haplotype C54 associated with African origin and was more frequent in patients from the Atlantic region with a high African component. In contrast, haplotype T45 associated with European origin and was more frequent in Andean patients with a higher European component. These results suggest that the human and M. leprae genomes have co-existed since the African and European origins of the disease, with leprosy ultimately arriving in Colombia during colonization. Distinct M. leprae strains followed European and African settlement in the country and can be detected in contemporary Colombian populations.

  18. Wildlife forensic science: A review of genetic geographic origin assignment.

    Science.gov (United States)

    Ogden, Rob; Linacre, Adrian

    2015-09-01

    Wildlife forensic science has become a key means of enforcing legislation surrounding the illegal trade in protected and endangered species. A relatively new dimension to this area of forensic science is to determine the geographic origin of a seized sample. This review focuses on DNA testing, which relies on assignment of an unknown sample to its genetic population of origin. Key examples of this are the trade in timber, fish and ivory and these are used only to illustrate the large number of species for which this type of testing is potentially available. The role of mitochondrial and nuclear DNA markers is discussed, alongside a comparison of neutral markers with those exhibiting signatures of selection, which potentially offer much higher levels of assignment power to address specific questions. A review of assignment tests is presented along with detailed methods for evaluating error rates and considerations for marker selection. The availability and quality of reference data are of paramount importance to support assignment applications and ensure reliability of any conclusions drawn. The genetic methods discussed have been developed initially as investigative tools but comment is made regarding their use in courts. The potential to compliment DNA markers with elemental assays for greater assignment power is considered and finally recommendations are made for the future of this type of testing. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. Complex genetic origin of Indian populations and its implications

    Indian Academy of Sciences (India)

    Rakesh Tamang; Lalji Singh; Kumarasamy Thangaraj

    2012-11-01

    Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000 years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.

  20. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

    Directory of Open Access Journals (Sweden)

    Omberg Larsson

    2012-06-01

    Full Text Available Abstract Background Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Results Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. Conclusions By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

  1. Genetic perspectives on the origin of clicks in Bantu languages from southwestern Zambia.

    Science.gov (United States)

    Barbieri, Chiara; Butthof, Anne; Bostoen, Koen; Pakendorf, Brigitte

    2013-04-01

    Some Bantu languages spoken in southwestern Zambia and neighboring regions of Botswana, Namibia, and Angola are characterized by the presence of click consonants, whereas their closest linguistic relatives lack such clicks. As clicks are a typical feature not of the Bantu language family, but of Khoisan languages, it is highly probable that the Bantu languages in question borrowed the clicks from Khoisan languages. In this paper, we combine complete mitochondrial genome sequences from a representative sample of populations from the Western Province of Zambia speaking Bantu languages with and without clicks, with fine-scaled analyses of Y-chromosomal single nucleotide polymorphisms and short tandem repeats to investigate the prehistoric contact that led to this borrowing of click consonants. Our results reveal complex population-specific histories, with female-biased admixture from Khoisan-speaking groups associated with the incorporation of click sounds in one Bantu-speaking population, while concomitant levels of potential Khoisan admixture did not result in sound change in another. Furthermore, the lack of sequence sharing between the Bantu-speaking groups from southwestern Zambia investigated here and extant Khoisan populations provides an indication that there must have been genetic substructure in the Khoisan-speaking indigenous groups of southern Africa that did not survive until the present or has been substantially reduced.

  2. A genome wide pattern of population structure and admixture in peninsular Malaysia Malays.

    Science.gov (United States)

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Etemad, Ali; Jin, Wenfei; Qin, Pengfei; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Limprasert, Pornprot; Feisal, Merican Amir; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2014-12-01

    The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit; the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative (PASNPI) Consortium and International HapMap project database. We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced back to have shared a common ancestor with the Proto-Malays and Chinese. These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided valuable information on the enigmatic demographical history as well as shed some insights into the origins of the Malays in the Malay Peninsula.

  3. Autosomal admixture levels are informative about sex bias in admixed populations.

    Science.gov (United States)

    Goldberg, Amy; Verdu, Paul; Rosenberg, Noah A

    2014-11-01

    Sex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and functions of quantities computed from sex chromosomes and autosomes have often been examined to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu and Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach suggests that it may be possible to use the effect of sex-biased admixture on autosomal DNA to assist with methods for inference of the history of complex sex-biased admixture processes.

  4. Origin and evolution of the genetic code: the universal enigma.

    Science.gov (United States)

    Koonin, Eugene V; Novozhilov, Artem S

    2009-02-01

    The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly nonrandom. The three main concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physicochemical affinity between amino acids and the cognate codons (anticodons); the coevolution theory, which posits that the code structure coevolved with amino acid biosynthesis pathways; and the error minimization theory under which selection to minimize the adverse effect of point mutations and translation errors was the principal factor of the code's evolution. These theories are not mutually exclusive and are also compatible with the frozen accident hypothesis, that is, the notion that the standard code might have no special properties but was fixed simply because all extant life forms share a common ancestor, with subsequent changes to the code, mostly, precluded by the deleterious effect of codon reassignment. Mathematical analysis of the structure and possible evolutionary trajectories of the code shows that it is highly robust to translational misreading but there are numerous more robust codes, so the standard code potentially could evolve from a random code via a short sequence of codon series reassignments. Thus, much of the evolution that led to the standard code could be a combination of frozen accident with selection for error minimization although contributions from coevolution of the code with metabolic pathways and weak affinities between amino acids and nucleotide triplets cannot be ruled out. However, such scenarios for the code evolution are based on formal schemes whose relevance to the actual primordial evolution is uncertain. A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system.

  5. Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping.

    Science.gov (United States)

    Marcano, Maria; Pugh, Tatiana; Cros, Emile; Morales, Sonia; Portillo Páez, Elvis A; Courtois, Brigitte; Glaszmann, Jean Christophe; Engels, Jan M M; Phillips, Wilbert; Astorga, Carlos; Risterucci, Ange Marie; Fouet, Olivier; González, Ventura; Rosenberg, Kai; Vallat, Isabelle; Dagert, Manuel; Lanaud, Claire

    2007-03-01

    A sound understanding of crop history can provide the basis for deriving novel genetic information through admixture mapping. We confirmed this, by using characterization data from an international collection of cocoa, collected 25 years ago, and from a contemporary plantation. We focus on the trees derived from three centuries of admixture between Meso-American Criollo and South American Forastero genomes. In both cacao sets of individuals, linkage disequilibrium extended over long genetic distances along chromosome regions, as expected in populations derived from recent admixture. Based on loose genome scans, genomic regions involved in useful traits were identified. Fifteen genomic regions involved in seed and fruit weight variation were highlighted. They correspond to ten previously identified QTLs and five novel ones. Admixture mapping can help to add value to genetic resources and thus, help to encourage investment in their conservation.

  6. Patterns of admixture and population structure in native populations of Northwest North America.

    Science.gov (United States)

    Verdu, Paul; Pemberton, Trevor J; Laurent, Romain; Kemp, Brian M; Gonzalez-Oliver, Angelica; Gorodezky, Clara; Hughes, Cris E; Shattuck, Milena R; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; William, Theresa; Worl, Rosita; Cybulski, Jerome S; Rosenberg, Noah A; Malhi, Ripan S

    2014-08-01

    The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

  7. Patterns of admixture and population structure in native populations of Northwest North America.

    Directory of Open Access Journals (Sweden)

    Paul Verdu

    2014-08-01

    Full Text Available The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

  8. North African populations carry the signature of admixture with Neandertals.

    Directory of Open Access Journals (Sweden)

    Federico Sánchez-Quinto

    Full Text Available One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

  9. Original Paper Patterns of genetic structure and phenotypic diversity ...

    African Journals Online (AJOL)

    Patterns of genetic structure and phenotypic diversity in sorghum landraces in relation to farmers' management in Burkina Faso ... the role of farmer practices in phenotypic and genetic evolution of sorghum. ... varieties to marginal environments such as ...... Supporting the Convention on Biological ... A new method to.

  10. Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method.

    Directory of Open Access Journals (Sweden)

    Emile R Chimusa

    Full Text Available Admixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes. We applied this approach to a complex, uniquely admixed South African population. Using genome-wide SNP data from over 764 individuals, we accurately estimate the genetic contributions from the best ancestral populations: isiXhosa [Formula: see text], ‡Khomani SAN [Formula: see text], European [Formula: see text], Indian [Formula: see text], and Chinese [Formula: see text]. We also demonstrate that the ancestral allele frequency differences correlate with increased linkage disequilibrium in the South African population, which originates from admixture events rather than population bottlenecks.The collective term for people of mixed ancestry in southern Africa is "Coloured," and this is officially recognized in South

  11. Shared genetic origins of allergy and autoimmune diseases

    DEFF Research Database (Denmark)

    Waage, J. E.; Kreiner-Møller, E.; Standl, M.

    2015-01-01

    Parallel increases in allergy and autoimmune disease prevalence in recent time suggest shared, but yet unknown, etiologies. Here, we investigated shared genetic loci and molecular pathways to identify possible shared disease mechanisms between allergy and autoimmune diseases....

  12. Calculating expected DNA remnants from ancient founding events in human population genetics

    Directory of Open Access Journals (Sweden)

    Stacey Andrew

    2008-10-01

    Full Text Available Abstract Background Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current human population studies and what these studies infer about past population structure. Final mean allele frequencies varied from 0.0005 to over 0.50, depending on the parameters. Conclusion The results of the simulations illustrate that, while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible.

  13. Ancestry inference in complex admixtures via variable-length Markov chain linkage models.

    Science.gov (United States)

    Rodriguez, Jesse M; Bercovici, Sivan; Elmore, Megan; Batzoglou, Serafim

    2013-03-01

    Inferring the ancestral origin of chromosomal segments in admixed individuals is key for genetic applications, ranging from analyzing population demographics and history, to mapping disease genes. Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes. In this paper we introduce ALLOY, an efficient method that incorporates generalized, but highly expressive, linkage disequilibrium models. ALLOY applies a factorial hidden Markov model to capture the parallel process producing the maternal and paternal admixed haplotypes, and models the background linkage disequilibrium in the ancestral populations via an inhomogeneous variable-length Markov chain. We test ALLOY in a broad range of scenarios ranging from recent to ancient admixtures with up to four ancestral populations. We show that ALLOY outperforms the previous state of the art, and is robust to uncertainties in model parameters.

  14. New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East.

    Science.gov (United States)

    Thomas, Mark G; Barnes, Ian; Weale, Michael E; Jones, Abigail L; Forster, Peter; Bradman, Neil; Pramstaller, Peter P

    2008-01-01

    The Alps are one of the most significant geographical barriers in Europe and several isolated Swiss and Italian valleys retain the distinctive Ladin and Romansch languages, alongside the modern majority of Italian and German languages. Linguistically, Ladin belongs to the Romance languages, but some studies on mitochondrial DNA (mtDNA) variation have suggested a major Middle Eastern component to their genealogical origin. Furthermore, an observed high degree of within-population diversity has been interpreted as reflecting long-standing differentiation from other European populations and the absence of a major bottleneck in Ladin population history. To explore these issues further, we examined Y chromosome and mtDNA variation in two samples of Ladin speakers, two samples of German speakers and one sample of metropolitan Italian speakers. Our results (1) indicate reduced diversity in the Ladin-speaking and isolated German-speaking populations when compared to a sample of metropolitan Italian speakers, (2) fail to identify haplotypes that are rare in other European populations that other researchers have identified, and (3) indicate different Middle Eastern components to Ladin ancestry in different localities. These new results, in combination with Bayesian estimation of demographic parameters of interest (population size, population growth rate, and Palaeolithic/Neolithic admixture proportions) and phylogeographic analysis, suggest that the Ladin groups under study are small genetically isolated populations (subject to strong genetic drift), having a predominantly European ancestry, and in one locality, may have a greater Palaeolithic component to that ancestry than their neighbours.

  15. Origins of biological information and the genetic code

    Science.gov (United States)

    Fox, S. W.

    1974-01-01

    Information, defined as the capacity of a molecule or system for selective interactions with other molecules or systems, is followed through its evolution from prebiological information to protoribosomes. Emphasis is on proteins and protein-like polymers, and later on ATP. The research will contribute more to the understanding of the essence of the genetic mechanism.

  16. Behavioral Genetic Toolkits: Toward the Evolutionary Origins of Complex Phenotypes.

    Science.gov (United States)

    Rittschof, C C; Robinson, G E

    2016-01-01

    The discovery of toolkit genes, which are highly conserved genes that consistently regulate the development of similar morphological phenotypes across diverse species, is one of the most well-known observations in the field of evolutionary developmental biology. Surprisingly, this phenomenon is also relevant for a wide array of behavioral phenotypes, despite the fact that these phenotypes are highly complex and regulated by many genes operating in diverse tissues. In this chapter, we review the use of the toolkit concept in the context of behavior, noting the challenges of comparing behaviors and genes across diverse species, but emphasizing the successes in identifying genetic toolkits for behavior; these successes are largely attributable to the creative research approaches fueled by advances in behavioral genomics. We have two general goals: (1) to acknowledge the groundbreaking progress in this field, which offers new approaches to the difficult but exciting challenge of understanding the evolutionary genetic basis of behaviors, some of the most complex phenotypes known, and (2) to provide a theoretical framework that encompasses the scope of behavioral genetic toolkit studies in order to clearly articulate the research questions relevant to the toolkit concept. We emphasize areas for growth and highlight the emerging approaches that are being used to drive the field forward. Behavioral genetic toolkit research has elevated the use of integrative and comparative approaches in the study of behavior, with potentially broad implications for evolutionary biologists and behavioral ecologists alike.

  17. Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci.

    Science.gov (United States)

    Chakraborty, R; Weiss, K M

    1988-12-01

    Admixture between genetically different populations may produce gametic association between gene loci as a function of the genetic difference between parental populations and the admixture rate. This association decays as a function of time since admixture and the recombination rate between the loci. Admixture between genetically long-separated human populations has been frequent in the centuries since the age of exploration and colonization, resulting in numerous hybrid descendant populations today, as in the Americas. This represents a natural experiment for genetic epidemiology and anthropology, in which to use polymorphic marker loci (e.g., restriction fragment length polymorphisms) and disequilibrium to infer a genetic basis for traits of interest. In this paper we show that substantial disequilibrium remains today under widely applicable situations, which can be detected without requiring inordinately close linkage between trait and marker loci. Very disparate parental allele frequencies produce large disequilibrium, but the sample size needed to detect such levels of disequilibrium can be large due to the skewed haplotype frequency distribution in the admixed population. Such situations, however, provide power to differentiate between disequilibrium due just to population mixing from that due to physical linkage of loci--i.e., to help map the genetic locus of the trait. A gradient of admixture levels between the same parental populations may be used to test genetic models by relating admixture to disequilibrium levels.

  18. Valorization of Local Mineral Admixtures in Concretes

    Directory of Open Access Journals (Sweden)

    Boudchicha Abdelaziz

    2014-04-01

    Full Text Available This study is an extension of previous researches on mortars with mineral admixtures and super-plasticizers. In this way, the same methodology was applied to concretes and the use of mineral admixture was limited to low cost materials available in Algeria as limestone, pozzolan and blast furnace slag, with current cement and super-plasticizer. The experimental methodology used was based on the volume substitution of the cement by admixtures in mixtures with the absolute volume of the solid phases and workability preserved constant. The main results achieved showed that the super-plasticizer demand of concretes depends on the nature and the quantity of the incorporated admixture. The combined use of admixtures and super-plasticizer has generally a favourable effect on compressive strengths at 07 and 28 days at low rates of cement substitution, which vary significantly with the nature, fineness and quantity of the used admixtures. At 07 days, limestone admixtures give better improvements and reach more than 20 % of gain to the compressive strength of the reference concrete with no admixtures or super-plasticizer, at 10 % of the cement substitution and still better until 30 %. At 28 days, blast furnace slag admixtures give better improvements at 28 days and reach more than 20 % of gain to the compressive strength of the reference concrete at 20 % of the cement substitution and still better until 30 %. This contribution to the compressive strength is explained on the one hand by the reduction of the quantity of water in the mixtures at the same consistency, by the use of the super-plasticizer and on another hand by the activity of Limestone admixtures at early ages and to the latent hydraulic properties of blast furnace slag at 28 days.

  19. The Evolutionary Origin and Genetic Makeup of Domestic Horses.

    Science.gov (United States)

    Librado, Pablo; Fages, Antoine; Gaunitz, Charleen; Leonardi, Michela; Wagner, Stefanie; Khan, Naveed; Hanghøj, Kristian; Alquraishi, Saleh A; Alfarhan, Ahmed H; Al-Rasheid, Khaled A; Der Sarkissian, Clio; Schubert, Mikkel; Orlando, Ludovic

    2016-10-01

    The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses. Copyright © 2016 by the Genetics Society of America.

  20. Archaeological and genetic insights into the origins of domesticated rice.

    Science.gov (United States)

    Gross, Briana L; Zhao, Zhijun

    2014-04-29

    Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world's population. Research into when, where, and how rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica. These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication.

  1. Archaeological and genetic insights into the origins of domesticated rice

    Science.gov (United States)

    Gross, Briana L.; Zhao, Zhijun

    2014-01-01

    Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world’s population. Research into when, where, and how rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica. These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication. PMID:24753573

  2. Population admixture, biological invasions and the balance between local adaptation and inbreeding depression

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Macel, M.; Wolfe, L.M.; Biere, A.

    2011-01-01

    When previously isolated populations meet and mix, the resulting admixed population can benefit from several genetic advantages, including increased genetic variation, the creation of novel genotypes and the masking of deleterious mutations. These admixture benefits are thought to play an important

  3. Population admixture, biological invasions and the balance between local adaptation and inbreeding depression

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Macel, M.; Wolfe, L.M.; Biere, A.

    2011-01-01

    When previously isolated populations meet and mix, the resulting admixed population can benefit from several genetic advantages, including increased genetic variation, the creation of novel genotypes and the masking of deleterious mutations. These admixture benefits are thought to play an important

  4. On the possible origin and evolution of the genetic code

    Science.gov (United States)

    Jukes, T. H.

    1974-01-01

    The genetic code is examined for indications of possible preceding codes that existed during early evolution. Eight of the 20 amino acids are coded by 'quartets' of codons with fourfold degeneracy, and 16 such quartets can exist, so that an earlier code could have provided for 15 or 16 amino acids, rather than 20. If twofold degeneracy is postulated for the first position of the codon, there could have been ten amino acids in the code. It is speculated that these may have been phenylalanine, valine, proline, alanine, histidine, glutamine, glutanic acid, aspartic acid, cysteine and glycine. There is a notable deficiency of arginine in proteins, despite the fact that it has six codons. Simultaneously, there is more lysine in proteins than would be expected from its two codons, if the four bases in mRNA are equiprobable and are arranged randomly. It is speculated that arginine is an 'intruder' into the genetic code, and that it may have displayed another amino acid such as ornithine, or may even have displayed lysine from some of its previous codon assignments. As a result, natural selection has favored lysine against the fact that it has only two codons.

  5. On the possible origin and evolution of the genetic code

    Science.gov (United States)

    Jukes, T. H.

    1974-01-01

    The genetic code is examined for indications of possible preceding codes that existed during early evolution. Eight of the 20 amino acids are coded by 'quartets' of codons with fourfold degeneracy, and 16 such quartets can exist, so that an earlier code could have provided for 15 or 16 amino acids, rather than 20. If twofold degeneracy is postulated for the first position of the codon, there could have been ten amino acids in the code. It is speculated that these may have been phenylalanine, valine, proline, alanine, histidine, glutamine, glutanic acid, aspartic acid, cysteine and glycine. There is a notable deficiency of arginine in proteins, despite the fact that it has six codons. Simultaneously, there is more lysine in proteins than would be expected from its two codons, if the four bases in mRNA are equiprobable and are arranged randomly. It is speculated that arginine is an 'intruder' into the genetic code, and that it may have displayed another amino acid such as ornithine, or may even have displayed lysine from some of its previous codon assignments. As a result, natural selection has favored lysine against the fact that it has only two codons.

  6. Etiology of valvular heart disease-genetic and developmental origins.

    Science.gov (United States)

    Lincoln, Joy; Garg, Vidu

    2014-01-01

    Valvular heart disease occurs as either a congenital or acquired condition and advances in medical care have resulted in valve disease becoming increasingly prevalent. Unfortunately, treatments remain inadequate because of our limited understanding of the genetic and molecular etiology of diseases affecting the heart valves. Therefore, surgical repair or replacement remains the most effective option, which comes with additional complications and no guarantee of life-long success. Over the past decade, there have been significant advances in our understanding of cardiac valve development and, not surprisingly, mutations in these developmental genes have been identified in humans with congenital valve malformations. Concurrently, there has been a greater realization that acquired valve disease is not simply a degenerative process. Molecular investigation of acquired valve disease has identified that numerous signaling pathways critical for normal valve development are re-expressed in diseased valves. This review will discuss recent advances in our understanding of the development of the heart valves, as well as the implications of these findings on the genetics of congenital and acquired valvular heart disease.

  7. Origin and Evolution of the Universal Genetic Code.

    Science.gov (United States)

    Koonin, Eugene V; Novozhilov, Artem S

    2017-08-30

    The standard genetic code (SGC) is virtually universal among extant life forms. Although many deviations from the universal code exist, particularly in organelles and prokaryotes with small genomes, they are limited in scope and obviously secondary. The universality of the code likely results from the combination of a frozen accident, i.e., the deleterious effect of codon reassignment in the SGC, and the inhibitory effect of changes in the code on horizontal gene transfer. The structure of the SGC is nonrandom and ensures high robustness of the code to mutational and translational errors. However, this error minimization is most likely a by-product of the primordial code expansion driven by the diversification of the repertoire of protein amino acids, rather than a direct result of selection. Phylogenetic analysis of translation system components, in particular aminoacyl-tRNA synthetases, shows that, at a stage of evolution when the translation system had already attained high fidelity, the correspondence between amino acids and cognate codons was determined by recognition of amino acids by RNA molecules, i.e., proto-tRNAs. We propose an experimentally testable scenario for the evolution of the code that combines recognition of amino acids by unique sites on proto-tRNAs (distinct from the anticodons), expansion of the code via proto-tRNA duplication, and frozen accident. Expected final online publication date for the Annual Review of Genetics Volume 51 is November 23, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  8. Origins of magic: review of genetic and epigenetic effects.

    Science.gov (United States)

    Ramagopalan, Sreeram V; Knight, Marian; Ebers, George C; Knight, Julian C

    2007-12-22

    To assess the evidence for a genetic basis to magic. Literature review. Harry Potter novels of J K Rowling. Muggles, witches, wizards, and squibs. Limited. Family and twin studies, magical ability, and specific magical skills. Magic shows strong evidence of heritability, with familial aggregation and concordance in twins. Evidence suggests magical ability to be a quantitative trait. Specific magical skills, notably being able to speak to snakes, predict the future, and change hair colour, all seem heritable. A multilocus model with a dominant gene for magic might exist, controlled epistatically by one or more loci, possibly recessive in nature. Magical enhancers regulating gene expressionmay be involved, combined with mutations at specific genes implicated in speech and hair colour such as FOXP2 and MCR1.

  9. A Novel Admixture-Based Pharmacogenetic Approach to Refine Warfarin Dosing in Caribbean Hispanics.

    Directory of Open Access Journals (Sweden)

    Jorge Duconge

    Full Text Available This study is aimed at developing a novel admixture-adjusted pharmacogenomic approach to individually refine warfarin dosing in Caribbean Hispanic patients.A multiple linear regression analysis of effective warfarin doses versus relevant genotypes, admixture, clinical and demographic factors was performed in 255 patients and further validated externally in another cohort of 55 individuals.The admixture-adjusted, genotype-guided warfarin dosing refinement algorithm developed in Caribbean Hispanics showed better predictability (R2 = 0.70, MAE = 0.72mg/day than a clinical algorithm that excluded genotypes and admixture (R2 = 0.60, MAE = 0.99mg/day, and outperformed two prior pharmacogenetic algorithms in predicting effective dose in this population. For patients at the highest risk of adverse events, 45.5% of the dose predictions using the developed pharmacogenetic model resulted in ideal dose as compared with only 29% when using the clinical non-genetic algorithm (p<0.001. The admixture-driven pharmacogenetic algorithm predicted 58% of warfarin dose variance when externally validated in 55 individuals from an independent validation cohort (MAE = 0.89 mg/day, 24% mean bias.Results supported our rationale to incorporate individual's genotypes and unique admixture metrics into pharmacogenetic refinement models in order to increase predictability when expanding them to admixed populations like Caribbean Hispanics.ClinicalTrials.gov NCT01318057.

  10. Complex patterns of genomic admixture within southern Africa.

    Directory of Open Access Journals (Sweden)

    Desiree C Petersen

    Full Text Available Within-population genetic diversity is greatest within Africa, while between-population genetic diversity is directly proportional to geographic distance. The most divergent contemporary human populations include the click-speaking forager peoples of southern Africa, broadly defined as Khoesan. Both intra- (Bantu expansion and inter-continental migration (European-driven colonization have resulted in complex patterns of admixture between ancient geographically isolated Khoesan and more recently diverged populations. Using gender-specific analysis and almost 1 million autosomal markers, we determine the significance of estimated ancestral contributions that have shaped five contemporary southern African populations in a cohort of 103 individuals. Limited by lack of available data for homogenous Khoesan representation, we identify the Ju/'hoan (n = 19 as a distinct early diverging human lineage with little to no significant non-Khoesan contribution. In contrast to the Ju/'hoan, we identify ancient signatures of Khoesan and Bantu unions resulting in significant Khoesan- and Bantu-derived contributions to the Southern Bantu amaXhosa (n = 15 and Khoesan !Xun (n = 14, respectively. Our data further suggests that contemporary !Xun represent distinct Khoesan prehistories. Khoesan assimilation with European settlement at the most southern tip of Africa resulted in significant ancestral Khoesan contributions to the Coloured (n = 25 and Baster (n = 30 populations. The latter populations were further impacted by 170 years of East Indian slave trade and intra-continental migrations resulting in a complex pattern of genetic variation (admixture. The populations of southern Africa provide a unique opportunity to investigate the genomic variability from some of the oldest human lineages to the implications of complex admixture patterns including ancient and recently diverged human lineages.

  11. Complex patterns of genomic admixture within southern Africa.

    Science.gov (United States)

    Petersen, Desiree C; Libiger, Ondrej; Tindall, Elizabeth A; Hardie, Rae-Anne; Hannick, Linda I; Glashoff, Richard H; Mukerji, Mitali; Fernandez, Pedro; Haacke, Wilfrid; Schork, Nicholas J; Hayes, Vanessa M

    2013-01-01

    Within-population genetic diversity is greatest within Africa, while between-population genetic diversity is directly proportional to geographic distance. The most divergent contemporary human populations include the click-speaking forager peoples of southern Africa, broadly defined as Khoesan. Both intra- (Bantu expansion) and inter-continental migration (European-driven colonization) have resulted in complex patterns of admixture between ancient geographically isolated Khoesan and more recently diverged populations. Using gender-specific analysis and almost 1 million autosomal markers, we determine the significance of estimated ancestral contributions that have shaped five contemporary southern African populations in a cohort of 103 individuals. Limited by lack of available data for homogenous Khoesan representation, we identify the Ju/'hoan (n = 19) as a distinct early diverging human lineage with little to no significant non-Khoesan contribution. In contrast to the Ju/'hoan, we identify ancient signatures of Khoesan and Bantu unions resulting in significant Khoesan- and Bantu-derived contributions to the Southern Bantu amaXhosa (n = 15) and Khoesan !Xun (n = 14), respectively. Our data further suggests that contemporary !Xun represent distinct Khoesan prehistories. Khoesan assimilation with European settlement at the most southern tip of Africa resulted in significant ancestral Khoesan contributions to the Coloured (n = 25) and Baster (n = 30) populations. The latter populations were further impacted by 170 years of East Indian slave trade and intra-continental migrations resulting in a complex pattern of genetic variation (admixture). The populations of southern Africa provide a unique opportunity to investigate the genomic variability from some of the oldest human lineages to the implications of complex admixture patterns including ancient and recently diverged human lineages.

  12. Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.

    Directory of Open Access Journals (Sweden)

    Rui Pereira

    Full Text Available Ancestry-informative markers (AIMs show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies. This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American. All markers are analyzed in short fragments (under 230 basepairs through a single PCR followed by capillary electrophoresis (CE allowing a very simple one tube PCR-to-CE approach. HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level. In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.

  13. Summary of evidence for an anticodonic basis for the origin of the genetic code

    Science.gov (United States)

    Lacey, J. C., Jr.; Mullins, D. W., Jr.

    1981-01-01

    This article summarizes data supporting the hypothesis that the genetic code origin was based on relationships (probably affinities) between amino acids and their anticodon nucleotides. Selective activation seems to follow from selective affinity and consequently, incorporation of amino acids into peptides can also be selective. It is suggested that these selectivities in affinity and activation, coupled with the base pairing specificities, allowed the origin of the code and the process of translation.

  14. Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates.

    Science.gov (United States)

    Cox, Murray P; Karafet, Tatiana M; Lansing, J Stephen; Sudoyo, Herawati; Hammer, Michael F

    2010-05-22

    The geographical region between mainland Asia and New Guinea is characterized by numerous small islands with isolated human populations. Phenotypically, groups in the west are similar to their neighbours in mainland Southeast Asia, eastern groups near New Guinea are similar to Melanesians, and intervening populations are intermediate in appearance. A long-standing question is whether this pattern primarily reflects mixing between groups with distinct origins or whether natural selection has shaped this range of variation by acting differentially on populations across the region. To address this question, we genotyped a set of 37 single nucleotide polymorphisms that are evolutionarily independent, putatively neutral and highly informative for Asian-Melanesian ancestry in 1430 individuals from 60 populations spanning mainland Asia to Melanesia. Admixture analysis reveals a sharp transition from Asian to Melanesian genetic variants over a narrow geographical region in eastern Indonesia. Interestingly, this admixture cline roughly corresponds to the human phenotypic boundary noted by Alfred Russell Wallace in 1869. We conclude that this phenotypic gradient probably reflects mixing of two long-separated ancestral source populations-one descended from the initial Melanesian-like inhabitants of the region, and the other related to Asian groups that immigrated during the Paleolithic and/or with the spread of agriculture. A higher frequency of Asian X-linked markers relative to autosomal markers throughout the transition zone suggests that the admixture process was sex-biased, either favouring a westward expansion of patrilocal Melanesian groups or an eastward expansion of matrilocal Asian immigrants. The matrilocal marriage practices that dominated early Austronesian societies may be one factor contributing to this observed sex bias in admixture rates.

  15. Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian–Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates

    Science.gov (United States)

    Cox, Murray P.; Karafet, Tatiana M.; Lansing, J. Stephen; Sudoyo, Herawati; Hammer, Michael F.

    2010-01-01

    The geographical region between mainland Asia and New Guinea is characterized by numerous small islands with isolated human populations. Phenotypically, groups in the west are similar to their neighbours in mainland Southeast Asia, eastern groups near New Guinea are similar to Melanesians, and intervening populations are intermediate in appearance. A long-standing question is whether this pattern primarily reflects mixing between groups with distinct origins or whether natural selection has shaped this range of variation by acting differentially on populations across the region. To address this question, we genotyped a set of 37 single nucleotide polymorphisms that are evolutionarily independent, putatively neutral and highly informative for Asian–Melanesian ancestry in 1430 individuals from 60 populations spanning mainland Asia to Melanesia. Admixture analysis reveals a sharp transition from Asian to Melanesian genetic variants over a narrow geographical region in eastern Indonesia. Interestingly, this admixture cline roughly corresponds to the human phenotypic boundary noted by Alfred Russell Wallace in 1869. We conclude that this phenotypic gradient probably reflects mixing of two long-separated ancestral source populations—one descended from the initial Melanesian-like inhabitants of the region, and the other related to Asian groups that immigrated during the Paleolithic and/or with the spread of agriculture. A higher frequency of Asian X-linked markers relative to autosomal markers throughout the transition zone suggests that the admixture process was sex-biased, either favouring a westward expansion of patrilocal Melanesian groups or an eastward expansion of matrilocal Asian immigrants. The matrilocal marriage practices that dominated early Austronesian societies may be one factor contributing to this observed sex bias in admixture rates. PMID:20106848

  16. Population evolution in 20th-century Easter Island: endogamy and admixture.

    Science.gov (United States)

    Hernández, M; García-Moro, C; Moral, P; González-Martín, A

    2000-04-01

    We studied the 20th-century evolution of the Rapanui population of Easter Island, the most geographically isolated in the world, to analyze the current process of admixture. Using parochial birth records, we determined origin of the birth parents based on their surnames. The origin of parents reveals two stages of population evolution: endogamy, due to the isolation of the island, but with a strong rejection of isonymous marriages; and admixture, beginning in 1965 with the opening of the island to the rest of the world. We used Lasker's coefficient (Lasker's Ri) and the Shannon-Weaver coefficient of diversity (H) to characterize both stages. The gene flow evaluated from admixture has increased significantly since 1965. Births from exogamous unions represented 3.5% of total births from 1937 to 1965. increased to 43.2% between 1966 and 1980, and constituted 50.8% of all births between 1981 and 1996.

  17. Estimating individual admixture proportions from next generation sequencing data

    DEFF Research Database (Denmark)

    Skotte, Line; Korneliussen, Thorfinn Sand; Albrechtsen, Anders

    2013-01-01

    Inference of population structure and individual ancestry is important both for population genetics and for association studies. With next generation sequencing technologies it is possible to obtain genetic data for all accessible genetic variations in the genome. Existing methods for admixture...... analysis rely on known genotypes. However, individual genotypes cannot be inferred from low-depth sequencing data without introducing errors. This article presents a new method for inferring an individual's ancestry that takes the uncertainty introduced in next generation sequencing data into account....... This is achieved by working directly with genotype likelihoods that contain all relevant information of the unobserved genotypes. Using simulations as well as publicly available sequencing data, we demonstrate that the presented method has great accuracy even for very low-depth data. At the same time, we...

  18. Admixture mapping identifies a locus on 6q25 associated with breast cancer risk in US Latinas

    Science.gov (United States)

    Fejerman, Laura; Chen, Gary K.; Eng, Celeste; Huntsman, Scott; Hu, Donglei; Williams, Amy; Pasaniuc, Bogdan; John, Esther M.; Via, Marc; Gignoux, Christopher; Ingles, Sue; Monroe, Kristine R.; Kolonel, Laurence N.; Torres-Mejía, Gabriela; Pérez-Stable, Eliseo J.; González Burchard, Esteban; Henderson, Brian E.; Haiman, Christopher A.; Ziv, Elad

    2012-01-01

    Among US Latinas and Mexican women, those with higher European ancestry have increased risk of breast cancer. We combined an admixture mapping and genome-wide association mapping approach to search for genomic regions that may explain this observation. Latina women with breast cancer (n= 1497) and Latina controls (n= 1272) were genotyped using Affymetrix and Illumina arrays. We inferred locus-specific genetic ancestry and compared the ancestry between cases and controls. We also performed single nucleotide polymorphism (SNP) association analyses in regions of interest. Correction for multiple-hypothesis testing was conducted using permutations (Pcorrected). We identified one region where genetic ancestry was significantly associated with breast cancer risk: 6q25 [odds ratio (OR) per Indigenous American chromosome 0.75, 95% confidence interval (CI): 0.65–0.85, P= 1.1 × 10−5, Pcorrected= 0.02]. A second region on 11p15 showed a trend towards association (OR per Indigenous American chromosome 0.77, 95% CI: 0.68–0.87, P= 4.3 × 10−5, Pcorrected= 0.08). In both regions, breast cancer risk decreased with higher Indigenous American ancestry in concordance with observations made on global ancestry. The peak of the 6q25 signal includes the estrogen receptor 1 (ESR1) gene and 5′ region, a locus previously implicated in breast cancer. Genome-wide association analysis found that a multi-SNP model explained the admixture signal in both regions. Our results confirm that the association between genetic ancestry and breast cancer risk in US Latinas is partly due to genetic differences between populations of European and Indigenous Americans origin. Fine-mapping within the 6q25 and possibly the 11p15 loci will lead to the discovery of the biologically functional variant/s behind this association. PMID:22228098

  19. Intrahepatic Cholestasis of Pregnancy (ICP) in U.S. Latinas and Chileans: Clinical features, Ancestry Analysis, and Admixture Mapping.

    Science.gov (United States)

    Bull, Laura N; Hu, Donglei; Shah, Sohela; Temple, Luisa; Silva, Karla; Huntsman, Scott; Melgar, Jennifer; Geiser, Mary T; Sanford, Ukina; Ortiz, Juan A; Lee, Richard H; Kusanovic, Juan P; Ziv, Elad; Vargas, Juan E

    2015-01-01

    In the Americas, women with Indigenous American ancestry are at increased risk of intrahepatic cholestasis of pregnancy (ICP), relative to women of other ethnicities. We hypothesized that ancestry-related genetic factors contribute to this increased risk. We collected clinical and laboratory data, and performed biochemical assays on samples from U.S. Latinas and Chilean women, with and without ICP. The study sample included 198 women with ICP (90 from California, U.S., and 108 from Chile) and 174 pregnant control women (69 from California, U.S., and 105 from Chile). SNP genotyping was performed using Affymetrix arrays. We compared overall genetic ancestry between cases and controls, and used a genome-wide admixture mapping approach to screen for ICP susceptibility loci. We identified commonalities and differences in features of ICP between the 2 countries and determined that cases had a greater proportion of Indigenous American ancestry than did controls (p = 0.034). We performed admixture mapping, taking country of origin into account, and identified one locus for which Native American ancestry was associated with increased risk of ICP at a genome-wide level of significance (P = 3.1 x 10(-5), Pcorrected = 0.035). This locus has an odds ratio of 4.48 (95% CI: 2.21-9.06) for 2 versus zero Indigenous American chromosomes. This locus lies on chromosome 2, with a 10 Mb 95% confidence interval which does not contain any previously identified hereditary 'cholestasis genes.' Our results indicate that genetic factors contribute to the risk of developing ICP in the Americas, and support the utility of clinical and genetic studies of ethnically mixed populations for increasing our understanding of ICP.

  20. Intrahepatic Cholestasis of Pregnancy (ICP in U.S. Latinas and Chileans: Clinical features, Ancestry Analysis, and Admixture Mapping.

    Directory of Open Access Journals (Sweden)

    Laura N Bull

    Full Text Available In the Americas, women with Indigenous American ancestry are at increased risk of intrahepatic cholestasis of pregnancy (ICP, relative to women of other ethnicities. We hypothesized that ancestry-related genetic factors contribute to this increased risk. We collected clinical and laboratory data, and performed biochemical assays on samples from U.S. Latinas and Chilean women, with and without ICP. The study sample included 198 women with ICP (90 from California, U.S., and 108 from Chile and 174 pregnant control women (69 from California, U.S., and 105 from Chile. SNP genotyping was performed using Affymetrix arrays. We compared overall genetic ancestry between cases and controls, and used a genome-wide admixture mapping approach to screen for ICP susceptibility loci. We identified commonalities and differences in features of ICP between the 2 countries and determined that cases had a greater proportion of Indigenous American ancestry than did controls (p = 0.034. We performed admixture mapping, taking country of origin into account, and identified one locus for which Native American ancestry was associated with increased risk of ICP at a genome-wide level of significance (P = 3.1 x 10(-5, Pcorrected = 0.035. This locus has an odds ratio of 4.48 (95% CI: 2.21-9.06 for 2 versus zero Indigenous American chromosomes. This locus lies on chromosome 2, with a 10 Mb 95% confidence interval which does not contain any previously identified hereditary 'cholestasis genes.' Our results indicate that genetic factors contribute to the risk of developing ICP in the Americas, and support the utility of clinical and genetic studies of ethnically mixed populations for increasing our understanding of ICP.

  1. [Human origin and evolution. A review of advances in paleoanthropology, comparative genetics, and evolutionary psychology].

    Science.gov (United States)

    Markov, A V

    2009-01-01

    In his main work, "On the origin of species", Darwin has refrained from discusion of the origin of man; be only mentioned that his theory would "throw light" on this problem. This famous Darwin's phrase turned out to be one of the most succesful scientific predictions. In the present paper some of the most important recent adavnces in paleoanthroplogy, comparative genetics and evolutionary psychology are reviewed. These three disciplines currently contribute most to our knowledge of anthropogenesis. The review demonstrates that Darwin's ideas not only "threw light" on human origin and evolution; they provided a comprehensive framework for a great variety of studies concerning different aspects of anthropogenesis.

  2. Beliefs about the etiology of homosexuality and about the ramifications of discovering its possible genetic origin.

    Science.gov (United States)

    Sheldon, Jane P; Pfeffer, Carla A; Jayaratne, Toby Epstein; Feldbaum, Merle; Petty, Elizabeth M

    2007-01-01

    Homosexuality is viewed by many as a social problem. As such, there is a keen interest in elucidating the origins of homosexuality among many scholars, from anthropologists to zoologists, from psychologists to theologians. Research has shown that those who believe sexual orientation is inborn are more likely to have tolerant attitudes toward gay men and lesbians, whereas those who believe it is a choice have less tolerant attitudes. The current qualitative study used in-depth, open-ended telephone interviews with 42 White and 44 Black Americans to gain insight into the public's beliefs about the possible genetic origins of homosexuality. Along with etiological beliefs (and the sources of information used to develop these beliefs), we asked respondents to describe the benefits and dangers of scientists discovering the possible genetic basis for homosexuality. We found that although limited understanding and biased perspectives likely led to simplistic reasoning concerning the origins and genetic basis of homosexuality, many individuals appreciated the complex and interactive etiological perspectives. These interactive perspectives often included recognition of some type of inherent aspect, such as a genetic factor(s), that served as an underlying predisposition that would be manifested after being influenced by other factors such as choice or environmental exposures. We also found that beliefs in a genetic basis for homosexuality could be used to support very diverse opinions including those in accordance with negative eugenic agendas.

  3. Tracing Behçet's disease origins along the Silk Road: an anthropological evolutionary genetics perspective.

    Science.gov (United States)

    Sazzini, Marco; Garagnani, Paolo; Sarno, Stefania; De Fanti, Sara; Lazzano, Teresa; Yang Yao, Daniele; Boattini, Alessio; Pazzola, Giulia; Maramotti, Sally; Boiardi, Luigi; Franceschi, Claudio; Salvarani, Carlo; Luiselli, Donata

    2015-01-01

    Behçet's disease is a multifactorial vasculitis that shows its highest prevalence in geographical areas historically involved in the Silk Road, suggesting that it might have originated somewhere along these ancient trade routes. This study aims to provide a first clue towards genetic evidence for this hypothesis by testing it via an anthropological evolutionary genetics approach. Behçet's disease variation at ancestry informative mitochondrial DNA control region and haplogroup diagnostic sites was characterised in 185 disease subjects of Italian descent and set into the Eurasian mitochondrial landscape by comparison with nearly 9,000 sequences representative of diversity observable in Italy and along the main Silk Road routes. Dissection of the actual genetic ancestry of disease individuals by means of population structure, spatial autocorrelation and haplogroup analyses revealed their closer relationships with some Middle Eastern and Central Asian groups settled along the Silk Road than with healthy Italians. These findings support the hypothesis that the Behçet's disease genetic risk has migrated to western Eurasia in parallel with ancestry components typical of Silk Road-related groups. This provided new insights that are useful to improve the understanding of disease origins and diffusion, as well as to inform future association studies aimed at properly accounting for the actual genetic ancestry of the examined Behçet's disease samples in order to minimise the detection of spurious associations and to improve the identification of genetic variants with actual clinical relevance.

  4. Analysis of the Genetic Diversity and Origin of Some Chinese Domestic Duck Breeds

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yang; CHEN Guo-hong; CHEN Yang; ZHEN Ting; HUANG Zheng-yang; CHEN Chang-yi; LI Xin-yu; DUAN Xiu-jun; DONG Biao; XU Qi

    2014-01-01

    Twelve lfuorescence-labeled microsatellite markers were used to analyze the genetic diversity of 12 domestic duck breeds and 2 wild duck breeds to determine the relationship and origin of Chinese domestic duck breeds. Gene frequency, effective number of alleles (Ne), expected heterozygosity (He), polymorphism information contents (PIC), inbreeding coefficient in population (Fis), standard genetic distance (DS), and genetic distance (DA) were calculated by FSTAT and distance and phylogenetic analysis after the dates which were output from the Microsatellite-Toolkit software. Genetic distances between 12 domestic duck breeds and 2 wild duck breeds were analyzed by variance analysis. Unweighted pair group method with arithmetic mean (UPGMA) and phylogenetic trees used for cluster analysis were structured. The results indicated that 11 loci had medium-or high-level genetic diversity among the 12 loci, which could be efifciently used in the detection of the genetic parameters of each population. The values of He were 0.5414 to 0.7343, those of PIC proved similar, and those of Fis were 0.1101 to 0.3381 among all populations. All breeds were clustered into three groups by UPGMA phylogenetic trees. Banzui duck was clustered into a separate group. Differences of the DA were analysed by t-test. The results showed that difference in DA between the 12 domestic duck breeds and Lvtou duck and the Banzui duck were very signiifcant (P<0.01), indicating that these 12 domestic duck breeds originated from Lvtou wild duck, but not Banzui duck.

  5. Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly.

    Directory of Open Access Journals (Sweden)

    Sofie Vandewoestijne

    selection on some flight morphology traits. MAIN CONCLUSIONS/SIGNIFICANCE: Clinal differentiation characterizes the population structure within the original woodland habitat. Genetic signatures of recent habitat expansion remain, notwithstanding high gene flow. After differentiation through drift was excluded, both latitude and landscape were significant factors inducing spatially variable phenotypic variation.

  6. Integrating social science and behavioral genetics: testing the origin of socioeconomic disparities in depression using a genetically informed design.

    Science.gov (United States)

    Mezuk, Briana; Myers, John M; Kendler, Kenneth S

    2013-10-01

    We tested 3 hypotheses-social causation, social drift, and common cause-regarding the origin of socioeconomic disparities in major depression and determined whether the relationship between socioeconomic status (SES) and major depression varied by genetic liability for major depression. Data were from a sample of female twins in the baseline Virginia Adult Twin Study of Psychiatric and Substance Use Disorders interviewed between 1987 and 1989 (n = 2153). We used logistic regression and structural equation twin models to evaluate these 3 hypotheses. Consistent with the social causation hypothesis, education (odds ratio [OR] = 0.78; 95% confidence interval [CI] = 0.66, 0.93; P social mobility was associated with lower risk of depression. There was no evidence that childhood SES was related to development of major depression (OR = 0.98; 95% CI = 0.89, 1.09; P > .1). Consistent with a common genetic cause, there was a negative correlation between the genetic components of major depression and education (r(2) = -0.22). Co-twin control analyses indicated a protective effect of education and income on major depression even after accounting for genetic liability. This study utilized a genetically informed design to address how social position relates to major depression. Results generally supported the social causation model.

  7. The time and place of European admixture in Ashkenazi Jewish history.

    Science.gov (United States)

    Xue, James; Lencz, Todd; Darvasi, Ariel; Pe'er, Itsik; Carmi, Shai

    2017-04-01

    The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60-80% of EU ancestry), with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25-50 generations ago.

  8. The time and place of European admixture in Ashkenazi Jewish history.

    Directory of Open Access Journals (Sweden)

    James Xue

    2017-04-01

    Full Text Available The Ashkenazi Jewish (AJ population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU and Middle-Eastern (ME components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60-80% of EU ancestry, with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25-50 generations ago.

  9. 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

  10. Genetic structure and natal origins of immature hawksbill turtles (Eretmochelys imbricata in Brazilian waters.

    Directory of Open Access Journals (Sweden)

    Maira C Proietti

    Full Text Available Understanding the connections between sea turtle populations is fundamental for their effective conservation. Brazil hosts important hawksbill feeding areas, but few studies have focused on how they connect with nesting populations in the Atlantic. Here, we (1 characterized mitochondrial DNA control region haplotypes of immature hawksbills feeding along the coast of Brazil (five areas ranging from equatorial to temperate latitudes, 157 skin samples, (2 analyzed genetic structure among Atlantic hawksbill feeding populations, and (3 inferred natal origins of hawksbills in Brazilian waters using genetic, oceanographic, and population size information. We report ten haplotypes for the sampled Brazilian sites, most of which were previously observed at other Atlantic feeding grounds and rookeries. Genetic profiles of Brazilian feeding areas were significantly different from those in other regions (Caribbean and Africa, and a significant structure was observed between Brazilian feeding grounds grouped into areas influenced by the South Equatorial/North Brazil Current and those influenced by the Brazil Current. Our genetic analysis estimates that the studied Brazilian feeding aggregations are mostly composed of animals originating from the domestic rookeries Bahia and Pipa, but some contributions from African and Caribbean rookeries were also observed. Oceanographic data corroborated the local origins, but showed higher connection with West Africa and none with the Caribbean. High correlation was observed between origins estimated through genetics/rookery size and oceanographic/rookery size data, demonstrating that ocean currents and population sizes influence haplotype distribution of Brazil's hawksbill populations. The information presented here highlights the importance of national conservation strategies and international cooperation for the recovery of endangered hawksbill turtle populations.

  11. Molecular genetic tools to infer the origin of forest plants and wood.

    Science.gov (United States)

    Finkeldey, Reiner; Leinemann, Ludger; Gailing, Oliver

    2010-02-01

    Most forest tree species exhibit high levels of genetic diversity that can be used to trace the origin of living plants or their products such as timber and processed wood. Recent progress to isolate DNA not only from living tissue but also from wood and wood products offers new opportunities to test the declared origin of material such as seedlings for plantation establishment or timber. However, since most forest tree populations are weakly differentiated, the identification of genetic markers to differentiate among spatially isolated populations is often difficult and time consuming. Two important fields of "forensic" applications are described: Molecular tools are applied to test the declared origin of forest reproductive material used for plantation establishment and of internationally traded timber and wood products. These applications are illustrated taking examples from Germany, where mechanisms have been developed to improve the control of the trade with forest seeds and seedlings, and from the trade with wood of the important Southeast Asian tree family Dipterocarpaceae. Prospects and limitations of the use of molecular genetic methods to conclude on the origin of forest plants, wood, and wood products are discussed.

  12. Origin and genetic differentiation of three Native Mexican groups (Purépechas, Triquis and Mayas): contribution of CODIS-STRs to the history of human populations of Mesoamerica.

    Science.gov (United States)

    Martínez-Cortés, G; Nuño-Arana, I; Rubi-Castellanos, R; Vilchis-Dorantes, G; Luna-Vázquez, A; Coral-Vázquez, R M; Canto-Cetina, T; Salazar-Flores, J; Muñoz-Valle, J F; Sandoval-Mendoza, K; López, Z; Gamero-Lucas, J J; Rangel-Villalobos, H

    2010-11-01

    CODIS-STRs in Native Mexican groups have rarely been analysed for human identification and anthropological purposes. To analyse the genetic relationships and population structure among three Native Mexican groups from Mesoamerica. 531 unrelated Native individuals from Mexico were PCR-typed for 15 and 9 autosomal STRs (Identifiler™ and Profiler™ kits, respectively), including five population samples: Purépechas (Mountain, Valley and Lake), Triquis and Yucatec Mayas. Previously published STR data were included in the analyses. Allele frequencies and statistical parameters of forensic importance were estimated by population. The majority of Native groups were not differentiated pairwise, excepting Triquis and Purépechas, which was attributable to their relative geographic and cultural isolation. Although Mayas, Triquis and Purépechas-Mountain presented the highest number of private alleles, suggesting recurrent gene flow, the elevated differentiation of Triquis indicates a different origin of this gene flow. Interestingly, Huastecos and Mayas were not differentiated, which is in agreement with the archaeological hypothesis that Huastecos represent an ancestral Maya group. Interpopulation variability was greater in Natives than in Mestizos, both significant. Although results suggest that European admixture has increased the similarity between Native Mexican groups, the differentiation and inconsistent clustering by language or geography stresses the importance of serial founder effect and/or genetic drift in showing their present genetic relationships.

  13. The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape

    Science.gov (United States)

    Busby, George B.J.; Hellenthal, Garrett; Montinaro, Francesco; Tofanelli, Sergio; Bulayeva, Kazima; Rudan, Igor; Zemunik, Tatijana; Hayward, Caroline; Toncheva, Draga; Karachanak-Yankova, Sena; Nesheva, Desislava; Anagnostou, Paolo; Cali, Francesco; Brisighelli, Francesca; Romano, Valentino; Lefranc, Gerard; Buresi, Catherine; Ben Chibani, Jemni; Haj-Khelil, Amel; Denden, Sabri; Ploski, Rafal; Krajewski, Pawel; Hervig, Tor; Moen, Torolf; Herrera, Rene J.; Wilson, James F.; Myers, Simon; Capelli, Cristian

    2015-01-01

    Summary Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [1, 2, 3, 4, 5, 6, 7]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [8, 9, 10, 11]. Here, using recently described haplotype-based techniques [11], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia. PMID:26387712

  14. [Genetic mechanism and evolutionary significance of the origin of parthenogenetic insects].

    Science.gov (United States)

    Wang, Cheng-Ye

    2011-12-01

    There is a high proportion of parthenogenesis in insecta, and the parthenogenetic potential of insects is an important but often ignored threaten factor for the agricultural and forestry production. The maintenance of parthenogenetic species is a puzzling issue in evolutionary biology. In recent years, although the cellular mechanisms during parthenogenesis in some species have been well studied, the underlying genetic mechanisms that cause the switch from sexual reproduction to parthenogenesis have not been defined. While, understanding the genetic mechanism and evolutionary significance of the origin of parthenogenetic insects is crucial for preventing the pests in agricultural and forestry production. Here we summarized recent studies aimed at identifying the underlying genetic mechanism of parthenogenesis in insects, and briefly discussed its potential application in this filed.

  15. Genetic architecture for the adaptive origin of annual wild rice, oryza nivara.

    Science.gov (United States)

    Grillo, Michael A; Li, Changbao; Fowlkes, Angela M; Briggeman, Trevor M; Zhou, Ailing; Schemske, Douglas W; Sang, Tao

    2009-04-01

    The wild progenitors of cultivated rice, Oryza nivara and Oryza rufipogon, provide an experimental system for characterizing the genetic basis of adaptation. The evolution of annual O. nivara from a perennial ancestor resembling its sister species, O. rufipogon, was associated with an ecological shift from persistently wet to seasonally dry habitats. Here we report a quantitative trait locus (QTL) analysis of phenotypic differentiation in life history, mating system, and flowering time between O. nivara and O. rufipogon. The exponential distribution of effect sizes of QTL fits the prediction of a recently proposed population genetic model of adaptation. More than 80% of QTL alleles of O. nivara acted in the same direction of phenotypic evolution, suggesting that they were fixed under directional selection. The loss of photoperiod sensitivity, which might be essential to the survival of the ancestral populations of O. nivara in the new environment, was controlled by QTL of relatively large effect. Mating system evolution from cross- to self-fertilization through the modification of panicle and floral morphology was controlled by QTL of small-to-moderate effect. The lack of segregation of the recessive annual habit in the F(2) mapping populations suggested that the evolution of annual from perennial life form had a complex genetic basis. The study captured the genetic architecture for the adaptive origin of O. nivara and provides a foundation for rigorous experimental tests of population genetic theories of adaptation.

  16. Effects of herd origin, AI stud and sire identification on genetic evaluation of Holstein Friesian bulls

    Directory of Open Access Journals (Sweden)

    Giovanni Bittante

    2010-01-01

    Full Text Available The purpose of this study was to estimate the effects of herd origin of bull, AI stud and sire identification number (ID  on official estimated breeding values (EBV for production traits of Holstein Friesian proven bulls. The data included 1,005  Italian Holstein-Friesian bulls, sons of 76 sires, born in 100 herds and progeny tested by 10 AI studs. Bulls were required  to have date of first proof between September 1992 and September 1997, to be born in a herd with at least one other  bull and to have sire and dam with official EBV when bull was selected for progeny testing. Records of sires with only one  son were also discarded. The dependent variable analyzed was the official genetic evaluation for a “quantity and quality  of milk” index (ILQ. The linear model to predict breeding values of bulls included the fixed class effects of herd origin of  bull, AI testing organization, birth year of bull, and estimated breeding values of sire and dam, both as linear covariates.  The R2of the model was 45% and a significant effect was found for genetic merit of sire (P   for herd origin of bull (P   nificant. The range of herd origin effect was 872 kg of ILQ. However, in this study, the causes of this result were not  clear; it may be due to numerous factors, one of which may be preferential treatment on dams of bulls. Analyses of resid-  uals on breeding value of proven bulls for ILQ showed a non significant effect of sire ID, after adjusting for parent aver-  age, herd origin effect and birth year effect. Although the presence of bias in genetic evaluation of dairy bulls is not evi-  dent, further research is recommended firstly to understand the reasons of the significant herd origin effect, secondly to  monitor and guarantee the greatest accuracy and reliability of genetic evaluation procedures. 

  17. A nearest neighbour approach by genetic distance to the assignment of individual trees to geographic origin.

    Science.gov (United States)

    Degen, Bernd; Blanc-Jolivet, Céline; Stierand, Katrin; Gillet, Elizabeth

    2017-03-01

    During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregates and intend to identify the most likely group of origin. Often this grouping does not have a biological but rather a historical or political justification, such as "country of origin". In this paper, we present a new nearest neighbour approach to individual assignment or classification within a given but potentially imperfect grouping of reference samples. This method, which is based on the genetic distance between individuals, functions better in many cases than commonly used methods. We demonstrate the operation of our assignment method using two data sets. One set is simulated for a large number of trees distributed in a 120km by 120km landscape with individual genotypes at 150 SNPs, and the other set comprises experimental data of 1221 individuals of the African tropical tree species Entandrophragma cylindricum (Sapelli) genotyped at 61 SNPs. Judging by the level of correct self-assignment, our approach outperformed the commonly used frequency and Bayesian approaches by 15% for the simulated data set and by 5-7% for the Sapelli data set. Our new approach is less sensitive to overlapping sources of genetic differentiation, such as genetic differences among closely-related species, phylogeographic lineages and isolation by distance, and thus operates better even for suboptimal grouping of individuals. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. Origin of microbial life: Nano- and molecular events, thermodynamics/entropy, quantum mechanisms and genetic instructions.

    Science.gov (United States)

    Trevors, J T

    2011-03-01

    Currently, there are no agreed upon mechanisms and supporting evidence for the origin of the first microbial cells on the Earth. However, some hypotheses have been proposed with minimal supporting evidence and experimentation/observations. The approach taken in this article is that life originated at the nano- and molecular levels of biological organization, using quantum mechanic principles that became manifested as classical microbial cell(s), allowing the origin of microbial life on the Earth with a core or minimal, organic, genetic code containing the correct instructions for cell(s) for growth and division, in a micron dimension environment, with a local entropy range conducive to life (present about 4 billion years ago), and obeying the laws of thermodynamics. An integrated approach that explores all encompassing factors necessary for the origin of life, may bring forth plausible hypotheses (and mechanisms) with much needed supporting experimentation and observations for an origin of life theory. Copyright © 2010 Elsevier B.V. All rights reserved.

  19. Early hydration cement Effect of admixtures superplasticizers

    Directory of Open Access Journals (Sweden)

    Puertas, F.

    2001-06-01

    Full Text Available Early hydration of portland cement with superplasticizer admixtures of different nature has been studied. These admixtures were: one based on melamine synthetic, other based on vinyl copolymer and other based on polyacrylate copolymers. The dosage of the formers were constant (1% weigth of cement and for the third, the influence of admixture dosage was also evaluated, giving dosage values among 1-0.3%. The pastes obtained were studied by conduction calorimetry, XRD and FTIR. Also the apparent fluidity was determined by "Minislump" test. The main results obtained were: a superplasticizers admixtures used, regardless of their nature and for the polycarboxilate one the dosage, retard the silicate hydration (specially, alite phase, b The ettringite formation is affected by the nature of the admixture. cA relationship between the dosage of admixture based on polycarboxilates and the time at the acceleration has been established. A lineal relation (y = 11.03 + 16.05x was obtained. From these results is possible to know, in function of dosage admixture, the time when the masive hydration products and the setting times are produced. Also the total heat releases in these reactions is independent of the nature and dosage of admixture, saying that in all cases the reactions are the same.

    En el presente trabajo se ha estudiado la hidratación inicial de un cemento portland aditivado con superplastificantes de diferente naturaleza. Dichos aditivos fueron: uno basado en melaminas sintéticas, otro en copolímeros vinilicos y otro en policarboxilatos. La dosificación de los dos primeros se fijó constante en 1% en peso con relación al cemento, mientras que para el tercero se evaluó, también, la influencia de la dosificación, tomando proporciones desde el 1% hasta el 0,3%. Las pastas obtenidas se estudiaron por: calorimetría de conducción, DRX y FTIR. También se determinó la fluidez de la pasta a través del ensayo del "Minislump ". Los

  20. An Autotrophic Origin for the Coded Amino Acids is Concordant with the Coevolution Theory of the Genetic Code.

    Science.gov (United States)

    Di Giulio, Massimo

    2016-10-01

    The coevolution theory of the origin of the genetic code maintains that the biosynthetic relationships between amino acids co-evolved with the genetic code organization. In other words, the metabolism of amino acids co-evolved with the organization of the genetic code because the biosynthetic pathways of amino acids occurred on tRNA-like molecules. Thus, a heterotrophic origin of amino acids-also only of those involved in the early phase of the structuring of the genetic code-would seem to contradict the main postulate of the coevolution theory. As a matter of fact, this origin not being linked to the metabolism of amino acids in any way-being taken from a physical setting-would seem to remove the possibility that this metabolism had instead heavily contributed to the structuring of the genetic code. Therefore, I have analyzed the structure of the genetic code and mechanisms that brought to its structuring for understanding if the coevolution theory is compatible with autotrophic or heterotrophic conditions. One of the arguments was that an autotrophic origin of amino acids would have the advantage to be able to directly link their metabolism to the structure of the genetic code if-as hypothesized by the coevolution theory-the biosyntheses of amino acids occurred on tRNA-like molecules. Simultaneously, a heterotrophic origin would not have been able to link the metabolism of amino acids to the structure of the genetic code for the absence of a precise determinism of allocation of amino acids, that is to say of a clear mechanism-linked to tRNA-like molecules, for example-that would have determined the specific pattern observed in the genetic code of the biosynthetic relationships between amino acids. The conclusion is that an autotrophic origin of coded amino acids would seem to be the condition under which the genetic code originated.

  1. Origin and evolution of the dependent lineages in the genetic caste determination system of Pogonomyrmex ants.

    Science.gov (United States)

    Sirviö, Anu; Pamilo, Pekka; Johnson, Robert A; Page, Robert E; Gadau, Jürgen

    2011-03-01

    Hybridizing harvester ants of the Pogonomyrmex barbatus/rugosus complex have an exceptional genetic caste determination (GCD) mechanism. We combined computer simulations, population genomics, and linkage mapping using >1000 nuclear AFLP markers and a partial mtDNA sequence to explore the genetic architecture and origin of the dependent lineages. Our samples included two pairs of hybridizing lineages, and the mitochondrial and nuclear data showed contradicting affinities between them. Clustering of individual genotypes based on nuclear markers indicated some exceptions to the general GCD system, that is, interlineage hybrid genes as well as some pure-line workers. A genetic linkage map of P. rugosus showed one of the highest recombination rates ever measured in insects (14.0 cM/Mb), supporting the view that social insects are characterized by high recombination rates. The population data had 165 markers in which sibling pairs showed a significant genetic difference depending on the caste. The differences were scattered in the genome; 13 linkage groups had loci with F(ST)>0.9 between the hybridizing lineages J1 and J2.The mapping results and the population data indicate that the dependent lineages have been initially formed through hybridization at different points in time but the role of introgression has been insignificant in their later evolution.

  2. Genetic insights into the origins of Tibeto-Burman populations in the Himalayas.

    Science.gov (United States)

    Gayden, Tenzin; Mirabal, Sheyla; Cadenas, Alicia M; Lacau, Harlette; Simms, Tanya M; Morlote, Diana; Chennakrishnaiah, Shilpa; Herrera, Rene J

    2009-04-01

    The Himalayan mountain range has played a dual role in shaping the genetic landscape of the region by (1) delineating east-west migrations including the Silk Road and (2) restricting human dispersals, especially from the Indian subcontinent into the Tibetan plateau. In this study, 15 hypervariable autosomal STR loci were employed to evaluate the genetic relationships of three populations from Nepal (Kathmandu, Newar and Tamang) and a general collection from Tibet. These Himalayan groups were compared to geographically targeted worldwide populations as well as Tibeto-Burman (TB) speaking groups from Northeast India. Our results suggest a Northeast Asian origin for the Himalayan populations with subsequent gene flow from South Asia into the Kathmandu valley and the Newar population, corroborating a previous Y-chromosome study. In contrast, Tamang and Tibet exhibit limited genetic contributions from South Asia, possibly due to the orographic obstacle presented by the Himalayan massif. The TB groups from Northeast India are genetically distinct compared to their counterparts from the Himalayas probably resulting from prolonged isolation and/or founder effects.

  3. On the origins and genetic diversity of South American chickens: one step closer.

    Science.gov (United States)

    Luzuriaga-Neira, A; Villacís-Rivas, G; Cueva-Castillo, F; Escudero-Sánchez, G; Ulloa-Nuñez, A; Rubilar-Quezada, M; Monteiro, R; Miller, M R; Beja-Pereira, A

    2017-06-01

    Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens. © 2017 Stichting International Foundation for Animal Genetics.

  4. Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations.

    Science.gov (United States)

    Haber, Marc; Mezzavilla, Massimo; Xue, Yali; Comas, David; Gasparini, Paolo; Zalloua, Pierre; Tyler-Smith, Chris

    2016-06-01

    The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain under-represented in genetic studies and have a complex history including a major geographic displacement during World War I. Here, we analyse genome-wide variation in 173 Armenians and compare them with 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3000 and ~2000 bce, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1200 bce when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of Armenian ancestry may originate from an ancestral population that is best represented by Neolithic Europeans.

  5. Functional and genetic deconstruction of the cellular origin in liver cancer

    DEFF Research Database (Denmark)

    Marquardt, Jens U; Andersen, Jesper B; Thorgeirsson, Snorri S

    2015-01-01

    During the past decade, research on primary liver cancers has particularly highlighted the uncommon plasticity of differentiated parenchymal liver cells (that is, hepatocytes and cholangiocytes (also known as biliary epithelial cells)), the role of liver progenitor cells in malignant transformation......, the importance of the tumour microenvironment and the molecular complexity of liver tumours. Whereas other reviews have focused on the landscape of genetic alterations that promote development and progression of primary liver cancers and the role of the tumour microenvironment, the crucial importance...... of the cellular origin of liver cancer has been much less explored. Therefore, in this Review, we emphasize the importance and complexity of the cellular origin in tumour initiation and progression, and attempt to integrate this aspect with recent discoveries in tumour genomics and the contribution...

  6. The Puzzle of Italian Rice Origin and Evolution: Determining Genetic Divergence and Affinity of Rice Germplasm from Italy and Asia

    Science.gov (United States)

    Jiang, Zhuxi; Basso, Barbara; Sala, Francesco; Spada, Alberto; Grassi, Fabrizio; Lu, Bao-Rong

    2013-01-01

    The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (He = 0.63-0.65) in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships. PMID:24265814

  7. The puzzle of Italian rice origin and evolution: determining genetic divergence and affinity of rice germplasm from Italy and Asia.

    Science.gov (United States)

    Cai, Xingxing; Fan, Jing; Jiang, Zhuxi; Basso, Barbara; Sala, Francesco; Spada, Alberto; Grassi, Fabrizio; Lu, Bao-Rong

    2013-01-01

    The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (H(e) = 0.63-0.65) in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships.

  8. The puzzle of Italian rice origin and evolution: determining genetic divergence and affinity of rice germplasm from Italy and Asia.

    Directory of Open Access Journals (Sweden)

    Xingxing Cai

    Full Text Available The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (H(e = 0.63-0.65 in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships.

  9. Molecular genetic diversity and maternal origin of Chinese black-bone chicken breeds.

    Science.gov (United States)

    Zhu, W Q; Li, H F; Wang, J Y; Shu, J T; Zhu, C H; Song, W T; Song, C; Ji, G G; Liu, H X

    2014-04-29

    Chinese black-bone chickens are valued for the medicinal properties of their meat in traditional Chinese medicine. We investigated the genetic diversity and systematic evolution of Chinese black-bone chicken breeds. We sequenced the DNA of 520 bp of the mitochondrial cyt b gene of nine Chinese black-bone chicken breeds, including Silky chicken, Jinhu black-bone chicken, Jiangshan black-bone chicken, Yugan black-bone chicken, Wumeng black-bone chicken, Muchuan black-bone chicken, Xingwen black-bone chicken, Dehua black-bone chicken, and Yanjin black-bone chicken. We found 13 haplotypes. Haplotype and nucleotide diversity of the nine black-bone chicken breeds ranged from 0 to 0.78571 and 0.00081 to 0.00399, respectively. Genetic diversity was the richest in Jinhu black-bone chickens and the lowest in Yanjin black-bone chickens. Analysis of phylogenetic trees for all birds constructed based on hyplotypes indicated that the maternal origin of black-bone chickens is predominantly from three subspecies of red jungle fowl. These results provide basic data useful for protection of black-bone chickens and help determine the origin of domestic chickens.

  10. Molecular genetic evidence for the place of origin of the Pacific rat, Rattus exulans.

    Directory of Open Access Journals (Sweden)

    Vicki Thomson

    Full Text Available Commensal plants and animals have long been used to track human migrations, with Rattus exulans (the Pacific rat a common organism for reconstructing Polynesian dispersal in the Pacific. However, with no knowledge of the homeland of R. exulans, the place of origin of this human-commensal relationship is unknown. We conducted a mitochondrial DNA phylogeographic survey of R. exulans diversity across the potential natural range in mainland and Island Southeast Asia in order to establish the origin of this human-commensal dyad. We also conducted allozyme electrophoresis on samples from ISEA to obtain a perspective on patterns of genetic diversity in this critical region. Finally, we compared molecular genetic evidence with knowledge of prehistoric rodent faunas in mainland and ISEA. We find that ISEA populations of R. exulans contain the highest mtDNA lineage diversity including significant haplotype diversity not represented elsewhere in the species range. Within ISEA, the island of Flores in the Lesser Sunda group contains the highest diversity in ISEA (across all loci and also has a deep fossil record of small mammals that appears to include R. exulans. Therefore, in addition to Flores harboring unusual diversity in the form of Homo floresiensis, dwarfed stegodons and giant rats, this island appears to be the homeland of R. exulans.

  11. Reflections on the Origins and Evolution of Genetic Toxicology and the Environmental Mutagen Society

    Energy Technology Data Exchange (ETDEWEB)

    Wassom, John S. [Oak Ridge National Laboratory (Retired); Malling, Heinrich V. [National Institute of Environmental Health Sciences (NIEHS); Sankaranarayanan, K. [Leiden University; Lu, Po-Yung [ORNL

    2010-01-01

    This article traces the development of the field of mutagenesis and its metamorphosis into the research area we now call genetic toxicology. In 1969 this transitional event led to the founding of the Environmental Mutagen Society (EMS). The charter of this new Society was to encourage interest in and study of mutagens in the human environment, particularly as these may be of concern to public health. As the mutagenesis field unfolded and expanded, the lexicon changed and new wording appeared to better describe this evolving area of research. The term genetic toxicology was coined and became an important subspecialty of the broad area of toxicology. Genetic toxicology is now set for a thorough reappraisal of its methods, goals, and priorities to meet the challenges of the 21st Century. To better understand these challenges, we have revisited the primary goal that the EMS founders had in mind for the Society s main mission and objective, namely, the quantitative assessment of genetic (hereditary) risks to human populations exposed to environmental agents. We also have reflected upon some of the seminal events over the last 40 years that have influenced the advancement of the genetic toxicology discipline and the extent to which the Society s major goal and allied objectives have been achieved. Additionally, we have provided suggestions on how EMS can further advance the science of genetic toxicology in the postgenome era. Chronicling all events and publications that influenced the development of the mutagenesis and genetic toxicology research area for this article was not possible, but some key happenings that contributed to the field s development have been reviewed. Events that led to the origin of EMS are also presented in celebration of the Society s 40th anniversary. Any historical accounting will have perceived deficiencies. Key people, publications, or events that some readers may feel have had significant impact on development of the subject under review may

  12. Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

    Directory of Open Access Journals (Sweden)

    Lunt David H

    2008-07-01

    has been maintained by selection. Conclusion The data strongly suggests the tropical root knot nematode apomicts have a recent origin and are not anciently asexual. The results support that interspecific hybridization has been involved in the origin of this asexual group and has played a role in shaping the patterns of genetic diversity observed. This study suggests that genetic signatures of ancient asexuality must be taken with caution due to the confounding effect of interspecific hybridization, which has long been implicated in the origins of apomictic species.

  13. Origins of albino and hooded rats: implications from molecular genetic analysis across modern laboratory rat strains.

    Directory of Open Access Journals (Sweden)

    Takashi Kuramoto

    Full Text Available Albino and hooded (or piebald rats are one of the most frequently used laboratory animals for the past 150 years. Despite this fact, the origin of the albino mutation as well as the genetic basis of the hooded phenotype remained unclear. Recently, the albino mutation has been identified as the Arg299His missense mutation in the Tyrosinase gene and the hooded (H locus has been mapped to the ∼460-kb region in which only the Kit gene exists. Here, we surveyed 172 laboratory rat strains for the albino mutation and the hooded (h mutation that we identified by positional cloning approach to investigate possible genetic roots and relationships of albino and hooded rats. All of 117 existing laboratory albino rats shared the same albino missense mutation, indicating they had only one single ancestor. Genetic fine mapping followed by de novo sequencing of BAC inserts covering the H locus revealed that an endogenous retrovirus (ERV element was inserted into the first intron of the Kit gene where the hooded allele maps. A solitary long terminal repeat (LTR was found at the same position to the ERV insertion in another allele of the H locus, which causes the so called Irish (h(i phenotype. The ERV and the solitary LTR insertions were completely associated with the hooded and Irish coat patterns, respectively, across all colored rat strains examined. Interestingly, all 117 albino rat strains shared the ERV insertion without any exception, which strongly suggests that the albino mutation had originally occurred in hooded rats.

  14. Geographic origins and population genetics of bats killed at wind-energy facilities.

    Science.gov (United States)

    Pylant, Cortney L; Nelson, David M; Fitzpatrick, Matthew C; Gates, J Edward; Keller, Stephen R

    2016-07-01

    An unanticipated impact of wind-energy development has been large-scale mortality of insectivorous bats. In eastern North America, where mortality rates are among the highest in the world, the hoary bat (Lasiurus cinereus) and the eastern red bat (L. borealis) comprise the majority of turbine-associated bat mortality. Both species are migratory tree bats with widespread distributions; however, little is known regarding the geographic origins of bats killed at wind-energy facilities or the diversity and population structure of affected species. We addressed these unknowns by measuring stable hydrogen isotope ratios (δ(2) H) and conducting population genetic analyses of bats killed at wind-energy facilities in the central Appalachian Mountains (USA) to determine the summering origins, effective size, structure, and temporal stability of populations. Our results indicate that ~1% of hoary bat mortalities and ~57% of red bat mortalities derive from non-local sources, with no relationship between the proportion of non-local bats and sex, location of mortality, or month of mortality. Additionally, our data indicate that hoary bats in our sample consist of an unstructured population with a small effective size (Ne ) and either a stable or declining history. Red bats also showed no evidence of population genetic structure, but in contrast to hoary bats, the diversity contained in our red bat samples is consistent with a much larger Ne that reflects a demographic expansion after a bottleneck. These results suggest that the impacts of mortality associated with intensive wind-energy development may affect bat species dissimilarly, with red bats potentially better able to absorb sustained mortality than hoary bats because of their larger Ne . Our results provide important baseline data and also illustrate the utility of stable isotopes and population genetics for monitoring bat populations affected by wind-energy development.

  15. Admixture into and within sub-Saharan Africa.

    Science.gov (United States)

    Busby, George Bj; Band, Gavin; Si Le, Quang; Jallow, Muminatou; Bougama, Edith; Mangano, Valentina D; Amenga-Etego, Lucas N; Enimil, Anthony; Apinjoh, Tobias; Ndila, Carolyne M; Manjurano, Alphaxard; Nyirongo, Vysaul; Doumba, Ogobara; Rockett, Kirk A; Kwiatkowski, Dominic P; Spencer, Chris Ca

    2016-06-21

    Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

  16. Origins.

    Science.gov (United States)

    Online-Offline, 1999

    1999-01-01

    Provides an annotated list of resources dealing with the theme of origins of life, the universe, and traditions. Includes Web sites, videos, books, audio materials, and magazines with appropriate grade levels and/or subject disciplines indicated; professional resources; and learning activities. (LRW)

  17. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes

    Science.gov (United States)

    Torgerson, Dara G.; Gignoux, Christopher R.; Galanter, Joshua M.; Drake, Katherine A.; Roth, Lindsey A.; Eng, Celeste; Huntsman, Scott; Torres, Raul; Avila, Pedro C.; Chapela, Rocio; Ford, Jean G.; Rodríguez-Santana, José R.; Rodríguez-Cintrón, William; Hernandez, Ryan D.; Burchard, Esteban G.

    2012-01-01

    Background Polymorphisms in more than 100 genes have been associated with asthma susceptibility, yet much of the heritability remains to be explained. Asthma disproportionately affects different racial and ethnic groups in the United States, suggesting that admixture mapping is a useful strategy to identify novel asthma-associated loci. Objective We sought to identify novel asthma-associated loci in Latino populations using case-control admixture mapping. Methods We performed genome-wide admixture mapping by comparing levels of local Native American, European, and African ancestry between children with asthma and nonasthmatic control subjects in Puerto Rican and Mexican populations. Within candidate peaks, we performed allelic tests of association, controlling for differences in local ancestry. Results Between the 2 populations, we identified a total of 62 admixture mapping peaks at a P value of less than 10−3 that were significantly enriched for previously identified asthma-associated genes (P = .0051). One of the peaks was statistically significant based on 100 permutations in the Mexican sample (6q15); however, it was not significant in Puerto Rican subjects. Another peak was identified at nominal significance in both populations (8q12); however, the association was observed with different ancestries. Conclusion Case-control admixture mapping is a promising strategy for identifying novel asthma-associated loci in Latino populations and implicates genetic variation at 6q15 and 8q12 regions with asthma susceptibility. This approach might be useful for identifying regions that contribute to both shared and population-specific differences in asthma susceptibility. PMID:22502797

  18. Turbulent diffusion of chemically reacting gaseous admixtures

    Science.gov (United States)

    Elperin, T.; Kleeorin, N.; Liberman, M.; Rogachevskii, I.

    2014-11-01

    We study turbulent diffusion of chemically reacting gaseous admixtures in a developed turbulence. In our previous study [Phys. Rev. Lett. 80, 69 (1998), 10.1103/PhysRevLett.80.69] using a path-integral approach for a delta-correlated in a time random velocity field, we demonstrated a strong modification of turbulent transport in fluid flows with chemical reactions or phase transitions. In the present study we use the spectral τ approximation that is valid for large Reynolds and Peclet numbers and show that turbulent diffusion of the reacting species can be strongly depleted by a large factor that is the ratio of turbulent and chemical times (turbulent Damköhler number). We have demonstrated that the derived theoretical dependence of a turbulent diffusion coefficient versus the turbulent Damköhler number is in good agreement with that obtained previously in the numerical modeling of a reactive front propagating in a turbulent flow and described by the Kolmogorov-Petrovskii-Piskunov-Fisher equation. We have found that turbulent cross-effects, e.g., turbulent mutual diffusion of gaseous admixtures and turbulent Dufour effect of the chemically reacting gaseous admixtures, are less sensitive to the values of stoichiometric coefficients. The mechanisms of the turbulent cross-effects differ from the molecular cross-effects known in irreversible thermodynamics. In a fully developed turbulence and at large Peclet numbers the turbulent cross-effects are much larger than the molecular ones. The obtained results are applicable also to heterogeneous phase transitions.

  19. Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids.

    Science.gov (United States)

    Kautt, Andreas F; Machado-Schiaffino, Gonzalo; Meyer, Axel

    2016-06-01

    The formation of species in the absence of geographic barriers (i.e. sympatric speciation) remains one of the most controversial topics in evolutionary biology. While theoretical models have shown that this most extreme case of primary divergence-with-gene-flow is possible, only a handful of accepted empirical examples exist. And even for the most convincing examples uncertainties remain; complex histories of isolation and secondary contact can make species falsely appear to have originated by sympatric speciation. This alternative scenario is notoriously difficult to rule out. Midas cichlids inhabiting small and remote crater lakes in Nicaragua are traditionally considered to be one of the best examples of sympatric speciation and lend themselves to test the different evolutionary scenarios that could lead to apparent sympatric speciation since the system is relatively small and the source populations known. Here we reconstruct the evolutionary history of two small-scale radiations of Midas cichlids inhabiting crater lakes Apoyo and Xiloá through a comprehensive genomic data set. We find no signs of differential admixture of any of the sympatric species in the respective radiations. Together with coalescent simulations of different demographic models our results support a scenario of speciation that was initiated in sympatry and does not result from secondary contact of already partly diverged populations. Furthermore, several species seem to have diverged simultaneously, making Midas cichlids an empirical example of multispecies outcomes of sympatric speciation. Importantly, however, the demographic models strongly support an admixture event from the source population into both crater lakes shortly before the onset of the radiations within the lakes. This opens the possibility that the formation of reproductive barriers involved in sympatric speciation was facilitated by genetic variants that evolved in a period of isolation between the initial founding

  20. On origin of genetic code and tRNA before translation

    Directory of Open Access Journals (Sweden)

    Szathmáry Eörs

    2011-02-01

    Full Text Available Abstract Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas. A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1 the fundamental veto on "foresight evolution", 2 modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3 the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code the anticodon(2-3/codon(1-2 tetramers to their anticodon(1-2/codon(2-3 counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator to the eventual 76 base

  1. Genetic origins of lactase persistence and the spread of pastoralism in Africa.

    Science.gov (United States)

    Ranciaro, Alessia; Campbell, Michael C; Hirbo, Jibril B; Ko, Wen-Ya; Froment, Alain; Anagnostou, Paolo; Kotze, Maritha J; Ibrahim, Muntaser; Nyambo, Thomas; Omar, Sabah A; Tishkoff, Sarah A

    2014-04-03

    In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ~2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ~198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa.

  2. Genetic enablers underlying the clustered evolutionary origins of C4 photosynthesis in angiosperms.

    Science.gov (United States)

    Christin, Pascal-Antoine; Arakaki, Mónica; Osborne, Colin P; Edwards, Erika J

    2015-04-01

    The evolutionary accessibility of novel adaptations varies among lineages, depending in part on the genetic elements present in each group. However, the factors determining the evolutionary potential of closely related genes remain largely unknown. In plants, CO2-concentrating mechanisms such as C4 and crassulacean acid metabolism (CAM) photosynthesis have evolved numerous times in distantly related groups of species, and constitute excellent systems to study constraints and enablers of evolution. It has been previously shown for multiple proteins that grasses preferentially co-opted the same gene lineage for C4 photosynthesis, when multiple copies were present. In this work, we use comparative transcriptomics to show that this bias also exists within Caryophyllales, a distantly related group with multiple C4 origins. However, the bias is not the same as in grasses and, when all angiosperms are considered jointly, the number of distinct gene lineages co-opted is not smaller than that expected by chance. These results show that most gene lineages present in the common ancestor of monocots and eudicots produced gene descendants that were recruited into C4 photosynthesis, but that C4-suitability changed during the diversification of angiosperms. When selective pressures drove C4 evolution, some copies were preferentially co-opted, probably because they already possessed C4-like expression patterns. However, the identity of these C4-suitable genes varies among clades of angiosperms, and C4 phenotypes in distant angiosperm groups thus represent genuinely independent realizations, based on different genetic precursors.

  3. Parent of origin, mosaicism, and recurrence risk: probabilistic modeling explains the broken symmetry of transmission genetics.

    Science.gov (United States)

    Campbell, Ian M; Stewart, Jonathan R; James, Regis A; Lupski, James R; Stankiewicz, Paweł; Olofsson, Peter; Shaw, Chad A

    2014-10-02

    Most new mutations are observed to arise in fathers, and increasing paternal age positively correlates with the risk of new variants. Interestingly, new mutations in X-linked recessive disease show elevated familial recurrence rates. In male offspring, these mutations must be inherited from mothers. We previously developed a simulation model to consider parental mosaicism as a source of transmitted mutations. In this paper, we extend and formalize the model to provide analytical results and flexible formulas. The results implicate parent of origin and parental mosaicism as central variables in recurrence risk. Consistent with empirical data, our model predicts that more transmitted mutations arise in fathers and that this tendency increases as fathers age. Notably, the lack of expansion later in the male germline determines relatively lower variance in the proportion of mutants, which decreases with paternal age. Subsequently, observation of a transmitted mutation has less impact on the expected risk for future offspring. Conversely, for the female germline, which arrests after clonal expansion in early development, variance in the mutant proportion is higher, and observation of a transmitted mutation dramatically increases the expected risk of recurrence in another pregnancy. Parental somatic mosaicism considerably elevates risk for both parents. These findings have important implications for genetic counseling and for understanding patterns of recurrence in transmission genetics. We provide a convenient online tool and source code implementing our analytical results. These tools permit varying the underlying parameters that influence recurrence risk and could be useful for analyzing risk in diverse family structures.

  4. Clinical and genetic data on Lafora disease patients of Serbian/Montenegrin origin.

    Science.gov (United States)

    Kecmanović, M; Jović, N; Keckarević-Marković, M; Keckarević, D; Stevanović, G; Ignjatović, P; Romac, S

    2016-01-01

    Lafora disease (LD) is an autosomal recessive, progressive disorder characterized by myoclonus and seizures, inexorable neurologic deterioration, cognitive decline and poor prognosis. LD is caused by mutations either in the EPM2A or in NHLRC1 genes. Here we report clinical and genetic findings on 14 LD patients from 10 families of Serbian/Montenegrin origin. Molecular diagnostics was performed by sequencing the coding regions of the EPM2A and NHLRC1 genes. In addition, haplotype analysis of the chromosomes carrying the two most frequent mutations (c.1048-1049delGA and deletion of the whole NHLRC1 gene) using eight different markers flanking the NHLRC1 gene was conducted. We identified one new mutation (c.1028T>C) along with the 3 previously reported mutations (c.1048-1049delGA, c.990delG, deletion of the whole NHLRC1 gene), all of which were located on the NHLRC1 gene. The two predominant mutations (c.1048-1049delGA and complete NHLRC1 gene deletion) appear to be founder mutations. In addition to documenting the genetic heterogeneity observed for LD, our study suggests that mutations in the NHLRC1 gene may be a common cause of LD in the Serbian/Montenegrin population, primarily because of a founder effect.

  5. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Whole genome sequence and analysis of the Marwari horse breed and its genetic origin.

    Science.gov (United States)

    Jun, JeHoon; Cho, Yun Sung; Hu, Haejin; Kim, Hak-Min; Jho, Sungwoong; Gadhvi, Priyvrat; Park, Kyung Mi; Lim, Jeongheui; Paek, Woon Kee; Han, Kyudong; Manica, Andrea; Edwards, Jeremy S; Bhak, Jong

    2014-01-01

    The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.

  7. Genetic analysis of individual origins supports isolation of grizzly bears in the Greater Yellowstone Ecosystem

    Science.gov (United States)

    Haroldson, Mark A.; Schwartz, Charles; Kendall, Katherine C.; Gunther, Kerry A.; Moody, David S.; Frey, Kevin L.; Paetkau, David

    2010-01-01

    The Greater Yellowstone Ecosystem (GYE) supports the southernmost of the 2 largest remaining grizzly bear (Ursus arctos) populations in the contiguous United States. Since the mid-1980s, this population has increased in numbers and expanded in range. However, concerns for its long-term genetic health remain because of its presumed continued isolation. To test the power of genetic methods for detecting immigrants, we generated 16-locus microsatellite genotypes for 424 individual grizzly bears sampled in the GYE during 1983–2007. Genotyping success was high (90%) and varied by sample type, with poorest success (40%) for hair collected from mortalities found ≥1 day after death. Years of storage did not affect genotyping success. Observed heterozygosity was 0.60, with a mean of 5.2 alleles/marker. We used factorial correspondence analysis (Program GENETIX) and Bayesian clustering (Program STRUCTURE) to compare 424 GYE genotypes with 601 existing genotypes from grizzly bears sampled in the Northern Continental Divide Ecosystem (NCDE) (FST  =  0.096 between GYE and NCDE). These methods correctly classified all sampled individuals to their population of origin, providing no evidence of natural movement between the GYE and NCDE. Analysis of 500 simulated first-generation crosses suggested that over 95% of such bears would also be detectable using our 16-locus data set. Our approach provides a practical method for detecting immigration in the GYE grizzly population. We discuss estimates for the proportion of the GYE population sampled and prospects for natural immigration into the GYE.

  8. Developmental plasticity and the origin of novel forms: unveiling cryptic genetic variation via "use and disuse".

    Science.gov (United States)

    Palmer, A Richard

    2012-09-01

    Natural selection eliminates phenotypic variation from populations, generation after generation-an observation that haunted Darwin. So, how does new phenotypic variation arise, and is it always random with respect to fitness? Repeated behavioral responses to a novel environment-particularly those that are learned-are typically advantageous. If those behaviors yield more extreme or novel morphological variants via developmental plasticity, then previously cryptic genetic variation may be exposed to natural selection. Significantly, because the mean phenotypic effect of "use and disuse" is also typically favorable, previously cryptic genetic variation can be transformed into phenotypic variation that is both visible to selection and biased in an adaptive direction. Therefore, use-induced developmental plasticity in a very real sense "creates" new phenotypic variation that is nonrandom with respect to fitness, in contrast to the random phenotypic effects of mutation, recombination, and "direct effects" of environment (stress, nutrition). I offer here (a) a brief review of the immense literature on the effects of "use and disuse" on morphology, (b) a simple yet general model illustrating how cryptic genetic variation may be exposed to selection by developmentally plastic responses that alter trait performance in response to "use and disuse," and (c) a more detailed model of a positive feedback loop between learning (handed behavior) and morphological plasticity (use-induced morphological asymmetry) that may rapidly generate novel phenotypic variation and facilitate the evolution of conspicuous morphological asymmetries. Evidence from several sources suggests that handed behaviors played an important role both in the origin of novel forms (asymmetries) and in their subsequent evolution. Copyright © 2011 Wiley Periodicals, Inc., A Wiley Company.

  9. Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code

    Science.gov (United States)

    Aggarwal, Neha; Vishwa Bandhu, Ashutosh; Sengupta, Supratim

    2016-06-01

    The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population. The establishment of such an optimal code depends on the probability of HGT events. Only when the probability of HGT events is above a critical threshold, we find that the ten amino acid code having a structure that is most consistent with the standard genetic code (SGC) often gets fixed in the population with the highest probability. We examine how the threshold is determined by factors like the population size, length of the sequences and selection coefficient. Our simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.

  10. Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code.

    Science.gov (United States)

    Aggarwal, Neha; Bandhu, Ashutosh Vishwa; Sengupta, Supratim

    2016-05-27

    The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population. The establishment of such an optimal code depends on the probability of HGT events. Only when the probability of HGT events is above a critical threshold, we find that the ten amino acid code having a structure that is most consistent with the standard genetic code (SGC) often gets fixed in the population with the highest probability. We examine how the threshold is determined by factors like the population size, length of the sequences and selection coefficient. Our simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.

  11. Genetic evidence from mitochondrial DNA corroborates the origin of Tibetan chickens

    Science.gov (United States)

    Zhu, Qing; Zhao, Xiaoling; Wang, Yan; Yin, Huadong; Hu, Yaodong; Liu, Aiping; Li, Diyan

    2017-01-01

    Chicken is the most common poultry species and is important to human societies. Tibetan chicken (Gallus gallus domesticus) is a breed endemic to China that is distributed mainly on the Qinghai-Tibet Plateau. However, its origin has not been well characterized. In the present study, we sequenced partial mitochondrial DNA (mtDNA) control region of 239 and 283 samples from Tibetan and Sichuan indigenous chickens, respectively. Incorporating 1091 published sequences, we constructed the matrilineal genealogy of Tibetan chickens to further document their domestication history. We found that the genetic structure of the mtDNA haplotypes of Tibetan chickens are dominated by seven major haplogroups (A-G). In addition, phylogenetic and network analyses showed that Tibetan chickens are not distinguishable from the indigenous chickens in surrounding areas. Furthermore, some clades of Tibetan chickens may have originated from game fowls. In summary, our results collectively indicated that Tibetan chickens may have diverged from indigenous chickens in the adjacent regions and hybridized with various chickens. PMID:28241078

  12. Genetic analysis identifies the region of origin of smuggled peach palm seeds.

    Science.gov (United States)

    Cristo-Araújo, Michelly; Molles, David Bronze; Rodrigues, Doriane Picanço; Clement, Charles R

    2017-04-01

    Seeds of a plant, supposedly a palm tree known popularly as peach palm (Bactris gasipaes), were seized by the Federal Police in the state of Pará, Brazil, without documentation of legal origin to authorize transportation and marketing in Brazil. They were alleged to be from the western part of Amazonas, Brazil, near the frontier with Peru and Colombia, justifying the lack of documentation. The species was confirmed to be peach palm. To determine the likely place of origin, a genetic analysis was performed to determine the relationship between the seized seeds and representative populations of peach palm from all of Amazonia, maintained in the Peach palm Core Collection, at the National Research Institute for Amazonia, using nine microsatellite loci. Reynolds' coancestry analysis showed a strong relationship between the seeds and the Pampa Hermosa landrace, around Yurimaguas, Peru. The Structure program, used to infer the probability of an individual belonging to a given population, showed that most seeds grouped with populations close to Yurimaguas, Peru, corroborating the coancestry analysis. The Pampa Hermosa landrace is the main source of spineless peach palm seeds used in the Brazilian heart-of-palm agribusiness, which motivated the smugglers to attempt this biopiracy.

  13. The application of genetics methods to differentiation of three Lactobacillus species of human origin.

    Science.gov (United States)

    Gosiewski, Tomasz; Chmielarczyk, Agnieszka; Strus, Magdalena; Brzychczy-Włoch, Monika; Heczko, Piotr B

    2012-12-01

    In recent decades, the interest in probiotics as diet supplements or drugs has increased. In order to determine a specific bacterial isolate to be probiotic, it is necessary to describe precisely its probiotic characteristics and taxonomic properties, including the strain level. Most of the well-known genotyping methods were designed for the commonly-found pathogenic bacteria. The objective of this study is to undertake an attempt at standardization of FISH, RAPD and PFGE methods to genotype and identify the bacteria belonging to Lactobacillus fermentum, L. gasseri and L. plantarum species. The FISH probes have been designed and tested for Lactobacillus fermentum, L. gasseri and L. plantarum species and an endeavor has been made at standardization of RAPD and PFGE methods for these bacterial species. Moreover, the MLST method was applied to differentiate Lactobacillus plantarum strains. L. plantarum isolated from humans could not be genetically diversified with the use of RAPD, PFGE or MLST methods; only the strains originating from plants have displayed diversification among themselves and have been different from the strains of human origin.

  14. Informativeness of the CODIS STR loci for admixture analysis.

    Science.gov (United States)

    Barnholtz-Sloan, Jill S; Pfaff, Carrie L; Chakraborty, Ranajit; Long, Jeffrey C

    2005-11-01

    Population admixture (or ancestry) is used as an approach to gene discovery in complex diseases, particularly when the disease prevalence varies widely across geographic populations. Admixture analysis could be useful for forensics because an indication of a perpetrator's ancestry would narrow the pool of suspects for a particular crime. The purpose of this study was to use Fisher's information to identify informative sets of markers for admixture analysis. Using published founding population allele frequencies we test three marker sets for efficacy for estimating admixture: the FBI CODIS Core STR loci, the HGDP-CEPH Human Genome Diversity Cell Line Panel and the set of 39 ancestry informative SNPS from the Shriver lab at Pennsylvania State University. We conclude that the FBI CODIS Core STR set is valid for admixture analysis, but not the most precise. We recommend using a combination of the most informative markers from the HGDP-CEPH and Shriver loci sets.

  15. Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina.

    Science.gov (United States)

    Parra, E J; Kittles, R A; Argyropoulos, G; Pfaff, C L; Hiester, K; Bonilla, C; Sylvester, N; Parrish-Gause, D; Garvey, W T; Jin, L; McKeigue, P M; Kamboh, M I; Ferrell, R E; Pollitzer, W S; Shriver, M D

    2001-01-01

    We analyzed admixture in samples of six different African-American populations from South Carolina: Gullah-speaking Sea Islanders in coastal South Carolina, residents of four counties in the "Low Country" (Berkeley, Charleston, Colleton, and Dorchester), and persons living in the city of Columbia, located in central South Carolina. We used a battery of highly informative autosomal, mtDNA, and Y-chromosome markers. Two of the autosomal markers (FY and AT3) are linked and lie 22 cM apart on chromosome 1. The results of this study indicate, in accordance with previous historical, cultural, and anthropological evidence, a very low level of European admixture in the Gullah Sea Islanders (m = 3.5 +/- 0.9%). The proportion of European admixture is higher in the Low Country (m ranging between 9. 9 +/- 1.8% and 14.0 +/- 1.9%), and is highest in Columbia (m = 17.7 +/- 3.1%). A sex-biased European gene flow and a small Native American contribution to the African-American gene pool are also evident in these data. We studied the pattern of pairwise allelic associations between the FY locus and the nine other autosomal markers in our samples. In the combined sample from the Low Country (N = 548), a high level of linkage disequilibrium was observed between the linked markers, FY and AT3. Additionally, significant associations were also detected between FY and 4 of the 8 unlinked markers, suggesting the existence of significant genetic structure in this population. A continuous gene flow model of admixture could explain the observed pattern of genetic structure. A test conditioning on the overall admixture of each individual showed association of ancestry between the two linked markers (FY and AT3), but not between any of the unlinked markers, as theory predicts. Thus, even in the presence of genetic structure due to continuous gene flow or some other factor, it is possible to differentiate associations due to linkage from spurious associations due to genetic structure.

  16. Information on genetic origins in donor-assisted conception: is knowing who you are a human rights issue?

    Science.gov (United States)

    Blyth, Eric

    2002-11-01

    It was not by my choice that my ancestral home is nothing more than a sample jar. (Whipp, 2000) There can be few more basic rights than a right to one's identity...a right not to be deceived about one's true origins. (Freeman, 1996) This article provides an overview of existing arrangements for the management of information on genetic origins in donor-assisted conception, that is, treatment involving sperm, eggs or embryo donation. The balance of this article reflects the fact that much of the debate on information on genetic origins in donor-assisted conception has been dominated by sperm donation. A detailed discussion of the rather different issues of egg and embryo donation would have added significantly to its complexity and length. The article considers what donor-conceived people wish to know about their genetic origins and how this might be seen as a human rights issue. The possibility of conflict between the interests and rights of donors and recipients of donated gametes or embryos is discussed, and possible policy and legislative options are outlined. The paper concludes that a donor-conceived person's own definition of their best interests should form the basis for the facilitation of access to information about their genetic origins.

  17. Genetic Structure of Water Chestnut Beetle: Providing Evidence for Origin of Water Chestnut

    Science.gov (United States)

    Qin, Jing; Lu, Ming-Xing; Du, Yu-Zhou

    2016-01-01

    Water chestnut beetle (Galerucella birmanica Jacoby) is a pest of the water chestnut (Trapa natans L.). To analyze the phylogeny and biogeography of the beetle and provide evidence for the origin of T. natans in China, we conducted this by using three mitochondrial genes (COI, COII and Cytb) and nuclear ITS2 ribosomal DNA of G. birmanica. As for mtDNA genes, the beetle could be subdivided into three groups: northeastern China (NEC), central-northern-southern China (CC-NC-SC) and southwestern China (SWC) based on SAMOVA, phylogenetic analyses and haplotype networks. But for ITS2, no obvious lineages were obtained but individuals which were from NEC region clustered into one clade, which might be due to sequence conservation of ITS2. Significant genetic variation was observed among the three groups with infrequent gene flow between groups, which may have been restricted due to natural barriers and events in the Late Pleistocene. Based on our analyses of genetic variation in the CC-NC-SC geographical region, the star-like haplotype networks, approximate Bayesian computation, niche modelling and phylogeographic variation of the beetle, we concluded that the beetle population has been lasting in the lower, central reaches of the Yangtze River Basin with its host plant, water chestnut, which is consistent with archaeological records. Moreover, we speculate that the CC-NC-SC population of G. birmanica may have undergone a period of expansion coincident with domestication of the water chestnut approximately 113,900–126,500 years ago. PMID:27459279

  18. Sero-genetic studies on the Ambo of Namibia.

    Science.gov (United States)

    Nurse, G T; Dunn, D S; Rootman, A J; Jenkins, T

    1987-08-01

    The Ambo are the largest population group of Namibia/South West Africa and consist of seven geographical and sociopolitical entities speaking different dialects of a common language. Nearly 600 individuals representing all the dialect groups were tested for 23 sero-genetic systems: the results reveal no evidence of significant San admixture and unusual alleles suggest an affinity with the Herero which confirms oral traditions of a common origin. Genetic distance measurements indicate that the Dama may also have a connection with these peoples and it is probable that most of the Bantu-speaking Negroes of Namibia/South West Africa come from the same stock.

  19. Development of admixture mapping panels for African Americans from commercial high-density SNP arrays

    Directory of Open Access Journals (Sweden)

    Dunston Georgia M

    2010-07-01

    Full Text Available Abstract Background Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels of ancestry-informative markers (AIMs for admixture mapping, markers have to be genotyped de novo for each admixed study sample and samples representing the ancestral parental populations. The increased availability of dense marker data on commercial chips has made it feasible to develop panels wherein the markers need not be predetermined. Results We developed two panels of AIMs (~2,000 markers each based on the Affymetrix Genome-Wide Human SNP Array 6.0 for admixture mapping with African American samples. These two AIM panels had good map power that was higher than that of a denser panel of ~20,000 random markers as well as other published panels of AIMs. As a test case, we applied the panels in an admixture mapping study of hypertension in African Americans in the Washington, D.C. metropolitan area. Conclusions Developing marker panels for admixture mapping from existing genome-wide genotype data offers two major advantages: (1 no de novo genotyping needs to be done, thereby saving costs, and (2 markers can be filtered for various quality measures and replacement markers (to minimize gaps can be selected at no additional cost. Panels of carefully selected AIMs have two major advantages over panels of random markers: (1 the map power from sparser panels of AIMs is higher than that of ~10-fold denser panels of random markers, and (2 clusters can be labeled based on information from the parental populations. With current technology, chip-based genome-wide genotyping is less expensive than genotyping ~20,000 random markers. The major advantage of using random markers is the absence of ascertainment effects resulting from the process of selecting markers. The ability to develop marker panels informative for ancestry from

  20. Dissecting the Genetic Susceptibility to Graves' Disease in a Cohort of Patients of Italian Origin.

    Science.gov (United States)

    Lombardi, Angela; Menconi, Francesca; Greenberg, David; Concepcion, Erlinda; Leo, Marenza; Rocchi, Roberto; Marinó, Michele; Keddache, Mehdi; Tomer, Yaron

    2016-01-01

    Graves' disease (GD) is an autoimmune oligogenic disorder with a strong hereditary component. Several GD susceptibility genes have been identified and confirmed during the last two decades. However, there are very few studies that evaluated susceptibility genes for GD in specific geographic subsets. Previously, we mapped a new locus on chromosome 3q that was unique to GD families of Italian origin. In the present study, we used association analysis of single-nucleotide polymorphism (SNPs) at the 3q locus in a cohort of GD patients of Italian origin in order to prioritize the best candidates among the known genes in this locus to choose the one(s) best supported by the association. DNA samples were genotyped using the Illumina GoldenGate genotyping assay analyzing 690 SNP in the linked 3q locus covering all 124 linkage disequilibrium blocks in this locus. Candidate non-HLA (human-leukocyte-antigen) genes previously reported to be associated with GD and/or other autoimmune disorders were analyzed separately. Three SNPs in the 3q locus showed a nominal association (p < 0.05): rs13097181, rs763313, and rs6792646. Albeit these could not be further validated by multiple comparison correction, we were prioritizing candidate genes at a locus already known to harbor a GD-related gene, not hypothesis testing. Moreover, we found significant associations with the thyroid-stimulating hormone receptor (TSHR) gene, the cytotoxic T-lymphocyte antigen-4 (CTLA-4) gene, and the thyroglobulin (TG) gene. In conclusion, we identified three SNPs on chromosome 3q that may map a new GD susceptibility gene in this region which is unique to the Italian population. Furthermore, we confirmed that the TSHR, the CTLA-4, and the TG genes are associated with GD in Italians. Our findings highlight the influence of ethnicity and geographic variations on the genetic susceptibility to GD.

  1. Using autonomous replication to physically and genetically define human origins of replication

    Energy Technology Data Exchange (ETDEWEB)

    Krysan, P.J.

    1993-01-01

    The author previously developed a system for studying autonomous replication in human cells involving the use of sequences from the Epstein-Barr virus (EBV) genome to provide extrachromosomal plasmids with a nuclear retention function. Using this system, it was demonstrated that large fragments of human genomic DNA could be isolated which replicate autonomously in human cells. In this study the DNA sequences which function as origins of replication in human cells are defined physically and genetically. These experiments demonstrated that replication initiates at multiple locations distributed throughout the plasmid. Another line of experiments addressed the DNA sequence requirements for autonomous replication in human cells. These experiments demonstrated that human DNA fragments have a higher replication activity than bacterial fragments do. It was also found, however, that the bacterial DNA sequence could support efficient replication if enough copies of it were present on the plasmid. These findings suggested that autonomous replication in human cells does not depend on extensive, specific DNA sequences. The autonomous replication system which the author has employed for these experiments utilizes a cis-acting sequence from the EBV origin and the trans-acting EBNA-1 protein to provide plasmids with a nuclear retention function. It was therefore relevant to verify that the autonomous replication of human DNA fragments did not depend on the replication activity associated with the EBV sequences utilized for nuclear retention. To accomplish this goal, the author demonstrated that plasmids carrying the EBV sequences and large fragments of human DNA could support long-term autonomous replication in hamster cells, which are not permissive for EBV replication.

  2. [Origin and genetic diversity of Mongolian and Chinese sheep using mitochondrial DNA D-loop sequences].

    Science.gov (United States)

    Luo, Yu-Zhu; Cheng, Shu-Ru; Batsuuri, Lkhagva; Badamdorj, D; Olivier, Hanotte; Han, Jian-Lin

    2005-12-01

    To determine the origin and gene diversity of the Chinese and Mongolian domestic sheep, a partial fragment of mitochondrial DNA D-loop was sequenced for total number of 314 individuals from nine Chinese sheep populations and 11 Mongolian sheep populations. The results show no difference in nucleotide composition between Chinese and Mongolian sheep mtDNA D-loop sequences. However, more variables were identified in Mongolian sheep (26.85% of the sites) than that in Chinese sheep (24.22%). In China, mtDNA haplotype diversity was the highest in Qinghai Tibetan sheep, followed then by Gansu Tibetan sheep, Gansu Alpine Merino, Qinghai Merino, Gannan Tibetan sheep, Small-tailed Han sheep, Tan sheep, Hu sheep and Minxian Black Fur sheep. In Mongolian sheep, mtDNA haplotype diversity was the highest in Bayad and Baidrag populations and the lowest in the Gobi-Altai population. In general, Mongolian sheep have a richer genetic diversity than the Chinese ones with larger number of haplotypes (86.06% (142/165) versus 78.83% (108/137)), higher haplotype diversity (Hd; 0.976 versus 0.936), higher nucleotide diversity (Pi (pi); 0. 036 versus 0.034) and higher average number of nucleotide differences (k; 23.50 versus 22.48). Phylogenetic analysis of the 217 haplotypes identified in both Mongolian and Chinese sheep supported the same origin of their domestication with three distinct maternal lineages defined as major haplotypes A, B and C, of which haplotype A are the commonest in all Chinese sheep populations and in the majority of Mongolian sheep populations (9/11) with an average frequency of 58.73%, followed by haplotype B present in eight of Chinese population and in all Mongolian sheep populations with an average frequency of 24.68%, and haplotype C present in eight Chinese and in 10 Mongolian sheep populations with an average frequency of 16.59%. Further network analysis of the phylogenetic relationship of the 87 haplotypes identified from 91 sequences retrieved from Gen

  3. Behavior of passive admixture in a vortical hydrodynamic field

    Directory of Open Access Journals (Sweden)

    R.O.Bobrov

    2006-01-01

    Full Text Available The motion of passive admixture of spherical particles in the stationary hydrodynamic field of a swirling flow is studied. A spherical particle of a given mass in the hydrodynamic field of a swirling flow is located on a certain circular orbit, where the centrifugal force is compensated by the radial drag force due to the sink. This leads to the separation of the host fluid and admixture. A theory of Brownian motion of admixture in dilute solutions with a non-uniform flow is constructed.

  4. Swarming, defensive and hygienic behaviour in honey bee colonies of different genetic origin in a pan-European experiment

    DEFF Research Database (Denmark)

    Uzunov, Aleksandar; Costa, Cecilia; Panasiuk, Beata;

    2014-01-01

    Honey bee colonies exhibit a wide range of variation in their behaviour, depending on their genetic origin and environmental factors. The COLOSS Genotype-Environment Interactions Experiment gave us the opportunity to investigate the phenotypic expression of the swarming, defensive and hygienic be...

  5. Genetic-evolutionary studies on cultivated cannas : VI. Origin and evolution of ornamental taxa.

    Science.gov (United States)

    Khoshoo, T N; Mukherjee, I

    1970-01-01

    Hybridization has played a dominant and decisive role in the origin of ornamental cannas. This has been made possible by the ecospecific differentiation of the parental species, which implies lack of barriers and a good deal of recombination associated with reasonably high fertility.Colour differences between species are controlled by a number of genes and their intensifiers, inhibitors, lethals, etc. From recombination in interspecific hybrids of such a wide range of genes, segregating simultaneously and involving complex segregation, arises a wide array of heterozygous genotypes with new colours and colour combinations, releasing much genetic diversity.Hybridization has also been responsible for transgressive segregation, particularly in length and breadth of staminodia and luxuriance, affecting not only plant height but also flower size. Perhaps the most important single factor responsible for the evolution of ornamental cannas has been the repeated cycles of hybridization which have led to the breakage of size and other barriers; this seems to have been exploited continuously until very large flower size was built up and combined with other useful vegetative and floral characters such as colour and number of flowers per inflorescence, extended blooming period, cold resistance, etc. The efficient vegetative propagation made fixing of the useful genotypes no problem, although they may contain a high degree of heterozygosity and sexual sterility.Along these lines, Année (hybrids between C. indica and C. glauca) and Ehemann (hybrids between C. iridiflora and C. warscwiczii) cannas came into being in 1848 and 1863 respectively. Although both were a distinct improvement over the original species, they were still relatively small-flowered and major improvements came roundabout 1868, when Crozy, Gladiolus or French Dwarf cannas (C. X generalis Bailey) were released. This group arose from hybrids and back crosses of the first two groups and contains diploids

  6. Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis

    Indian Academy of Sciences (India)

    K Ikehara

    2002-03-01

    We have investigated the origin of genes, the genetic code, proteins and life using six indices (hydropathy, -helix, -sheet and -turn formabilities, acidic amino acid content and basic amino acid content) necessary for appropriate three-dimensional structure formation of globular proteins. From the analysis of microbial genes, we have concluded that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GC-NSF(a)] and from SNS repeating sequences [(SNS)n] similar to the GC-NSF(a) (S and N mean G or C and either of four bases, respectively). We have also proposed that the universal genetic code used by most organisms on the earth presently could be derived from a GNC-SNS primitive genetic code. We have further presented the [GADV]-protein world hypothesis of the origin of life as well as a hypothesis of protein production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions termed as GNC-, SNS- and GC-NSF(a)-0th order structures of proteins. The [GADV]-protein world hypothesis is primarily derived from the GNC-primitive genetic code hypothesis. It is also expected that basic properties of extant genes and proteins could be revealed by considerations based on the scenario with four stages.

  7. Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.

    Science.gov (United States)

    Caetano-Anollés, Gustavo; Wang, Minglei; Caetano-Anollés, Derek

    2013-01-01

    The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the 'operational' RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment. Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation. Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.

  8. Sequence analysis of mitochondrial ND1 gene can reveal the genetic structure and origin of Bactrocera dorsalis s.s.

    Science.gov (United States)

    Wu, Zhong-Zhen; Li, Hong-Mei; Bin, Shu-Ying; Ma, Jun; He, Hua-Liang; Li, Xian-Feng; Gong, Fei-Liang; Lin, Jin-Tian

    2014-03-21

    The oriental fruit fly, Bactrocera dorsalis s.s., is one of the most important quarantine pests in many countries, including China. Although the oriental fruit fly has been investigated extensively, its origins and genetic structure remain disputed. In this study, the NADH dehydrogenase subunit 1 (ND1) gene was used as a genetic marker to examine the genetic diversity, population structure, and gene flow of B. dorsalis s.s. throughout its range in China and southeast Asia. Haplotype networks and phylogenetic analysis indicated two distinguishable lineages of the fly population but provided no strong support for geographical subdivision in B. philippinensis. Demographic analysis revealed rapid expansion of B. dorsalis s.s. populations in China and Southeast Asia in the recent years. The greatest amount of genetic diversity was observed in Manila, Pattaya, and Bangkok, and asymmetric migration patterns were observed in different parts of China. The data collected here further show that B. dorsalis s.s. in Yunnan, Guangdong, and Fujian Provinces, and in Taiwan might have different origins within southeast Asia. Using the mitochondrial ND1 gene, the results of the present study showed B. dorsalis s.s. from different parts of China to have different genetic structures and origins. B. dorsalis s.s. in China and southeast Asia was found to have experienced rapid expansion in recent years. Data further support the existence of two distinguishable lineages of B. dorsalis s.s. in China and indicate genetic diversity and gene flow from multiple origins.The sequences in this paper have been deposited in GenBank/NCBI under accession numbers KC413034-KC413367.

  9. Implications of the Admixture Process in Skin Color Molecular Assessment

    Science.gov (United States)

    de Cerqueira, Caio Cesar Silva; Hünemeier, Tábita; Gomez-Valdés, Jorge; Ramallo, Virgínia; Volasko-Krause, Carla Daiana; Barbosa, Ana Angélica Leal; Vargas-Pinilla, Pedro; Dornelles, Rodrigo Ciconet; Longo, Danaê; Rothhammer, Francisco; Bedoya, Gabriel; Canizales-Quinteros, Samuel; Acuña-Alonzo, Victor; Gallo, Carla; Poletti, Giovanni; González-José, Rolando; Salzano, Francisco Mauro; Callegari-Jacques, Sídia Maria; Schuler-Faccini, Lavínia; Ruiz-Linares, Andrés; Cátira Bortolini, Maria

    2014-01-01

    The understanding of the complex genotype-phenotype architecture of human pigmentation has clear implications for the evolutionary history of humans, as well as for medical and forensic practices. Although dozens of genes have previously been associated with human skin color, knowledge about this trait remains incomplete. In particular, studies focusing on populations outside the European-North American axis are rare, and, until now, admixed populations have seldom been considered. The present study was designed to help fill this gap. Our objective was to evaluate possible associations of 18 single nucleotide polymorphisms (SNPs), located within nine genes, and one pseudogene with the Melanin Index (MI) in two admixed Brazilian populations (Gaucho, N = 352; Baiano, N = 148) with different histories of geographic and ethnic colonization. Of the total sample, four markers were found to be significantly associated with skin color, but only two (SLC24A5 rs1426654, and SLC45A2 rs16891982) were consistently associated with MI in both samples (Gaucho and Baiano). Therefore, only these 2 SNPs should be preliminarily considered to have forensic significance because they consistently showed the association independently of the admixture level of the populations studied. We do not discard that the other two markers (HERC2 rs1129038 and TYR rs1126809) might be also relevant to admixed samples, but additional studies are necessary to confirm the real importance of these markers for skin pigmentation. Finally, our study shows associations of some SNPs with MI in a modern Brazilian admixed sample, with possible applications in forensic genetics. Some classical genetic markers in Euro-North American populations are not associated with MI in our sample. Our results point out the relevance of considering population differences in selecting an appropriate set of SNPs as phenotype predictors in forensic practice. PMID:24809478

  10. An analysis of the metabolic theory of the origin of the genetic code

    Science.gov (United States)

    Amirnovin, R.; Bada, J. L. (Principal Investigator)

    1997-01-01

    A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared. It was determined that many codon correlations are also present within random genetic codes and that among the random codes there are always several which have many more correlations than that found in the universal code. Although the number of correlations depends on the choice of biosynthetically related amino acids, the probability of choosing a random genetic code with the same or greater number of codon correlations as the universal genetic code was found to vary from 0.1% to 34% (with respect to a fairly complete listing of related amino acids). Thus, Wong's theory that the genetic code arose by coevolution with the biosynthetic pathways of amino acids, based on codon correlations between biosynthetically related amino acids, is statistical in nature.

  11. Genetic structures at the origin of acquisition of the beta-lactamase bla KPC gene.

    Science.gov (United States)

    Naas, Thierry; Cuzon, Gaelle; Villegas, Maria-Virginia; Lartigue, Marie-Frédérique; Quinn, John P; Nordmann, Patrice

    2008-04-01

    Genetic structures surrounding the carbapenem-hydrolyzing Ambler class A bla KPC gene were characterized in several KPC-positive Klebsiella pneumoniae and Pseudomonas aeruginosa strains isolated from the United States, Colombia, and Greece. The bla KPC genes were associated in all cases with transposon-related structures. In the K. pneumoniae YC isolate from the United States, the beta-lactamase bla KPC-2 gene was located on a novel Tn3-based transposon, Tn4401. Tn4401 was 10 kb in size, was delimited by two 39-bp imperfect inverted repeat sequences, and harbored, in addition to the beta-lactamase bla KPC-2 gene, a transposase gene, a resolvase gene, and two novel insertion sequences, ISKpn6 and ISKpn7. Tn4401 has been identified in all isolates. However, two isoforms of this transposon were found: Tn4401a was found in K. pneumoniae YC and K. pneumoniae GR from the United States and Greece, respectively, and differed by a 100-bp deletion, located just upstream of the bla KPC-2 gene, compared to the sequence of Tn4401b, which was found in the Colombian isolates. In all isolates tested, Tn4401 was flanked by a 5-bp target site duplication, the signature of a recent transposition event, and was inserted in different open reading frames located on plasmids that varied in size and nature. Tn4401 is likely at the origin of carbapenem-hydrolyzing beta-lactamase KPC mobilization to plasmids and its further insertion into various-sized plasmids identified in nonclonally related K. pneumoniae and P. aeruginosa isolates.

  12. A genetic approach to the origin of Millepora sp. in the eastern Atlantic

    Science.gov (United States)

    López, C.; Clemente, S.; Almeida, C.; Brito, A.; Hernández, M.

    2015-06-01

    Many species have experienced recent range expansions due to human-mediated processes, such as the unintentional transport on ships or plastic waste and ocean warming, which facilitates many tropical species to tolerate living beyond their normal limit of distribution, with a potential impact on autochthonous assemblages. In September 2008, three colonies of the fire coral Millepora sp. (Cnidaria: Hydrozoa) were found on the southeastern coast of Tenerife (Canary Islands), though this species had been previously described to have a circumtropical distribution with Cape Verde Islands as its northern limit of distribution in the eastern Atlantic. The aim of this study was to determine the origin of these new colonies in the Canary Islands (11°N of its previously known northernmost limit of distribution) using variation in the cytochrome oxidase subunit I (COI) gene as a molecular marker. In order to do that, Millepora samples from Tenerife and Cape Verde Islands were collected for molecular analyses, and COI sequences from Caribbean samples listed in GenBank were also included in the analysis. Our results showed that all the specimens from Tenerife were genetically identical, suggesting that the colonization of the Canary Islands was the result of a very recent and strong founder effect. The nucleotide sequences of the samples from the Cape Verde and the Canary Islands were closer to the Caribbean than between themselves, pointing to the Caribbean population as the source population for both archipelagos, through independent founder events. The fact that Millepora sp. arrived to Cape Verde long before arriving to the Canaries (pleistocene fossils have been found in that archipelago) suggests that the habitat requirements for this species did not exist before in the Canarian archipelago. Therefore, the rising seawater temperatures recently registered in the Canary Islands could have facilitated the settlement of reef-forming corals drifting across the two basins of

  13. Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms.

    Science.gov (United States)

    Ginja, C; Penedo, M C T; Melucci, L; Quiroz, J; Martínez López, O R; Revidatti, M A; Martínez-Martínez, A; Delgado, J V; Gama, L T

    2010-04-01

    The ancestry of New World cattle was investigated through the analysis of mitochondrial and Y chromosome variation in Creoles from Argentina, Brazil, Mexico, Paraguay and the United States of America. Breeds that influenced the Creoles, such as Iberian native, British and Zebu, were also studied. Creoles showed high mtDNA diversity (H = 0.984 +/- 0.003) with a total of 78 haplotypes, and the European T3 matriline was the most common (72.1%). The African T1a haplogroup was detected (14.6%), as well as the ancestral African-derived AA matriline (11.9%), which was absent in the Iberian breeds. Genetic proximity among Creoles, Iberian and Atlantic Islands breeds was inferred through their sharing of mtDNA haplotypes. Y-haplotype diversity in Creoles was high (H = 0.779 +/- 0.019), with several Y1, Y2 and Y3 haplotypes represented. Iberian patrilines in Creoles were more difficult to infer and were reflected by the presence of H3Y1 and H6Y2. Y-haplotypes confirmed crossbreeding with British cattle, mainly of Hereford with Pampa Chaqueño and Texas Longhorn. Male-mediated Bos indicus introgression into Creoles was found in all populations, except Argentino1 (herd book registered) and Pampa Chaqueño. The detection of the distinct H22Y3 patriline with the INRA189-90 allele in Caracú suggests introduction of bulls directly from West Africa. Further studies of Spanish and African breeds are necessary to elucidate the origins of Creole cattle, and determine the exact source of their African lineages.

  14. Intramolecular interactions in aminoacyl nucleotides: Implications regarding the origin of genetic coding and protein synthesis

    Science.gov (United States)

    Lacey, J. C., Jr.; Mullins, D. W., Jr.; Watkins, C. L.; Hall, L. M.

    1986-01-01

    Cellular organisms store information as sequences of nucleotides in double stranded DNA. This information is useless unless it can be converted into the active molecular species, protein. This is done in contemporary creatures first by transcription of one strand to give a complementary strand of mRNA. The sequence of nucleotides is then translated into a specific sequence of amino acids in a protein. Translation is made possible by a genetic coding system in which a sequence of three nucleotides codes for a specific amino acid. The origin and evolution of any chemical system can be understood through elucidation of the properties of the chemical entities which make up the system. There is an underlying logic to the coding system revealed by a correlation of the hydrophobicities of amino acids and their anticodonic nucleotides (i.e., the complement of the codon). Its importance lies in the fact that every amino acid going into protein synthesis must first be activated. This is universally accomplished with ATP. Past studies have concentrated on the chemistry of the adenylates, but more recently we have found, through the use of NMR, that we can observe intramolecular interactions even at low concentrations, between amino acid side chains and nucleotide base rings in these adenylates. The use of this type of compound thus affords a novel way of elucidating the manner in which amino acids and nucleotides interact with each other. In aqueous solution, when a hydrophobic amino acid is attached to the most hydrophobic nucleotide, AMP, a hydrophobic interaction takes place between the amino acid side chain and the adenine ring. The studies to be reported concern these hydrophobic interactions.

  15. Dense packing properties of mineral admixtures in cementitious material

    Institute of Scientific and Technical Information of China (English)

    Yanzhou Peng; Shuguang Hu; Qingjun Ding

    2009-01-01

    The effect of ultra-fine fly ash (UFFA), steel slag (SS) and silica fume (SF) on packing density of binary, ternary and quaternary cementitious materials was studied in this paper in terms of minimum water requirement of cement. The influence of mineral admixtures on the relative density of pastes with low water/binder ratios was analyzed and the relationship between paste density and compressive strength of the corresponding hardened mortars was discussed. The results indicate that the incorporation of mineral admixtures can effectively improve the packing density of cementitious materials; the increase in packing density of a composite with incorporation of two or three kinds of mineral admixtures is even more obvious than that with only one mineral admixture. Moreover, an optimal amount of mineral admixture imparts to the mixture maximum packing density. The dense packing effect of a mineral admixture can increase the packing density of the resulting cementitious material and also the density of paste with low water/binder ratio, which evidently enhances the compressive strength of the hardened mortar.

  16. Assessing individual interethnic admixture and population substructure using a 48-insertion-deletion (INSEL) ancestry-informative marker (AIM) panel.

    Science.gov (United States)

    Santos, Ney P C; Ribeiro-Rodrigues, Elzemar M; Ribeiro-Dos-Santos, Andrea K C; Pereira, Rui; Gusmão, Leonor; Amorim, António; Guerreiro, Joáo F; Zago, Marco A; Matte, Cecília; Hutz, Mara H; Santos, Sidney E B

    2010-02-01

    Estimating the proportions of different ancestries in admixed populations is very important in population genetics studies, and it is particularly important for detecting population substructure effects in case-control association studies. In this work, a set of 48 ancestry-informative insertion-deletion polymorphisms (INDELs) were selected with the goal of efficiently measuring the proportions of three different ancestries (sub-Saharan African, European, and Native American) in mixed populations. All selected markers can be easily analyzed via multiplex PCR and detected with standard capillary electrophoresis. A total of 593 unrelated individuals representative of European, African, and Native American parental populations were typed, as were 380 individuals from three Brazilian populations with known admixture patterns. As expected, the interethnic admixture estimates show that individuals from southern Brazil present an almost exclusively European ancestry; Afro-descendant communities in the Amazon region, apart from the major African contribution, present some degree of admixture with Europeans and Native Americans; and a sample from Belém, in the northeastern Amazon, shows a significant contribution of the three ethnic groups, although with a greater European proportion. In summary, a panel of ancestry-informative INDELs was optimized and proven to be a valuable tool for estimating individual and global ancestry proportions in admixed populations. The ability to accurately infer interethnic admixtures highlights the usefulness of this marker set for assessing population substructure in association studies, particularly those conducted in Brazilian and other Latin American populations sharing trihybrid ancestry patterns.

  17. International Veterinary Epilepsy Task Force's current understanding of idiopathic epilepsy of genetic or suspected genetic origin in purebred dogs

    DEFF Research Database (Denmark)

    Hülsmeyer, Velia-Isabel; Fischer, Andrea; Mandigers, Paul J. J.;

    2015-01-01

    Canine idiopathic epilepsy is a common neurological disease affecting both purebred and crossbred dogs. Various breed-specific cohort, epidemiological and genetic studies have been conducted to date, which all improved our knowledge and general understanding of canine idiopathic epilepsy, and in ...

  18. International Veterinary Epilepsy Task Force's current understanding of idiopathic epilepsy of genetic or suspected genetic origin in purebred dogs

    DEFF Research Database (Denmark)

    Hülsmeyer, Velia-Isabel; Fischer, Andrea; Mandigers, Paul J. J.

    2015-01-01

    of the dog with epilepsy in everyday clinical practice and furthermore may promote canine epilepsy research. The following manuscript reviews the evidence available for breeds which have been identified as being predisposed to idiopathic epilepsy with a proven or suspected genetic background, and highlights...

  19. History shaped the geographic distribution of genomic admixture on the island of Puerto Rico.

    Directory of Open Access Journals (Sweden)

    Marc Via

    Full Text Available 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.

  20. Glioblastomas with Oligodendroglial Component – Common Origin of the Different Histological Parts and Genetic Subclassification

    Directory of Open Access Journals (Sweden)

    Barbara Klink

    2010-01-01

    Full Text Available Background: Glioblastomas are the most common and most malignant brain tumors in adults. A small subgroup of glioblastomas contains areas with histological features of oligodendroglial differentiation (GBMO. Our objective was to genetically characterize the oligodendroglial and the astrocytic parts of GBMOs and correlate morphologic and genetic features with clinical data.

  1. Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift?

    Directory of Open Access Journals (Sweden)

    Jobson Richard W

    2008-10-01

    Full Text Available Abstract Background The C↔U substitution types of RNA editing have been observed frequently in organellar genomes of land plants. Although various attempts have been made to explain why such a seemingly inefficient genetic mechanism would have evolved, no satisfactory explanation exists in our view. In this study, we examined editing patterns in chloroplast genomes of the hornwort Anthoceros formosae and the fern Adiantum capillus-veneris and in mitochondrial genomes of the angiosperms Arabidopsis thaliana, Beta vulgaris and Oryza sativa, to gain an understanding of the question of how RNA editing originated. Results We found that 1 most editing sites were distributed at the 2nd and 1st codon positions, 2 editing affected codons that resulted in larger hydrophobicity and molecular size changes much more frequently than those with little change involved, 3 editing uniformly increased protein hydrophobicity, 4 editing occurred more frequently in ancestrally T-rich sequences, which were more abundant in genes encoding membrane-bound proteins with many hydrophobic amino acids than in genes encoding soluble proteins, and 5 editing occurred most often in genes found to be under strong selective constraint. Conclusion These analyses show that editing mostly affects functionally important and evolutionarily conserved codon positions, codons and genes encoding membrane-bound proteins. In particular, abundance of RNA editing in plant organellar genomes may be associated with disproportionately large percentages of genes in these two genomes that encode membrane-bound proteins, which are rich in hydrophobic amino acids and selectively constrained. These data support a hypothesis that natural selection imposed by protein functional constraints has contributed to selective fixation of certain editing sites and maintenance of the editing activity in plant organelles over a period of more than four hundred millions years. The retention of genes encoding RNA

  2. Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

    Science.gov (United States)

    Brandenburg, Jean-Tristan; Mary-Huard, Tristan; Rigaill, Guillem; Corti, Hélène; Vitte, Clémentine; Charcosset, Alain; Tenaillon, Maud I.

    2017-01-01

    Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans. PMID:28301472

  3. Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

    Science.gov (United States)

    Lacey, J. C., Jr.; Mullins, D. W., Jr.

    1983-01-01

    A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

  4. Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

    Science.gov (United States)

    Lacey, J. C., Jr.; Mullins, D. W., Jr.

    1983-01-01

    A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

  5. The genetic origin of Klinefelter syndrome and its effect on spermatogenesis.

    Science.gov (United States)

    Maiburg, Merel; Repping, Sjoerd; Giltay, Jacques

    2012-08-01

    Klinefelter syndrome is the most prevalent chromosome abnormality and genetic cause of azoospermia in males. The availability of assisted reproductive technology (ART) has allowed men with Klinefelter syndrome to father their own genetic offspring. When providing ART to men with Klinefelter syndrome, it is important to be able to counsel them properly on both the chance of finding sperm and the potential effects on their offspring. The aim of this review is twofold: [1] to describe the genetic etiology of Klinefelter syndrome and [2] to describe how spermatogenesis occurs in men with Klinefelter syndrome and the consequences this has for children born from men with Klinefelter syndrome.

  6. Linking individual migratory behaviour of Atlantic salmon to their genetic origin

    DEFF Research Database (Denmark)

    Jepsen, Niels; Eg Nielsen, Einar; Deacon, M.

    2005-01-01

    by increased aquaculture activities. The interpretation of results from studies of survival and behaviour of fish from such “mixed stocks” require information of the genetic background of individual fish. We used genetic analysis combined with radiotelemetry to study upstream migration of Atlantic salmon....... The results indicate that stocked, foreign salmon had a slightly higher mortality and moved more up and down in the river than the native salmon did, but all salmon had problems passing the physical obstructions in the river. The DNA analyses enabled us to compare the behaviour of fish of different genetic...

  7. Independent origins of cultivated coconut (Cocos nucifera L.) in the old world tropics.

    Science.gov (United States)

    Gunn, Bee F; Baudouin, Luc; Olsen, Kenneth M

    2011-01-01

    As a portable source of food, water, fuel, and construction materials, the coconut (Cocos nucifera L.) played a fundamental role in human migrations and the development of civilization across the humid tropics. Here we investigated the coconut's domestication history and its population genetic structure as it relates to human dispersal patterns. A sample of 1,322 coconut accessions, representing the geographical and phenotypic diversity of the species, was examined using ten microsatellite loci. Bayesian analyses reveal two highly genetically differentiated subpopulations that correspond to the Pacific and Indo-Atlantic oceanic basins. This pattern suggests independent origins of coconut cultivation in these two world regions, with persistent population structure on a global scale despite long-term human cultivation and dispersal. Pacific coconuts show additional genetic substructure corresponding to phenotypic and geographical subgroups; moreover, the traits that are most clearly associated with selection under human cultivation (dwarf habit, self-pollination, and "niu vai" fruit morphology) arose only in the Pacific. Coconuts that show evidence of genetic admixture between the Pacific and Indo-Atlantic groups occur primarily in the southwestern Indian Ocean. This pattern is consistent with human introductions of Pacific coconuts along the ancient Austronesian trade route connecting Madagascar to Southeast Asia. Admixture in coastal east Africa may also reflect later historic Arab trading along the Indian Ocean coastline. We propose two geographical origins of coconut cultivation: island Southeast Asia and southern margins of the Indian subcontinent.

  8. Independent origins of cultivated coconut (Cocos nucifera L. in the old world tropics.

    Directory of Open Access Journals (Sweden)

    Bee F Gunn

    Full Text Available As a portable source of food, water, fuel, and construction materials, the coconut (Cocos nucifera L. played a fundamental role in human migrations and the development of civilization across the humid tropics. Here we investigated the coconut's domestication history and its population genetic structure as it relates to human dispersal patterns. A sample of 1,322 coconut accessions, representing the geographical and phenotypic diversity of the species, was examined using ten microsatellite loci. Bayesian analyses reveal two highly genetically differentiated subpopulations that correspond to the Pacific and Indo-Atlantic oceanic basins. This pattern suggests independent origins of coconut cultivation in these two world regions, with persistent population structure on a global scale despite long-term human cultivation and dispersal. Pacific coconuts show additional genetic substructure corresponding to phenotypic and geographical subgroups; moreover, the traits that are most clearly associated with selection under human cultivation (dwarf habit, self-pollination, and "niu vai" fruit morphology arose only in the Pacific. Coconuts that show evidence of genetic admixture between the Pacific and Indo-Atlantic groups occur primarily in the southwestern Indian Ocean. This pattern is consistent with human introductions of Pacific coconuts along the ancient Austronesian trade route connecting Madagascar to Southeast Asia. Admixture in coastal east Africa may also reflect later historic Arab trading along the Indian Ocean coastline. We propose two geographical origins of coconut cultivation: island Southeast Asia and southern margins of the Indian subcontinent.

  9. Reflections on the origins and evolution of genetic toxicology and the Environmental Mutagen Society.

    Science.gov (United States)

    Wassom, John S; Malling, Heinrich V; Sankaranarayanan, K; Lu, Po-Yung

    2010-01-01

    This article traces the development of the field of mutagenesis and its metamorphosis into the research area we now call genetic toxicology. In 1969, this transitional event led to the founding of the Environmental Mutagen Society (EMS). The charter of this new Society was to "encourage interest in and study of mutagens in the human environment, particularly as these may be of concern to public health." As the mutagenesis field unfolded and expanded, new wording appeared to better describe this evolving area of research. The term "genetic toxicology" was coined and became an important subspecialty of the broad area of toxicology. Genetic toxicology is now set for a thorough reappraisal of its methods, goals, and priorities to meet the challenges of the 21st Century. To better understand these challenges, we have revisited the primary goal that the EMS founders had in mind for the Society's main mission and objective, namely, the quantitative assessment of genetic (hereditary) risks to human populations exposed to environmental agents. We also have reflected upon some of the seminal events over the last 40 years that have influenced the advancement of the genetic toxicology discipline and the extent to which the Society's major goal and allied objectives have been achieved. Additionally, we have provided suggestions on how EMS can further advance the science of genetic toxicology in the postgenome era. Any oversight or failure to make proper acknowledgment of individuals, events, or the citation of relevant references in this article is unintentional.

  10. Consumer preferences of genetically modified foods of vegetal and animal origin in Chile

    Directory of Open Access Journals (Sweden)

    Berta Schnettler

    2012-03-01

    Full Text Available Given the debate generated by Genetically Modified (GM foods in developed and developing countries, the aim was to evaluate the importance of determining factors in the preference of consumers in Temuco and Talca in central-southern Chile for GM foods using conjoint analysis and to determine the existence of different market segments using a survey of 800 people. Using conjoint analysis, it was established that, in general, genetic modification was a more important factor than either brand or price in the consumer's decision to purchase either food. Cluster analysis identified three segments: the largest (51.4% assigned greatest importance to brand and preferred genetically modified milk and tomato sauce; the second group (41.0% gave greatest importance to the existence of genetic manipulation and preferred non-genetically modified foods; the smallest segment (7.6% mainly valued price and preferred milk and tomato sauce with no genetic manipulation. The three segments rejected the store brand and preferred to pay less for both foods. The results are discussed based on studies conducted in developed and developing countries.

  11. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle.

    Directory of Open Access Journals (Sweden)

    Jared E Decker

    2014-03-01

    Full Text Available The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

  12. Codon size reduction as the origin of the triplet genetic code.

    Directory of Open Access Journals (Sweden)

    Pavel V Baranov

    Full Text Available The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon

  13. Individual differences in executive functions are almost entirely genetic in origin.

    Science.gov (United States)

    Friedman, Naomi P; Miyake, Akira; Young, Susan E; Defries, John C; Corley, Robin P; Hewitt, John K

    2008-05-01

    Recent psychological and neuropsychological research suggests that executive functions--the cognitive control processes that regulate thought and action--are multifaceted and that different types of executive functions are correlated but separable. The present multivariate twin study of 3 executive functions (inhibiting dominant responses, updating working memory representations, and shifting between task sets), measured as latent variables, examined why people vary in these executive control abilities and why these abilities are correlated but separable from a behavioral genetic perspective. Results indicated that executive functions are correlated because they are influenced by a highly heritable (99%) common factor that goes beyond general intelligence or perceptual speed, and they are separable because of additional genetic influences unique to particular executive functions. This combination of general and specific genetic influences places executive functions among the most heritable psychological traits. These results highlight the potential of genetic approaches for uncovering the biological underpinnings of executive functions and suggest a need for examining multiple types of executive functions to distinguish different levels of genetic influences.

  14. Establish nesting beach origins for all turtles in CA via genetic techniques

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — To examine the stock origin and evaluate current life-history hypotheses of green turtles foraging in southern California, 780 bp of the mitochondrial (mtDNA)...

  15. Spontaneous mutations and the origin and maintenance of quantitative genetic variation.

    Science.gov (United States)

    Huang, Wen; Lyman, Richard F; Lyman, Rachel A; Carbone, Mary Anna; Harbison, Susan T; Magwire, Michael M; Mackay, Trudy Fc

    2016-05-23

    Mutation and natural selection shape the genetic variation in natural populations. Here, we directly estimated the spontaneous mutation rate by sequencing new Drosophila mutation accumulation lines maintained with minimal natural selection. We inferred strong stabilizing natural selection on quantitative traits because genetic variation among wild-derived inbred lines was much lower than predicted from a neutral model and the mutational effects were much larger than allelic effects of standing polymorphisms. Stabilizing selection could act directly on the traits, or indirectly from pleiotropic effects on fitness. However, our data are not consistent with simple models of mutation-stabilizing selection balance; therefore, further empirical work is needed to assess the balance of evolutionary forces responsible for quantitative genetic variation.

  16. Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy.

    Science.gov (United States)

    Kusuma, Pradiptajati; Brucato, Nicolas; Cox, Murray P; Pierron, Denis; Razafindrazaka, Harilanto; Adelaar, Alexander; Sudoyo, Herawati; Letellier, Thierry; Ricaut, François-Xavier

    2016-05-18

    The Austronesian expansion, one of the last major human migrations, influenced regions as distant as tropical Asia, Remote Oceania and Madagascar, off the east coast of Africa. The identity of the Asian groups that settled Madagascar is particularly mysterious. While language connects Madagascar to the Ma'anyan of southern Borneo, haploid genetic data are more ambiguous. Here, we screened genome-wide diversity in 211 individuals from the Ma'anyan and surrounding groups in southern Borneo. Surprisingly, the Ma'anyan are characterized by a distinct, high frequency genomic component that is not found in Malagasy. This novel genetic layer occurs at low levels across Island Southeast Asia and hints at a more complex model for the Austronesian expansion in this region. In contrast, Malagasy show genomic links to a range of Island Southeast Asian groups, particularly from southern Borneo, but do not have a clear genetic connection with the Ma'anyan despite the obvious linguistic association.

  17. Genetic Diversity of mtDNA D-loop and Maternal Origin of Three Chinese Native Horse Breeds.

    Science.gov (United States)

    Zhang, Tao; Lu, Hongzhao; Chen, Chen; Jiang, Hai; Wu, Sanqiao

    2012-07-01

    In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G), indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G). The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.

  18. Genetic Diversity of mtDNA D-loop and Maternal Origin of Three Chinese Native Horse Breeds

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    2012-07-01

    Full Text Available In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G, indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G. The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.

  19. Genetic origins of the Dogon population in the Arrondissement of Boni (Mali).

    Science.gov (United States)

    Cazes, M H

    1986-07-01

    A study of probabilities of origin of genes was carried out on a Dogon population in Mali, spread over four massifs separated from each other by about 20 kilometers. Within each village, the founder contributions are very disparate and show that each village has a very specific origin. Therefore, the exchange of wives between massifs has not resulted in a homogenization of the population, which has remained strongly structured into four relatively independent isolates.

  20. The contribution of dormant origins to genome stability: from cell biology to human genetics.

    Science.gov (United States)

    Alver, Robert C; Chadha, Gaganmeet Singh; Blow, J Julian

    2014-07-01

    The ability of a eukaryotic cell to precisely and accurately replicate its DNA is crucial to maintain genome stability. Here we describe our current understanding of the process by which origins are licensed for DNA replication and review recent work suggesting that fork stalling has exerted a strong selective pressure on the positioning of licensed origins. In light of this, we discuss the complex and disparate phenotypes observed in mouse models and humans patients that arise due to defects in replication licensing proteins.

  1. A colorful origin for the genetic code: information theory, statistical mechanics and the emergence of molecular codes.

    Science.gov (United States)

    Tlusty, Tsvi

    2010-09-01

    The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the problem of the code's origin and discuss the results of a recent work that treats the code in terms of an evolving, error-prone information channel. Our model - which utilizes the rate-distortion theory of noisy communication channels - suggests that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources. The description of the code as an information channel allows us to mathematically identify the fitness of the code and locate its emergence at a second-order phase transition when the mapping of codons to amino-acids becomes nonrandom. The noise in the channel brings about an error-graph, in which edges connect codons that are likely to be confused. The emergence of the code is governed by the topology of the error-graph, which determines the lowest modes of the graph-Laplacian and is related to the map coloring problem. (c) 2010 Elsevier B.V. All rights reserved.

  2. Remediating Viking Origins: Genetic Code as Archival Memory of the Remote Past.

    Science.gov (United States)

    Scully, Marc; King, Turi; Brown, Steven D

    2013-10-01

    This article introduces some early data from the Leverhulme Trust-funded research programme, 'The Impact of the Diasporas on the Making of Britain: evidence, memories, inventions'. One of the interdisciplinary foci of the programme, which incorporates insights from genetics, history, archaeology, linguistics and social psychology, is to investigate how genetic evidence of ancestry is incorporated into identity narratives. In particular, we investigate how 'applied genetic history' shapes individual and familial narratives, which are then situated within macro-narratives of the nation and collective memories of immigration and indigenism. It is argued that the construction of genetic evidence as a 'gold standard' about 'where you really come from' involves a remediation of cultural and archival memory, in the construction of a 'usable past'. This article is based on initial questionnaire data from a preliminary study of those attending DNA collection sessions in northern England. It presents some early indicators of the perceived importance of being of Viking descent among participants, notes some emerging patterns and considers the implications for contemporary debates on migration, belonging and local and national identity.

  3. Genetic evidence for the origin and relationships of Hawaiian honeycreepers (Aves: Fringillidae)

    Science.gov (United States)

    Ned K. Johnson; Jill A. Marten; C. John Ralph

    1989-01-01

    Using starch gel electrophoresis of proteins, we examined variation at 36 genetic loci in nine species (eight genera) of Hawaiian honeycreepers (Class Aves; Family Fringillidae; Subfamily Drepanidinae). Two species of cardueline finches and two emberizids served as outgroup taxa. Twenty-three loci (64%) were either polymorphic within taxa and/or were fixed at...

  4. The legend of the Canadian horse: genetic diversity and breed origin.

    Science.gov (United States)

    Khanshour, Anas; Juras, Rytis; Blackburn, Rick; Cothran, E Gus

    2015-01-01

    The Canadian breed of horse invokes a fascinating chapter of North American history and as such it is now a heritage breed and the national horse of Canada. The aims of this study were to determine the level of genetic diversity in the Canadian, investigate the possible foundation breeds and the role it had in the development of the US horse breeds, such as Morgan Horse. We tested a total of 981 horses by using 15 microsatellite markers. We found that Canadian horses have high values of genetic diversity indices and show no evidence of a serious loss of genetic diversity and the inbreeding coefficient was not significantly different from zero. Belgian, Percheron, Breton and Dales Pony, unlike the light French horses, may have common ancestries with the Canadian and could be important founders. However, the Shire and Clydesdale influenced the Canadian to a lesser extent than French and Belgian draft breeds. Furthermore, our finding indicated that there was no evidence of a clear relationship between Canadian and Oriental or Iberian breeds. Also, the Canadian likely contributed to the early development of the Morgan. Finally, these findings support the ancient legends of the Canadian Horse as North America’s first equine breed and the foundation bloodstock to many American breeds and may help in the management and breeding program of this outstanding breed in North America. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Genome-wide analysis in Brazilian Xavante Indians reveals low degree of admixture.

    Science.gov (United States)

    Kuhn, Patricia C; Horimoto, Andréa R V Russo; Sanches, José Maurício; Vieira Filho, João Paulo B; Franco, Luciana; Fabbro, Amaury Dal; Franco, Laercio Joel; Pereira, Alexandre C; Moises, Regina S

    2012-01-01

    Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise F(st) statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

  6. Genome-wide analysis in Brazilian Xavante Indians reveals low degree of admixture.

    Directory of Open Access Journals (Sweden)

    Patricia C Kuhn

    Full Text Available Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise F(st statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

  7. Origin of the Genetic Components of the Vomeronasal System in the Common Ancestor of all Extant Vertebrates

    Science.gov (United States)

    Grus, Wendy E.; Zhang, Jianzhi

    2009-01-01

    Comparative genomics provides a valuable tool for inferring the evolutionary history of physiological systems, particularly when this information is difficult to ascertain by morphological traits. One such example is the vomeronasal system (VNS), a vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants. The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. To determine when the genetic components of the VNS originated, we searched for the VNS-specific genes in the genomes of two early diverging vertebrate lineages: the sea lamprey from jawless fishes and the elephant shark from cartilaginous fishes. Genes encoding vomeronasal type 1 receptors (V1Rs) and Trpc2, two components of the vomeronasal signaling pathway, are present in the sea lamprey genome, and both are expressed in the olfactory organ, revealing that the genetic components of the present-day VNS existed in the common ancestor of all extant vertebrates. Additionally, all three VNS genes, Trpc2, V1Rs, and vomeronasal type 2 receptors (V2Rs), are found in the elephant shark genome. Because V1Rs and V2Rs are related to two families of taste receptors, we also searched the early diverging vertebrate genomes for taste system genes and found them in the shark genome but not in the lamprey. Coupled with known distributions of the genetic components of the vertebrate main olfactory system, our results suggest staggered origins of vertebrate sensory systems. These findings are important for understanding the evolution of vertebrate sensory systems and illustrate the utility of the genome sequences of early diverging vertebrates for uncovering the evolution of vertebrate-specific traits. PMID:19008528

  8. Genetics and the origin of species: the continuing synthesis a symposium in honor of Richard G. Harrison

    Science.gov (United States)

    Grosberg, Richard K.; Rand, David M.; Normark, Benjamin B.

    2013-01-01

    This is a special issue of Genetica that has its origins in a symposium held in honor of Richard G. Harrison at Ithaca, New York on July 22–23. Former students of Rick Harrison organized the symposium and most of the speakers were former students, as well. The quality and breadth of the talks were a testament to Rick’s influence as a thinker, synthesizer, and mentor and it is only appropriate to reflect on Rick’s contributions to the fields of evolutionary ecology, systematics, and genetics in this preface to the symposium articles. PMID:21152955

  9. Ontogeny of an adventurous mind: the origin of Antonio García-Bellido's contributions to developmental genetics.

    Science.gov (United States)

    García-Bellido, Antonio

    2009-01-01

    This interview with Antonio Garcia-Bellido explores three aspects of his work. First and foremost is the origin of his contributions: trying to define what allowed him to become a pioneer of developmental genetics. The second part deals with the nature of his major contributions, as seen by himself. In a third section he expresses his views on a number of subjects that relate mostly to the future of developmental biology and to evolution. A list of his most significant publications is appended as an annex.

  10. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

    Science.gov (United States)

    Miller, Webb; Schuster, Stephan C.; Welch, Andreanna J.; Ratan, Aakrosh; Bedoya-Reina, Oscar C.; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C.; Drautz, Daniela I.; Wittekindt, Nicola E.; Tomsho, Lynn P.; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K.; Rode, Karyn; Obbard, Martyn E.; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Ólafur; Aars, Jon; Mailund, Thomas; Wiig, Øystein; Talbot, Sandra L.; Lindqvist, Charlotte

    2012-01-01

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

  11. The Place of RNA in the Origin and Early Evolution of the Genetic Machinery

    OpenAIRE

    Günter Wächtershäuser

    2014-01-01

    The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that l...

  12. Acceptance of a food of animal origin obtained through genetic modification and cloning in South America

    DEFF Research Database (Denmark)

    Schnettler, Berta; Velásquez, Carlos; Miranda, Horacio

    2015-01-01

    With the aim of comparing the acceptance of milk obtained from cloned, genetically modified (GM) and conventionally bred cows among working adults and university students, and identifying and characterizing typologies among both subsamples in terms of their preferences, a survey was applied to 400...... of cloning was greatest among university students, whereas a higher proportion of working adults rejected GM. The segments differed in terms of area of residence, knowledge about GM, and milk consumption habits. Contrary to w...

  13. miRNA Nomenclature : A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants

    NARCIS (Netherlands)

    Desvignes, T.; Batzel, P.; Berezikov, E.; Eilbeck, K.; Eppig, J. T.; McAndrews, M. S.; Singer, A.; Postlethwait, J. H.

    2015-01-01

    High-throughput sequencing of miRNAs has revealed the diversity and variability of mature and functional short noncoding RNAs, including their genomic origins, biogenesis pathways, sequence variability, and newly identified products such as miRNA-offset RNAs (moRs). Here we review known cases of alt

  14. miRNA Nomenclature : A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants

    NARCIS (Netherlands)

    Desvignes, T.; Batzel, P.; Berezikov, E.; Eilbeck, K.; Eppig, J. T.; McAndrews, M. S.; Singer, A.; Postlethwait, J. H.

    2015-01-01

    High-throughput sequencing of miRNAs has revealed the diversity and variability of mature and functional short noncoding RNAs, including their genomic origins, biogenesis pathways, sequence variability, and newly identified products such as miRNA-offset RNAs (moRs). Here we review known cases of

  15. The Place of RNA in the Origin and Early Evolution of the Genetic Machinery

    Directory of Open Access Journals (Sweden)

    Günter Wächtershäuser

    2014-12-01

    Full Text Available The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that life began as an autotrophic metabolism in hot volcanic-hydrothermal fluids and evolved with organic products turning into ligands for transition metal catalysts thereby eliciting feedback and feed-forward effects. In this latter context it is posited that the three polymers of the genetic machinery essentially coevolved from monomers through oligomers to polymers, operating functionally first as ligands for ligand-accelerated transition metal catalysis with later addition of base stacking and base pairing, whereby the functional dichotomy between hereditary DNA with stability on geologic time scales and transient, catalytic RNA with stability on metabolic time scales existed since the dawn of the genetic machinery. Both approaches are assessed comparatively for chemical soundness.

  16. Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

    Science.gov (United States)

    Remington, David L

    2015-12-01

    Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  17. Probable relationship between partitions of the set of codons and the origin of the genetic code.

    Science.gov (United States)

    Salinas, Dino G; Gallardo, Mauricio O; Osorio, Manuel I

    2014-03-01

    Here we study the distribution of randomly generated partitions of the set of amino acid-coding codons. Some results are an application from a previous work, about the Stirling numbers of the second kind and triplet codes, both to the cases of triplet codes having four stop codons, as in mammalian mitochondrial genetic code, and hypothetical doublet codes. Extending previous results, in this work it is found that the most probable number of blocks of synonymous codons, in a genetic code, is similar to the number of amino acids when there are four stop codons, as well as it could be for a primigenious doublet code. Also it is studied the integer partitions associated to patterns of synonymous codons and it is shown, for the canonical code, that the standard deviation inside an integer partition is one of the most probable. We think that, in some early epoch, the genetic code might have had a maximum of the disorder or entropy, independent of the assignment between codons and amino acids, reaching a state similar to "code freeze" proposed by Francis Crick. In later stages, maybe deterministic rules have reassigned codons to amino acids, forming the natural codes, such as the canonical code, but keeping the numerical features describing the set partitions and the integer partitions, like a "fossil numbers"; both kinds of partitions about the set of amino acid-coding codons. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  18. The humankind genome: from genetic diversity to the origin of human diseases.

    Science.gov (United States)

    Belizário, Jose E

    2013-12-01

    Genome-wide association studies have failed to establish common variant risk for the majority of common human diseases. The underlying reasons for this failure are explained by recent studies of resequencing and comparison of over 1200 human genomes and 10 000 exomes, together with the delineation of DNA methylation patterns (epigenome) and full characterization of coding and noncoding RNAs (transcriptome) being transcribed. These studies have provided the most comprehensive catalogues of functional elements and genetic variants that are now available for global integrative analysis and experimental validation in prospective cohort studies. With these datasets, researchers will have unparalleled opportunities for the alignment, mining, and testing of hypotheses for the roles of specific genetic variants, including copy number variations, single nucleotide polymorphisms, and indels as the cause of specific phenotypes and diseases. Through the use of next-generation sequencing technologies for genotyping and standardized ontological annotation to systematically analyze the effects of genomic variation on humans and model organism phenotypes, we will be able to find candidate genes and new clues for disease's etiology and treatment. This article describes essential concepts in genetics and genomic technologies as well as the emerging computational framework to comprehensively search websites and platforms available for the analysis and interpretation of genomic data.

  19. The place of RNA in the origin and early evolution of the genetic machinery.

    Science.gov (United States)

    Wächtershäuser, Günter

    2014-12-19

    The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that life began as an autotrophic metabolism in hot volcanic-hydrothermal fluids and evolved with organic products turning into ligands for transition metal catalysts thereby eliciting feedback and feed-forward effects. In this latter context it is posited that the three polymers of the genetic machinery essentially coevolved from monomers through oligomers to polymers, operating functionally first as ligands for ligand-accelerated transition metal catalysis with later addition of base stacking and base pairing, whereby the functional dichotomy between hereditary DNA with stability on geologic time scales and transient, catalytic RNA with stability on metabolic time scales existed since the dawn of the genetic machinery. Both approaches are assessed comparatively for chemical soundness.

  20. North African populations carry the signature of admixture with Neandertals

    DEFF Research Database (Denmark)

    Sánchez-Quinto, Federico; Botigué, Laura R; Civit, Sergi

    2012-01-01

    One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient popu...

  1. Premixed intravenous admixtures: a positive development for hospital pharmacy.

    Science.gov (United States)

    Lee, H E

    1983-06-01

    The development of premixed intravenous admixtures is reviewed in a historical context, and its effects on hospital pharmacy practice are discussed. As pharmaceutical manufacturers introduce more i.v. medications in ready-to-use containers, the same complaints that were voiced by pharmacists about unit dose packaging and ready-to-dispense tablets and capsules are being aired. But premixed i.v. admixtures are a logical extension of the basic unit dose principle of providing a readily identifiable and ready-to-administer dose. The time and cost savings these products offer are needed in hospital pharmacies. Some of the disadvantages of these products--including storage and freezer space and multiplicity of administration systems--are overcome by proper planning and education of personnel. If fewer personnel are now needed to prepare i.v. admixtures, then those personnel should be used to improve patient care in other ways. The use of premixed i.v. admixtures is a positive technological advance in drug packaging. Its advantages outweight its disadvantages, and it will soon be become the universally accepted form of i.v. drug packaging.

  2. Worldwide patterns of genomic variation and admixture in gray wolves.

    Science.gov (United States)

    Fan, Zhenxin; Silva, Pedro; Gronau, Ilan; Wang, Shuoguo; Armero, Aitor Serres; Schweizer, Rena M; Ramirez, Oscar; Pollinger, John; Galaverni, Marco; Ortega Del-Vecchyo, Diego; Du, Lianming; Zhang, Wenping; Zhang, Zhihe; Xing, Jinchuan; Vilà, Carles; Marques-Bonet, Tomas; Godinho, Raquel; Yue, Bisong; Wayne, Robert K

    2016-02-01

    The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. To address questions about wolf relationships to each other and dogs, we assembled and analyzed a data set of 34 canine genomes. The divergence between New and Old World wolves is the earliest branching event and is followed by the divergence of Old World wolves and dogs, confirming that the dog was domesticated in the Old World. However, no single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population. All extant wolves have a surprisingly recent common ancestry and experienced a dramatic population decline beginning at least ∼30 thousand years ago (kya). We suggest this crisis was related to the colonization of Eurasia by modern human hunter-gatherers, who competed with wolves for limited prey but also domesticated them, leading to a compensatory population expansion of dogs. We found extensive admixture between dogs and wolves, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry. Dogs have influenced the recent history of wolves through admixture and vice versa, potentially enhancing adaptation. Simple scenarios of dog domestication are confounded by admixture, and studies that do not take admixture into account with specific demographic models are problematic. © 2016 Fan et al.; Published by Cold Spring Harbor Laboratory Press.

  3. Performance of alusilica as mineral admixture in cementitious systems

    DEFF Research Database (Denmark)

    Chi, Lin; Jensen, Ole Mejlhede

    2016-01-01

    This paper presents a preliminary study of the effect of alusilica (ALS) as a mineral admixture on the fresh properties and development of mechanical properties of cementitious systems. Cement was substituted with ALS with the ratio of 10% during grinding or blended during mixing. The produced ALS......, it is believed that ALS can be a useful cement substitution....

  4. North African populations carry the signature of admixture with Neandertals

    DEFF Research Database (Denmark)

    Sánchez-Quinto, Federico; Botigué, Laura R.; Civit, Sergi

    2012-01-01

    One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient popu...

  5. Genomic Characterization of Interspecific Hybrids and an Admixture Population Derived from Panicum amarum × P. virgatum

    Directory of Open Access Journals (Sweden)

    Christopher Heffelfinger

    2015-07-01

    Full Text Available Switchgrass ( L. and its relatives are regarded as top bioenergy crop candidates; however, one critical barrier is the introduction of useful genetic diversity and the development of new cultivars and hybrids. Combining genomes from related cultivars and species provides an opportunity to introduce new traits. In switchgrass, a breeding advantage would be achieved by combining the genomes of intervarietal ecotypes or interspecific hybrids. The recovery of wide crosses, however, is often tedious and may involve complicated embryo rescue and numerous backcrosses. Here, we demonstrate a straightforward approach to wide crosses involving the use of a selectable transgene for recovery of interspecific [ cv. Alamo × Ell var or Atlantic Coastal Panicgrass (ACP] F hybrids followed by backcrossing to generate a nontransgenic admixture population. A nontransgenic herbicide-sensitive (HbS admixture population of 83 FBC progeny was analyzed by genotyping-by-sequencing (GBS to characterize local ancestry, parental contribution, and patterns of recombination. These results demonstrate a widely applicable breeding strategy that makes use of transgenic selectable resistance to identify and recover true hybrids.

  6. Beliefs about the Etiology of Homosexuality and about the Ramifications of Discovering Its Possible Genetic Origin

    OpenAIRE

    Sheldon, Jane P.; Pfeffer, Carla A.; Jayaratne, Toby Epstein; Feldbaum, Merle; Petty, Elizabeth M

    2007-01-01

    Homosexuality is viewed by many as a social problem. As such, there has been keen interest in elucidating the origins of homosexuality among many scholars, from anthropologists to zoologists, psychologists to theologians. Research has shown that those who believe sexual orientation is inborn are more likely to have tolerant attitudes toward gay men and lesbians, whereas those who believe it is a choice have less tolerant attitudes. The current qualitative study used in-depth, open-ended telep...

  7. ENVIRONMENTAL AND GENETIC EFFECTS ON PRODUCTION TRAITS OF EWES ORIGINALLY FROM DISTINCT ENVIRONMENTS

    Directory of Open Access Journals (Sweden)

    Nelson Manzoni de Oliveira

    1993-12-01

    Full Text Available Wool production and reproductive performance components of similar genotypes, brought from distinct production areas, were evaluated during five years trial at similar environments, such as, joining season and stocking rate on winter improved pasture. The least squares means revealed that the origin (breed effect concentrated upon the Corriedale ewes wool production, whereas in Romney females it affected the reproductive performance. In the abscence of interaction between origin (breed and year for most variables, it was assumed that the farm management procedures and/or selection criteria applied on hoggets were determinant of the subsequent lifetime production within each genotype examined. Expecting a better reproductive performance in Romneys, mainly rate of lambs born, weaned and lambs weaning weight, comments were made on the selection criteria employed on this breed over many years. The work has demonstrated that "property of origin (breed" of sheep composing any experiment aiming at breed comparisons, should be considered as a potential factor capable of biasing information on productive aspects.

  8. Developmental origins of the adipocyte lineage: new insights from genetics and genomics studies.

    Science.gov (United States)

    Billon, Nathalie; Dani, Christian

    2012-03-01

    The current epidemic of obesity and overweight has caused a surge of interest in the study of adipose tissue formation. Much progress has been made in defining the transcriptional networks controlling the terminal differentiation of adipocyte progenitors into mature adipocytes. However, the early steps of adipocyte development and the embryonic origin of this lineage have been largely disregarded until recently. In mammals, two functionally different types of adipose tissues coexist, which are both involved in energy balance but assume opposite functions. White adipose tissue (WAT) stores energy, while brown adipose tissue (BAT) is specialized in energy expenditure. WAT and BAT can be found as several depots located in various sites of the body. Individual fat depots exhibit different timing of appearance during development, as well as distinct functional properties, suggesting possible differences in their developmental origin. This hypothesis has recently been revisited through large-scale genomics studies and in vivo lineage tracing approaches, which are reviewed in this report. These studies have provided novel fundamental insights into adipocyte biology, pointing out distinct developmental origins for WAT and BAT, as well as for individual WAT depots. They suggest that the adipose tissue is composed of distinct mini-organs, exhibiting developmental and functional differences, as well as variable contribution to obesity-related metabolic diseases.

  9. A Genome-Wide Study of Modern-Day Tuscans: Revisiting Herodotus's Theory on the Origin of the Etruscans

    Science.gov (United States)

    Gómez-Carballa, Alberto; Amigo, Jorge; Martinón-Torres, Federico

    2014-01-01

    Background The origin of the Etruscan civilization (Etruria, Central Italy) is a long-standing subject of debate among scholars from different disciplines. The bulk of the information has been reconstructed from ancient texts and archaeological findings and, in the last few years, through the analysis of uniparental genetic markers. Methods By meta-analyzing genome-wide data from The 1000 Genomes Project and the literature, we were able to compare the genomic patterns (>540,000 SNPs) of present day Tuscans (N = 98) with other population groups from the main hypothetical source populations, namely, Europe and the Middle East. Results Admixture analysis indicates the presence of 25–34% of Middle Eastern component in modern Tuscans. Different analyses have been carried out using identity-by-state (IBS) values and genetic distances point to Eastern Anatolia/Southern Caucasus as the most likely geographic origin of the main Middle Eastern genetic component observed in the genome of modern Tuscans. Conclusions The data indicate that the admixture event between local Tuscans and Middle Easterners could have occurred in Central Italy about 2,600–3,100 years ago (y.a.). On the whole, the results validate the theory of the ancient historian Herodotus on the origin of Etruscans. PMID:25230205

  10. Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis.

    Science.gov (United States)

    Cavalier-Smith, T

    2001-01-01

    I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects. Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the outer surface of an 'inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later

  11. Mitochondrial Genetic Structure and Matrilineal Origin of White Sharks, Carcharodon carcharias, in the Northeastern Pacific: Implications for Their Conservation.

    Science.gov (United States)

    Oñate-González, Erick C; Rocha-Olivares, Axayácatl; Saavedra-Sotelo, Nancy C; Sosa-Nishizaki, Oscar

    2015-01-01

    White sharks (Carcharodon carcharias, WS henceforth) are globally and regionally threatened. Understanding their patterns of abundance and connectivity, as they relate to habitat use, is central for delineating conservation units and identifying priority areas for conservation. We analyzed mitochondrial data to test the congruence between patterns of genetic connectivity and of individual movements in the Northeastern Pacific (NEP) and to trace the matrilineal origin of immature WS from coastal California and Baja California to adult aggregation areas. We analyzed 186 mitochondrial control region sequences from sharks sampled in Central California (CC; n = 61), Southern California Bight (SCB; n = 25), Baja California Pacific coast (BCPC; n = 9), Bahía Vizcaíno (BV; n = 39), Guadalupe Island (GI; n = 45), and the Gulf of California (GC; n = 7). Significant mitochondrial differentiation between adult aggregation areas (CC, GI) revealed two reproductive populations in the NEP. We found general concordance between movement patterns of young and adult WS with genetic results. Young sharks from coastal California and Baja California were more likely born from females from GI. Mitochondrial differentiation of young-of-the-year from SCB and BV suggests philopatry to nursery areas in females from GI. These results provide a genetic basis of female reproductive behavior at a regional scale and point to a preponderance of sharks from GI in the use of the sampled coastal region as pupping habitat. These findings should be considered in Mexican and US management and conservation strategies of the WS NEP population.

  12. Reduced lipid oxidation in skeletal muscle from type 2 diabetic subjects may be of genetic origin: evidence from cultured myotubes.

    Science.gov (United States)

    Gaster, Michael; Rustan, Arild C; Aas, Vigdis; Beck-Nielsen, Henning

    2004-03-01

    Insulin resistance in skeletal muscle in vivo is associated with reduced lipid oxidation and lipid accumulation. It is still uncertain whether changes in lipid metabolism represent an adaptive compensation at the cellular level or a direct expression of a genetic trait. Studies of palmitate metabolism in human myotubes established from control and type 2 diabetic subjects may solve this problem, as genetic defects are preserved and expressed in vitro. In this study, total uptake of palmitic acid was similar in myotubes established from both control and type 2 diabetic subjects under basal conditions and acute insulin stimulation. Myotubes established from diabetic subjects expressed a primary reduced palmitic acid oxidation to carbon dioxide with a concomitantly increased esterification of palmitic acid into phospholipids compared with control myotubes under basal conditions. Triacylglycerol (TAG) content and the incorporation of palmitic acid into diacylglycerol (DAG) and TAG at basal conditions did not vary between the groups. Acute insulin treatment significantly increased palmitate uptake and incorporation of palmitic acid into DAG and TAG in myotubes established from both study groups, but no difference was found in myotubes established from control and diabetic subjects. These results indicate that the reduced lipid oxidation in diabetic skeletal muscle in vivo may be of genetic origin; it also appears that TAG metabolism is not primarily affected in diabetic muscles under basal physiological conditions.

  13. Patterns of genetic diversity of the cryptogenic red alga Polysiphonia morrowii (Ceramiales, Rhodophyta) suggest multiple origins of the Atlantic populations.

    Science.gov (United States)

    Geoffroy, Alexandre; Destombe, Christophe; Kim, Byeongseok; Mauger, Stéphane; Raffo, María Paula; Kim, Myung Sook; Le Gall, Line

    2016-08-01

    The red alga Polysiphonia morrowii, native to the North Pacific (Northeast Asia), has recently been reported worldwide. To determine the origin of the French and Argentine populations of this introduced species, we compared samples from these two areas with samples collected in Korea and at Hakodate, Japan, the type locality of the species. Combined analyses of chloroplastic (rbcL) and mitochondrial (cox1) DNA revealed that the French and Argentine populations are closely related and differ substantially from the Korean and Japanese populations. The genetic structure of P. morrowii populations from South Atlantic and North Atlantic, which showed high haplotype diversity compared with populations from the North Pacific, suggested the occurrence of multiple introduction events from areas outside of the so-called native regions. Although similar, the French and Argentine populations are not genetically identical. Thus, the genetic structure of these two introduced areas may have been modified by cryptic and recurrent introduction events directly from Asia or from other introduced areas that act as introduction relays. In addition, the large number of private cytoplasmic types identified in the two introduced regions strongly suggests that local populations of P. morrowii existed before the recent detection of these invasions. Our results suggest that the most likely scenario is that the source population(s) of the French and Argentine populations was not located only in the North Pacific and/or that P. morrowii is a cryptogenic species.

  14. Genetic diversity and relationship between cultivated clones of Dalbergia sissoo of wide geographical origin using RAPD markers

    Institute of Scientific and Technical Information of China (English)

    H. S. Ginwal; S. S. Maurya; P. Chauhan

    2011-01-01

    Random Amplified Polymorphic DNA (RAPD) polymorphism was employed to assess the genetic diversity in the elite germplasm of Dalbergia sissoo.Sixty-seven clones that are under cultivation in northern India,originated from six different states of India and Nepal were analyzed with 30 RAPD primers that generated a total of 342 fragments out of which 290 were polymorphic.Total genetic diversity (Ht) varied between 0.01 and 0.37,with an average of 0.19.Shannon's Information index (I) varied between 0.02 and 0.54,with an average of 0.31.Marker attributes like Polymorphism Information Content (PIC),Marker Index (MI) and Effective Multiplex Ratio (EMR) values were calculated to assess the discriminatory power of 30 primers used.The PIC values ranged from 0.01 to 0.37 with an average of 0.17 per primer and the EMR ranged from 0.17 to 21.00 with a mean of 8.66 across all genotypes.Closely related clones were CA9 and C51 with similarity index of 0.86 while the least similar or most dissimilar clones were C14 and S-DB showing similarity index of 0.58.The UPGMA-phenogram categorized the 67 clones into six clusters based on genetic similarity and dissimilarity.The clustering of clones in relation to their geographical location has been discussed.

  15. Evaluation of Genetic Diversity Using Parameters Based on Probability of Gene Origin in the Slovak Spotted Bulls

    Directory of Open Access Journals (Sweden)

    E. Hazuchová

    2012-05-01

    Full Text Available The aim of this study was to assess the diversity based on probability of gene origin in Slovak Spotted bulls. The pedigree information was available from The Breeding Services of the Slovak Republic, s. e. The pedigree file consisted of 752 individuals. The 62 sires born from 1995 to 2009 and registered in Herd book set up the analyzed reference (RP population. Total number of founders in the RP was 308, effective number of founders was 115 and the effective number of ancestors was 37. The number of ancestors explaining 50 % of the diversity was 15 and founder’s genome equivalent was 20.46. The sire GS Malf and Horwein were with 16 offspring’s the most frequently used bulls in the artificial insemination. We found that the genetic conservation index for RP was 16.34 %. Results will be used in genetic management of breeding work in Slovak Spotted and monitoring of parameters characterizing genetic diversity and their development, as well.

  16. Evaluation of Population Structure, Genetic Diversity and Origin of Northeast Asia Weedy Rice Based on Simple Sequence Repeat Markers

    Directory of Open Access Journals (Sweden)

    Li Mao-bai

    2015-07-01

    Full Text Available Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon's diversity index (I of 0.748 and the heterozygosity (He of 0.434. In each regional population, I value varied widely. The widest range of I (0.228–0.489 was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea (0.168–0.270. The F-statistics of regional populations (Fis, Fit and Fst also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea. All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.

  17. Genetic diversity among different physiological traits of Sorghum bicolor cultivars of subtropical origin.

    Science.gov (United States)

    Bafeel, S O

    2015-08-21

    The genetic diversity of Saudi locally growing sorghum (Sorghum bicolor) cultivars has not been thoroughly characterized. To understand the genomic patterns of diversification in Saudi sorghum cultivars (N = 7), random amplified polymorphic DNA (RAPD) was used as a rapid, inexpensive method for providing information regarding genomic variability below the species level. Six commercially available primers were initially used to select a single primer based on availability, universality, and its use with standard polymerase chain reaction (PCR) conditions. PCR-amplified molecular markers were reproducibly detected in Saudi cultivars. The single primer 2 produced clear bands and revealed variability among the cultivars. Seven tested cultivars were categorized into 2 major groups, indicating 2 genomogroups for the Saudi-cultivars. Five cultivars (S2, S3, S4, S5, and S6) showed identical banding patterns and were grouped in the same clade, although their panicles varied in size, shape, and color. Two cultivars (S1 and S7) showed different banding patterns. In this study, a single primer (P2) was used to demonstrate the effectiveness of genotype detection among sorghum cultivars. This is the first report describing genetic variation among S. bicolor cultivars in Saudi Arabia. The commercial primer (P2) and PCR reaction mixture used in this study are readily available and can be used in sorghum improvement programs.

  18. Genetics reveal the origin and timing of a cryptic insular introduction of muskrats in North America.

    Directory of Open Access Journals (Sweden)

    Alexis M Mychajliw

    Full Text Available The muskrat, Ondatra zibethicus, is a semiaquatic rodent native to North America that has become a highly successful invader across Europe, Asia, and South America. It can inflict ecological and economic damage on wetland systems outside of its native range. Anecdotal evidence suggests that, in the early 1900s, a population of muskrats was introduced to the Isles of Shoals archipelago, located within the Gulf of Maine, for the purposes of fur harvest. However, because muskrats are native to the northeastern coast of North America, their presence on the Isles of Shoals could be interpreted as part of the native range of the species, potentially obscuring management planning and biogeographic inferences. To investigate their introduced status and identify a historic source population, muskrats from Appledore Island of the Isles of Shoals, and from the adjacent mainland of Maine and New Hampshire, were compared for mitochondrial cytochrome b sequences and allele frequencies at eight microsatellite loci. Appledore Island muskrats consistently exhibited reduced genetic diversity compared with mainland populations, and displayed signatures of a historic bottleneck. The distribution of mitochondrial haplotypes is suggestive of a New Hampshire source population. The data presented here are consistent with a human-mediated introduction that took place in the early 1900s. This scenario is further supported by the zooarchaeological record and island biogeographic patterns. This is the first genetic study of an introduced muskrat population within US borders and of any island muskrat population, and provides an important contrast with other studies of introduced muskrat populations worldwide.

  19. Interpersonal and Genetic Origins of Adult Attachment Styles: A Longitudinal Study from Infancy to Early Adulthood

    Science.gov (United States)

    Fraley, R. Chris; Roisman, Glenn I.; Booth-LaForce, Cathryn; Owen, Margaret Tresch; Holland, Ashley S.

    2013-01-01

    One of the assumptions of attachment theory is that individual differences in adult attachment styles emerge from individuals’ developmental histories. To examine this assumption empirically the authors report data from an age 18 follow-up (Booth-LaForce & Roisman, 2012) of the NICHD Study of Early Child Care and Youth Development, a longitudinal investigation that tracked a cohort of children and their parents from birth to age 15. Analyses indicate that individual differences in adult attachment can be traced to variations in the quality of individuals’ caregiving environments, their emerging social competence, and the quality of their best friendship. Analyses also indicate that assessments of temperament and most of the specific genetic polymorphisms thus far examined in the literature on genetic correlates of attachment styles were essentially uncorrelated with adult attachment, with the exception of a polymorphism in the serotonin receptor gene (HTR2A rs6313), which modestly predicted higher attachment anxiety and that revealed a G × E interaction such that changes in maternal sensitivity across time predicted attachment-related avoidance. The implications of these data for contemporary perspectives and debates concerning adult attachment theory are discussed. PMID:23397970

  20. Epidemiology of the American Indians' burden and its likely genetic origins.

    Science.gov (United States)

    Carey, Martin C; Paigen, Beverly

    2002-10-01

    It was not known until recently whether the endemic of cholesterol gallstones among certain southwestern American Indian tribes was unique among this ethnic group. With use of ultrasonography of the gallbladder and standard diagnostic criteria, gallstones are now found in epidemic proportions in 13 diverse American Indian tribes and communities living in Arizona, Oklahoma, and the Dakotas. We speculate that this predisposition is polygenic involving "thrifty" genes that conferred survival advantages when Paleo-Indians migrated from present-day Siberia to the Americas during the last Great Ice Age approximately 50,000 to 10,000 years ago. A reasonable hypothesis is that functioning of these genes promoted more efficient calorie utilization and storage in the form of adipose tissue. Beneficial results would have been operative during the isolation of Paleo-Indians in the Bering Strait land bridge (Beringia) when thrifty genes would have ensured sufficient fat reserves for survival of prolonged winters, successful pregnancy outcomes, and extended lactation periods. The authors' conjoint work on genetics of experimental cholesterol cholelithiasis in inbred mice promises help in pinpointing orthologous genetic loci (LITH genes) in the human genome. Moreover, the shared environments and homogeneity of American Indian tribes and communities should facilitate discovery of the ensembles of their common and rarer cholesterol gallstone genes. It is anticipated that knowledge of expression, polymorphisms, and functionality of LITH genes will help resolve the molecular mechanisms of this complex heterogeneous trait and thereby provide targets for novel therapies to prevent cholesterol cholelithiasis worldwide.

  1. Interpersonal and genetic origins of adult attachment styles: a longitudinal study from infancy to early adulthood.

    Science.gov (United States)

    Fraley, R Chris; Roisman, Glenn I; Booth-LaForce, Cathryn; Owen, Margaret Tresch; Holland, Ashley S

    2013-05-01

    One of the assumptions of attachment theory is that individual differences in adult attachment styles emerge from individuals' developmental histories. To examine this assumption empirically, the authors report data from an age 18 follow-up (Booth-LaForce & Roisman, 2012) of the National Institute of Child Health and Human Development Study of Early Child Care and Youth Development, a longitudinal investigation that tracked a cohort of children and their parents from birth to age 15. Analyses indicate that individual differences in adult attachment can be traced to variations in the quality of individuals' caregiving environments, their emerging social competence, and the quality of their best friendship. Analyses also indicate that assessments of temperament and most of the specific genetic polymorphisms thus far examined in the literature on genetic correlates of attachment styles are essentially uncorrelated with adult attachment, with the exception of a polymorphism in the serotonin receptor gene (HTR2A rs6313), which modestly predicted higher attachment anxiety and which revealed a Gene × Environment interaction such that changes in maternal sensitivity across time predicted attachment-related avoidance. The implications of these data for contemporary perspectives and debates concerning adult attachment theory are discussed. PsycINFO Database Record (c) 2013 APA, all rights reserved

  2. Ancestry analysis reveals a predominant Native American component with moderate European admixture in Bolivians.

    Science.gov (United States)

    Heinz, Tanja; Alvarez-Iglesias, Vanesa; Pardo-Seco, Jacobo; Taboada-Echalar, Patricia; Gómez-Carballa, Alberto; Torres-Balanza, Antonio; Rocabado, Omar; Carracedo, Angel; Vullo, Carlos; Salas, Antonio

    2013-09-01

    We have genotyped 46 Ancestry Informative Markers (AIMs) in two of the most populated areas in Bolivia, namely, La Paz (Andean region; n=105), and Chuquisaca (Sub-Andean region; n=73). Using different analytical tools, we inferred admixture proportions of these two American communities by comparing the genetic profiles with those publicly available from the CEPH (Centre d'Etude du Polymorphisme Humain) panel representing three main continental groups (Africa, Europe, and America). By way of simulations, we first evaluated the minimum sample size needed in order to obtain accurate estimates of ancestry proportions. The results indicated that sample sizes above 30 individuals could be large enough to estimate main continental ancestry proportions using the 46 AIMs panel. With the exception of a few individuals, the results also indicated that Bolivians showed a predominantly Native American ancestry with variable levels of European admixture. The proportions of ancestry were statistically different in La Paz and Chuquisaca: the Native American component was 86% and 77% (Mann-Whitney U-test: un-adjusted P-value=2.1×10(-5)), while the European ancestry was 13% and 21% (Mann-Whitney U-test: un-adjusted P-value=3.6×10(-5)), respectively. The African ancestry in Bolivians captured by the AIMs analyzed in the present study was below 2%. The inferred ancestry of Bolivians fits well with previous studies undertaken on haplotype data, indicating a major proportion of Native American lineages. The genetic differences observed in these two groups suggest that forensic genetic analysis should be better performed based on local databases built in the main Bolivian areas.

  3. Carbonado: Physical and chemical properties, a critical evaluation of proposed origins, and a revised genetic model

    Science.gov (United States)

    Haggerty, Stephen E.

    2014-03-01

    Carbonado-diamond is the most controversial of all diamond types and is found only in Brazil, and the Central African Republic (Bangui). Neither an affinity to Earth's mantle, nor an origin in the crust can be unequivocally established. Carbonado-diamond is at least 3.8 Ga old, an age about 0.5 Ga older than the oldest diamonds yet reported in kimberlites and lamproites on Earth. Derived from Neo- to Mid-Proterozoic meta-conglomerates, the primary magmatic host rock has not been identified. Discovered in 1841, the material is polycrystalline, robust and coke-like, and is best described as a strongly bonded micro-diamond ceramic. It is characteristically porous, which precludes an origin at high pressures and high temperatures in Earth's deep interior, yet it is also typically patinated, with a glass-like surface that resembles melting. With exotic inclusions of highly reduced metals, carbides, and nitrides the origin of carbonado-diamond is made even more challenging. But the challenge is important because a new diamondiferous host rock may be involved, and the development of a new physical process for generating diamond is possibly assured. The combination of micro-crystals and random crystal orientation leads to extreme mechanical toughness, and a predicable super-hardness. The physical and chemical properties of carbonado are described with a view to the development of a mimetic strategy to synthesize carbonado and to duplicate its extreme toughness and super-hardness. Textural variations are described with an emphasis on melt-like surface features, not previously discussed in the literature, but having a very clear bearing on the history and genesis of carbonado. Selected physical properties are presented and the proposed origins, diverse in character and imaginatively novel, are critically reviewed. From our present knowledge of the dynamic Earth, all indications are that carbonado is unlikely to be of terrestrial origin. A revised model for the origin of

  4. Historical environmental change in Africa drives divergence and admixture of Aedes aegypti mosquitoes: a precursor to successful worldwide colonization?

    Science.gov (United States)

    Bennett, Kelly Louise; Shija, Fortunate; Linton, Yvonne-Marie; Misinzo, Gerald; Kaddumukasa, Martha; Djouaka, Rousseau; Anyaele, Okorie; Harris, Angela; Irish, Seth; Hlaing, Thaung; Prakash, Anil; Lutwama, Julius; Walton, Catherine

    2016-09-01

    Increasing globalization has promoted the spread of exotic species, including disease vectors. Understanding the evolutionary processes involved in such colonizations is both of intrinsic biological interest and important to predict and mitigate future disease risks. The Aedes aegypti mosquito is a major vector of dengue, chikungunya and Zika, the worldwide spread of which has been facilitated by Ae. aegypti's adaption to human-modified environments. Understanding the evolutionary processes involved in this invasion requires characterization of the genetic make-up of the source population(s). The application of approximate Bayesian computation (ABC) to sequence data from four nuclear and one mitochondrial marker revealed that African populations of Ae. aegypti best fit a demographic model of lineage diversification, historical admixture and recent population structuring. As ancestral Ae. aegypti were dependent on forests, this population history is consistent with the effects of forest fragmentation and expansion driven by Pleistocene climatic change. Alternatively, or additionally, historical human movement across the continent may have facilitated their recent spread and mixing. ABC analysis and haplotype networks support earlier inferences of a single out-of-Africa colonization event, while a cline of decreasing genetic diversity indicates that Ae. aegypti moved first from Africa to the Americas and then to Asia. ABC analysis was unable to verify this colonization route, possibly because the genetic signal of admixture obscures the true colonization pathway. By increasing genetic diversity and forming novel allelic combinations, divergence and historical admixture within Africa could have provided the adaptive potential needed for the successful worldwide spread of Ae. aegypti. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  5. A population genetics view of animal domestication.

    Science.gov (United States)

    Larson, Greger; Burger, Joachim

    2013-04-01

    The fundamental shift associated with the domestication of plants and animals allowed for a dramatic increase in human population sizes and the emergence of modern society. Despite its importance and the decades of research devoted to studying it, questions regarding the origins and processes of domestication remain. Here, we review recent theoretical advances and present a perspective that underscores the crucial role that population admixture has played in influencing the genomes of domestic animals over the past 10000 years. We then discuss novel approaches to generating and analysing genetic data, emphasising the importance of an explicit hypothesis-testing approach for the inference of the origins and subsequent evolution and demography of domestic animals. By applying next-generation sequencing technology alongside appropriate biostatistical methodologies, a substantially deeper understanding of domestication is on the horizon.

  6. Some pungent arguments against the physico-chemical theories of the origin of the genetic code and corroborating the coevolution theory.

    Science.gov (United States)

    Di Giulio, Massimo

    2017-02-07

    Whereas it is extremely easy to prove that "if the biosynthetic relationships between amino acids were fundamental in the structuring of the genetic code, then their physico-chemical properties might also be revealed in the genetic code table"; it is, on the contrary, impossible to prove that "if the physico-chemical properties of amino acids were fundamental in the structuring of the genetic code, then the presence of the biosynthetic relationships between amino acids should not be revealed in the genetic code". And, given that in the genetic code table are mirrored both the biosynthetic relationships between amino acids and their physico-chemical properties, all this would be a test that would falsify the physico-chemical theories of the origin of the genetic code. That is to say, if the physico-chemical properties of amino acids had a fundamental role in organizing the genetic code, then we would not have duly revealed the presence - in the genetic code - of the biosynthetic relationships between amino acids, and on the contrary this has been observed. Therefore, this falsifies the physico-chemical theories of genetic code origin. Whereas, the coevolution theory of the origin of the genetic code would be corroborated by this analysis, because it would be able to give a description of evolution of the genetic code more coherent with the indisputable empirical observations that link both the biosynthetic relationships of amino acids and their physico-chemical properties to the evolutionary organization of the genetic code. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. The evolutionary and genetic origins of consciousness in the Cambrian Period over 500 million years ago

    Science.gov (United States)

    Feinberg, Todd E.; Mallatt, Jon

    2013-01-01

    Vertebrates evolved in the Cambrian Period before 520 million years ago, but we do not know when or how consciousness arose in the history of the vertebrate brain. Here we propose multiple levels of isomorphic or somatotopic neural representations as an objective marker for sensory consciousness. All extant vertebrates have these, so we deduce that consciousness extends back to the group's origin. The first conscious sense may have been vision. Then vision, coupled with additional sensory systems derived from ectodermal placodes and neural crest, transformed primitive reflexive systems into image forming brains that map and perceive the external world and the body's interior. We posit that the minimum requirement for sensory consciousness and qualia is a brain including a forebrain (but not necessarily a developed cerebral cortex/pallium), midbrain, and hindbrain. This brain must also have (1) hierarchical systems of intercommunicating, isomorphically organized, processing nuclei that extensively integrate the different senses into representations that emerge in upper levels of the neural hierarchy; and (2) a widespread reticular formation that integrates the sensory inputs and contributes to attention, awareness, and neural synchronization. We propose a two-step evolutionary history, in which the optic tectum was the original center of multi-sensory conscious perception (as in fish and amphibians: step 1), followed by a gradual shift of this center to the dorsal pallium or its cerebral cortex (in mammals, reptiles, birds: step 2). We address objections to the hypothesis and call for more studies of fish and amphibians. In our view, the lamprey has all the neural requisites and is likely the simplest extant vertebrate with sensory consciousness and qualia. Genes that pattern the proposed elements of consciousness (isomorphism, neural crest, placodes) have been identified in all vertebrates. Thus, consciousness is in the genes, some of which are already known. PMID

  8. The evolutionary and genetic origins of consciousness in the Cambrian Period over 500 million years ago

    Directory of Open Access Journals (Sweden)

    Todd E Feinberg

    2013-10-01

    Full Text Available Vertebrates evolved in the Cambrian Period before 520 million years ago, but we do not know when or how consciousness arose in the history of the vertebrate brain. Here we propose multiple levels of isomorphic or somatotopic neural representations as an objective marker for sensory consciousness. All extant vertebrates have these, so we deduce that consciousness extends back to the group’s origin. The first conscious sense may have been vision. Then vision, coupled with additional sensory systems derived from ectodermal placodes and neural crest, transformed primitive reflexive systems into image forming brains that map and perceive the external world and the body’s interior. We posit that the minimum requirement for sensory consciousness and qualia is a brain including a forebrain (but not necessarily a developed cerebral cortex/pallium, midbrain and hindbrain. This brain must also have 1 hierarchical systems of intercommunicating, isomorphically organized, processing nuclei that extensively integrate the different senses into representations that emerge in upper levels of the neural hierarchy; and 2 a widespread reticular formation that integrates the sensory inputs and contributes to attention, awareness, and neural synchronization. We propose a two-step evolutionary history, in which the optic tectum was the original center of multi-sensory conscious perception (as in fish and amphibians: step 1, followed by a gradual shift of this center to the dorsal pallium or its cerebral cortex (in mammals, reptiles, birds: step 2. We address objections to the hypothesis and call for more studies of fish and amphibians. In our view, the lamprey has all the neural requisites and is likely the simplest extant vertebrate with sensory consciousness and qualia. Genes that pattern the proposed elements of consciousness (isomorphism, neural crest, placodes have been identified in all vertebrates. Thus, consciousness is in the genes, some of which are

  9. Macromolecular recognition: Structural aspects of the origin of the genetic system

    Science.gov (United States)

    Rein, Robert; Barak, Dov; Luo, Ning; Zielinski, Theresa Julia; Shibata, Masayuki

    1991-01-01

    Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and

  10. Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

    Science.gov (United States)

    Ruiz-Linares, Andrés; Adhikari, Kaustubh; Acuña-Alonzo, Victor; Quinto-Sanchez, Mirsha; Jaramillo, Claudia; Arias, William; Fuentes, Macarena; Pizarro, María; Everardo, Paola; de Avila, Francisco; Gómez-Valdés, Jorge; León-Mimila, Paola; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C.; Burley, Mari-Wyn; Konca, Esra; de Oliveira, Marcelo Zagonel; Veronez, Mauricio Roberto; Rubio-Codina, Marta; Attanasio, Orazio; Gibbon, Sahra; Ray, Nicolas; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Schuler-Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Balding, David; Gonzalez-José, Rolando

    2014-01-01

    The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry. PMID:25254375

  11. Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals.

    Directory of Open Access Journals (Sweden)

    Andrés Ruiz-Linares

    2014-09-01

    Full Text Available The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú. These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.

  12. Genetic stock compositions and natal origin of green turtle (Chelonia mydas foraging at Brunei Bay

    Directory of Open Access Journals (Sweden)

    Juanita Joseph

    2016-04-01

    Full Text Available Knowledge of genetics composition and growth stages of endangered green turtles, as well as the connectivity between nesting and foraging grounds is important for effective conservation. A total of 42 green turtles were captured at Brunei Bay with curved carapace length ranging from 43.8 to 102.0 cm, and most sampled individuals were adults and large juveniles. Twelve haplotypes were revealed in mitochondrial DNA control region sequences. Most haplotypes contained identical sequences to haplotypes previously found in rookeries in the Western Pacific, Southeast Asia, and the Indian Ocean. Haplotype and nucleotide diversity indices of the Brunei Bay were 0.8444±0.0390 and 0.009350±0.004964, respectively. Mixed-stock analysis (for both uninformative and informative prior weighting by population size estimated the main contribution from the Southeast Asian rookeries of the Sulu Sea (mean ≥45.31%, Peninsular Malaysia (mean ≥17.42%, and Sarawak (mean ≥12.46%. Particularly, contribution from the Sulu Sea rookery was estimated to be the highest and lower confidence intervals were more than zero (≥24.36%. When estimating contributions by region rather than individual rookeries, results showed that Brunei Bay was sourced mainly from the Southeast Asian rookeries. The results suggest an ontogenetic shift in foraging grounds and provide conservation implications for Southeast Asian green turtles.

  13. Morphology vs Genetics: the hybrid origin of a sea turtle disproved by DNA

    Directory of Open Access Journals (Sweden)

    L. GAROFALO

    2013-01-01

    Full Text Available A putative hybrid sea turtle juvenile was evaluated with discriminant DNA markers. When compared with standard values for sea turtles, the general morphological features assigned the specimen to Caretta caretta, while the shape and coloration of the head and the beak profile fell within the Eretmochelys imbricata range; the front flippers were instead like those of a Chelonia mydas. Moreover, prefrontal scale number was outside the putative parental species’ ranges. The mitochondrial D-loop sequence was from C. caretta, and matched haplotype CC-A2.1, the most common in the Mediterranean. Sequence profiles at three nuclear loci withspecies-specific substitutions (Cmos, BDNF and R35 revealed only C. caretta variants, thus excluding that the individual wasan F1 hybrid. This study highlights the importance of integrating different methodological approaches to understand reproductive animal biology and to set the boundaries for specific morphological traits. In particular, we propose the genetic analysis of a new combination of mitochondrial and nuclear markers as a standard procedure which can be adopted in the identification of sea turtlehybrids.

  14. Global prostate cancer incidence and the migration, settlement, and admixture history of the Northern Europeans.

    Science.gov (United States)

    Gunderson, Kristin; Wang, Christopher Y; Wang, Ruoxiang

    2011-08-01

    The most salient feature of prostate cancer is its striking ethnic disparity. High incidences of the disease are documented in two ethnic groups: descendents of the Northern Europeans and African Americans. Other groups, including native Africans, are much less susceptible to the disease. Given that many risk factors may contribute to carcinogenesis, an etiological cause for the ethnic disparity remains to be defined. By analyzing the global prostate cancer incidence data, we found that distribution of prostate cancer incidence coincides with the migration and settlement history of Northern Europeans. The incidences in other ethnic groups correlate to the settlement history and extent of admixture of the Europeans. This study suggests that prostate cancer has been spread by the transmission of a genetic susceptibility that resides in the Northern European genome.

  15. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

    DEFF Research Database (Denmark)

    Librado, Pablo; Der Sarkissian, Clio; Ermini, Luca

    2015-01-01

    , extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens......Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below −70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations...... dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski’s horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid...

  16. Compatibility of repair mortar with migrating corrosion inhibiting admixtures

    Energy Technology Data Exchange (ETDEWEB)

    Bjegovic, D.; Ukrainczyk, V. [Univ. of Zagreb (Croatia). Faculty of Civil Engineering; Ukrainczyk, B. [LGM, Zagreb (Croatia); Miksic, B. [CORTEC Corp., St. Paul, MN (United States)

    1997-08-01

    One of the methods for corrosion protection of reinforced concrete is the use of migrating corrosion inhibitor as an admixture in repair mortars. The admixture must be effective for corrosion protection and compatible with polymers added to repair mortar to improve properties of fresh and hardened mortar. This paper presents experimental results on compatibility of a migrating corrosion inhibitor added to two repair mortars based on an inorganic binder modified with polymers. The influence of a migrating inhibitor on the properties of fresh and hardened mortars was tested. The effectiveness on reinforcement corrosion protection has been tested according to ASTM G 109. Test results prove that the investigated migrating inhibitor is compatible with repair mortars and that it delays corrosion of the reinforcement.

  17. [Helicobacter pylori infection in Uruguayan patients of African origin: clinical, endoscopic and genetic characteristics].

    Science.gov (United States)

    González, Nicolás; Fernández, Lucía; Pérez Pérez, Guillermo; Saona, Gustavo; Raisler, Katherine; Eugenia Torres, María; Olivares, Asalia; Stein, Silvana; Cohen, Henry

    2010-09-01

    Prevalence of H pylori varies in different regions around the world and its associated clinical manifestations are more severe in certain ethnic groups. Prevalence of H pylori in different groups is scarcely known in Uruguay. To determine the prevalence, clinical and endoscopic characteristics of H pylori infection in Uruguayan patients of African origin. Fifty Afro-descendant patients attending the Clinics of Gastroenterology at Hospital de Clínicas in Montevideo, were studied. They were all examined by upper endoscopy and H pylori infection was determined by histology, urease test and culture. Presence of cagA was ascertained by PCR. The prevalence of H pylori infection determined by histology and urease test in Afro-descendants was 70%. No relationship was found between symptoms that led to consultation and the presence of infection. It was not possible either to establish a relationship between H pylori and endoscopic findings. CagA gene was detected in 62% of cases, but there was no relationship between its presence and the endoscopic findings. The prevalence of H pylori infection in Afro-descendant Uruguayan patients is high, comparable with that found in other developing regions. However, an association of the presence of infection with symptoms or endoscopic findings was not found. CagA did not result in a risk factor for the presence of more severe gastroduodenal lesions in this group of patients.

  18. The origins of genetic variation between individual human oocytes and embryos: implications for infertility.

    Science.gov (United States)

    Delhanty, Joy D A

    2013-12-01

    Human fertility is low in comparison with that seen in other well-studied mammals. The main reason for this state of affairs seems to be the frequent occurrence and persistence of chromosomal errors in the human conceptus. Evidence obtained over the past two decades shows that the exceptionally high incidence of chromosomal anomalies seen in human preimplantation embryos is the result of errors that may occur at various stages during gamete and embryo formation. In rare cases, an error may exist or arise in the premeiotic germ cells; much more commonly it may arise during the first or second meiotic division in the male or female. Highly efficient cell cycle checkpoints in the male ensure that the incidence of aneuploidy in mature sperm is low compared to that in the oocyte. Most 3-day-old embryos created by IVF are chromosomal mosaics, and this persists to a lesser degree to the blastocyst stage on day 5. While aneuploidy of meiotic origin is a major factor affecting the fertility of older women, embryos from most younger women will have predominantly post-zygotic mitotic errors. Couples experiencing RIF are particularly likely to produce highly abnormal (chaotic) embryos by post-zygotic mechanisms.

  19. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  20. High Frequency of Hb E-Saskatoon (HBB: c.67G > A) in Brazilians: A New Genetic Origin?

    Science.gov (United States)

    Wagner, Sandrine C; Lindenau, Juliana D; Castro, Simone M de; Santin, Ana Paula; Zaleski, Carina F; Azevedo, Laura A; Ribeiro Dos Santos, Ândrea K C; Dos Santos, Sidney E B; Hutz, Mara H

    2016-08-01

    Hb E-Saskatoon [β22(B4)Glu→Lys, HBB: c.67G > A] is a rare, nonpathological β-globin variant that was first described in a Canadian woman of Scottish and Dutch ancestry and has since then been detected in several populations. The aim of the present study was to identify the origin of Hb E-Saskatoon in Brazil using β-globin haplotypes and genetic ancestry in carriers of this hemoglobin (Hb) variant. Blood samples were investigated by isoelectric focusing (IEF) and high performance liquid chromatography (HPLC) using commercial kits. Hb E-Saskatoon was confirmed by amplification of the HBB gene, followed by sequence analysis. Haplotypes of the β-globin gene were determined by polymerase chain reaction (PCR), followed by digestion with specific restriction enzymes. Individual ancestry was estimated with 48 biallelic insertion/deletions using three 16-plex PCR amplifications. The IEF pattern was similar to Hbs C (HBB: c.19G > A) and Hb E (HBB: c.79G > A) [isoelectric point (pI): 7.59-7.65], and HPLC results showed an elution in the Hb S (HBB: c.20A > T) window [retention time (RT): 4.26-4.38]. DNA sequencing of the amplified β-globin gene showed a mutation at codon 22 (GAA>AAA) corresponding to Hb E-Saskatoon. A total of 11 cases of this variant were identified. In nine unrelated individuals, Hb E-Saskatoon was in linkage disequilibrium with haplotype 2 [+ - - - -]. All subjects showed a high degree of European contribution (mean = 0.85). Hb E-Saskatoon occurred on the β-globin gene of haplotype 2 in all Brazilian carriers. These findings suggest a different genetic origin for this Hb variant from that previously described.

  1. Assessment of Commercial Corrosion Inhibiting Admixtures for Reinforced Concrete

    OpenAIRE

    Brown, Michael Carey

    1999-01-01

    Corrosion of reinforcing steel in concrete exposed to chloride-laden environments is a well-known and documented phenomenon. The need for cost effective systems for protection against corrosion has become increasingly clear since the first observations of severe corrosion damage to interstate bridges in the 1960's. As one potential solution to the mounting problem of corrosion deterioration of structures, corrosion-inhibiting admixtures have been researched and introduced into service. ...

  2. Multiple genetic origins of histidine-rich protein 2 gene deletion in Plasmodium falciparum parasites from Peru.

    Science.gov (United States)

    Akinyi, Sheila; Hayden, Tonya; Gamboa, Dionicia; Torres, Katherine; Bendezu, Jorge; Abdallah, Joseph F; Griffing, Sean M; Quezada, Wilmer Marquiño; Arrospide, Nancy; De Oliveira, Alexandre Macedo; Lucas, Carmen; Magill, Alan J; Bacon, David J; Barnwell, John W; Udhayakumar, Venkatachalam

    2013-09-30

    The majority of malaria rapid diagnostic tests (RDTs) detect Plasmodium falciparum histidine-rich protein 2 (PfHRP2), encoded by the pfhrp2 gene. Recently, P. falciparum isolates from Peru were found to lack pfhrp2 leading to false-negative RDT results. We hypothesized that pfhrp2-deleted parasites in Peru derived from a single genetic event. We evaluated the parasite population structure and pfhrp2 haplotype of samples collected between 1998 and 2005 using seven neutral and seven chromosome 8 microsatellite markers, respectively. Five distinct pfhrp2 haplotypes, corresponding to five neutral microsatellite-based clonal lineages, were detected in 1998-2001; pfhrp2 deletions occurred within four haplotypes. In 2003-2005, outcrossing among the parasite lineages resulted in eight population clusters that inherited the five pfhrp2 haplotypes seen previously and a new haplotype; pfhrp2 deletions occurred within four of these haplotypes. These findings indicate that the genetic origin of pfhrp2 deletion in Peru was not a single event, but likely occurred multiple times.

  3. Mirror matter admixtures in K_L to mu^+ mu^-

    CERN Document Server

    Sánchez-Colón, G; Sanchez-Colon, Gabriel; Garcia, Augusto

    2006-01-01

    Our previous analysis on the contributions of mirror matter admixtures in ordinary hadrons to K_L to gamma gamma is extended to study the relevance of such contributions to the K_L to mu^+ mu^- rare decay. The mixing angle of the admixtures previously determined to describe the enhancement phenomenon in two body non-leptonic decays of strange hadrons is used, along with recent results for the description of the strong and electromagnetic interaction parts of the transition amplitudes. We find that these admixtures give a significant contribution with a small SU(3) breaking of only 2.8%, we also find a value of \\sim -17.9^{\\circ} for the eta-eta' mixing angle consistent with some of its determinations in the literature and a preferred negative value around -16 for the local counter-term contribution chi_1 + chi_2 consistent with the existence of a unique counter-term assuming lepton universality. We conclude that those mixings may be relevant in low energy physics and should not be ignored.

  4. Experimental study of admixture on soil's physical and mechanical characteristics

    Science.gov (United States)

    Guo, Zihong; Li, Tangyong; Yu, Dongke; Tang, Hua; Zhang, Yang; Li, Zhaochen; He, Dan

    2017-08-01

    Earth building is a traditional architectural form. With respect to environment protection, low cost, convenient advantages, its practical value is recognizing carefully. Due to poor mechanical properties and durability of earth, the development of earth building has been prevented. This experiment selects two kinds of soil. Sawdust and straw serve as admixture. More than 300 specimens have been performed to verify the effects of various factors on soil's physical and mechanical characteristics. Some useful characteristics are acquired by the experiment, such as soil's optimal moisture content, maximum dry density, optimal length of straw and contraction ratio. Testing the influence of admixture on soil's strength and deformation, this experiment shows that mixing straw and sawdust reduce soil's compressive and tensile strength. However, it may reduce soil's contraction ratio. Considering the influence of admixture on soil's contraction and strength, when soil 1 mixes with 0.1% sawdust, its contraction ratio decreases obviously and strength decreases slightly. It is a good choice according to the experiments.

  5. The rights of donor inseminated children to know their genetic origins in Australia.

    Science.gov (United States)

    Schneller, Edwina Anne

    2005-12-01

    Twenty years after it was recognised that adopted children have rights to understand their origins, the dawn has finally broken with respect to children conceived as a result of the Assisted Reproductive Technologies (ART), specifically donor insemination (DI). Recipients and practitioners of conception technologies focus their energies and ethical deliberation on the achievement of pregnancy and the successful birth of the child. Law, in contrast, must focus beyond birth to enshrine respect for the rights of the child, who is 'not legally capable of defending [his or her] own future interests.' This article undertakes an assessment of what is in the best interests of a child using empirical studies to ground a position that should be adopted by law in Australia. This article also critically evaluates the current legal position of the various States and Territories with regards to a DI conceived child's rights to know of their form of conception; access to identifying information of their donor; at what age they may access information; the position of DI children born before existing legislation; record-keeping; and finally whether international law grants such children rights. Australian children must enjoy the right in theory and practice to know they were donor conceived and the identity of their donor. It is disappointing that New South Wales, as the most recent State to propose legislation on ART, has not utilised international empirical research on the best interests of DI children or even followed the Infertility Treatment Act 1995 (Vic) which seems to be far more progressive in recognising how best to protect the rights of DI children. The current legal position is chaotic. States and Territories should confer power on the Federal Government to legislate uniform and explicit regulation of ART for the benefit of DI children.

  6. The Chemical Basis for the Origin of the Genetic Code and the Process of Protein Synthesis

    Science.gov (United States)

    Lacey, James C., Jr.

    1990-01-01

    A model for the origin of protein synthesis. The essential features of the model are that 5'-AMP and perhaps other monoribonucleotides can serve as catalysts for the selective synthesis of L-based peptides. A unique set of characteristics of 5'-AMP is responsible for the selective catalysts and these characteristics are described in detail. The model involves the formation of diesters as intermediates and selectivity for use of the L-isomer occurs principally at the step of forming the diester. However, in the formation of acetyl phenylalanine-AMP monoester there is a selectivity for esterification by the D-isomer. Data showing this selectivity is presented. This selectivity for D-isomer disappears after the first step. The identity was confirmed of all four of possible diesters of acetyl-D- and -L phenylaline with 5'-AMP by nuclear magnetic resonance (NMR). The data using flourescence and NMR show the Trp ring can associate with the adenine ring more strongly when the D-isomer is in the 2' position than it can when in the 3' position. These same data also suggest a molecular mechanisim for the faster esterificaton of 5'-AMP by acetyl-D-phenylaline. Some new data is also presented on the possible structure of the 2' isomer of acetyl-D-tryptophan-AMP monoester. The HPLC elution times of all four possible acetyl diphenylalanine esters of 5'-AMP were studied, these peptidyl esters will be products in the studies of peptide formation on the ribose of 5'-AMP. Other studies were on the rate of synthesis and the identity of the product when producing 3'Ac-Phe-2'tBOC-Phe-AMP diester. HPLC purification and identification of this product were accomplished.

  7. Characterization of genetic defects of hemophilia A in patients of Chinese origin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Shu-Wha; Lin, Shu-Rung; Shen, Ming-Ching (National Taiwan Univ., Taipei (Taiwan, Province of China))

    1993-12-01

    The molecular characterization of hemophilia A of Chinese origin was carried out by the polymerase chain reaction (PCR) and direct sequencing of patient's factor VIII genes. Single-strand conformation polymorphism (SSCP) and dideoxy fingerprinting (ddF) were used as screening methods to detect mutated DNAs. A total of 102 individuals from 87 different families, including 10 patients (10 families) with mild-to-moderate and 92 patients (77 families) with severe hemophilia A, were analyzed by PCR-SSCP and PCR-ddF. Of the 87 independent cases, 40 revealed a single mutation in the coding regions of their factor VIII genes. These mutations include 21 with single base changes resulting in 8 nonsense and 13 missense codons, 16 with deletion or insertion of 1-11 nucleotides, and 3 with deletion of large DNA fragments. The frequency of 8 of the identified factor VIII polymorphisms or silent mutations was also determined among Chinese. The frequencies for codons 1241, 1269, and 2223 (the numbering system follows J. Gitschier et al., 1984, Nature 312: 326-330) were found to be different from those reported for other populations. As for the 47 severe cases whose mutational events were not readily detected by PCR-SSCP and PCR-ddF, the reverse transcriptase PCR method was applied. In 24 such cases analyzed, 17 were found to be of the [open quotes]intron 22 mutations[close quotes] as described by Naylor et al. (1992, The Lancet, 342: 1066-1067), accounting for 39% of Chinese patients with hemophilia A. 31 refs., 2 figs., 6 tabs.

  8. Genome-wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate.

    Science.gov (United States)

    Sim, Zijian; Hall, Jocelyn C; Jex, Bill; Hegel, Troy M; Coltman, David W

    2016-08-01

    Past glaciation events have played a major role in shaping the genetic diversity and distribution of wild sheep in North America. The advancement of glaciers can isolate populations in ice-free refugia, where they can survive until the recession of ice sheets. The major Beringian refugium is thought to have held thinhorn sheep (Ovis dalli) populations during times of glacial advance. While isolation in the major refugium can account for much of the genetic and morphological diversity seen in extant thinhorn sheep populations, mounting evidence suggests the persistence of populations in smaller minor refugia. We investigated the refugial origins of thinhorn sheep using ~10 000 SNPs obtained via a cross-species application of the domestic sheep ovine HD BeadChip to genotype 52 thinhorn sheep and five bighorn sheep (O. canadensis) samples. Phylogenetic inference revealed a distinct lineage of thinhorn sheep inhabiting British Columbia, which is consistent with the survival of a group of thinhorn sheep in a minor refugium separate from the Beringian refugium. Isolation in separate glacial refugia probably mediated the evolution of the two thinhorn sheep subspecies, the white Dall's sheep (O. d. dalli), which persisted in Beringia, and the dark Stone's sheep (O. d. stonei), which utilized the minor refugium. We also found the first genetic evidence for admixture between sheep from different glacial refugia in south-central Yukon as a consequence of post glacial expansion and recolonization. These results show that glaciation events can have a major role in the evolution of species inhabiting previously glaciated habitats and the need to look beyond established refugia when examining the evolutionary history of such species.

  9. Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences.

    Science.gov (United States)

    Haber, Marc; Doumet-Serhal, Claude; Scheib, Christiana; Xue, Yali; Danecek, Petr; Mezzavilla, Massimo; Youhanna, Sonia; Martiniano, Rui; Prado-Martinez, Javier; Szpak, Michał; Matisoo-Smith, Elizabeth; Schutkowski, Holger; Mikulski, Richard; Zalloua, Pierre; Kivisild, Toomas; Tyler-Smith, Chris

    2017-08-03

    The Canaanites inhabited the Levant region during the Bronze Age and established a culture that became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole genomes from ∼3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalog modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with recorded massive population movements in Mesopotamia during the mid-Holocene. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate that this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  10. Male ancestry structure and interethnic admixture in African-descent communities from the Amazon as revealed by Y-chromosome Strs.

    Science.gov (United States)

    Palha, Teresinha de Jesus Brabo Ferreira; Ribeiro-Rodrigues, Elzemar Martins; Ribeiro-dos-Santos, Andrea; Guerreiro, João Farias; de Moura, Luciene Soraya Souza; Santos, Sidney

    2011-03-01

    Some genetic markers on both the Y chromosome and mtDNA are highly polymorphic and population-specific in humans, representing useful tools for reconstructing the past history of populations with poor historical records. Such lack of information is usually true in the case of recent African-descent populations of the New World founded by fugitive slaves throughout the slavery period in the Americas, particularly in Brazil, where those communities are known as quilombos. Aiming to recover male-derived ethnic structure of nine quilombos from the Brazilian Amazon, a total of 300 individuals, belonging to Mazagão Velho (N = 24), Curiaú (N = 48), Mazagão (N = 36), Trombetas (N = 20), Itacoã (N = 22), Saracura (N = 46), Marajó (N = 58), Pitimandeua (N = 26), and Pontal (N = 20), were investigated for nine Y-STRs (DYS393, DYS19, DYS390, DYS389 I, DYS389 II, DYS392, DYS391, DYS385 I/II). From the 169 distinct haplotypes obtained, 120 were singletons. The results suggest the West African coast as the main origin of slaves brought to Brazil (54% of male contribution); the European contribution was high (41%), while the Amerindian's was low (5%). Those results contrast with previous mtDNA data that showed high Amerindian female contribution (46.6%) in African-descent populations. AMOVA suggests that the genetic differentiation among the quilombos is mainly influenced by admixture with European. However, when restricting AMOVA to African-specific haplotypes, low differentiation was detected, suggesting great genetic homogeneity of the African founding populations and/or a later homogenization by intense slave trade inside Brazil.

  11. Genetic structure and natural variation associated with host of origin in Penicillium expansum strains causing blue mould.

    Science.gov (United States)

    Sanzani, S M; Montemurro, C; Di Rienzo, V; Solfrizzo, M; Ippolito, A

    2013-07-15

    Blue mould, caused by Penicillium expansum, is one of the most economically damaging postharvest diseases of pome fruits, although it may affect a wider host range, including sweet cherries and table grapes. Several reports on the role of mycotoxins in plant pathogenesis have been published, but few focussed on the influence of mycotoxins on the variation in host preference amongst producing fungi. In the present study the influence of the host on P. expansum pathogenicity/virulence was investigated, focussing mainly on the relationship with patulin production. Three P. expansum strain groups, originating from apples, sweet cherries, and table grapes (7 strains per host) were grown on their hosts of isolation and on artificial media derived from them. Strains within each P. expansum group proved to be more aggressive and produced more patulin than the other two groups under evaluation when grown on the host from which they originated. Table grape strains were the most aggressive (81% disease incidence) and strongest patulin producers (up to 554μg/g). The difference in aggressiveness amongst strains was appreciable only in the presence of a living host, suggesting that the complex pathogen-host interaction significantly influenced the ability of P. expansum to cause the disease. Incidence/severity of the disease and patulin production proved to be positively correlated, supporting the role of patulin as virulence/pathogenicity factor. The existence of genetic variation amongst isolates was confirmed by the High Resolution Melting method that was set up herein, which permitted discrimination of P. expansum from other species (P. chrysogenum and P. crustosum) and, within the same species, amongst the host of origin. Host effect on toxin production appeared to be exerted at a transcriptional level.

  12. Origins and divergence of the Roma (gypsies).

    Science.gov (United States)

    Gresham, D; Morar, B; Underhill, P A; Passarino, G; Lin, A A; Wise, C; Angelicheva, D; Calafell, F; Oefner, P J; Shen, P; Tournev, I; de Pablo, R; Kuĉinskas, V; Perez-Lezaun, A; Marushiakova, E; Popov, V; Kalaydjieva, L

    2001-12-01

    The identification of a growing number of novel Mendelian disorders and private mutations in the Roma (Gypsies) points to their unique genetic heritage. Linguistic evidence suggests that they are of diverse Indian origins. Their social structure within Europe resembles that of the jatis of India, where the endogamous group, often defined by profession, is the primary unit. Genetic studies have reported dramatic differences in the frequencies of mutations and neutral polymorphisms in different Romani populations. However, these studies have not resolved ambiguities regarding the origins and relatedness of Romani populations. In this study, we examine the genetic structure of 14 well-defined Romani populations. Y-chromosome and mtDNA markers of different mutability were analyzed in a total of 275 individuals. Asian Y-chromosome haplogroup VI-68, defined by a mutation at the M82 locus, was present in all 14 populations and accounted for 44.8% of Romani Y chromosomes. Asian mtDNA-haplogroup M was also identified in all Romani populations and accounted for 26.5% of female lineages in the sample. Limited diversity within these two haplogroups, measured by the variation at eight short-tandem-repeat loci for the Y chromosome, and sequencing of the HVS1 for the mtDNA are consistent with a small group of founders splitting from a single ethnic population in the Indian subcontinent. Principal-components analysis and analysis of molecular variance indicate that genetic structure in extant endogamous Romani populations has been shaped by genetic drift and differential admixture and correlates with the migrational history of the Roma in Europe. By contrast, social organization and professional group divisions appear to be the product of a more recent restitution of the caste system of India.

  13. The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

    Science.gov (United States)

    Di Giulio, Massimo

    2017-11-07

    The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal

  14. Admixture and population structure in Mexican-Mestizos based on paternal lineages.

    Science.gov (United States)

    Martínez-Cortés, Gabriela; Salazar-Flores, Joel; Fernández-Rodríguez, Laura Gabriela; Rubi-Castellanos, Rodrigo; Rodríguez-Loya, Carmen; Velarde-Félix, Jesús Salvador; Muñoz-Valle, José Franciso; Parra-Rojas, Isela; Rangel-Villalobos, Héctor

    2012-09-01

    In the nonrecombining region of the Y-chromosome, there are single-nucleotide polymorphisms (Y-SNPs) that establish haplogroups with particular geographical origins (European, African, Native American, etc.). The complex process of admixture that gave rise to the majority of the current Mexican population (~93%), known as Mestizos, can be examined with Y-SNPs to establish their paternal ancestry and population structure. We analyzed 18 Y-SNPs in 659 individuals from 10 Mexican-Mestizo populations from different regions of the country. In the total population sample, paternal ancestry was predominately European (64.9%), followed by Native American (30.8%) and African (4.2%). However, the European ancestry was prevalent in the north and west (66.7-95%) and, conversely, Native American ancestry increased in the center and southeast (37-50%), whereas the African ancestry was low and relatively homogeneous (0-8.8%). Although this paternal landscape concurs with previous studies based on genome-wide SNPs and autosomal short tandem repeats (STRs), this pattern contrasts with the maternal ancestry, mainly of Native American origin, based on maternal lineages haplogroups. In agreement with historical records, these results confirm a strong gender-biased admixture history between European males and Native American females that gave rise to Mexican-Mestizos. Finally, pairwise comparisons and analysis of molecular variance tests demonstrated significant population structure (F(ST)=4.68%; P<0.00005), delimiting clusters that were geographically defined as the following: north-west, center-south and southeast.

  15. Genetic structure of the populations migrating from San Luis Potosi and Zacatecas to Nuevo León in Mexico.

    Science.gov (United States)

    Cerda-Flores, R M; Kshatriya, G K; Barton, S A; Leal-Garza, C H; Garza-Chapa, R; Schull, W J; Chakraborty, R

    1991-06-01

    The Mexicans residing in the Monterrey metropolitan area in Nuevo León, Mexico, were grouped by generation and birthplace [Monterrey Metropolitan Area (MMA), San Luis Potosi (SLP), and Zacatecas (ZAC)] of the four grandparents to determine the extent of genetic variation within this population and the genetic differences, if any, between the natives living in the MMA and the immigrant populations from SLP and ZAC. Nine genetic marker systems were analyzed. The genetic distance analysis indicates that SLP and ZAC are similar to the MMA, irrespective of birthplace and generation. Gene diversity analysis (GST) suggests that more than 96% of the total gene diversity (HT) can be attributed to individual variation within the population. The genetic admixture analysis suggests that the Mexicans of the MMA, SLP, and ZAC, stratified by birthplace and generation, have received a predominantly Spanish contribution (78.5%), followed by a Mexican Indian contribution (21.5%). Similarly, admixture analysis, conducted on the population of Nuevo León and stratified by generation, indicates a substantial contribution from the MMA (64.6%), followed by ZAC (22.1%) and SLP (13.3%). Finally, we demonstrate that there is no nonrandom association of alleles among the genetic marker systems (i.e., no evidence of gametic disequilibrium) despite the Mestizo origin of this population.

  16. Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers

    Directory of Open Access Journals (Sweden)

    A. A. Maw

    2015-01-01

    Full Text Available The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels markers. Most of the indels loci were polymorphic (71% to 96%, and the genetic variability was similar in all populations. The average observed heterozygosities (HO and expected heterozygosities (HE ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088 than Myanmar (0.041 and Laotian (0.024 populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ tree, using Nei’s genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3 from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

  17. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.

    Science.gov (United States)

    Librado, Pablo; Der Sarkissian, Clio; Ermini, Luca; Schubert, Mikkel; Jónsson, Hákon; Albrechtsen, Anders; Fumagalli, Matteo; Yang, Melinda A; Gamba, Cristina; Seguin-Orlando, Andaine; Mortensen, Cecilie D; Petersen, Bent; Hoover, Cindi A; Lorente-Galdos, Belen; Nedoluzhko, Artem; Boulygina, Eugenia; Tsygankova, Svetlana; Neuditschko, Markus; Jagannathan, Vidhya; Thèves, Catherine; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Sicheritz-Ponten, Thomas; Popov, Ruslan; Grigoriev, Semyon; Alekseev, Anatoly N; Rubin, Edward M; McCue, Molly; Rieder, Stefan; Leeb, Tosso; Tikhonov, Alexei; Crubézy, Eric; Slatkin, Montgomery; Marques-Bonet, Tomas; Nielsen, Rasmus; Willerslev, Eske; Kantanen, Juha; Prokhortchouk, Egor; Orlando, Ludovic

    2015-12-15

    Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.

  18. Complete genetic analysis of plasmids carrying mcr-1 and other resistance genes in an Escherichia coli isolate of animal origin.

    Science.gov (United States)

    Li, Ruichao; Xie, Miaomiao; Lv, Jingzhang; Wai-Chi Chan, Edward; Chen, Sheng

    2017-03-01

    To investigate the genetic features of three plasmids recovered from an MCR-1 and ESBL-producing Escherichia coli strain, HYEC7, and characterize the transmission mechanism of mcr-1 . The genetic profiles of three plasmids were determined by PCR, S1-PFGE, Southern hybridization and WGS analysis. The ability of the mcr-1 -bearing plasmid to undergo conjugation was also assessed. The mcr-1 -bearing transposon Tn 6330 was characterized by PCR and DNA sequencing. Complete sequences of three plasmids were obtained. A non-conjugative phage P7-like plasmid, pHYEC7- mcr1 , was found to harbour the mcr-1 -bearing transposon Tn 6330 , which could be excised from the plasmid by generating a circular intermediate harbouring mcr-1 and the IS Apl1 element. The insertion of the circular intermediate into another plasmid, pHYEC7-IncHI2, could form pHNSHP45-2, the original IncHI2-type mcr-1 -carrying plasmid that was reported. The third plasmid, pHYEC7-110, harboured two replicons, IncX1 and IncFIB, and comprised multiple antimicrobial resistance mobile elements, some of which were shared by pHYEC7-IncHI2. The Tn 6330 element located in the phage-like plasmid pHYEC7- mcr1 could be excised from the plasmid and formed a circular intermediate that could be integrated into plasmids containing the IS Apl1 element. This phenomenon indicated that Tn 6330 is a key element responsible for widespread dissemination of mcr-1 among various types of plasmids and bacterial chromosomes. The dissemination rate of such an element may be further enhanced upon translocation into phage-like vectors, which may also be transmitted via transduction events.

  19. Genetic Heterogeneity in Algerian Human Populations.

    Science.gov (United States)

    Bekada, Asmahan; Arauna, Lara R; Deba, Tahria; Calafell, Francesc; Benhamamouch, Soraya; Comas, David

    2015-01-01

    The demographic history of human populations in North Africa has been characterized by complex processes of admixture and isolation that have modeled its current gene pool. Diverse genetic ancestral components with different origins (autochthonous, European, Middle Eastern, and sub-Saharan) and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample. In order to evaluate the genetic heterogeneity of Algeria, Y-chromosome, mtDNA and autosomal genome-wide makers have been analyzed in several Berber- and Arab-speaking groups. Our results show that the genetic heterogeneity found in Algeria is not correlated with geography or linguistics, challenging the idea of Berber groups being genetically isolated and Arab groups open to gene flow. In addition, we have found that external sources of gene flow into North Africa have been carried more often by females than males, while the North African autochthonous component is more frequent in paternally transmitted genome regions. Our results highlight the different demographic history revealed by different markers and urge to be cautious when deriving general conclusions from partial genomic information or from single samples as representatives of the total population of a region.

  20. Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction.

    Science.gov (United States)

    Sánchez-Quinto, Federico; Lalueza-Fox, Carles

    2015-01-19

    Nearly two decades since the first retrieval of Neanderthal DNA, recent advances in next-generation sequencing technologies have allowed the generation of high-coverage genomes from two archaic hominins, a Neanderthal and a Denisovan, as well as a complete mitochondrial genome from remains which probably represent early members of the Neanderthal lineage. This genomic information, coupled with diversity exome data from several Neanderthal specimens is shedding new light on evolutionary processes such as the genetic basis of Neanderthal and modern human-specific adaptations-including morphological and behavioural traits-as well as the extent and nature of the admixture events between them. An emerging picture is that Neanderthals had a long-term small population size, lived in small and isolated groups and probably practised inbreeding at times. Deleterious genetic effects associated with these demographic factors could have played a role in their extinction. The analysis of DNA from further remains making use of new large-scale hybridization-capture-based methods as well as of new approaches to discriminate contaminant DNA sequences will provide genetic information in spatial and temporal scales that could help clarify the Neanderthal's-and our very own-evolutionary history.

  1. Effect of Anti-freezing Admixtures on Alkali-silica Reaction in Mortars

    Institute of Scientific and Technical Information of China (English)

    LIU Junzhe; LI Yushun; LV Lihua

    2005-01-01

    The influence of anti-freezing admixture on the alkali aggregate reaction in mortar was analyzed with accelerated methods. It is confirmed that the addition of sodium salt ingredients of anti-freezing admixture accelerates the alkali silica reaction to some extent, whereas calcium salt ingredient of anti-freezing admixture reduces the expansion of alkali silica reaction caused by high alkali cement. It is found that the addition of the fly ash considerably suppresses the expansion of alkali silica reaction induced by the anti-freezing admixtures.

  2. Practical handling of AIO admixtures – Guidelines on Parenteral Nutrition, Chapter 10

    Directory of Open Access Journals (Sweden)

    Stanga, Z.

    2009-11-01

    Full Text Available All-in-one admixtures (AIO-admixtures provide safe, effective and low-risk PN (parenteral nutrition for practically all indications and applications. Water, energy (carbohydrates and lipids, amino acids, vitamins and trace elements are infused together with PN either as industrially-manufactured AIO admixtures provided as two- or three-chamber bags (shelf life usually more than 12 months completed with electrolytes and micronutrients where appropriate or as individually compounded ready-to-use AIO admixtures (compounding, usually prepared by a pharmacy on either a daily or weekly basis and stored at 2–8°C. Physico-chemical and microbial stability of an AIO admixture is essential for the safety and effectiveness of patient-specific PN, and its assurance requires specialist pharmaceutical knowledge. The stability should be documented for an application period of 24 (–48 hours. It is advisable to offer a limited selection of different PN regimes in each hospital. For reasons of drug and medication safety, PN admixtures prepared for individual patients must be correctly labelled and specifications for storage conditions must also be followed during transport. Monitoring is required where applicable. Micronutrients are usually administered separately to AIO admixtures. In case compatibility and stability have been well documented trace elements and/or combination preparations including water-soluble or water-soluble/fat soluble vitamin supplements can be added to PN admixtures under strict aseptic conditions. AIO admixtures are usually not used as vehicles for drugs (incompatibilities.

  3. Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups.

    Science.gov (United States)

    Martínez-Cortés, Gabriela; Salazar-Flores, Joel; Haro-Guerrero, Javier; Rubi-Castellanos, Rodrigo; Velarde-Félix, Jésus S; Muñoz-Valle, José F; López-Casamichana, Mavil; Carrillo-Tapia, Eduardo; Canseco-Avila, Luis M; Bravi, Claudio M; López-Armenta, Mauro; Rangel-Villalobos, Héctor

    2013-08-01

    The maternal ancestry (mtDNA) has important applications in different research fields, such as evolution, epidemiology, identification, and human population history. This is particularly interesting in Mestizos, which constitute the main population in Mexico (∼93%) resulting from post-Columbian admixture between Spaniards, Amerindians, and African slaves, principally. Consequently, we conducted minisequencing analysis (SNaPshot) of 11 mitochondrial single-nucleotide polymorphisms in 742 Mestizos of 10 populations from different regions in Mexico. The predominant maternal ancestry was Native American (92.9%), including Haplogroups A, B, C, and D (47, 23.7, 15.9, and 6.2%, respectively). Conversely, European and African ancestries were less frequent (5.3 and 1.9%, respectively). The main characteristics of the maternal lineages observed in Mexican-Mestizos comprised the following: 1) contrasting geographic gradient of Haplogroups A and C; 2) increase of European lineages toward the Northwest; 3) low or absent, but homogeneous, African ancestry throughout the Mexican territory; 4) maternal lineages in Mestizos roughly represent the genetic makeup of the surrounding Amerindian groups, particularly toward the Southeast, but not in the North and West; 5) continuity over time of the geographic distribution of Amerindian lineages in Mayas; and 6) low but significant maternal population structure (FST  = 2.8%; P = 0.0000). The average ancestry obtained from uniparental systems (mtDNA and Y-chromosome) in Mexican-Mestizos was correlated with previous ancestry estimates based on autosomal systems (genome-wide single-nucleotide polymorphisms and short tandem repeats). Finally, the comparison of paternal and maternal lineages provided additional information concerning the gender bias admixture, mating patterns, and population structure in Mestizos throughout the Mexican territory.

  4. Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks.

    Science.gov (United States)

    Stamatoyannopoulos, George; Bose, Aritra; Teodosiadis, Athanasios; Tsetsos, Fotis; Plantinga, Anna; Psatha, Nikoletta; Zogas, Nikos; Yannaki, Evangelia; Zalloua, Pierre; Kidd, Kenneth K; Browning, Brian L; Stamatoyannopoulos, John; Paschou, Peristera; Drineas, Petros

    2017-05-01

    Peloponnese has been one of the cradles of the Classical European civilization and an important contributor to the ancient European history. It has also been the subject of a controversy about the ancestry of its population. In a theory hotly debated by scholars for over 170 years, the German historian Jacob Philipp Fallmerayer proposed that the medieval Peloponneseans were totally extinguished by Slavic and Avar invaders and replaced by Slavic settlers during the 6th century CE. Here we use 2.5 million single-nucleotide polymorphisms to investigate the genetic structure of Peloponnesean populations in a sample of 241 individuals originating from all districts of the peninsula and to examine predictions of the theory of replacement of the medieval Peloponneseans by Slavs. We find considerable heterogeneity of Peloponnesean populations exemplified by genetically distinct subpopulations and by gene flow gradients within Peloponnese. By principal component analysis (PCA) and ADMIXTURE analysis the Peloponneseans are clearly distinguishable from the populations of the Slavic homeland and are very similar to Sicilians and Italians. Using a novel method of quantitative analysis of ADMIXTURE output we find that the Slavic ancestry of Peloponnesean subpopulations ranges from 0.2 to 14.4%. Subpopulations considered by Fallmerayer to be Slavic tribes or to have Near Eastern origin, have no significant ancestry of either. This study rejects the theory of extinction of medieval Peloponneseans and illustrates how genetics can clarify important aspects of the history of a human population.

  5. The influence of shrinkage reducing admixtures on plastic shrinkage

    Directory of Open Access Journals (Sweden)

    Mora, J.

    2003-12-01

    Full Text Available Shrinkage reducing admixtures (SRAs are viable alternatives for reducing plastic shrinkage cracking in concrete. The objective of the present paper is to study early age plastic shrinkage in restrained concrete elements, where three different SRAs have been used. The influence of the admixture is analyzed through the following measurements: capillary pressure, evaporation, temperature evolution, crack evolution and settlement. The tests for studying the cracking and deformation were made on two different configurations (i.e., restrained prisms with reduced cross-section and restrained panel, in a wind tunnel, with controlled wind temperature and velocity. The conclusions obtained indicate the viability of the use of this type of admixture and the usefulness of the test methods.

    Los aditivos reductores de retracción (SRAs se plantean, hoy en día, como una alternativa viable para reducir la fisuración por retracción plástica. El objetivo del presente artículo es conocer mejor y predecir el comportamiento a primeras edades de la retracción plástica en elementos estructurales coaccionados, a los que se les ha añadido diversos aditivos reductores de retracción (tres tipos diferentes. Esta influencia se analiza a través de las siguientes propiedades: presión capilar, evaporación, evolución de temperaturas, evolución de fisuración, y deformaciones verticales de asentamiento. Los ensayos para estudiar la fisuración y las deformaciones se han realizado sobre diferentes configuraciones (prisma restringido con estrangulamiento y panel restringido, en un túnel de viento, con temperaturas y velocidades de viento controladas. Las conclusiones obtenidas señalan la viabilidad del empleo de este tipo de aditivos y la bondad de los métodos experimentales utilizados.

  6. Phenolic Contents and Compositions in Skins of Red Wine Grape Cultivars among Various Genetic Backgrounds and Originations

    Directory of Open Access Journals (Sweden)

    Lei Zhu

    2012-03-01

    Full Text Available In order to analyze and compare the phenolic characteristics of red wine grapes with diverse genetic backgrounds, skin phenolics among 21 different cultivars belonging to Vitis vinifera L., East Asian and North American Vitis species and hybrids, as well as 2 varieties of muscadine grapes were estimated by HPLC-MS/MS. There were 45 anthocyanins, 28 flavonols, 8 flavan-3-ols, 9 cinnamic acids, 5 benzoic acids, 5 ellagic acids and 2 stilbenes detected in all the samples. Total contents of each phenolic type varied significantly among the different grape cultivars investigated. There was also a large variability in the phenolic compositions of different grape groups. The differences in anthocyanin composition were obvious between V. vinifera and non-V. vinifera grapes and also between the grapes originating from Eurasia and North America. Quercetin-3-glucuronide and quercetin-3-glucoside were marker flavonol compounds for Euvitis grape skins. Flavan-3-ol monomers were dominant in the skins of muscadine and non-V. amurensis East Asian grapes, whereas polymers were more common in V. vinifera and North American grapes. The muscadine grapes were very rich in flavonols, flavan-3-ols and ellagic acids. Via principal component analysis, these grape cultivars were clustered into three groups according to their characteristic phenolic content and composition.

  7. Whistler Solitons in Plasma with Anisotropic Hot Electron Admixture

    Science.gov (United States)

    Khazanov, G. V.; Krivorutsky, E. N.; Gallagher, D. L.

    1999-01-01

    The longitudinal and transverse modulation instability of whistler waves in plasma, with a small admixture of hot anisotropic electrons, is discussed. If the hot particles temperature anisotropy is positive, it is found that, in such plasma, longitudinal perturbations can lead to soliton formation for frequencies forbidden in cold plasma. The soliton is enriched by hot particles. The frequency region unstable to transverse modulation in cold plasma in the presence of hot electrons is divided by stable domains. For both cases the role of hot electrons is more significant for whistlers with smaller frequencies.

  8. Mirror matter admixtures in K_S to gamma gamma

    CERN Document Server

    Sánchez-Colón, G; Sanchez-Colon, Gabriel; Garcia, Augusto

    2006-01-01

    The latest measurement of the K_S to gamma gamma branching ratio clearly shows an enhancement over the current theoretical prediction. As in other K and B meson decays, this invites to consider the possibility of the contribution of new physics. We study a particular form of the latter, which may be referred to as manifest mirror symmetry. The experimental data are described using previously determined values for the mixing angles of the admixtures of mirror matter in ordinary hadrons and by assuming that for pi^0, eta, eta', the mirror decay amplitudes have the same magnitudes as their ordinary counterparts.

  9. Symmetry limit properties of decay amplitudes with mirror matter admixtures

    CERN Document Server

    Sánchez-Colón, G; Sanchez-Colon, Gabriel; Garcia, Augusto

    2006-01-01

    We extend our previous analysis on the symmetry limit properties of non-leptonic and weak radiative decay amplitudes of hyperons in a scheme of mirror matter admixtures in physical hadrons to include the two-body non-leptonic decays of $\\Omega^-$ and the two photon and two pion decays of kaons. We show that the so-called parity-conserving amplitudes predicted for all the decays vanish in the strong flavor SU(3) symmetry limit. We also establish the specific conditions under which the corresponding so-called parity-violating amplitudes vanish in the same limit.

  10. Gas genetic type and origin of hydrogen sulfide in the Zhongba gas field of the western Sichuan Basin, China

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Guangyou; Zhang Shuichang [Research Institute of Petroleum Exploration and Development, PetroChina, Beijing 100083 (China)] [State Key Laboratory for Enhanced Oil Recovery, Beijing 100083 (China); Huang Haiping, E-mail: huah@ucalgary.ca [School of Energy Resource, China University of Geosciences, Beijing 100083 (China)] [Department of Geosciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4 (Canada); Liang Yingbo; Meng, Shucui [Research Institute of Petroleum Exploration and Development, PetroChina, Beijing 100083 (China); Li Yuegang [Northwest Sichuan Gas Field, PetroChina Southwest Oil and Gas Field Company, Jiangyou, 621101 Sichuan (China)

    2011-07-15

    Highlights: > Natural gases discovered from the Zhongba gas field have two genetic types. > TSR is the main origin of H{sub 2}S. > Supportive evidences of TSR are derived from gas carbon isotopic values, sulfur isotopic values and formation water compositions. > Incomplete TSR reaction ceased in the Late Cretaceous. - Abstract: Natural gases and associated condensate oils from the Zhongba gas field in the western Sichuan Basin, China were investigated for gas genetic types and origin of H{sub 2}S by integrating gaseous and light hydrocarbon geochemistry, formation water compositions, S isotopes ({delta}{sup 34}S) and geological data. There are two types of natural gas accumulations in the studied area. Gases from the third member of the Middle Triassic Leikoupo Formation (T{sub 2}l{sup 3}) are reservoired in a marine carbonate sequence and are characterized by high gas dryness, high H{sub 2}S and CO{sub 2} contents, slightly heavy C isotopic values of CH{sub 4} and widely variable C isotopic values of wet gases. They are highly mature thermogenic gases mainly derived from the Permian type II kerogens mixed with a small proportion of the Triassic coal-type gases. Gases from the second member of the Upper Triassic Xujiahe Formation (T{sub 3}x{sup 2}) are reservoired in continental sandstones and characterized by low gas dryness, free of H{sub 2}S, slightly light C isotopic values of CH{sub 4}, and heavy and less variable C isotopic values of wet gases. They are coal-type gases derived from coal in the Triassic Xujiahe Formation. The H{sub 2}S from the Leikoupo Formation is most likely formed by thermochemical SO{sub 4} reduction (TSR) even though other possibilities cannot be fully ruled out. The proposed TSR origin of H{sub 2}S is supported by geochemical compositions and geological interpretations. The reservoir in the Leikoupo Formation is dolomite dominated carbonate that contains gypsum and anhydrite. Petroleum compounds dissolved in water react with aqueous SO

  11. Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism

    Institute of Scientific and Technical Information of China (English)

    YANG LiuQi; TAN SiJie; YU HaiJing; ZHENG BingRong; QIAO EnFa; DONG YongLi; ZAN RuiGuang; XIAO ChunJie

    2008-01-01

    To evaluate the gene admixture on the current genetic landscape in Gansu Corridor (GC) in China, the upper part of the ancient Silk Road which connects the Eastern and Central Asia, we examined mitochondrial DNA (mtDNA) polymorphisms of five ethnic populations in this study. Using PCR-RFLP and sequencing, we analyzed mtDNA haplotypes in 242 unrelated samples in three ethnic populations from the GC region and two ethnic populations from the adjacent Xinjiang Uygur Autonomous Region of China. We analyzed the data in comparison with the previously reported data from Eastern, Central and Western Asia and Europe. We found that both European-specific haplogroups and Eastern Asian-specific haplogroups exist in the Gansu Corridor populations, while a modest matrilineal gene flow from Europeans to this region was revealed. The Gansu Corridor populations are genetically located between Eastern Asians and Central Asians, both of who contributed significantly to the maternal lineages of the GC populations. This study made the landscape of the gene flow and admixture along the Silk Road from Europe, through Central Asia, to the upper part of the Silk Road more complete.

  12. Quaternary origin and genetic divergence of the endemic cactus Mammillaria pectinifera in a changing landscape in the Tehuacán Valley, Mexico.

    Science.gov (United States)

    Cornejo-Romero, A; Medina-Sánchez, J; Hernández-Hernández, T; Rendón-Aguilar, B; Valverde, P L; Zavala-Hurtado, A; Rivas-Arancibia, S P; Pérez-Hernández, M A; López-Ortega, G; Jiménez-Sierra, C; Vargas-Mendoza, C F

    2014-01-08

    The endemic Mexican cactus, Mammillaria pectinifera, shows low dispersal capabilities and isolated populations within the highly dissected landscape of Tehuacán Valley. These characteristics can restrict gene flow and act upon the genetic divergence and speciation in arid plants. We conducted a phylogeographic study to determine if the origin, current distribution, and genetic structure of M. pectinifera were driven by Quaternary geomorphic processes. Sequences of the plastids psbA-trnH and trnT-trnL obtained from 66 individuals from seven populations were used to estimate genetic diversity. Population differentiation was assessed by an analysis of molecular variance. We applied a stepwise phylogenetic calibration test to determine whether species origin and genetic divergence among haplotypes were temporally concordant with recognizable episodes of geomorphic evolution. The combination of plastid markers yielded six haplotypes, with high levels of haplotype diversity (h = 0.622) and low nucleotide diversity (π = 0.00085). The populations were found to be genetically structured (F(ST) = 0.682; P < 0.00001), indicating that geographic isolation and limited dispersal were the primary causes of genetic population differentiation. The estimated origin and divergence time among haplotypes were 0.017-2.39 and 0.019-1.237 mya, respectively, which correlates with Pleistocene tectonics and erosion events, supporting a hypothesis of geomorphically-driven geographical isolation. Based on a Bayesian skyline plot, these populations showed long term demographic stability, indicating that persistence in confined habitats has been the main response of this species to landscape changes. We conclude that the origin and haplotype divergence of M. pectinifera were a response to local Quaternary geomorphic evolution.

  13. Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.

    Science.gov (United States)

    Simčič, Mojca; Smetko, Anamarija; Sölkner, Johann; Seichter, Doris; Gorjanc, Gregor; Kompan, Dragomir; Medugorac, Ivica

    2015-01-01

    The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had

  14. Performance Using Bamboo Fiber Ash Concrete as Admixture Adding Superplasticizer

    Science.gov (United States)

    Vasudevan, Gunalaan

    2017-06-01

    The increasing demand on natural resources for housing provisions in developing countries have called for sourcing and use of sustainable local materials for building and housing delivery. Natural materials to be considered sustainable for building construction should be ‘green’ and obtained from local sources, including rapidly renewable plant materials like palm fronds and bamboo, recycled materials and other products that are reusable and renewable. Each year, tens of millions of tons of bamboo are utilized commercially, generating a vast amount of waste. Besides that, bamboo fiber is easy availability, low density, low production cost and satisfactory mechanical properties. One solution is to activate this waste by using it as an additive admixture in concrete to keep it out of landfills and save money on waste disposal. The research investigates the mechanical and physical properties of bamboo fiber powder in a blended Portland cement. The structural value of the bamboo fiber powder in a blended Portland cement was evaluated with consideration for its suitability in concrete. Varied percentage of bamboo fiber powder (BFP) at 0%, 5%, 10%, 15%, and 20% as an admixture in 1:2:4 concrete mixes. The workability of the mix was determined through slump; standard consistency test was carried on the cement. Compressive strength of hardened cured (150 x 150 x 150) mm concrete cubes at 7days, 14days and 28days were tested.

  15. Incorporation of Mineral Admixtures in Sustainable High Performance Concrete

    Directory of Open Access Journals (Sweden)

    Nima Farzadnia

    2011-07-01

    Full Text Available Concrete is a widely used construction material around the world, and its properties have been undergoing changes through technological advancement. Numerous types of concrete have been developed to enhance the different properties of concrete. So far, this development can be divided into four stages. The earliest is the traditional normal strength concrete which is composed of only four constituent materials, which are cement, water, fine and coarse aggregates. With a fast population growth and a higher demand for housing and infrastructure, accompanied by recent developments in civil engineering, such as high-rise buildings and long-span bridges, higher compressive strength concrete was needed. At the beginning, reducing the water-cement ratio was the easiest way to achieve the high compressive strength. Thereafter, the fifth ingredient, a water reducing agent or super plasticizer, was indispensable. However, sometimes the compressive strength was not as important as some other properties, such as low permeability, durability and workability. Thus, high performance concrete was proposed and widely studied at the end of the last century. Currently, high-performance concrete is used in massive volumes due to its technical and economic advantages. Such materials are characterized by improved mechanical and durability properties resulting from the use of chemical and mineral admixtures as well as specialized production processes. This paper reviews the incorporation of mineral admixtures in binary, ternary and quaternary blended mortars in concrete.

  16. Prevalence and diversity of enterotoxin genes with genetic background of Staphylococcus aureus isolates from different origins in China.

    Science.gov (United States)

    Chao, Guoxiang; Bao, Guangyu; Cao, Yongzhong; Yan, Wenguang; Wang, Yan; Zhang, Xiaorong; Zhou, Liping; Wu, Yantao

    2015-10-15

    Staphylococcal enterotoxins (SE) induce toxin-mediated diseases, such as food poisoning. In the present study, 568 isolates from different sources were tested for the prevalence of 18 SE genes and performed spa typing. In addition, we characterized the relationships between the distribution of SE genes and molecular clones based on multilocus sequence typing (MLST), spa and staphylococcal cassette chromosome mec (SCCmec) typing in selected 250 isolates. Approximately 54.40% of the isolates from different sources harbored one or more SE genes forming 120 distinct gene profiles. Seven genes, sea, seb, seg, seo, sem, seq, and sel were more frequently detected. The distributions of the SE genes among the isolates from human, animals, and foodborne origins were highly different with isolates from environments (P0.05). We identified two important gene clusters, sea-sek-seq, which is closely related to hospital-acquired (HA) methicillin-resistant Staphylococcus aureus (MRSA)-III, and the egc cluster, which accounts for nearly half of all genes. Approximately 71% isolates could be typed by spa, yielding 103 spa types, of which 18 spa types were primary types. In clonal complex (CC) 239, an important Asian HA-MRSA-III clone from humans, nearly all isolates harbored complete or partial sea-sek-seq cluster; the main spa types were t030 and t037. In CC630, an important new community-associated (CA) MRSA-V CC in China, only sporadic SE genes, three main spa types, t4549, t2196, and t377 were observed. The egc cluster coexisting with other genes was present in isolates of CC5, CC9, CC1281, CC1301, CC30 and sequence type (ST) 25, but completely absent in isolates of CC239, CC59, CC7, and CC88. The results illustrate the genetic clonal diversity and the identity of S. aureus isolates from different sources with respect to SE genes and highlight a correlation between SE genes or gene clusters and CCs, spa, and MRSA clones. The foodborne and human origin isolates were the main

  17. Relationship of prevalence of non-insulin-dependent diabetes mellitus to Amerindian admixture in the Mexican Americans of San Antonio, Texas.

    Science.gov (United States)

    Chakraborty, R; Ferrell, R E; Stern, M P; Haffner, S M; Hazuda, H P; Rosenthal, M

    1986-01-01

    A genetic and epidemiological survey of non-insulin-dependent diabetes mellitus (NIDDM) was conducted among the Mexican Americans residing in three socioeconomically distinct areas of San Antonio, Texas: a low socioeconomic (SES) traditional area (barrio), a middle SES, ethnically balanced area (transitional), and a high SES, predominantly Anglo area (suburb). Seventeen polymorphic markers were used to relate the prevalences of NIDDM with the extent of Amerindian ancestry of 1,237 Mexican Americans of these three residential areas. While only the RH and haptoglobin loci showed evidence of association with NIDDM, an admixture analysis of the combined allele frequency data revealed a pattern of decreasing NIDDM prevalence with increasing socioeconomic status (as approximated by neighborhood of residence) and a parallel decrease in Amerindian ancestry. The rank-order correlation between NIDDM prevalence and Amerindian admixture is 0.943 (P less than .001) for the crude prevalence rate and 0.829 (P less than .02) for the age-adjusted rate. Nested gene diversity analysis revealed that the heterogeneity of allele frequencies is more pronounced when individuals were classified by their NIDDM disease status as compared to the classification by neighborhood. Estimation of Amerindian ancestry of each individual did not reveal any significant change in the shape of the distributions of individual admixture proportions in diabetics as compared to the controls. Nevertheless, the results suggest that genetic factors partially explain the differences in NIDDM prevalence observed between the Mexican American and Anglo populations in the southwestern United States.

  18. Harmful admixtures assessment in sinter mixtures used in iron ore sinter plants in Poland

    Directory of Open Access Journals (Sweden)

    J. Korol

    2014-10-01

    Full Text Available In this study composition of sinter mixtures used in Polish sinter plants were established. Seven sinter mixtures composition were examined, based on iron-bearing materials, admixtures and fuels. Contents of harmful admixtures were examined according to three kinds of environmental impacts: emissions of SOx, heavy metals, polychlorinated dibenzodioxins and polychlorinated dibenzofurans (PCDDs/PCDFs.

  19. Effects of Different Mineral Admixtures on the Properties of Fresh Concrete

    Science.gov (United States)

    Nuruddin, Muhammad Fadhil; Shafiq, Nasir

    2014-01-01

    This paper presents a review of the properties of fresh concrete including workability, heat of hydration, setting time, bleeding, and reactivity by using mineral admixtures fly ash (FA), silica fume (SF), ground granulated blast furnace slag (GGBS), metakaolin (MK), and rice husk ash (RHA). Comparison of normal and high-strength concrete in which cement has been partially supplemented by mineral admixture has been considered. It has been concluded that mineral admixtures may be categorized into two groups: chemically active mineral admixtures and microfiller mineral admixtures. Chemically active mineral admixtures decrease workability and setting time of concrete but increase the heat of hydration and reactivity. On the other hand, microfiller mineral admixtures increase workability and setting time of concrete but decrease the heat of hydration and reactivity. In general, small particle size and higher specific surface area of mineral admixture are favourable to produce highly dense and impermeable concrete; however, they cause low workability and demand more water which may be offset by adding effective superplasticizer. PMID:24701196

  20. Dating the age of admixture via wavelet transform analysis of genome-wide data

    NARCIS (Netherlands)

    I. Pugach (Irina); R. Matveyev (Rostislav); A. Wollstein (Andreas); M.H. Kayser (Manfred); M. Stoneking (Mark)

    2011-01-01

    textabstractWe describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixe

  1. Population genetics structure of glyphosate-resistant Johnsongrass (Sorghum halepense L. Pers) does not support a single origin of the resistance.

    Science.gov (United States)

    Fernández, Luis; de Haro, Luis Alejandro; Distefano, Ana J; Carolina Martínez, Maria; Lía, Verónica; Papa, Juan C; Olea, Ignacio; Tosto, Daniela; Esteban Hopp, Horacio

    2013-09-01

    Single sequence repeats (SSR) developed for Sorghum bicolor were used to characterize the genetic distance of 46 different Sorghum halepense (Johnsongrass) accessions from Argentina some of which have evolved toward glyphosate resistance. Since Johnsongrass is an allotetraploid and only one subgenome is homologous to cultivated sorghum, some SSR loci amplified up to two alleles while others (presumably more conserved loci) amplified up to four alleles. Twelve SSR providing information of 24 loci representative of Johnsongrass genome were selected for genetic distance characterization. All of them were highly polymorphic, which was evidenced by the number of different alleles found in the samples studied, in some of them up to 20. UPGMA and Mantel analysis showed that Johnsongrass glyphosate-resistant accessions that belong to different geographic regions do not share similar genetic backgrounds. In contrast, they show closer similarity to their neighboring susceptible counterparts. Discriminant Analysis of Principal Components using the clusters identified by K-means support the lack of a clear pattern of association among samples and resistance status or province of origin. Consequently, these results do not support a single genetic origin of glyphosate resistance. Nucleotide sequencing of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) encoding gene from glyphosate-resistant and susceptible accessions collected from different geographic origins showed that none presented expected mutations in aminoacid positions 101 and 106 which are diagnostic of target-site resistance mechanism.

  2. Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo.

    Science.gov (United States)

    Brucato, Nicolas; Kusuma, Pradiptajati; Cox, Murray P; Pierron, Denis; Purnomo, Gludhug A; Adelaar, Alexander; Kivisild, Toomas; Letellier, Thierry; Sudoyo, Herawati; Ricaut, François-Xavier

    2016-09-01

    Malagasy genetic diversity results from an exceptional protoglobalization process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy highlighted Borneo broadly as a potential source, but so far no firm source populations were identified. Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data from populations across the Indian Ocean region. We find strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing presence of a Malay Empire trading post in Southeast Borneo, which favored admixture between the Malay and an autochthonous Borneo group, the Ma'anyan. Reconciling genetic, historical, and linguistic data, we show that the Banjar, in Malay-led voyages, were the most probable Asian source among the analyzed groups in the founding of the Malagasy gene pool.

  3. Techniques and methods of characterization of admixtures for the concrete

    Directory of Open Access Journals (Sweden)

    Palacios, M.

    2003-03-01

    Full Text Available Admixtures are defined as those products that are incorporated in the moment of the process of mixture of the concrete in a quantity not bigger than 5 by mass of the cement %, with relationship to the cement content in the concrete, with object of modifying the properties of the mixture in .state fresh and/or hardened. The behaviour of the admixtures depends on its chemical and ionic composition, the organic functional groups present, and the structure of the polymer and the distribution of molecular weight of the different polymers. In the present work the techniques and methods of characterization physical-chemistry, chemistry and ionic, structural, as well as of the polymers that constitute this admixtures, are described. A lot of techniques have been employed like: ionic chromatography, ultraviolet-visible spectroscopy (UV-VIS, Fourier transform infrared spectroscopy (FTIR, Fourier transform Raman spectroscopy (FT-Raman, nuclear magnetic resonance spectroscopy (1H-RMN and 13C-RMN, gel permeation chromatography (GPC. Two commercial admixtures have been selected to carry out this characterization, a superplastificant based on policarboxilates, and a reducer of the shrinkage based on polipropilenglycol.

    RESUMEN Se definen los aditivos como aquellos productos que son incorporados en el momento del amasado del hormigón en una cantidad no mayor del 5% en masa, con relación al contenido de cemento en el hormigón, con objeto de modificar las propiedades de la mezcla en estado fresco y/o endurecido. El comportamiento de los aditivos depende de su composición química e iónica, de los grupos funcionales orgánicos presentes, de la estructura del polímero y de la distribución de pesos moleculares de los diferentes polímeros que lo constituyen. En el presente trabajo se describen diferentes técnicas y métodos de caracterización físico-química, química e iónica, estructural, así como de los polímeros que

  4. Strength characteristics of light weight concrete blocks using mineral admixtures

    Science.gov (United States)

    Bhuvaneshwari, P.; Priyadharshini, U.; Gurucharan, S.; Mithunram, B.

    2017-07-01

    This paper presents an experimental study to investigate the characteristics of light weight concrete blocks. Cement was partially replaced with mineral admixtures like Fly ash (FA), limestone powder waste (LPW), Rice husk ash (RHA), sugarcane fiber waste (SCW) and Chrysopogonzizanioides (CZ). The maximum replacement level achieved was 25% by weight of cement and sand. Total of 56 cubes (150 mm x 150 mm x150 mm) and 18 cylinders (100mmφ and 50mm depth) were cast. The specimens being (FA, RHA, SCW, LPW, CZ, (FA-RHA), (FA-LPW), (FA-CZ), (LPW-CZ), (FA-SCW), (RHA-SCW)).Among the different combination, FA,FA-SCW,CZ,FA-CZ showed enhanced strength and durability, apart from achieving less density.

  5. Used cooking oil as a green chemical admixture in concrete

    Science.gov (United States)

    Salmia, B.; Che Muda, Zakaria; Ashraful Alam, Md; Sidek, L. M.; Hidayah, B.

    2013-06-01

    According to National Statistics Approximately 1.35 billion gallons of used oil are generated yearly. With the increasing of the concrete usage, a more cost effective and economic new type of admixtures may give positive impacts on the Malaysian construction building as well as worldwide concrete usage. To objective of this is study is to investigate the effect of used cooking oil in terms of slump test, compressive strength test and rebound hammer. By adding the used cooking oil to the concrete, it increases the slump value from 4% to 72%. And the compressive strength have an increment from 1% to 16.8%. The used cooking oil obtains the optimum contribution to the concrete mix proportion of containing used cooking oil of 1.50% from the cement content. The result of used cooking oil from experimental program of slump value and compressive strength proved that used cooking oil have positive effects on replacement of commercially available superplasticizer.

  6. Genetic Structure of the Spanish Population

    Directory of Open Access Journals (Sweden)

    Gutiérrez Marta

    2010-05-01

    Full Text Available Abstract Background Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias. Results In this study we have sampled over 800 unrelated individuals from the population of Spain, and have genotyped them with a genome-wide coverage. We have carried out linkage disequilibrium, haplotype, population structure and copy-number variation (CNV analyses, and have compared these estimates of the Spanish population with existing data from similar efforts. Conclusions In general, the Spanish population is similar to the Western and Northern Europeans, but has a more diverse haplotypic structure. Moreover, the Spanish population is also largely homogeneous within itself, although patterns of micro-structure may be able to predict locations of origin from distant regions. Finally, we also present the first characterization of a CNV map of the Spanish population. These results and original data are made available to the scientific community.

  7. High level of genetic compatibility between swine-origin H1N1 and highly pathogenic avian H5N1 influenza viruses.

    Science.gov (United States)

    Octaviani, Cássio Pontes; Ozawa, Makoto; Yamada, Shinya; Goto, Hideo; Kawaoka, Yoshihiro

    2010-10-01

    Reassortment is an important mechanism for the evolution of influenza viruses. Here, we coinfected cultured cells with the pandemic swine-origin influenza virus (S-OIV) and a contemporary H5N1 virus and found that these two viruses have high genetic compatibility. Studies of human lung cell lines indicated that some reassortants had better growth kinetics than their parental viruses. We conclude that reassortment between these two viruses can occur and could create pandemic H5N1 viruses.

  8. 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.

  9. Finding new solutions in pediatric parenteral admixtures: how to improve quality and to deal with shortages

    Directory of Open Access Journals (Sweden)

    Dorota Watrobska-Swietlikowska

    2014-07-01

    Full Text Available Introduction: Pediatric parenteral nutrition enables normal growth even of preterm infants. Those children require, however, tailored parenteral nutrition and the creation of such can be challenging due to the risk of instability and shortages. Objective: Prototypical parenteral admixtures were created using different calcium salts (organic and inorganic and different lipid emulsions and tested for stability. 36 of parenteral admixtures containing two types of calcium salts: chloride or gluconolactobionate and different lipid emulsions (SMOFlipid® or Lipofundin MCT/LCT® were under investigation. Methods: Preliminary admixtures were prepared in two-chamber bags whereas lipid emulsions were placed separately in the second chamber. Pre-admixtures were stored for up to 21 days at +4ºC. Contents of the two chambers were combined at t = 0 or after 21 days of storage. Physical analysis of completed admixtures (visual inspection, microscopic observation, pH measurement and determination of the size distribution of oily droplets was carried out after 21 days of the storage. Stability of lipid, commercial emulsions stored in ethylene vinyl acetate (EVA bags for 42 days was also studied. Results: Irrespectively of the time of storage of preadmixtures and type of calcium salt and different lipid emulsions among 36 total parenteral admixtures only one showed signs of destabilization after preparation and one was unstable when stored for longer than 14 days. All other formulations were qualified to be stable during the study. All investigated commercial lipid emulsions were physically stable in EVA bags even when stored at room temperature. Conclusion: The study proved that it was possible to store pre-admixture in EVA bags for 21 days at 4ºC as well as that CAN (critical aggregation number and CaxP (the products of multiplication of calcium and phosphate ions concentration should not be used as reliable indicators of admixture physical stability. No

  10. Analyzing the genetic structure of the Tepehua in relation to other neighbouring Mesoamerican populations. A study based on allele frequencies of STR markers.

    Science.gov (United States)

    González-Martín, Antonio; Gorostiza, Amaya; Rangel-Villalobos, Héctor; Acunha, Víctor; Barrot, Carme; Sánchez, Cristina; Ortega, Monserrat; Gené, Manel; Calderón, Rosario

    2008-01-01

    We report data on the genetic variation of the Tepehua population based on 15 autosomal microsatellites. The Tepehua, whose language belongs to the Totonac family, are settled throughout the Sierra Madre Oriental in Mexico and constitute a group in demographic decline. The results suggest that the Tepehua population remained isolated throughout a large part of its history. Phylogenetic analyses performed with other indigenous and admixed populations of Mesoamerica allow us to address their biological history. The results suggest a genetic affinity between the Tepehua and the Huastecos due to their previous shared history, and a certain degree of differentiation from the Otomões groups and the Choles (who are of Mayan origin). A clear genetic differentiation is also apparent between native and admixed populations within the greater region of Mesoamerica. It is currently accepted that the genetic composition of the American populations fits a trihybrid model of admixture. The genetic structure based on comparison of 34 populations throughout the continent (9 indigenous and 23 admixed) using hierarchical cluster analysis with an explained variance of 61.17% suggests the existence of four large groups distinguished according to the degree of admixture between Amerindians, Europeans, and Africans. (c) 2008 Wiley-Liss, Inc.

  11. Variation Revealed by SNP Genotyping and Morphology Provides Insight into the Origin of the Tomato

    Science.gov (United States)

    Cordero, Laura; Pascual, Laura; Diez, María José; Nuez, Fernando

    2012-01-01

    Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato. The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 S. pimpinellifolium, 106 S. l. cerasiforme, 95 S. l. lycopersicum and 8 derived from hybridization processes) were morphologically and genetically using the SolCap platform (7,414 SNPs). The two species were distinguished in a PCA analysis and displayed a rich geographic structure. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured S. l. cerasiforme might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took plants from

  12. Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato.

    Science.gov (United States)

    Blanca, Jose; Cañizares, Joaquín; Cordero, Laura; Pascual, Laura; Diez, María José; Nuez, Fernando

    2012-01-01

    Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato.The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 S. pimpinellifolium, 106 S. l. cerasiforme, 95 S. l. lycopersicum and 8 derived from hybridization processes) were morphologically and genetically using the SolCap platform (7,414 SNPs). The two species were distinguished in a PCA analysis and displayed a rich geographic structure. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured S. l. cerasiforme might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took plants from

  13. Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato.

    Directory of Open Access Journals (Sweden)

    Jose Blanca

    Full Text Available Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato.The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 S. pimpinellifolium, 106 S. l. cerasiforme, 95 S. l. lycopersicum and 8 derived from hybridization processes were morphologically and genetically using the SolCap platform (7,414 SNPs. The two species were distinguished in a PCA analysis and displayed a rich geographic structure. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured S. l. cerasiforme might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took

  14. Hydration Characteristics of Metakaolin Admixtured Cement using DTA, XRD and SEM Techniques

    Science.gov (United States)

    Govindarajan, D.; Gopalakrishnan, R.

    2008-04-01

    The paper aims to investigate hydration and pozzolanic reaction in Portland cement paste with different replacement percentages (0%, 10%, 20% and 30%) of metakaolin. The compressive strength of the metakaolin admixtured cement was measured at 1 day, 1 week and 4 weeks. The compressive strength developments of the metakaolin admixtured cement are compared with Portland cement. It is found that metakaolin contributes significantly to strength development as an accelerating admixture for Portland cement. The pozzolanic reactions and the reaction products were determined by DTA, XRD and SEM.

  15. 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...

  16. Effect of polycarboxylate admixture structure on cement paste rheology

    Directory of Open Access Journals (Sweden)

    Aranda, M. A. G.

    2007-06-01

    Full Text Available The purpose of the present study was to analyze the effect of the structural differences in four polycarboxylate and polyether admixtures on the rheological properties of cement pastes with different chemical and mineralogical compositions and different active additions (CEM I 42.5 R, CEM I 52.5 R, CEM I 52.5 N/SR, CEM II/AV 42.5R, CEM II/B-L 32.5 R, CEM III/B 32.5R, BL I 52.5R and CAC – European standard EN 197-1:2000. The results of the minislump test concurred with the variations observed in the values of the rheological parameters (shear stress and plastic viscosity. The structural characteristic of the admixtures found to play the most prominent role in their fluidizing effect was the proportion of carboxylate (CG and polyether (EG group components. In cements characteristics such as fineness and the C3A/calcium sulphate and C3S/C3A ratios were also observed to be essential to admixture effectiveness. In this regard, the rheological parameters varied most widely in CEM I 52.5N/SR pastes and least in BL I 52.5R cement pastes. Of the additioned cements, the CEM III/B 32.5R pastes, which contained granulated blast furnace slag, showed the highest rises in flowability. Finally, the fluidizing effect of polycarboxylate superplasticizers was much more intense in calcium aluminate cements, although flowability declined rapidly in this material.El objetivo de este trabajo ha sido estudiar el efecto de las diferencias estructurales de cuatro aditivos basados en policarboxilatos y poliéteres sobre las propiedades reológicas de pastas de cemento con diferente composición química, mineralógica y con distintas adiciones activas (CEM I 42,5 R, CEM I 52,5 R, CEM I 52,5 N/SR, CEM II/AV 42,5R, CEM II/ B-L 32,5 R, CEM III/B 32,5R, BL I 52,5R y CAC - Norma EN 197-1:2000. Los resultados obtenidos sobre la fluidez de la pasta en el ensayo del “Minislump” coinciden con la evolución de los valores de los parámetros reológicos (esfuerzo de

  17. Search for an admixture of sterile neutrino in the electron spectrum from tritium $\\beta$-decay

    CERN Document Server

    Abdurashitov, D; Likhovid, N; Lokhov, A; Tkachev, I; Yants, V

    2014-01-01

    We propose an experiment intended for search for an admixture of sterile neutrino with mass m$_s$ in the range of 1-8 keV that may be detected as specific distortion of the electron energy spectrum during tritium decay. The distortion is spread over large part of the spectrum so to reveal it one can use a detector with relatively poor (near 10-15%) energy resolution. A classic proportional counter is a simple natural choice for a tritium $\\beta$-decay detector. The method we are proposing is original in two respects. First, the counter is produced as a whole from fully-fused quartz tube allowing to measure current pulse directly from anode while providing high stability for a long time. Second, a modern digital acquisition technique can be used in measurements at ultrahigh count rate - up to 10$^6$ Hz. As a result an energy spectrum of tritium electrons containing up to 10$^{12}$ counts may be collected in a month of live time measurements. Due to high statistics an upper limit down to 10$^{-3}$..10$^{-5}$ ca...

  18. Validation of the polysemen admixture on viability and acrosomal morphology of boar spermatozoa

    Directory of Open Access Journals (Sweden)

    Ogbuewu IP

    2007-07-01

    Full Text Available Semen were collected using artificial vagina (AV, from 5 large white boars aged 2-2.5 years twice a week for 16 weeks in each of the two seasons, early rainy (ER and late rainy (LR seasons, to determine the effects of multiple semen pool admixture on the viability and acrosomal morphology. The semen qualities studied were sperm motility, live sperm and sperm concentration, while the acrosomal parameters includes normal apical ridge (NAR, damaged apical ridge (DAR, missing apical ridge (MAR and loose apical ridge (LAC. There were no significant (P>0.05 seasonal effects. Three-boar semen admixture gave the highest percentage NAR, motility, live sperm concentration and least DAR and LAC, although these were not significantly (P>0.05 different from the 2-boar semen admixture. The result of this study suggests that 3-boar semen admixture is most suitable for use in artificial insemination program.

  19. A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population.

    Science.gov (United States)

    Downie, Jonathan M; Tashi, Tsewang; Lorenzo, Felipe Ramos; Feusier, Julie Ellen; Mir, Hyder; Prchal, Josef T; Jorde, Lynn B; Koul, Parvaiz A

    2016-01-01

    The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley in northern India. A longstanding hypothesis is that this population derives ancestry from Jewish and/or Greek sources. There is historical and archaeological evidence of ancient Greek presence in India and Kashmir. Further, some historical accounts suggest ancient Hebrew ancestry as well. To date, it has not been determined whether signatures of Greek or Jewish admixture can be detected in the Kashmiri population. Using genome-wide genotyping and admixture detection methods, we determined there are no significant or substantial signs of Greek or Jewish admixture in modern-day Kashmiris. The ancestry of Kashmiri Tibetans was also determined, which showed signs of admixture with populations from northern India and west Eurasia. These results contribute to our understanding of the existing population structure in northern India and its surrounding geographical areas.

  20. Parenteral Admixture Compatibility in Neurosurgery Ward in Prof. Dr. Margono Soekarjo Regional Public Hospital

    Directory of Open Access Journals (Sweden)

    Laksmi Maharani

    2014-03-01

    Full Text Available Parenteral admixtures (intravenous admixtures have been done commonly in hospitals. However, it has a possibility of failures, like incompatibilities and changes in drug stabilities. The aim of this study was to determine the rate of drug incompatibilities in mixing parenteral preparations in neurosurgery ward in Prof. Dr. Margono Soekarjo Regional Public Hospital which undergo physical incompatibility observed in organoleptic. This study was a prospective descriptive research for one month period. Data were collected and analyzed descriptively. The results showed that from 667 parenteral admixtures in neurosurgery ward in Prof Dr Margono Soekarjo Hospital in February 2010, there were 0.45% potential incompatibility and 2.55% actual incompatibility happened. Actual incompatibility shown as crystal 0.17%, sediment 0.17%, and 2.04% was non-permanent haze in phenytoin and sodium chloride or ringer lactate admixtures.

  1. A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population

    Science.gov (United States)

    Tashi, Tsewang; Lorenzo, Felipe Ramos; Feusier, Julie Ellen; Mir, Hyder

    2016-01-01

    The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley in northern India. A longstanding hypothesis is that this population derives ancestry from Jewish and/or Greek sources. There is historical and archaeological evidence of ancient Greek presence in India and Kashmir. Further, some historical accounts suggest ancient Hebrew ancestry as well. To date, it has not been determined whether signatures of Greek or Jewish admixture can be detected in the Kashmiri population. Using genome-wide genotyping and admixture detection methods, we determined there are no significant or substantial signs of Greek or Jewish admixture in modern-day Kashmiris. The ancestry of Kashmiri Tibetans was also determined, which showed signs of admixture with populations from northern India and west Eurasia. These results contribute to our understanding of the existing population structure in northern India and its surrounding geographical areas. PMID:27490348

  2. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells.

    Science.gov (United States)

    Francis, Brian R

    2015-02-11

    Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and

  3. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

    Directory of Open Access Journals (Sweden)

    Brian R. Francis

    2015-02-01

    Full Text Available Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid. Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of

  4. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

    Science.gov (United States)

    Francis, Brian R.

    2015-01-01

    Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and

  5. A cybernetic approach to the origin of the genetic coding mechanism. II. Formation of the code series.

    Science.gov (United States)

    Batchinsky, A G; Ratner, V A

    1976-08-01

    The sequential fulfillment of the principle of succession necessarily guides the main steps of the genetic code evolution to be reflected in its structure. The general scheme of the code series formation is proposed basing on the idea of "group coding" (Woese, 1970). The genetic code supposedly evolved by means of successive divergence of pra-ARS's loci, accompanied by increasing specification of recognition capacity of amino acids and triplets. The sense of codons had not been changed on any step of stochastic code evolution. The formulated rules for code series formation produce a code version, similar to the contemporary one. Based on these rules the scheme of pra-ARS's divergence is proposed resulting in the grouping of amino acids by their polarity and size. Later steps in the evolution of the genetic code were probably based on more detailed features of the amino acids (for example, on their functional similarities like their interchangeabilities in isofunctional proteins).

  6. Profile of Intravenous Admixture Compatibility in the Intensive Care Unit (ICU Patients

    Directory of Open Access Journals (Sweden)

    Sharly Dwijayanti

    2016-06-01

    Full Text Available which may directly impact to the outcome of treatment to the Intensive Care Unit (ICU patients. The objective of this study was to identify the profile of compatibility and incompatibility among IV admixtures given to the ICU patients. This observational research was conducted prospectively to the patients admitted in the ICU at a private hospital in Surabaya from October–December 2014. In this research, compatibility data of IV drug and its solution was compared with drug brochure and Handbook on Injectable Drugs 17th ed (2013 as references to analyze the compatibility of IV admixtures. The admixture between IV drug and its solvent was classified as compatible, incompatible, no information (NI, not applicable (NA, and not clear (NC, using a specific criteria. There were 1.186 IV drug‑solvent admixtures observed in 39 ICU patients. There were no IV drug-solvent admixtures classified as incompatible in both adult and child patients. Most of IV drugs were admixed with compatible solvents (adults: 72.31%; children: 69.84%. However, according to two of IV drugs compatibility references used in this research, there were some IV drug-solvent admixtures with unknown information about its compatibility that were classified as NI (adults: 19.68%; children: 30.16%. There were a few of IV drug-solvent admixtures classified as NA and NC, of 7.48% and 0.53%, respectively. The lack of information related to compatibility and stability of the IV admixtures emphasize the importance to continually monitor patients’ condition and drug concentration.

  7. Admixture mapping scans identify a locus affecting retinal vascular caliber in hypertensive African Americans: the Atherosclerosis Risk in Communities (ARIC study.

    Directory of Open Access Journals (Sweden)

    Ching-Yu Cheng

    2010-04-01

    Full Text Available Retinal vascular caliber provides information about the structure and health of the microvascular system and is associated with cardiovascular and cerebrovascular diseases. Compared to European Americans, African Americans tend to have wider retinal arteriolar and venular caliber, even after controlling for cardiovascular risk factors. This has suggested the hypothesis that differences in genetic background may contribute to racial/ethnic differences in retinal vascular caliber. Using 1,365 ancestry-informative SNPs, we estimated the percentage of African ancestry (PAA and conducted genome-wide admixture mapping scans in 1,737 African Americans from the Atherosclerosis Risk in Communities (ARIC study. Central retinal artery equivalent (CRAE and central retinal vein equivalent (CRVE representing summary measures of retinal arteriolar and venular caliber, respectively, were measured from retinal photographs. PAA was significantly correlated with CRVE (rho = 0.071, P = 0.003, but not CRAE (rho = 0.032, P = 0.182. Using admixture mapping, we did not detect significant admixture association with either CRAE (genome-wide score = -0.73 or CRVE (genome-wide score = -0.69. An a priori subgroup analysis among hypertensive individuals detected a genome-wide significant association of CRVE with greater African ancestry at chromosome 6p21.1 (genome-wide score = 2.31, locus-specific LOD = 5.47. Each additional copy of an African ancestral allele at the 6p21.1 peak was associated with an average increase in CRVE of 6.14 microm in the hypertensives, but had no significant effects in the non-hypertensives (P for heterogeneity <0.001. Further mapping in the 6p21.1 region may uncover novel genetic variants affecting retinal vascular caliber and further insights into the interaction between genetic effects of the microvascular system and hypertension.

  8. Influences of a New Admixture MX on Concrete Durability

    Institute of Scientific and Technical Information of China (English)

    MA Baoguo; DONG Rongzhen; ZHU Hongbo; ZHANG Li; ZHONG Kaihong; HE Xingyang; LI Zongjin

    2005-01-01

    The performance of concrete with a new admixture MX was studied by using the freeze-thaw cycle, permeability and chemical attack test. The experimental results show that MX improves the durability of concrete. Within the optimum proportion ranges from 0.1%to 1%,the compressive strength of concrete after freeze-thaw is increased by 20%-50%,and Young's modulus can be increased by 3.76-5.64 times.The strength and weight loss of concrete with 0.4%MX are respectively decreased by 28% and 60% after hydrochloric acid attack.The strength and weight loss of concrete with 0.4% MX are decreased by 5%-20% after sulfuric acid and sodium sulfate attack.The permeability of concrete with 1% MX at 28 days can be decreased by more than 30%. The investigation of the negative temperature property of MX and analysis on concrete composition and microstructure by MIP reveal that the heat conduction is resisted and the freezing procedure of solution in concrete pore is retarded due to the adding of MX. Moreover,the pore structure of concrete with MX is improved, thus improving the durability. Based on this study, a resistance model of MX to block the heat and mass transference was proposed, and the mechanism of durability improvement of concrete with MX was explained.

  9. Research on Development and Performance of Active Admixture

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Comparing with that of low-calcium fly ash (LF) or fly dreg (FD), chemical content of high-calcium fly ash (HF) waves more much. Coarse grain, which existing in HF, would determine soundness more seriously than fine one. Grinding it is a simple method to result this problem. Because of with thiner specific surface and higher CaO content, fine grain exhibits higher activity of hydration than coarse one. Activity of active admixture (AF), which is produced by ways of grinding HF together with calcium carbide sludge (CS), desulfurize gypsum (DG), calcine desulfurize gypsum (CG) and NS (Na2SO4+FeSO4), can catch up with that of grinding blast furnace slag (GBFS) powder with about 400 m2/kg specific surface. AF costs lower than GBFS. 20% cement replaced by the equal amount of AF, compression strength of concrete is similar to that control one, and electrifies coulomb of concrete at 90 day's age reduces to about half of control one.

  10. Strong Selection at MHC in Mexicans since Admixture.

    Directory of Open Access Journals (Sweden)

    Quan Zhou

    2016-02-01

    Full Text Available Mexicans are a recent admixture of Amerindians, Europeans, and Africans. We performed local ancestry analysis of Mexican samples from two genome-wide association studies obtained from dbGaP, and discovered that at the MHC region Mexicans have excessive African ancestral alleles compared to the rest of the genome, which is the hallmark of recent selection for admixed samples. The estimated selection coefficients are 0.05 and 0.07 for two datasets, which put our finding among the strongest known selections observed in humans, namely, lactase selection in northern Europeans and sickle-cell trait in Africans. Using inaccurate Amerindian training samples was a major concern for the credibility of previously reported selection signals in Latinos. Taking advantage of the flexibility of our statistical model, we devised a model fitting technique that can learn Amerindian ancestral haplotype from the admixed samples, which allows us to infer local ancestries for Mexicans using only European and African training samples. The strong selection signal at the MHC remains without Amerindian training samples. Finally, we note that medical history studies suggest such a strong selection at MHC is plausible in Mexicans.

  11. Gene frequencies and admixture estimates in four Mexican urban centers.

    Science.gov (United States)

    Lisker, R; Ramirez, E; Briceño, R P; Granados, J; Babinsky, V

    1990-12-01

    We studied 202 individuals from the city of Leon in Guanajuato state, 228 from Merida, Yucatan, 220 from Oaxaca, Oaxaca, and 257 from Saltillo, Coahuila, to learn the distribution of the ABO, MN, Rh, and Duffy blood groups, serum haptoglobin, albumin, and factor Bf types, and red cell hemoglobin and glucose-6-phosphate dehydrogenase types. With the gene frequencies obtained, we performed admixture measurements with a maximum likelihood method, obtaining a trihybrid model for black, Indian, and white ancestry with the following proportions: 0.084, 0.513, and 0.403 in Leon: 0.059, 0.512, and 0.429 in Merida; 0.018, 0.676, and 0.306 in Oaxaca; and 0.073, 0.547, and 0.380 in Saltillo. The general pattern has high Indian ancestry followed by white and black ancestry. This pattern is congruent with most other studies performed in Mexico, including the east coast, where Indian ancestry predominates despite a clear increase in the black contribution.

  12. Performance of alusilica as mineral admixture in cementitious systems

    DEFF Research Database (Denmark)

    Chi, Lin; Jensen, Ole Mejlhede

    The aim of this project is to study the effect of alusilica (ALS) as a mineral admixture on the fresh properties and development of mechanical properties of cementitious systems. ALS consists of relatively pure, amorphous silicium-dioxide – a chemical compound which is known to be useful as mineral...... to the total binder mass (cement+ALS). The water/binder-ratio (w/b) is 0.5 for all mixtures. The produced ALS-substituted powder was studied by scanning electron microscopy (SEM) and Energy Dispersive X-ray Analysis (EDAX) to investigate if the ALS agglomerates in the raw material were broken by the grinding...... procedure. On the fresh mortar air content was measured by the pressure method, ASTM C231/C231M-14 and the flow was measured by ASTM C1437-13. Casting was done in standard mortar molds 4×4×16 cm3. After demolding, each mortar specimen was weighed over and under water to evaluate their homogeneity and air...

  13. The Influence of Admixtures on the Technological Properties of Fresh Concrete Mixture

    Directory of Open Access Journals (Sweden)

    Albertas KLOVAS

    2015-11-01

    Full Text Available In this research superplasticizing (SP, air voids removing (AVR, viscosity modifying (VM and air entraining admixtures (AE were used. The dosage of admixtures was chosen from minimum to maximum values recommended by the manufacturers. To sum up, 7 concrete mixture compositions with SP, 6 with AVR and 6 with VM and the last 6 with AE admixture were prepared. Water and cement ratio for all the compositions was kept at the same value. According to the results obtained, the usage of SP admixture resulted in significant increase of mixture`s slump and flow however it reduced mixture`s air content and increased its density. Concrete mixture`s properties: slump and flow were almost not affected by the increase of AVR and VM admixtures, however the air content slightly decreased and the density of concrete mixture slightly increased. With the incline of air entraining admixture, mixture`s slump, flow and air content increased, but the density declined. The authors of this study wanted to express the importance of the close link between concrete mixture`s technological and rheological properties. According to the yield stress of concrete mixture it is possible to prognosticate the future problems or various outcomes during or after the concrete mixture`s casting process.DOI: http://dx.doi.org/10.5755/j01.ms.21.4.5170

  14. Genetic relatedness between pneumococcal populations originating from the nasopharynx, adenoid, and tympanic cavity of children with otitis media.

    NARCIS (Netherlands)

    Tonnaer, E.L.G.M.; Rijkers, G.T.; Meis, J.F.G.M.; Klaassen, C.H.W.; Bogaert, D.; Hermans, P.W.M.; Curfs, J.H.A.J.

    2005-01-01

    Previous studies have shown that Streptococcus pneumoniae exists in both middle ear effusions and the upper respiratory region from children with otitis media with effusion (OME), but it remains unclear whether these strains represent genetically identical clones. Therefore, it cannot be determined

  15. Genetic diversity of Phytophthora infestans sensu lato in Ecuador provides new insight into the origin of this important plant pathogen

    NARCIS (Netherlands)

    Adler, N.E.; Erselius, L.J.; Chacón, G.M.; Flier, W.G.; Ordonez, M.E.; Kroon, L.P.N.M.; Forbes, G.A.

    2004-01-01

    The metapopulation structure of Phytophthora infestans sensu lato is genetically diverse in the highlands of Ecuador. Previous reports documented the diversity associated with four putative clonal lineages of the pathogen collected from various hosts in the genus Solanum. This paper simultaneously a

  16. Genetic differentiation, origin and dispersal of Gammarus gauthieri from the Iberian peninsula and North Africa (Crustacea, Amphipoda)

    NARCIS (Netherlands)

    Scheepmaker, Maarten

    1990-01-01

    Genetic differentiation among population samples of G. gauthieri on both sides of the Strait of Gibraltar was investigated by enzyme electrophoresis at 20 enzyme loci with reference to G. gauthieri and G. ibericus from different areas in the Iberian peninsula. Levels of divergence resolved suggest t

  17. Comparing genetic ancestry and self-reported race/ethnicity in a multiethnic population in New York City

    Indian Academy of Sciences (India)

    Yin Leng Lee; Susan Teitelbaum; Mary S. Wolff; James G. Wetmur; Jia Chen

    2010-12-01

    Self-reported race/ethnicity is frequently used in epidemiological studies to assess an individual’s background origin. However, in admixed populations such as Hispanic, self-reported race/ethnicity may not accurately represent them genetically because they are admixed with European, African and Native American ancestry. We estimated the proportions of genetic admixture in an ethnically diverse population of 396 mothers and 188 of their children with 35 ancestry informative markers (AIMs) using the STRUCTURE version 2.2 program. The majority of the markers showed significant deviation from Hardy–Weinberg equilibrium in our study population. In mothers self-identified as Black and White, the imputed ancestry proportions were 77.6% African and 75.1% European respectively, while the racial composition among self-identified Hispanics was 29.2% European, 26.0% African, and 44.8% Native American.We also investigated the utility of AIMs by showing the improved fitness of models in paraoxanase-1 genotype–phenotype associations after incorporating AIMs; however, the improvement was moderate at best. In summary, a minimal set of 35 AIMs is sufficient to detect population stratification and estimate the proportion of individual genetic admixture; however, the utility of these markers remains questionable.

  18. Comparing genetic ancestry and self-reported race/ethnicity in a multiethnic population in New York City.

    Science.gov (United States)

    Lee, Yin Leng; Teitelbaum, Susan; Wolff, Mary S; Wetmur, James G; Chen, Jia

    2010-12-01

    Self-reported race/ethnicity is frequently used in epidemiological studies to assess an individual's background origin. However, in admixed populations such as Hispanic, self-reported race/ethnicity may not accurately represent them genetically because they are admixed with European, African and Native American ancestry. We estimated the proportions of genetic admixture in an ethnically diverse population of 396 mothers and 188 of their children with 35 ancestry informative markers (AIMs) using the STRUCTURE version 2.2 program. The majority of the markers showed significant deviation from Hardy-Weinberg equilibrium in our study population. In mothers self-identified as Black and White, the imputed ancestry proportions were 77.6% African and 75.1% European respectively, while the racial composition among self-identified Hispanics was 29.2% European, 26.0% African, and 44.8% Native American. We also investigated the utility of AIMs by showing the improved fitness of models in paraoxanase-1 genotype-phenotype associations after incorporating AIMs; however, the improvement was moderate at best. In summary, a minimal set of 35 AIMs is sufficient to detect population stratification and estimate the proportion of individual genetic admixture; however, the utility of these markers remains questionable.

  19. Screening Out Controversy: Human Genetics, Emerging Techniques of Diagnosis, and the Origins of the Social Issues Committee of the American Society of Human Genetics, 1964-1973.

    Science.gov (United States)

    Mitchell, M X

    2017-05-01

    In the years following World War II, and increasingly during the 1960s and 1970s, professional scientific societies developed internal sub-committees to address the social implications of their scientific expertise (Moore, Disrupting Science: Social Movements, American Scientists, and the Politics of the Military, 1945-1975. Princeton: Princeton University Press, 2008). This article explores the early years of one such committee, the American Society of Human Genetics' "Social Issues Committee," founded in 1967. Although the committee's name might suggest it was founded to increase the ASHG's public and policy engagement, exploration of the committee's early years reveals a more complicated reality. Affronted by legislators' recent unwillingness to seek the expert advice of human geneticists before adopting widespread neonatal screening programs for phenylketonuria (PKU), and feeling pressed to establish their relevance in an increasingly resource-scarce funding environment, committee members sought to increase the discipline's expert authority. Painfully aware of controversy over abortion rights and haunted by the taint of the discipline's eugenic past, however, the committee proceeded with great caution. Seeking to harness interest in and assert professional control over emerging techniques of genetic diagnosis, the committee strove to protect the society's image by relegating ethical and policy questions about their use to the individual consciences of member scientists. It was not until 1973, after the committee's modest success in organizing support for a retrospective public health study of PKU screening and following the legalization of abortion on demand, that the committee decided to take a more publicly engaged stance.

  20. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil

    Directory of Open Access Journals (Sweden)

    Almeida Leonardo D

    2007-12-01

    Full Text Available Abstract Background Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists on the Brazilian Creole breeds very little is known on their genetic composition. The objective of this study was to assess the levels of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture among ten cattle breeds raised in Brazil. Results Significant reduction of heterozygosity exists due both to within-population inbreeding and to breed differentiation in both subspecies (taurine and zebuine. For taurine breeds the number of markers that contribute to breed differentiation is larger than for zebuine. A consistently similar number of alleles was seen in both subspecies for all microsatellites. Four Creole breeds were the most genetically diverse followed by the zebuine breeds, the two specialized taurine breeds and the Creole Caracu. Pairwise genetic differentiation were all significant indicating that all breeds can be considered as genetically independent entities. A STRUCTURE based diagram indicated introgression of indicine genes in the local Creole breeds and suggested that occasional Creole introgression can be detected in some Zebuine animals. Conclusion This study reports on a comprehensive study of the genetic structure and diversity of cattle breeds in Brazil. A significant amount of genetic variation is maintained in the local cattle populations. The genetic data show that Brazilian Creole breeds constitute an important and diverse reservoir of genetic diversity for bovine breeding and conservation. The

  1. The genetic origin of honey bee colonies used in the COLOSS Genotype-Environment Interactions Experiment: a comparison of methods

    DEFF Research Database (Denmark)

    Francis, Roy M; Kryger, Per; Meixner, Marina;

    2014-01-01

    to describe the genetic background and population allocation of the bees used in this experiment. Two wing morphometric and two genetic methods were employed to discriminate bee populations. Classical morphometry of 11 angles on the wings were carried out on 350 bees. Geometric morphometry on 19 wing...... landmarks was carried out on 381 individuals. DNA microsatellite analysis was carried out on 315 individuals using 24 loci. Allozyme analysis was performed on 90 individuals using six enzyme systems. DNA microsatellite markers produced the best discrimination between the subspecies (Apis mellifera carnica......, A. m. ligustica, A. m. macedonica, A. m. mellifera and A. m. siciliana) used in the experiment. Morphometric methods generally showed an intermediate level of discrimination, usually best separating A. m. siciliana and A. m. ligustica from the remaining populations. Allozyme markers lack power...

  2. Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

    Science.gov (United States)

    Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

    2011-01-01

    Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

  3. Genetic origin of Behçet's disease population in Denizli, Turkey; population genetics data analysis; historical demography and geographical perspectives based on β-globin gene cluster haplotype variation.

    Science.gov (United States)

    Ozturk, O; Arikan, S; Bahadir, A; Atalay, A; Atalay, E O

    2017-01-01

    In our study, we aimed to investigate the possible genetic drift, relationships, expansion and historical origin based on haplotype frequencies of the β-globin gene cluster of normal and Behçet's disease (BD) population in Denizli, Turkey. We examined blood DNA samples obtained from our DNA bank. The association of population genetic parameters such as haplotypes, diversity, differentiation, Hardy-Weinberg equilibrium and demographic analysis for two populations was performed by Arlequin ver. 3.5. Our results show that both populations have high similarity in genetic parameters in terms of development and expansion based on haplotype diversity through the history. We found that historical levels of gene flow were significantly higher between the two populations. According to historical population, growth parameter of τ values for normal and BD populations dated approximately 42 000 to 38 000 ybp, respectively. In conclusion, historically, two populations show similar genetic parameters and unimodal growth distribution. Our results are consistent with the view that the BD may have occurred in area, independent from Silk Road.

  4. Genetic structure of the paternal lineage of the Roma people.

    Science.gov (United States)

    Pamjav, Horolma; Zalán, Andrea; Béres, Judit; Nagy, Melinda; Chang, Yuet Meng

    2011-05-01

    According to written sources, Roma (Romanies, Gypsies) arrived in the Balkans around 1,000 years ago from India and have subsequently spread through several parts of Europe. Genetic data, particularly from the Y chromosome, have supported this model, and can potentially refine it. We now provide an analysis of Y-chromosomal markers from five Roma and two non-Roma populations (N = 787) in order to investigate the genetic relatedness of the Roma population groups to one another, and to gain further understanding of their likely Indian origins, the genetic contribution of non-Roma males to the Roma populations, and the early history of their splits and migrations in Europe. The two main sources of the Roma paternal gene pool were identified as South Asian and European. The reduced diversity and expansion of H1a-M82 lineages in all Roma groups imply shared descent from a single paternal ancestor in the Indian subcontinent. The Roma paternal gene pool also contains a specific subset of E1b1b1a-M78 and J2a2-M67 lineages, implying admixture during early settlement in the Balkans and the subsequent influx into the Carpathian Basin. Additional admixture, evident in the low and moderate frequencies of typical European haplogroups I1-M253, I2a-P37.2, I2b-M223, R1b1-P25, and R1a1-M198, has occurred in a more population-specific manner.

  5. Extensive Admixture and Selective Pressure Across the Sahel Belt.

    Science.gov (United States)

    Triska, Petr; Soares, Pedro; Patin, Etienne; Fernandes, Veronica; Cerny, Viktor; Pereira, Luisa

    2015-11-26

    Genome-wide studies of African populations have the potential to reveal powerful insights into the evolution of our species, as these diverse populations have been exposed to intense selective pressures imposed by infectious diseases, diet, and environmental factors. Within Africa, the Sahel Belt extensively overlaps the geographical center of several endemic infections such as malaria, trypanosomiasis, meningitis, and hemorrhagic fevers. We screened 2.5 million single nucleotide polymorphisms in 161 individuals from 13 Sahelian populations, which together with published data cover Western, Central, and Eastern Sahel, and include both nomadic and sedentary groups. We confirmed the role of this Belt as a main corridor for human migrations across the continent. Strong admixture was observed in both Central and Eastern Sahelian populations, with North Africans and Near Eastern/Arabians, respectively, but it was inexistent in Western Sahelian populations. Genome-wide local ancestry inference in admixed Sahelian populations revealed several candidate regions that were significantly enriched for non-autochthonous haplotypes, and many showed to be under positive selection. The DARC gene region in Arabs and Nubians was enriched for African ancestry, whereas the RAB3GAP1/LCT/MCM6 region in Oromo, the TAS2R gene family in Fulani, and the ALMS1/NAT8 in Turkana and Samburu were enriched for non-African ancestry. Signals of positive selection varied in terms of geographic amplitude. Some genomic regions were selected across the Belt, the most striking example being the malaria-related DARC gene. Others were Western-specific (oxytocin, calcium, and heart pathways), Eastern-specific (lipid pathways), or even population-restricted (TAS2R genes in Fulani, which may reflect sexual selection).

  6. Genetic and environmental determinants of type II diabetes in Mexico City and San Antonio.

    Science.gov (United States)

    Stern, M P; Gonzalez, C; Mitchell, B D; Villalpando, E; Haffner, S M; Hazuda, H P

    1992-04-01

    To study genetic and environmental determinants of non-insulin-dependent (type II) diabetes, we compared a random sample of 35- to 64-yr-old Mexican-American men and women living in several low-income barrio neighborhoods of San Antonio to similarly aged Mexicans living in a low-income colonia of Mexico City (Colonia Liberales). A total of 1138 Mexican Americans, representing 64.3% of the original sample, and 646 Mexicans, representing 69.2% of the original sample, participated in the survey. Diabetes was diagnosed using World Health Organization criteria. Genetic susceptibility to type II diabetes was inferred from the percentage of Native American genetic admixture as estimated from skin reflectance measurements. The prevalence of diabetes was 36% higher among San Antonio Mexican Americans than among Mexicans in Mexico City; this difference was highly statistically significant (age- and sex-adjusted prevalence ratio 1.36, P = 0.006). This excess was observed despite the fact that genetic susceptibility, as inferred from the admixture estimates, was similar in the two cities. On the other hand, Mexicans were somewhat leaner as measured by body mass index and skin folds. Mexican women consumed fewer total calories than Mexican-American women, but there was no difference in the caloric intake of men. Mexico City residents ate less fat (18-19% of total calories vs. 31-32% in San Antonio, P less than 0.001), more carbohydrate (64-65 vs. 49%, P less than 0.001), and performed more physical activity than San Antonio Mexican Americans. Mexicans appeared to consume more refined sugar than Mexican Americans.(ABSTRACT TRUNCATED AT 250 WORDS)

  7. The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia.

    Directory of Open Access Journals (Sweden)

    Bayazit Yunusbayev

    2015-04-01

    Full Text Available The Turkic peoples represent a diverse collection of ethnic groups defined by the Turkic languages. These groups have dispersed across a vast area, including Siberia, Northwest China, Central Asia, East Europe, the Caucasus, Anatolia, the Middle East, and Afghanistan. The origin and early dispersal history of the Turkic peoples is disputed, with candidates for their ancient homeland ranging from the Transcaspian steppe to Manchuria in Northeast Asia. Previous genetic studies have not identified a clear-cut unifying genetic signal for the Turkic peoples, which lends support for language replacement rather than demic diffusion as the model for the Turkic language's expansion. We addressed the genetic origin of 373 individuals from 22 Turkic-speaking populations, representing their current geographic range, by analyzing genome-wide high-density genotype data. In agreement with the elite dominance model of language expansion most of the Turkic peoples studied genetically resemble their geographic neighbors. However, western Turkic peoples sampled across West Eurasia shared an excess of long chromosomal tracts that are identical by descent (IBD with populations from present-day South Siberia and Mongolia (SSM, an area where historians center a series of early Turkic and non-Turkic steppe polities. While SSM matching IBD tracts (> 1cM are also observed in non-Turkic populations, Turkic peoples demonstrate a higher percentage of such tracts (p-values ≤ 0.01 compared to their non-Turkic neighbors. Finally, we used the ALDER method and inferred admixture dates (~9th-17th centuries that overlap with the Turkic migrations of the 5th-16th centuries. Thus, our results indicate historical admixture among Turkic peoples, and the recent shared ancestry with modern populations in SSM supports one of the hypothesized homelands for their nomadic Turkic and related Mongolic ancestors.

  8. Stability investigation of total parenteral nutrition admixture prepared in a hospital pharmacy

    Directory of Open Access Journals (Sweden)

    Mirković Dušica

    2008-01-01

    Full Text Available Background/Aim. In the cases when nutrition of patients can not be orally nor enterally performed, parenteral nutrition is a method of the therapy that provides more successful and rapid recovery. In that way, hospitalization can be significantly shorter, healing costs reduced and mortality minimized. Total parenteral nutrition (TPN admixtures are the most complex systems which contain amino acids, carbohydrates, lipid emulsion, macroelectrolytes (Na+, K+, Ca2+, Mg2+, Cl-, SO42-, PO43-, oligoelements, hydro- and liposoluble vitamines, heparin, insulin and water. Concerning the mentioned complexity, special attention should be payed to physicochemical and microbiological stability of a mixture, because of interactions among components, that can be very hard to analyze. The aim of this study was to investigate the problem of stability of TPN admixtures prepared in a hospital pharmacy. Methods. Admixture TPN was aseptically prepared in laminar air - flow environment on the basis of the specified order in supplementing components and additives to basic solutions. Solutions were kept in sterile multicompartment ethylene-vinyl-acetate bags. After preparation and slow homogenization, TPN admixtures were submitted to physicochemical and microbiological stability analyses in various period of time. The assessment of physical stability of TPN admixture was done on the basis of visual inspection, determination of pH value and measuring of particle size. The investigation of sterility and pyrogenic test were performed according to Ph. Yug. V regulations. Results. Physico-chemical and microbiological analyses were applied and no significant changes in visual sense, pH value and droplet size stability of the TPN admixture were observed during the period of 60 hours. The lipid droplets were smaller in size than 5 μm, that is the most common pharmacopoeia requirement. Conclusion. The results of our study confirmed that a TPN admixture prepared in a hospital

  9. Porosity Parameters Of Cement Stone Containing Chemical Admixtures Of Different Purpose

    Directory of Open Access Journals (Sweden)

    Lukas Venčkauskas

    2013-12-01

    Full Text Available The conducted research has established a complex influenceand the impact of separate chemical admixtures of differentpurpose on the parameters of the porosity of hardened cementpaste such as open and closed porosity, the average size of poresand the rates of pore inequality. According to the parametersof the porosity of hardened cement paste, on the basis of A. E.Sheikin’s methodology, the number of freezing-thawing cycleswas predicted. This research used plasticizing, viscosity modifyingand antifoaming admixtures. It has been found that, when theamount of plasticizing admixture in cement paste (W/C–0.45 isconstant and makes 1.1% of the cement mass, and the amountof viscosity modifying and antifoaming the admixture increasesfrom 0.1 to 0.6% and from 0.05 to 0.3% respectively, the openporosity of hardened cement paste varies between 30.21% and31.06%, while closed porosity varies between 5.39% and 6.22%.When the amount of the plasticizing admixture in cement paste(W/C–0.45 exceeds 1.1% of the cement mass, the open porosityof hardened cement paste increases by 1.4 times and closedporosity decreases by 2.5 times. While adding 0.1% of the viscositymodifying admixture to cement paste, the open porosityof hardened cement paste is increased by 1.5 times and closedporosity decreases by 2.4 times. The amount of 0.05% of thecement mass of the antifoaming admixture results in the increasedopen porosity of hardened cement paste by 1.5 times and reducedclosed porosity by 3.5 times.

  10. A review on the genetic, environmental, and lifestyle aspects of the early-life origins of cardiovascular disease.

    Science.gov (United States)

    Kelishadi, Roya; Poursafa, Parinaz

    2014-03-01

    This article is a comprehensive review on developmental origins of health and disease regarding various factors related to the origins of cardiovascular diseases from early life. It presents a summary of the impacts of various factors such as epigenetics; gene-environment interaction; ethnic predisposition to cardiovascular diseases and their underlying risk factors; prenatal factors; fetal programming; maternal weight status and weight gain during pregnancy; type of feeding during infancy; growth pattern during childhood; obesity; stunting; socioeconomic status; dietary and physical activity habits; active, secondhand, and thirdhand smoking, as well as environmental factors including air pollution and global climate change on the development and progress of cardiovascular diseases and their risk factors. The importance of early identification of predisposing factors for cardiovascular diseases for primordial and primary prevention of cardiovascular diseases from early life is highlighted.

  11. Admixture mapping scans identify a locus affecting retinal vascular caliber in hypertensive African Americans: the Atherosclerosis Risk in Communities (ARIC) study.

    Science.gov (United States)

    Cheng, Ching-Yu; Reich, David; Wong, Tien Y; Klein, Ronald; Klein, Barbara E K; Patterson, Nick; Tandon, Arti; Li, Man; Boerwinkle, Eric; Sharrett, A Richey; Kao, W H Linda

    2010-04-15

    Retinal vascular caliber provides information about the structure and health of the microvascular system and is associated with cardiovascular and cerebrovascular diseases. Compared to European Americans, African Americans tend to have wider retinal arteriolar and venular caliber, even after controlling for cardiovascular risk factors. This has suggested the hypothesis that differences in genetic background may contribute to racial/ethnic differences in retinal vascular caliber. Using 1,365 ancestry-informative SNPs, we estimated the percentage of African ancestry (PAA) and conducted genome-wide admixture mapping scans in 1,737 African Americans from the Atherosclerosis Risk in Communities (ARIC) study. Central retinal artery equivalent (CRAE) and central retinal vein equivalent (CRVE) representing summary measures of retinal arteriolar and venular caliber, respectively, were measured from retinal photographs. PAA was significantly correlated with CRVE (rho = 0.071, P = 0.003), but not CRAE (rho = 0.032, P = 0.182). Using admixture mapping, we did not detect significant admixture association with either CRAE (genome-wide score = -0.73) or CRVE (genome-wide score = -0.69). An a priori subgroup analysis among hypertensive individuals detected a genome-wide significant association of CRVE with greater African ancestry at chromosome 6p21.1 (genome-wide score = 2.31, locus-specific LOD = 5.47). Each additional copy of an African ancestral allele at the 6p21.1 peak was associated with an average increase in CRVE of 6.14 microm in the hypertensives, but had no significant effects in the non-hypertensives (P for heterogeneity retinal vascular caliber and further insights into the interaction between genetic effects of the microvascular system and hypertension.

  12. Origins of the classical gene concept, 1900-1950: genetics, mechanistic, philosophy, and the capitalization of agriculture.

    Science.gov (United States)

    Allen, Garland E

    2014-01-01

    In the period of "classical genetics" (roughly 1915-950), the common view of the gene was mechanistic--hat is, genes were seen as individual, atomistic units, as material components of the chromosomes. Although it was recognized early on that genes could interact and influence each other's expression, they were still regarded as individually functioning units, much like the chemists' atoms or molecules. Although geneticists in particular knew the story was more complex, the atomistic gene remained the central view for a variety of reasons. It fit the growing philosophy of mechanistic materialism in the life sciences, as biologists tried to make their field more quantitative,rigorous, and predictive, like physics and chemistry. Conceptually and pedagogically, it provided a simple way to depict genes (as beads on a string) that fit with the exciting new work on chromosomal mapping. The atomistic gene also fit well with the increasing drive to move capital into agriculture, both for potential patenting purposes and for ease of experimental manipulation and prediction. It is the latter point that the present essay explores most thoroughly. The rise of agriculture as an industrialized process provided a context and material support that fueled much of the rapid growth of genetics in the first half of the 20th century.

  13. Solving cryptogenic histories using host and parasite molecular genetics: the resolution of Littorina littorea's North American origin.

    Science.gov (United States)

    Blakeslee, April M H; Byers, James E; Lesser, Michael P

    2008-08-01

    Even after decades of investigation using multiple sources of evidence, the natural histories of some species remain unclear (i.e. cryptogenic). A key example is Littorina littorea, the most abundant intertidal snail in northeastern North America. Native to Europe, the snail's ecological history in North America has been debated for over 100 years with no definitive resolution. To resolve its cryptogenic status, we used molecular genetics from a novel combination of the snail and a highly associated trematode parasite, Cryptocotyle lingua. Based on mitochondrial sequences of 370 L. littorea and 196 C. lingua individuals, our results demonstrate a significant reduction in genetic diversity in North America vs. Europe, North American haplotypes nested within European haplotypes, and mean divergence estimates of approxiamtely 500 years ago from Europe for both host and parasite--thus supporting a recent introduction of both host and parasite to North America from Europe. Our study therefore resolves not only a specific cryptogenic history, but it also demonstrates the success of our approach generally and could be used in resolving difficult invasion histories worldwide.

  14. Genome-wide association and admixture analysis of glaucoma in the Women's Health Initiative.

    Science.gov (United States)

    Hoffmann, Thomas J; Tang, Hua; Thornton, Timothy A; Caan, Bette; Haan, Mary; Millen, Amy E; Thomas, Fridtjof; Risch, Neil

    2014-12-15

    We report a genome-wide association study (GWAS) and admixture analysis of glaucoma in 12 008 African-American and Hispanic women (age 50-79 years) from the Women's Health Initiative (WHI). Although GWAS of glaucoma have been conducted on several populations, this is the first to look at glaucoma in individuals of African-American and Hispanic race/ethnicity. Prevalent and incident glaucoma was determined by self-report from study questionnaires administered at baseline (1993-1998) and annually through 2005. For African Americans, there was a total of 658 prevalent cases, 1062 incident cases and 6067 individuals who never progressed to glaucoma. For our replication cohort, we used the WHI Hispanics, including 153 prevalent cases, 336 incident cases and 2685 non-cases. We found an association of African ancestry with glaucoma incidence in African Americans (hazards ratio 1.62, 95% CI 1.023-2.56, P = 0.038) and in Hispanics (hazards ratio 3.21, 95% CI 1.32-7.80, P = 0.011). Although we found that no previously identified glaucoma SNPs replicated in either the WHI African Americans or Hispanics, a risk score combining all previously reported hits was significant in African-American prevalent cases (P = 0.0046), and was in the expected direction in the incident cases, as well as in the Hispanic incident cases. Additionally, after imputing to 1000 Genomes, two less common independent SNPs were suggestive in African Americans, but had too low of an allele frequency in Hispanics to test for replication. These results suggest the possibility of a distinct genetic architecture underlying glaucoma in individuals of African ancestry.

  15. Population structure and paternal admixture landscape on present-day Mexican-Mestizos revealed by Y-STR haplotypes.

    Science.gov (United States)

    Salazar-Flores, J; Dondiego-Aldape, R; Rubi-Castellanos, R; Anaya-Palafox, M; Nuño-Arana, I; Canseco-Avila, L M; Flores-Flores, G; Morales-Vallejo, M E; Barojas-Pérez, N; Muñoz-Valle, J F; Campos-Gutiérrez, R; Rangel-Villalobos, H

    2010-01-01

    Mestizos currently represent most of the Mexican population (>90%); they are defined as individuals born in the country having a Spanish-derived last name, with family antecedents of Mexican ancestors back at least to the third generation. Mestizos are result of 500 years of admixture mainly among Spaniards, Amerindians, and African slaves. Consequently, a complex genetic pattern has been generated throughout the country that has been scarcely studied from the paternal point of view. This fact is important, taking into account that gene flow toward the New World comprised largely males. We analyzed the population structure and paternal admixture of present-day Mexican-Mestizo populations based on Y-STRs. We genotyped at least 12 Y-STRs in DNA samples of 986 males from five states: Aguascalientes (n = 293); Jalisco (n = 185); Guanajuato (n = 168); Chiapas (n = 170); and Yucatán (n = 170). AmpFlSTR Y-filer and Powerplex-Y(R) kits were used. Inclusion of North and Central Y-STR databases in the analyses allowed obtaining a Y-STR variability landscape from Mexico. Results confirmed the population differentiation gradient previously noted in Mestizos with SNPs and autosomal STRs throughout the Mexican territory: European ancestry increments to the Northwest and, correspondingly, Amerindian ancestry increments to the Center and Southeast. In addition, SAMOVA test and Autocorrelation Index for DNA Analysis autocorrelogram plot suggested preferential gene flow of males with neighboring populations in agreement with the isolation-by-distance model. Results are important for disease-risk studies (principally male-related) and for human identification purposes, because Y-STR databases are not available on the majority of Mexican-Mestizo populations.

  16. Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme.

    Science.gov (United States)

    Ranc, Nicolas; Muños, Stephane; Xu, Jiaxin; Le Paslier, Marie-Christine; Chauveau, Aurélie; Bounon, Rémi; Rolland, Sophie; Bouchet, Jean-Paul; Brunel, Dominique; Causse, Mathilde

    2012-08-01

    Genome-wide association mapping is an efficient way to identify quantitative trait loci controlling the variation of phenotypes, but the approach suffers severe limitations when one is studying inbred crops like cultivated tomato (Solanum lycopersicum). Such crops exhibit low rates of molecular polymorphism and high linkage disequilibrium, which reduces mapping resolution. The cherry type tomato (S. lycopersicum var. cerasiforme) genome has been described as an admixture between the cultivated tomato and its wild ancestor, S. pimpinellifolium. We have thus taken advantage of the properties of this admixture to improve the resolution of association mapping in tomato. As a proof of concept, we sequenced 81 DNA fragments distributed on chromosome 2 at different distances in a core collection of 90 tomato accessions, including mostly cherry type tomato accessions. The 81 Sequence Tag Sites revealed 352 SNPs and indels. Molecular diversity was greatest for S. pimpinellifolium accessions, intermediate for S. l. cerasiforme accessions, and lowest for the cultivated group. We assessed the structure of molecular polymorphism and the extent of linkage disequilibrium over genetic and physical distances. Linkage disequilibrium decreased under r(2) = 0.3 within 1 cM, and minimal estimated value (r(2) = 0.13) was reached within 20 kb over the physical regions studied. Associations between polymorphisms and fruit weight, locule number, and soluble solid content were detected. Several candidate genes and quantitative trait loci previously identified were validated and new associations detected. This study shows the advantages of using a collection of S. l. cerasiforme accessions to overcome the low resolution of association mapping in tomato.

  17. Southeast Asian origins of five Hill Tribe populations and correlation of genetic to linguistic relationships inferred with genome-wide SNP data.

    Science.gov (United States)

    Listman, J B; Malison, R T; Sanichwankul, K; Ittiwut, C; Mutirangura, A; Gelernter, J

    2011-02-01

    In Thailand, the term Hill Tribe is used to describe populations whose members traditionally practice slash and burn agriculture and reside in the mountains. These tribes are thought to have migrated throughout Asia for up to 5,000 years, including migrations through Southern China and/or Southeast Asia. There have been continuous migrations southward from China into Thailand for approximately the past thousand years and the present geographic range of any given tribe straddles multiple political borders. As none of these populations have autochthonous scripts, written histories have until recently, been externally produced. Northern Asian, Tibetan, and Siberian origins of Hill Tribes have been proposed. All purport endogamy and have nonmutually intelligible languages. To test hypotheses regarding the geographic origins of these populations, relatedness and migrations among them and neighboring populations, and whether their genetic relationships correspond with their linguistic relationships, we analyzed 2,445 genome-wide SNP markers in 118 individuals from five Thai Hill Tribe populations (Akha, Hmong, Karen, Lahu, and Lisu), 90 individuals from majority Thai populations, and 826 individuals from Asian and Oceanean HGDP and HapMap populations using a Bayesian clustering method. Considering these results within the context of results ofrecent large-scale studies of Asian geographic genetic variation allows us to infer a shared Southeast Asian origin of these five Hill Tribe populations as well ancestry components that distinguish among them seen in successive levels of clustering. In addition, the inferred level of shared ancestry among the Hill Tribes corresponds well to relationships among their languages.

  18. ADSORPTION OF CHROMIUM (VI FROM AQUEOUS SOLUTIONS BY DIFFERENT ADMIXTURES – A BATCH EQUILIBRIUM TEST STUDY

    Directory of Open Access Journals (Sweden)

    K. SHIVA PRASHANTH KUMAR

    2014-08-01

    Full Text Available Wide variety of inorganic compounds such as nutrients and trace metals, organic chemicals, radioactive contaminants and pathogens are commonly present as contaminants in the groundwater. Migration of contaminants in soil involves important mechanisms such as molecular diffusion, dispersion under physical processes, adsorption, precipitation and oxidation - reduction under chemical processes and biodegradation under biological process. Cr (VI is a major and dangerous contaminant as per the ground water is concerned. There are numerous research work carried out with concentrated efforts by the researchers towards removal of Cr (VI contaminant from aqueous solutions. There are few studies relevant to Cr (VI removal with respect to utilization of low cost admixtures and also soil type. In the present study, different low cost admixtures like rice husk (RH, shredded tyre (ST and fly ash (FA are used to understand the performance in removal of Cr (VI from aqueous solution and also two different soil types are used along with the admixture. The results are discussed in terms of sorption capacity and performance of individual admixture and combination of admixture with soil in removal of contaminant. The fly ash, rice husk and shredded tyre admixtures are used and the results revealed that the shredded tyre showed higher performance in removal of contaminant concentration. Also, the soil which has more fine particle content (size<0.075 mm IS sieve showed reasonable reduction in concentration of contaminant at the lower levels of contaminant initial concentration. The sorption capacity results of Cr (VI contaminant, treated with various admixtures are further validated with the published work of other investigators. The shredded tyre (ST showed more adsorption capacity, i.e., 3.283 mg/g at pH of 4.8. For other admixtures, adsorption capacity value is varying in the range of 0.07 mg/g to 1.7 mg/g. Only in case of activated alumina and modified saw dust

  19. Outcrossing and coexistence of genetically modified with (genetically) unmodified crops: a case study of the situation in the Netherlands.

    NARCIS (Netherlands)

    Wiel, van de C.C.M.; Lotz, L.A.P.

    2006-01-01

    With the introduction of genetically modified (GM) crops the EU has demanded that individual member states enact measures to prevent inadvertent admixture ¿ through outcrossing ¿ of genetically modified organisms (GMOs) with products from conventional and organic farming. A literature review on outc

  20. MECHANISMS OF RESISTANCE TO CIPROFLOXACIN AND GENETIC DIVERSITY OF ESCHERICHIA COLI STRAINS ORIGINATING FROM URINE CULTURES PERFORMED FOR ROMANIAN ADULTS.

    Science.gov (United States)

    Cristea, Violeta Corina; Oprea, Mihaela; Neacşu, Gabriela; Gîlcă, Ramona; Popa, Mircea Ioan; Usein, Codruţa-Romaniţa

    2015-01-01

    Urinary tract infections (UTI) with Escherichia coli are among the most common infections presenting in general practice. Fluoroquinolones (FQs) are relied on for their empirical therapy but recent reports indicate a concerning increase in the percentage of FQ-resistant E. coli isolates in many countries, including Romania. Sixty E. coli strains with ciprofloxacin resistance and cephalosporin susceptibility isolated from urine specimens of non-hospitalized patients during a five-month period (October 2014 - February 2015) were further analyzed to determine the molecular basis of FQ resistance (i.e. mutations in chromosomal gyrA, gyrB, parC genes and presence of plasmid-borne qnrA, qnrB, qnrS, and aac(6'-Ib-cr genes), the phylogenetic background (i.e. phylogenetic groups A, B1, B2, C, D, E, F or clade I), O25b/ST131 status, and genetic relatedness inferred from the XbaI pulsed-field gel electrophoresis (PFGE) profiles as a measure of isolate-specific genetic composition. The PCR-based phylotyping showed that most strains were assigned to non-B2 phylogenetic groups (i.e. group A/21 strains, group B1/14 strains, group B2/10 strains, group C/8 strains, group D/3 strains, group F/4 strains). Already described chromosomal mutations associated to FQ resistance were found, the strains being double gyrA mutants (i.e. Ser83Leu, Asp87Asn) with one or two parC mutations (e.g. Ala56Thr, Ser80Ile, Glu84Gly). Seven percent of the strains harboured plasmid-borne genes qnrS1 (2 strains) and aac(6'-Ib-cr (2 strains). Based on the PCR results, 15% of the strains were members of the O25b/ST131 clone and possessed the gyrA/parC allele combination which is considered as hallmark of H30 subclone. PFGE genotyping revealed a genetically diverse population of FQ-resistant E. coli. ST131 strains displayed more homogeneous PFGE profiles than non-ST131. The ST131 cluster extended to 77.74% similarity versus 60% overall. These findings underscore the need for ongoing surveillance to capture the

  1. Molybdenum isotopic evidence for the origin of chondrules and a distinct genetic heritage of carbonaceous and non-carbonaceous meteorites

    Science.gov (United States)

    Budde, Gerrit; Burkhardt, Christoph; Brennecka, Gregory A.; Fischer-Gödde, Mario; Kruijer, Thomas S.; Kleine, Thorsten

    2016-11-01

    Nucleosynthetic isotope anomalies are powerful tracers to determine the provenance of meteorites and their components, and to identify genetic links between these materials. Here we show that chondrules and matrix separated from the Allende CV3 chondrite have complementary nucleosynthetic Mo isotope anomalies. These anomalies result from the enrichment of a presolar carrier enriched in s-process Mo into the matrix, and the corresponding depletion of this carrier in the chondrules. This carrier most likely is a metal and so the uneven distribution of presolar material probably results from metal-silicate fractionation during chondrule formation. The Mo isotope anomalies correlate with those reported for W isotopes on the same samples in an earlier study, suggesting that the isotope variations for both Mo and W are caused by the heterogeneous distribution of the same carrier. The isotopic complementary of chondrules and matrix indicates that both components are genetically linked and formed together from one common reservoir of solar nebula dust. As such, the isotopic data require that most chondrules formed in the solar nebula and are not a product of protoplanetary impacts. Allende chondrules and matrix together with bulk carbonaceous chondrites and some iron meteorites (groups IID, IIIF, and IVB) show uniform excesses in 92Mo, 95Mo, and 97Mo that result from the addition of supernova material to the solar nebula region in which these carbonaceous meteorites formed. Non-carbonaceous meteorites (enstatite and ordinary chondrites as well as most iron meteorites) do not contain this material, demonstrating that two distinct Mo isotope reservoirs co-existed in the early solar nebula that remained spatially separated for several million years. This separation was most likely achieved through the formation of the gas giants, which cleared the disk between the inner and outer solar system regions parental to the non-carbonaceous and carbonaceous meteorites. The Mo isotope

  2. Mechanical Characteristics of Hardened Concrete with Different Mineral Admixtures: A Review

    Science.gov (United States)

    2014-01-01

    The available literature identifies that the addition of mineral admixture as partial replacement of cement improves the microstructure of the concrete (i.e., porosity and pore size distribution) as well as increasing the mechanical characteristics such as drying shrinkage and creep, compressive strength, tensile strength, flexural strength, and modulus of elasticity; however, no single document is available in which review and comparison of the influence of the addition of these mineral admixtures on the mechanical characteristics of the hardened pozzolanic concretes are presented. In this paper, based on the reported results in the literature, mechanical characteristics of hardened concrete partially containing mineral admixtures including fly ash (FA), silica fume (SF), ground granulated blast furnace slag (GGBS), metakaolin (MK), and rice husk ash (RHA) are discussed and it is concluded that the content and particle size of mineral admixture are the parameters which significantly influence the mechanical properties of concrete. All mineral admixtures enhance the mechanical properties of concrete except FA and GGBS which do not show a significant effect on the strength of concrete at 28 days; however, gain in strength at later ages is considerable. Moreover, the comparison of the mechanical characteristics of different pozzolanic concretes suggests that RHA and SF are competitive. PMID:24688443

  3. Mechanical Characteristics of Hardened Concrete with Different Mineral Admixtures: A Review

    Directory of Open Access Journals (Sweden)

    Tehmina Ayub

    2014-01-01

    Full Text Available The available literature identifies that the addition of mineral admixture as partial replacement of cement improves the microstructure of the concrete (i.e., porosity and pore size distribution as well as increasing the mechanical characteristics such as drying shrinkage and creep, compressive strength, tensile strength, flexural strength, and modulus of elasticity; however, no single document is available in which review and comparison of the influence of the addition of these mineral admixtures on the mechanical characteristics of the hardened pozzolanic concretes are presented. In this paper, based on the reported results in the literature, mechanical characteristics of hardened concrete partially containing mineral admixtures including fly ash (FA, silica fume (SF, ground granulated blast furnace slag (GGBS, metakaolin (MK, and rice husk ash (RHA are discussed and it is concluded that the content and particle size of mineral admixture are the parameters which significantly influence the mechanical properties of concrete. All mineral admixtures enhance the mechanical properties of concrete except FA and GGBS which do not show a significant effect on the strength of concrete at 28 days; however, gain in strength at later ages is considerable. Moreover, the comparison of the mechanical characteristics of different pozzolanic concretes suggests that RHA and SF are competitive.

  4. Origin and population structure of the Icelanders.

    Science.gov (United States)

    Williams, J T

    1993-04-01

    The Norse and Celtic contributions to the founding population of Iceland have been estimated previously on a pan-Icelandic basis using gene frequency data for the entire island. Accounts of the settlement of Iceland, however, suggest that different regions received different proportions of Norse and Celtic settlers, indicating the need to incorporate geographic variation into Icelandic admixture studies. A formal likelihood ratio test rejects the null hypothesis of regional homogeneity in admixture proportions. Here, regional admixture estimates for Iceland are reported; they are in agreement with the settlement pattern inferred from historical accounts. The western, northern, and southern regions of Iceland exhibit a moderate Celtic component, consistent with historical indications that these regions were settled by Norse Vikings from the British Isles, accompanied by Celtic wives and slaves. Eastern Iceland, believed to have been settled chiefly by Vikings from Scandinavia, is characterized by a large Norse component of admixture. The northwestern peninsula is also found to be predominantly Norse. Regional genetic data are used to elucidate the contemporary population structure of Iceland. The observed structure correlates well with patterns of Icelandic geography, history, economy, marriage, urbanization, and internal migration. The northeastern region is strongly isolated, the urbanized areas of the north and southwest are representative of the overall population, and the remaining regions exhibit small-scale variation about the genetic central tendency. A high level of genetic homogeneity is indicated (RST = 0.0005), consistent with the high internal migration rate of the Icelanders. A regression of mean per-locus heterozygosity on distance from the gene frequency centroid reveals a greater than average external gene flow into the eastern region, whereas the northwestern peninsula has received less than average external gene flow. Iceland is compared with

  5. Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region.

    Science.gov (United States)

    Quéméré, Erwan; Amelot, Xavier; Pierson, Julie; Crouau-Roy, Brigitte; Chikhi, Lounès

    2012-08-07

    The impact of climate change and anthropogenic deforestation on biodiversity is of growing concern worldwide. Disentangling how past anthropogenic and natural factors contributed to current biome distribution is thus a crucial issue to understand their complex interactions on wider time scales and to improve predictions and conservation strategies. This is particularly important in biodiversity hotspots, such as Madagascar, dominated by large open habitats whose origins are increasingly debated. Although a dominant narrative argues that Madagascar was originally entirely covered by woodlands, which were destroyed by humans, a number of recent studies have suggested that past climatic fluctuations played a major role in shaping current biome distributions well before humans arrived. Here, we address the question of the origin of open habitats in the Daraina region in northern Madagascar, using a multiproxy approach combining population genetics modeling and remote-sensing analyses. We show that (i) contrary to most regions of Madagascar, the forest cover in Daraina remained remarkably stable over the past 60 y, and (ii) the golden-crowned sifaka (Propithecus tattersalli), a forest-dwelling lemur, underwent a strong population contraction before the arrival of the first humans, hence excluding an anthropogenic cause. Prehuman Holocene droughts may have led to a significant increase of grasslands and a reduction in the species' habitat. This contradicts the prevailing narrative that land cover changes are necessarily anthropogenic in Madagascar but does not preclude the later role played by humans in other regions in which recent lemur bottlenecks have been observed.

  6. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides.

    Directory of Open Access Journals (Sweden)

    Shuhong Ouyang

    Full Text Available Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90 via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172.

  7. Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection, and seasonal periodicity of the VP1 gene.

    Science.gov (United States)

    Tee, Kok Keng; Lam, Tommy Tsan-Yuk; Chan, Yoke Fun; Bible, Jon M; Kamarulzaman, Adeeba; Tong, C Y William; Takebe, Yutaka; Pybus, Oliver G

    2010-04-01

    Human enterovirus 71 (EV-71) is one of the major etiologic causes of hand, foot, and mouth disease (HFMD) among young children worldwide, with fatal instances of neurological complications becoming increasingly common. Global VP1 capsid sequences (n = 628) sampled over 4 decades were collected and subjected to comprehensive evolutionary analysis using a suite of phylogenetic and population genetic methods. We estimated that the common ancestor of human EV-71 likely emerged around 1941 (95% confidence interval [CI], 1929 to 1952), subsequently diverging into three genogroups: B, C, and the now extinct genogroup A. Genealogical analysis revealed that diverse lineages of genogroup B and C (subgenogroups B1 to B5 and C1 to C5) have each circulated cryptically in the human population for up to 5 years before causing large HFMD outbreaks, indicating the quiescent persistence of EV-71 in human populations. Estimated phylogenies showed a complex pattern of spatial structure within well-sampled subgenogroups, suggesting endemicity with occasional lineage migration among locations, such that past HFMD epidemics are unlikely to be linked to continuous transmission of a single strain of virus. In addition, rises in genetic diversity are correlated with the onset of epidemics, driven in part by the emergence of novel EV-71 subgenogroups. Using subgenogroup C1 as a model, we observe temporal strain replacement through time, and we investigate the evidence for positive selection at VP1 immunogenic sites. We discuss the consequences of the evolutionary dynamics of EV-71 for vaccine design and compare its phylodynamic behavior with that of influenza virus.

  8. High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region

    Science.gov (United States)

    Douaihy, Bouchra; Vendramin, Giovanni G.; Boratyński, Adam; Machon, Nathalie; Bou Dagher-Kharrat, Magda

    2011-01-01

    Background and aims Juniperus excelsa is an important woody species in the high mountain ecosystems of the eastern Mediterranean Basin where it constitutes the only coniferous species found at the tree line. The genetic diversity within and among J. excelsa populations of the eastern Mediterranean Basin is studied in the light of their historical fragmentation. Methodology Nuclear microsatellites originally developed for Juniperus communis and J. przewalskii were tested on 320 individuals from 12 different populations originating from Lebanon, Turkey, Cyprus, Greece and the Ukraine. Principal results Among the 31 nuclear microsatellite primers tested, only three produced specific amplification products, with orthology confirmed by sequence analysis. They were then used for genetic diversity studies. The mean number of alleles and the expected heterozygosity means were Na=8.78 and He=0.76, respectively. The fixation index showed a significant deviation from Hardy–Weinberg equilibrium and an excess of homozygotes (FIS=0.27–0.56). A moderate level of genetic differentiation was observed among the populations (FST=0.075, P2000 m) in Lebanon. These populations were differentiated from the other populations that are grouped into three sub-clusters. Conclusions High levels of genetic diversity were observed at species and population levels. The high level of differentiation in the high-mountain Lebanese populations reflects a long period of isolation or possibly a different origin. The admixture observed in other populations from Lebanon suggests a more recent separation from the Turkish–southeastern European populations. PMID:22476474

  9. High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region.

    Science.gov (United States)

    Douaihy, Bouchra; Vendramin, Giovanni G; Boratyński, Adam; Machon, Nathalie; Bou Dagher-Kharrat, Magda

    2011-01-01

    Juniperus excelsa is an important woody species in the high mountain ecosystems of the eastern Mediterranean Basin where it constitutes the only coniferous species found at the tree line. The genetic diversity within and among J. excelsa populations of the eastern Mediterranean Basin is studied in the light of their historical fragmentation. Nuclear microsatellites originally developed for Juniperus communis and J. przewalskii were tested on 320 individuals from 12 different populations originating from Lebanon, Turkey, Cyprus, Greece and the Ukraine. Among the 31 nuclear microsatellite primers tested, only three produced specific amplification products, with orthology confirmed by sequence analysis. They were then used for genetic diversity studies. The mean number of alleles and the expected heterozygosity means were N(a)=8.78 and H(e)=0.76, respectively. The fixation index showed a significant deviation from Hardy-Weinberg equilibrium and an excess of homozygotes (F(IS)=0.27-0.56). A moderate level of genetic differentiation was observed among the populations (F(ST)=0.075, P2000 m) in Lebanon. These populations were differentiated from the other populations that are grouped into three sub-clusters. High levels of genetic diversity were observed at species and population levels. The high level of differentiation in the high-mountain Lebanese populations reflects a long period of isolation or possibly a different origin. The admixture observed in other populations from Lebanon suggests a more recent separation from the Turkish-southeastern European populations.

  10. Coagulated silica - a-SiO2 admixture in cement paste

    Science.gov (United States)

    Pokorný, Jaroslav; Pavlíková, Milena; Záleská, Martina; Rovnaníková, Pavla; Pavlík, Zbyšek

    2016-07-01

    Amorphous silica (a-SiO2) in fine-grained form possesses a high pozzolanic activity which makes it a valuable component of blended binders in concrete production. The origin of a-SiO2 applied in cement-based composites is very diverse. SiO2 in amorphous form is present in various amounts in quite a few supplementary cementing materials (SCMs) being used as partial replacement of Portland cement. In this work, the applicability of a commercially produced coagulated silica powder as a partial replacement of Portland cement in cement paste mix design is investigated. Portland cement CEM I 42.5R produced according to the EU standard EN 197-1 is used as a reference binder. Coagulated silica is applied in dosages of 5 and 10 % by mass of cement. The water/binder ratio is kept constant in all the studied pastes. For the applied silica, specific surface area, density, loss on ignition, pozzolanic activity, chemical composition, and SiO2 amorphous phase content are determined. For the developed pastes on the basis of cement-silica blended binder, basic physical properties as bulk density, matrix density, and total open porosity are accessed. Pore size distribution is determined using MIP analysis. Initial and final setting times of fresh mixtures are measured by automatic Vicat apparatus. Effect of silica admixture on mechanical resistivity is evaluated using compressive strength, bending strength, and dynamic Young's modulus measurement. The obtained data gives evidence of a decreased workability of paste mixtures with silica, whereas the setting process is accelerated. On the other hand, reaction activity of silica with Portland cement minerals results in a slight decrease of porosity and improvement of mechanical resistivity of cement pastes containing a-SiO2.

  11. Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

    Science.gov (United States)

    Banda, Yambazi; Kvale, Mark N.; Hoffmann, Thomas J.; Hesselson, Stephanie E.; Ranatunga, Dilrini; Tang, Hua; Sabatti, Chiara; Croen, Lisa A.; Dispensa, Brad P.; Henderson, Mary; Iribarren, Carlos; Jorgenson, Eric; Kushi, Lawrence H.; Ludwig, Dana; Olberg, Diane; Quesenberry, Charles P.; Rowell, Sarah; Sadler, Marianne; Sakoda, Lori C.; Sciortino, Stanley; Shen, Ling; Smethurst, David; Somkin, Carol P.; Van Den Eeden, Stephen K.; Walter, Lawrence; Whitmer, Rachel A.; Kwok, Pui-Yan; Schaefer, Catherine; Risch, Neil

    2015-01-01

    Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian–European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent–child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent–child pairs was largely due to intermarriage. The parent–child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies. PMID:26092716

  12. The genetic structure of Mexican Mestizos of different locations: tracking back their origins through MHC genes, blood group systems, and microsatellites.

    Science.gov (United States)

    Gorodezky, C; Alaez, C; Vázquez-García, M N; de la Rosa, G; Infante, E; Balladares, S; Toribio, R; Pérez-Luque, E; Muñoz, L

    2001-09-01

    Mexican Mestizos, who are the result of the admixture of Spanish, Indian, and Black genes, were analyzed for different systems. Three populations from geographical distinct areas were studied: the north (State of Nuevo Leon ), the center (State of Guanajuato), and the highlands (mainly Mexico City). Ten blood group systems (N = 229), STRs (N = 107), HLA-A*, B*, C* (N = 116-167), and DRB1, DQA1, and DQB1 (N = 40, 101, 160, respectively) were analyzed in the samples of the highlands. The three groups cluster together in the same branch: Mestizos from Venezuela, Mediterranean and Jews close to the cluster of Orientals, followed by Amerindians. All markers demonstrate that Indian genes are strongly represented in the highlands: Di(a), O, D(-)(+), s, A*0201, *0206, B*1539 (*1541), *3902, *3905, *3512, *3517, *4002, *4005, Cw*0801, *0304, *0401 among others. Cw*0501, *1203, *1204, and *1601 are of White ancestry. The most frequent haplotypes *0407-*03011-*0302 and *0802-*0401-*0402 are of Indian descent as well. The center and mainly the north show a more Caucasian and Semitic profile. The results demonstrate the high variability resulting from interethnic admixture, suggesting that this mechanism is the main factor responsible for the large diversity found in urban populations.

  13. Geographic population structure analysis of worldwide human populations infers their biogeographical origins

    Science.gov (United States)

    Elhaik, Eran; Tatarinova, Tatiana; Chebotarev, Dmitri; Piras, Ignazio S.; Maria Calò, Carla; De Montis, Antonella; Atzori, Manuela; Marini, Monica; Tofanelli, Sergio; Francalacci, Paolo; Pagani, Luca; Tyler-Smith, Chris; Xue, Yali; Cucca, Francesco; Schurr, Theodore G.; Gaieski, Jill B.; Melendez, Carlalynne; Vilar, Miguel G.; Owings, Amanda C.; Gómez, Rocío; Fujita, Ricardo; Santos, Fabrício R.; Comas, David; Balanovsky, Oleg; Balanovska, Elena; Zalloua, Pierre; Soodyall, Himla; Pitchappan, Ramasamy; GaneshPrasad, ArunKumar; Hammer, Michael; Matisoo-Smith, Lisa; Wells, R. Spencer; Acosta, Oscar; Adhikarla, Syama; Adler, Christina J.; Bertranpetit, Jaume; Clarke, Andrew C.; Cooper, Alan; Der Sarkissian, Clio S. I.; Haak, Wolfgang; Haber, Marc; Jin, Li; Kaplan, Matthew E.; Li, Hui; Li, Shilin; Martínez-Cruz, Begoña; Merchant, Nirav C.; Mitchell, John R.; Parida, Laxmi; Platt, Daniel E.; Quintana-Murci, Lluis; Renfrew, Colin; Lacerda, Daniela R.; Royyuru, Ajay K.; Sandoval, Jose Raul; Santhakumari, Arun Varatharajan; Soria Hernanz, David F.; Swamikrishnan, Pandikumar; Ziegle, Janet S.

    2014-01-01

    The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing. PMID:24781250

  14. GENETIC CIVERSITH AND MATERNAL ORIGIN OF CHINESE DONKEY BREEDS%中国家驴品种遗传多样性及母系起源研究

    Institute of Scientific and Technical Information of China (English)

    王全喜; 陈建兴; 闵令江; 乌日图那生; 乌云

    2012-01-01

    为了给中国家驴遗传资源的评价、保护和利用提供一些分子生物学基础,本研究通过自行设计引物,采用PCR-SSCP技术对中国家驴线粒体DNA( Mitochondrial DNA,mtDNA)细胞色素b(Cytochrome b,Cytb)基因308bp片段序列的变异进行检测来探讨其遗传多样性和母系起源.发现了3种基因型,结合GenBank已公布的数据进行分析发现在中国家驴品种中共存在15个突变位点,17个单倍型,通过计算各群体的遗传多样性指数发现中国家驴的遗传多样性比较丰富.另外,还通过与两种非洲野驴的Cytb序列进行比对和网络聚类分析方法对所有家驴的样品进行了母系起源的研究,证明家驴起源于非洲的索马里驴和努比亚驴.%To provide molecular biological foundation for the evaluation, conservation and utilization of Chinese domestic donkey genetic resources, we investigated the genetic diversity and maternal origin of domestic donkeys by detecting the variations of 308bp fragment of mtDNA Cytb gene sequence in Chinese donkey samples with self designed primers, using PCR - SSCP technique. Three genotypes were found by this way, and 15 variable sites were revealed and 17 haplotypes were determined after alignment with all the homologous 308nt Chinese donkey Cytb sequences deposited in CenBank. The results showed that abundant genetic diversity was revealed in the researched region of donkey Cytb, by calculating the genetic diversity indexes of all Chinese donkey populations. Additionally, it was demonstrated that the maternal origins of domestic donkeys are Nubian and Somali asses, two kinds of African wild asses, by comparison and Network analyses with the Cytb sequences of two different kinds of African wild asses.

  15. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

    Directory of Open Access Journals (Sweden)

    Wan Isa Hatin

    Full Text Available Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis. To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

  16. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

    Science.gov (United States)

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-04-05

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

  17. Effects of GH Admixture on the Early Strength of Fly Ash Concrete and Mortar

    Institute of Scientific and Technical Information of China (English)

    KANG Jingfu; WANG Xiufen

    2008-01-01

    The enhancement effects of GH admixture on the early strengths of fly ash concrete and mortar were studied, and the mechanism was analyzed by X-ray diffraction (XRD) and scanning electro microscope (SEM). Experimental results show that, by the incorporation of GH admixture, both of cement hydration and pozzolanic reaction of fly ash are accelerated, the strengths of fly ash concrete and mortar are enhanced noticeably, especially the early strength. With a mixture design of 200 kg/m3 OPC (Ordinary Portland Cement), 200 kg/m3 fly ash and 50 kg/m3 GH admixture, the strength of concrete at 1 d, 3 d and 28 d reaches 25 Mpa, 50 Mpa and 70 Mpa respectively.

  18. Effect of Functional Chemical Admixtures on the Performance of Cement Asphalt Mortar Used in Ballastless Track

    Institute of Scientific and Technical Information of China (English)

    JIANG Jinyang; SHE Wei; LI Wei; PAN Li

    2015-01-01

    Chemical admixtures are of paramount importance to the performance of modern cement based composites. In this paper, we performed a series of tests to investigate the effects of chemical admixtures on the cement asphalt mortar (CA mortar), i e, compressive strength, frost resistance, permeability, fatigue resistance, pore structure and microstructure. In particular, two types of chemical admixtures were tested,i e, defoamer (tributyl phosphate (TBP)) and polycarboxylate superplasticizer (PS). The results indicate that the addition of TBP and PS eliminates big bubbles and promotes small non-connected pores forming in matrix. Besides, an optimum dosage of TBP and PS may be determined with respect to the frost resistance, permeability and fatigue resistance of CA mortar. Further elaborative discussions are presented as well as experimental evidences from mercury intrusion porosimetry, scanning electron microscopy and energy dispersive spectroscopy.

  19. Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2.

    Science.gov (United States)

    Curk, Franck; Ancillo, Gema; Garcia-Lor, Andres; Luro, François; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Navarro, Luis; Ollitrault, Patrick

    2014-12-29

    The most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity. Modern breeding of these species is hampered by their complex heterozygous genomic structures that determine species phenotype and are broken by sexual hybridisation. Nevertheless, a large amount of diversity is present in the citrus gene pool, and breeding to allow inclusion of desirable traits is of paramount importance. However, the efficient mobilization of citrus biodiversity in innovative breeding schemes requires previous understanding of Citrus origins and genomic structures. Haplotyping of multiple gene fragments along the whole genome is a powerful approach to reveal the admixture genomic structure of current species and to resolve the evolutionary history of the gene pools. In this study, the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species was assessed by analysis of 16 gene fragments on chromosome 2. 454 amplicon libraries were established using the Fluidigm array system for 48 genotypes and 16 gene fragments from chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed using the haplotypic data for each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins, (ii) was

  20. Genetic basis, nutritional challenges and adaptive responses in the prenatal origin of obesity and type-2 diabetes.

    Science.gov (United States)

    Gonzalez-Bulnes, Antonio; Ovilo, Cristina

    2012-03-01

    Obesity and type-2 diabetes are currently considered global pandemics. A large set of epidemiological evidences are addressing both the importance of a genetic predisposition -starting with the thrifty genotype hypothesis- and the determinant role of the maternal nutrition during pregnancy -starting with longitudinal studies of individuals born during the Dutch famine- on the adult onset of the disease. Compelling evidences suggest that both over- and undernutrition may modify the intrauterine environment of the conceptus and may alter the expression of its genome, predisposing to disease in the adult life. However, the most recent data indicate that the consequences of this phenomenon, termed as prenatal programming, are influenced both by timing, degree and duration of the challenge and by the adaptive response of the mother and the conceptus; thus, the information acquired by interventional studies modifying these parameters is becoming increasingly important. Obviously, interventional research in human beings is limited by ethical issues; hence, investigations need to be conducted on animal models, either rodents or large animals. This review summarizes the results of epidemiological human studies and translational animal research in unraveling the interaction between genome, nutritional status and adaptive response on the establishment of postnatal obesity, insulin resistance and type-2 diabetes.

  1. Independent Origins of Yeast Associated with Coffee and Cacao Fermentation.

    Science.gov (United States)

    Ludlow, Catherine L; Cromie, Gareth A; Garmendia-Torres, Cecilia; Sirr, Amy; Hays, Michelle; Field, Colburn; Jeffery, Eric W; Fay, Justin C; Dudley, Aimée M

    2016-04-04

    Modern transportation networks have facilitated the migration and mingling of previously isolated populations of plants, animals, and insects. Human activities can also influence the global distribution of microorganisms. The best-understood example is yeasts associated with winemaking. Humans began making wine in the Middle East over 9,000 years ago [1, 2]. Selecting favorable fermentation products created specialized strains of Saccharomyces cerevisiae [3, 4] that were transported along with grapevines. Today, S. cerevisiae strains residing in vineyards around the world are genetically similar, and their population structure suggests a common origin that followed the path of human migration [3-7]. Like wine, coffee and cacao depend on microbial fermentation [8, 9] and have been globally dispersed by humans. Theobroma cacao originated in the Amazon and Orinoco basins of Colombia and Venezuela [10], was cultivated in Central America by Mesoamerican peoples, and was introduced to Europeans by Hernán Cortés in 1530 [11]. Coffea, native to Ethiopia, was disseminated by Arab traders throughout the Middle East and North Africa in the 6(th) century and was introduced to European consumers in the 17(th) century [12]. Here, we tested whether the yeasts associated with coffee and cacao are genetically similar, crop-specific populations or genetically diverse, geography-specific populations. Our results uncovered populations that, while defined by niche and geography, also bear signatures of admixture between major populations in events independent of the transport of the plants. Thus, human-associated fermentation and migration may have affected the distribution of yeast involved in the production of coffee and chocolate. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Portland cement hydration in the presence of admixtures: black gram pulse and superplasticizer

    Directory of Open Access Journals (Sweden)

    Viveka Nand Dwivedi

    2008-12-01

    Full Text Available Effect of admixtures such as black gram pulse (BGP and sulfonated naphthalene based superplasticizer (SP on the hydration of Portland cement has been studied. The hydration characteristics of OPC in the presence of BGP and SP were studied with the help of non evaporable water content determinations, calorimetric method, Mössbauer spectroscopic and atomic force microscopic techniques. Results have shown that both BGP and SP get adsorbed at the surface of cement and its hydration products. The hydration of Portland cement is retarded in the presence of both the admixtures and nanosize hydration products are formed.

  3. Further characterization of theobroma oil-beeswax admixtures as lipid matrices for improved drug delivery systems.

    Science.gov (United States)

    Attama, A A; Schicke, B C; Müller-Goymann, C C

    2006-11-01

    There is an increasing interest in lipid based drug delivery systems due to factors such as better characterization of lipidic excipients and formulation versatility and the choice of different drug delivery systems. It is important to know the thermal characteristics, crystal habit, texture, and appearance of a new lipid matrix when determining its suitability for use in certain pharmaceutical application. It is line with this that this research was embarked upon to characterize mixtures of beeswax and theobroma oil with a view to applying their admixtures in drug delivery systems such as solid lipid nanoparticles and nanostructured lipid carriers. Admixtures of theobroma oil and beeswax were prepared to contain 25% w/w, 50% w/w, and 75% w/w of theobroma oil. The admixtures were analyzed by differential scanning calorimetry (DSC), small angle X-ray diffraction (SAXD), wide angle X-ray diffraction (WAXD), and isothermal heat conduction microcalorimetry (IMC). The melting behavior and microstructures of the lipid admixtures were monitored by polarized light microscopy (PLM). Transmission electron microscopy (TEM) was used to study the internal structures of the lipid bases. DSC traces indicated that the higher melting peaks were roughly constant for the different admixtures, but lower melting peaks significantly increased (p beeswax in all the lipid matrix admixtures at all stages of the study. PLM micrographs revealed differences with regard to the thermal and optical behaviors depending on the composition of the matrix. The lipid matrix consisting of 75% w/w of theobroma oil showed a spherulite texture after 4 weeks of isothermal storage. Crystallization exotherms of lipid matrices containing 50% w/w and 25% w/w of theobroma oil showed change in modification after 30 min with the latter having a greater time-dependent crystallization. Generally, low non-integral Avrami exponents and growth rate constants were obtained for all the lipid matrices, with the admixture

  4. On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary centre of diversity.

    Science.gov (United States)

    Roullier, C; Kambouo, R; Paofa, J; McKey, D; Lebot, V

    2013-06-01

    New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers' management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change.

  5. Some Molecular and Clinical Aspects of Genetic Predisposition to Malignant Melanoma and Tumours of Various Site of Origin

    Directory of Open Access Journals (Sweden)

    Dębniak Tadeusz

    2007-06-01

    Full Text Available Abstract Based on epidemiological data we can assume that at least some malignant melanoma (MM and breast cancer cases can be caused by the same genetic factors. CDKN2A, which encodes the p16 protein, a cyclin-dependent kinase inhibitor suppressing cell proliferation, is regarded as a major melanoma susceptibility gene and the literature has also implicated this gene in predisposition to breast cancer. Genes also known to predispose to MM include XPD and MC1R. We studied CDKN2A/ARF, XPD and MC1R for their associations with melanoma and breast cancer risk in Polish patients and controls. We found that CDKN2A and ARF do not contribute significantly to either familial melanoma or malignant melanoma within the context of a cancer familial aggregation of disease with breast cancer. However, the common variant of the CDKN2A gene A148T, previously regarded as non-pathogenic, may predispose to malignant melanoma, early-onset breast cancer and lung cancer. Compound carriers of common XPD variants may be at slightly increased risk of breast cancer or late–onset malignant melanoma. Common recurrent variants of the MC1R gene (V60L, R151C, R163Q and R160W may predispose to malignant melanoma. In general, the establishment of surveillance protocols proposed as an option for carriers of common alterations in CDKN2A, XPD or MC1R variants requires additional studies. It is possible that missense variants of genes for which truncating mutations are clearly pathogenic may also be deleterious, but with reduced penetrance. This may be overlooked unless large numbers of patients and controls are studied. A registry that includes 2000 consecutive breast cancer cases, 3500 early onset breast cancer patients, 500 unselected malignant melanoma and over 700 colorectal cancer patients has been established in the International Hereditary Cancer Centre and can contribute to these types of large association studies.

  6. A specific scenario for the origin of life and the genetic code based on peptide/oligonucleotide interdependence.

    Science.gov (United States)

    Griffith, Robert W

    2009-12-01

    Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurred within a surface hydrophilic layer and at its aqueous and atmospheric interfaces. Replication of nucleic acids and translation of peptides began at the emulsified interface between hydrophobic and aqueous layers. At the core of the protobiont was a family of short nucleic acids bearing arginine's codon and anticodon that added this amino acid to pre-formed peptides. In turn, the survival and replication of nucleic acid was aided by the peptides. The arginine-enriched peptides served to sequester and transfer phosphate bond energy and acted as cohesive agents, aggregating nucleic acids and keeping them at the interface.

  7. Nutrient overlap, genetic relatedness and spatial origin influence interaction-mediated shifts in inhibitory phenotype among Streptomyces spp.

    Science.gov (United States)

    Vaz Jauri, Patricia; Kinkel, Linda L

    2014-10-01

    Chemical communication among kin bacteria modulates diverse activities. Despite the general consensus that signaling among non-kin organisms is likely to influence microbial behavior, there is limited information on the potential for microbial interactions to alter microbial phenotypes in natural habitats. We explored patterns of interaction that alter inhibitory phenotypes among Streptomyces isolates from distinct communities. Shifts in inhibition in response to the presence of a partner were evaluated for 861 isolate combinations, and were considered in relation to nutrient use, 16S sequence, inhibition phenotype and community origin. The frequency of inhibition-shifting interactions was significantly higher among isolates from the same (0.40) than from different (0.33) communities, suggesting local selection for inhibition-shifting interactions. Communities varied in the frequency with which Streptomyces isolates responded to a partner but not in the frequency with which isolates induced changes in partners. Streptomyces isolates were more likely to exhibit increased inhibition of a target bacterium in response to isolates that compete for the same nutrients, are closely-related or are strongly inhibited by their antibiotics. This work documents a high frequency of interactions among Streptomyces that shift the capacity of Streptomyces to inhibit other microbes, and suggests significant potential for such interactions to shape microbial community dynamics.

  8. Genetic interaction of an origin recognition complex subunit and the Polycomb group gene MEDEA during seed development.

    Science.gov (United States)

    Collinge, Margaret A; Spillane, Charles; Köhler, Claudia; Gheyselinck, Jacqueline; Grossniklaus, Ueli

    2004-04-01

    The eukaryotic origin recognition complex (ORC) is made up of six subunits and functions in nuclear DNA replication, chromatin structure, and gene silencing in both fungi and metazoans. We demonstrate that disruption of a plant ORC subunit homolog, AtORC2 of Arabidopsis (Arabidopsis thaliana), causes a zygotic lethal mutant phenotype (orc2). Seeds of orc2 abort early, typically producing embryos with up to eight cells. Nuclear division in the endosperm is arrested at an earlier developmental stage: only approximately four nuclei are detected in orc2 endosperm. The endosperm nuclei in orc2 are dramatically enlarged, a phenotype that is most similar to class B titan mutants, which include mutants in structural maintenance of chromosomes (SMC) cohesins. The highest levels of ORC2 gene expression were found in preglobular embryos, coinciding with the stage at which homozygous orc2 mutant seeds arrest. The homologs of the other five Arabidopsis ORC subunits are also expressed at this developmental stage. The orc2 mutant phenotype is partly suppressed by a mutation in the Polycomb group gene MEDEA. In double mutants between orc2 and medea (mea), orc2 homozygotes arrest later with a phenotype intermediate between those of mea and orc2 single mutants. Either alterations in chromatin structure or the release of cell cycle checkpoints by the mea mutation may allow more cell and nuclear divisions to occur in orc2 homozygous seeds.

  9. Genetic relatedness of Plasmodium falciparum isolates and the origin of allelic diversity at the merozoite surface protein-1 (MSP-1 locus in Brazil and Vietnam

    Directory of Open Access Journals (Sweden)

    Ferreira Marcelo U

    2003-07-01

    Full Text Available Abstract Background Despite the extensive polymorphism at the merozoite surface protein-1 (MSP-1 locus of Plasmodium falciparum, that encodes a major repetitive malaria vaccine candidate antigen, identical and nearly identical alleles frequently occur in sympatric parasites. Here we used microsatellite haplotyping to estimate the genetic distance between isolates carrying identical and nearly identical MSP-1 alleles. Methods We analyzed 28 isolates from hypoendemic areas in north-western Brazil, collected between 1985 and 1998, and 23 isolates obtained in mesoendemic southern Vietnam in 1996. MSP-1 alleles were characterized by combining PCR typing with allele-specific primers and partial DNA sequencing. The following single-copy microsatellite markers were typed : Polyα, TA42 (only for Brazilian samples, TA81, TA1, TA87, TA109 (only for Brazilian samples, 2490, ARAII, PfG377, PfPK2, and TA60. Results The low pair-wise average genetic distance between microsatellite haplotypes of isolates sharing identical MSP-1 alleles indicates that epidemic propagation of discrete parasite clones originated most identical MSP-1 alleles in parasite populations from Brazil and Vietnam. At least one epidemic clone propagating in Brazil remained relatively unchanged over more than one decade. Moreover, we found no evidence that rearrangements of MSP-1 repeats, putatively created by mitotic recombination events, generated new alleles within clonal lineages of parasites in either country. Conclusion Identical MSP-1 alleles originated from co-ancestry in both populations, whereas nearly identical MSP-1 alleles have probably appeared independently in unrelated parasite lineages.

  10. Microsatellites reveal origin and genetic diversity of Eurasian invasions by one of the world's most notorious marine invader, Mnemiopsis leidyi (Ctenophora).

    Science.gov (United States)

    Reusch, Thorsten B H; Bolte, Sören; Sparwel, Maximiliane; Moss, Anthony G; Javidpour, Jamileh

    2010-07-01

    Marine invasions are taking place at an increasing rate. When occurring in blooms, zooplanktivorous comb jellies of the genus Mnemiopsis are able to cause pelagic regime shifts in coastal areas and may cause the collapse of commercially important fish populations. Using microsatellites, developed for the first time in the phylum Ctenophora, we show that Mnemiopsis leidyi has colonized Eurasia from two source regions. Our preliminary data set included four sites within the putative source region (US East Coast and Gulf of Mexico) and 10 invaded locations in Eurasian waters. Bayesian clustering and phylogeographic approaches revealed the origin of earlier invasions of the Black and Caspian Sea in the 1980s/1990s within or close to the Gulf of Mexico, while the 2006 invasion of the North and Baltic Seas can be directly traced to New England (pairwise F(ST) = 0). We found no evidence for mixing among both gene pools in the invaded areas. While the genetic diversity (allelic richness) remained similar in the Baltic Sea compared to the source region New England, it was reduced in the North Sea, supporting the view of an initial invasion of Northern Europe to a Baltic Sea port. In Black and Caspian Sea samples, we found a gradual decline in allelic richness compared to the Gulf of Mexico region, supporting a stepping-stone model of colonization with two sequential genetic founder events. Our data also suggest that current practices of ballast water treatment are insufficient to prevent repeated invasions of gelatinous zooplankton.

  11. Replication of a gene-environment interaction Via Multimodel inference: additive-genetic variance in adolescents' general cognitive ability increases with family-of-origin socioeconomic status.

    Science.gov (United States)

    Kirkpatrick, Robert M; McGue, Matt; Iacono, William G

    2015-03-01

    The present study of general cognitive ability attempts to replicate and extend previous investigations of a biometric moderator, family-of-origin socioeconomic status (SES), in a sample of 2,494 pairs of adolescent twins, non-twin biological siblings, and adoptive siblings assessed with individually administered IQ tests. We hypothesized that SES would covary positively with additive-genetic variance and negatively with shared-environmental variance. Important potential confounds unaddressed in some past studies, such as twin-specific effects, assortative mating, and differential heritability by trait level, were found to be negligible. In our main analysis, we compared models by their sample-size corrected AIC, and base our statistical inference on model-averaged point estimates and standard errors. Additive-genetic variance increased with SES-an effect that was statistically significant and robust to model specification. We found no evidence that SES moderated shared-environmental influence. We attempt to explain the inconsistent replication record of these effects, and provide suggestions for future research.

  12. Genetic differentiation, niche divergence, and the origin and maintenance of the disjunct distribution in the Blossomcrown Anthocephala floriceps (Trochilidae).

    Science.gov (United States)

    Lozano-Jaramillo, María; Rico-Guevara, Alejandro; Cadena, Carlos Daniel

    2014-01-01

    Studies of the origin and maintenance of disjunct distributions are of special interest in biogeography. Disjunct distributions can arise following extinction of intermediate populations of a formerly continuous range and later maintained by climatic specialization. We tested hypotheses about how the currently disjunct distribution of the Blossomcrown (Anthocephala floriceps), a hummingbird species endemic to Colombia, arose and how is it maintained. By combining molecular data and models of potential historical distributions we evaluated: (1) the timing of separation between the two populations of the species, (2) whether the disjunct distribution could have arisen as a result of fragmentation of a formerly widespread range due to climatic changes, and (3) if the disjunct distribution might be currently maintained by specialization of each population to different climatic conditions. We found that the two populations are reciprocally monophyletic for mitochondrial and nuclear loci, and that their divergence occurred ca. 1.4 million years before present (95% credibility interval 0.7-2.1 mybp). Distribution models based on environmental data show that climate has likely not been suitable for a fully continuous range over the past 130,000 years, but the potential distribution 6,000 ybp was considerably larger than at present. Tests of climatic divergence suggest that significant niche divergence between populations is a likely explanation for the maintenance of their disjunct ranges. However, based on climate the current range of A. floriceps could potentially be much larger than it currently is, suggesting other ecological or historical factors have influenced it. Our results showing that the distribution of A. floriceps has been discontinous for a long period of time and that populations exhibit different climatic niches have taxonomic and conservation implications.

  13. Genetic Differentiation, Niche Divergence, and the Origin and Maintenance of the Disjunct Distribution in the Blossomcrown Anthocephala floriceps (Trochilidae)

    Science.gov (United States)

    Lozano-Jaramillo, María; Rico-Guevara, Alejandro; Cadena, Carlos Daniel

    2014-01-01

    Studies of the origin and maintenance of disjunct distributions are of special interest in biogeography. Disjunct distributions can arise following extinction of intermediate populations of a formerly continuous range and later maintained by climatic specialization. We tested hypotheses about how the currently disjunct distribution of the Blossomcrown (Anthocephala floriceps), a hummingbird species endemic to Colombia, arose and how is it maintained. By combining molecular data and models of potential historical distributions we evaluated: (1) the timing of separation between the two populations of the species, (2) whether the disjunct distribution could have arisen as a result of fragmentation of a formerly widespread range due to climatic changes, and (3) if the disjunct distribution might be currently maintained by specialization of each population to different climatic conditions. We found that the two populations are reciprocally monophyletic for mitochondrial and nuclear loci, and that their divergence occurred ca. 1.4 million years before present (95% credibility interval 0.7–2.1 mybp). Distribution models based on environmental data show that climate has likely not been suitable for a fully continuous range over the past 130,000 years, but the potential distribution 6,000 ybp was considerably larger than at present. Tests of climatic divergence suggest that significant niche divergence between populations is a likely explanation for the maintenance of their disjunct ranges. However, based on climate the current range of A. floriceps could potentially be much larger than it currently is, suggesting other ecological or historical factors have influenced it. Our results showing that the distribution of A. floriceps has been discontinous for a long period of time and that populations exhibit different climatic niches have taxonomic and conservation implications. PMID:25251766

  14. Some introductory formalizations on the affine Hilbert spaces model of the origin of life. I. On quantum mechanical measurement and the origin of the genetic code: a general physical framework theory.

    Science.gov (United States)

    Balázs, András

    2006-08-01

    A physical (affine Hilbert spaces) frame is developed for the discussion of the interdependence of the problem of the origin (symbolic assignment) of the genetic code and a possible endophysical (a kind of "internal") quantum measurement in an explicite way, following the general considerations of Balázs (Balázs, A., 2003. BioSystems 70, 43-54; Balázs, A., 2004a. BioSystems 73, 1-11). Using the Everett (a dynamic) interpretation of quantum mechanics, both the individual code assignment and the concatenated linear symbolism is discussed. It is concluded that there arises a skewed quantal probability field, with a natural dynamic non-linearity in codon assignment within the physical model adopted (essentially corresponding to a much discussed biochemical frame of self-catalyzed binding (charging) of t RNA like proto RNAs (ribozymes) with amino acids). This dynamic specific molecular complex assumption of individual code assignment, and the divergence of the code in relation to symbol concatenation, are discussed: our frame supports the former and interpret the latter as single-type codon (triplet), also unambiguous and extended assignment, selection in molecular evolution, corresponding to converging towards the fixedpoint of the internal dynamics of measurement, either in a protein- or RNA-world. In this respect, the general physical consequence is the introduction of a fourth rank semidiagonal energy tensor (see also Part II) ruling the internal dynamics as a non-linear in principle second-order one. It is inferred, as a summary, that if the problem under discussion could be expressed by the concepts of the Copenhagen interpretation of quantum mechanics in some yet not quite specified way, the matter would be particularly interesting with respect to both the origin of life and quantum mechanics, as a dynamically supported natural measurement-theoretical split between matter ("hardware") and (internal) symbolism ("software") aspects of living matter.

  15. A case study on the genetic origin of the high oleic acid trait through FAD2-1 DNA sequence variation in safflower (Carthamus tinctorius L.

    Directory of Open Access Journals (Sweden)

    Sara eRapson

    2015-09-01

    Full Text Available The safflower (Carthamus tinctorius L. is considered a strongly domesticated species with a long history of cultivation. The hybridization of safflower with its wild relatives has played an important role in the evolution of cultivars and is of particular interest with regards to their production of high quality edible oils. Original safflower varieties were all rich in linoleic acid, while varieties rich in oleic acid have risen to prominence in recent decades. The high oleic acid trait is controlled by a partially recessive allele ol at a single locus OL. The ol allele was found to be a defective microsomal oleate desaturase FAD2-1. Here we present DNA sequence data and DNA Southern blot analysis suggesting that there has been an ancient hybridization and introgression of the FAD2-1 gene into C. tinctorius from its wild relative C. palaestinus. It is from this gene that FAD2-1Δ was derived more recently. Identification and characterization of the genetic origin and diversity of FAD2-1 could aid safflower breeders in reducing population size and generations required for the development of new high oleic acid varieties by using perfect molecular marker-assisted selection.

  16. Genetic evidence for a worldwide chaotic dispersion pattern of the arbovirus vector, Aedes albopictus

    Science.gov (United States)

    Manni, Mosè; Guglielmino, Carmela R.; Scolari, Francesca; Vega-Rúa, Anubis; Failloux, Anna-Bella; Somboon, Pradya; Lisa, Antonella; Savini, Grazia; Bonizzoni, Mariangela; Gomulski, Ludvik M.; Malacrida, Anna R.

    2017-01-01

    Background Invasive species represent a global concern for their rapid spread and the possibility of infectious disease transmission. This is the case of the global invader Aedes albopictus, the Asian tiger mosquito. This species is a vector of medically important arboviruses, notably chikungunya (CHIKV), dengue (DENV) and Zika (ZIKV). The reconstruction of the complex colonization pattern of this mosquito has great potential for mitigating its spread and, consequently, disease risks. Methodology/Principal findings Classical population genetics analyses and Approximate Bayesian Computation (ABC) approaches were combined to disentangle the demographic history of Aedes albopictus populations from representative countries in the Southeast Asian native range and in the recent and more recently colonized areas. In Southeast Asia, the low differentiation and the high co-ancestry values identified among China, Thailand and Japan indicate that, in the native range, these populations maintain high genetic connectivity, revealing their ancestral common origin. China appears to be the oldest population. Outside Southeast Asia, the invasion process in La Réunion, America and the Mediterranean Basin is primarily supported by a chaotic propagule distribution, which cooperates in maintaining a relatively high genetic diversity within the adventive populations. Conclusions/Significance From our data, it appears that independent and also trans-continental introductions of Ae. albopictus may have facilitated the rapid establishment of adventive populations through admixture of unrelated genomes. As a consequence, a great amount of intra-population variability has been detected, and it is likely that this variability may extend to the genetic mechanisms controlling vector competence. Thus, in the context of the invasion process of this mosquito, it is possible that both population ancestry and admixture contribute to create the conditions for the efficient transmission of

  17. Genetic Footprints of Iberian Cattle in America 500 Years after the Arrival of Columbus

    Science.gov (United States)

    Martínez, Amparo M.; Gama, Luis T.; Cañón, Javier; Ginja, Catarina; Delgado, Juan V.; Dunner, Susana; Landi, Vincenzo; Martín-Burriel, Inmaculada; Penedo, M. Cecilia T.; Rodellar, Clementina; Vega-Pla, Jose Luis; Acosta, Atzel; Álvarez, Luz A.; Camacho, Esperanza; Cortés, Oscar; Marques, Jose R.; Martínez, Roberto; Martínez, Ruben D.; Melucci, Lilia; Martínez-Velázquez, Guillermo; Muñoz, Jaime E.; Postiglioni, Alicia; Quiroz, Jorge; Sponenberg, Philip; Uffo, Odalys; Villalobos, Axel; Zambrano, Delsito; Zaragoza, Pilar

    2012-01-01

    Background American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of the genetic status of Creole cattle is essential for the establishment of conservation programs of these historical resources. Methodology/Principal Findings We sampled 27 Creole populations, 39 Iberian, 9 European and 6 Zebu breeds. We used microsatellite markers to assess the origins of Creole cattle, and to investigate the influence of different breeds on their genetic make-up. The major ancestral contributions are from breeds of southern Spain and Portugal, in agreement with the historical ports of departure of ships sailing towards the Western Hemisphere. This Iberian contribution to Creoles may also include some African influence, given the influential role that African cattle have had in the development of Iberian breeds, but the possibility of a direct influence on Creoles of African cattle imported to America can not be discarded. In addition to the Iberian influence, the admixture with other European breeds was minor. The Creoles from tropical areas, especially those from the Caribbean, show clear signs of admixture with Zebu. Conclusions/Significance Nearly five centuries since cattle were first brought to the Americas, Creoles still show a strong and predominant signature of their Iberian ancestors. Creole breeds differ widely from each other, both in genetic structure and influences from other breeds. Efforts are needed to avoid their extinction or further genetic erosion, which would compromise centuries of selective adaptation to a wide range of

  18. Genetic footprints of Iberian cattle in America 500 years after the arrival of Columbus.

    Directory of Open Access Journals (Sweden)

    Amparo M Martínez

    Full Text Available BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of the genetic status of Creole cattle is essential for the establishment of conservation programs of these historical resources. METHODOLOGY/PRINCIPAL FINDINGS: We sampled 27 Creole populations, 39 Iberian, 9 European and 6 Zebu breeds. We used microsatellite markers to assess the origins of Creole cattle, and to investigate the influence of different breeds on their genetic make-up. The major ancestral contributions are from breeds of southern Spain and Portugal, in agreement with the historical ports of departure of ships sailing towards the Western Hemisphere. This Iberian contribution to Creoles may also include some African influence, given the influential role that African cattle have had in the development of Iberian breeds, but the possibility of a direct influence on Creoles of African cattle imported to America can not be discarded. In addition to the Iberian influence, the admixture with other European breeds was minor. The Creoles from tropical areas, especially those from the Caribbean, show clear signs of admixture with Zebu. CONCLUSIONS/SIGNIFICANCE: Nearly five centuries since cattle were first brought to the Americas, Creoles still show a strong and predominant signature of their Iberian ancestors. Creole breeds differ widely from each other, both in genetic structure and influences from other breeds. Efforts are needed to avoid their extinction or further genetic erosion, which would compromise centuries of selective adaptation

  19. Chimpanzee genomic diversity reveals ancient admixture with bonobos

    DEFF Research Database (Denmark)

    de Manuel, Marc; Kuhlwilm, Martin; Frandsen, Peter

    2016-01-01

    Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor o...

  20. Authentic, Original, and Valuable

    DEFF Research Database (Denmark)

    Tupasela, Aaro Mikael; Tamminen, Sakari

    2015-01-01

    The idea of genetic authenticity and origin has been an important issue within genetics for decades for scientific, political, and economic reasons. The question of where species and populations come from, as well as the linking of genetic traits to particular geographical locations, has resurfaced...... as both a scientific and political site of interest more recently through the study of population genetics in both humans and non-humans. This article explores the ways in which genetics and notions of ‘authentic’, ‘indigenous’, and ‘endemic’ have become intertwined with everyday practices in research....... Using the case of human and non-human genetics to compare and contrast the various facets associated with genetic identity, we seek to develop a broader picture of the ways in which genetics plays an important role in stabilizing categories of origin....

  1. Shrinkage-reducing admixtures and early-age desiccation in cement pastes and mortars

    DEFF Research Database (Denmark)

    Bentz, D. P.; Geiker, Mette Rica; Hansen, Kurt Kielsgaard

    2001-01-01

    Fundamental studies of the early-age desiccation of cement-based materials with and without a shrinkage-reducing admixture (SRA) have been performed. Studies have been conducted under both sealed and drying conditions. Physical measurements include mass loss, surface tension, X-ray absorption...

  2. Rare earth metals appliance for magnetic admixtures recovery from mineral premixes

    Directory of Open Access Journals (Sweden)

    A. A. Shevtsov

    2012-01-01

    Full Text Available The analysis of the material composition metallomagnetic admixtures of mineral premix. It is shown that the dressed metallomagnetic impurity includes low-magnetic particles with low magnetic susceptibility. Removing these particles from the product stream in process of magnetic separation using high-energy rare earth magnets is a challenging task.

  3. Diffusion Decay Coefficient for Chloride Ions of Concrete Containing Mineral Admixtures

    Directory of Open Access Journals (Sweden)

    Jae-Im Park

    2016-01-01

    Full Text Available The diffusion coefficient for chloride ions and the diffusion decay coefficient for chloride ions are essential variables for a service life evaluation of concrete structures. They are influenced by water-binder ratio, exposure condition, curing temperature, cement type, and the type and use of mineral admixture. Mineral admixtures such as ground granulated blast furnace slag, fly ash, and silica fume have been increasingly used to improve resistance against chloride ions penetration in concrete structures built in an offshore environment. However, there is not enough measured data to identify the statistical properties of diffusion decay coefficient for chloride ions in concrete using mineral admixtures. This paper is aimed at evaluating the diffusion decay coefficient for chloride ions of concrete using ordinary Portland cement or blended cement. NT BUILD 492 method, an electrophoresis experiment, was used to measure the diffusion coefficient for chloride ions with ages. It was revealed from the test results that the diffusion decay coefficient for chloride ions was significantly influenced by W/B and the replacement ratio of mineral admixtures.

  4. Genetic structure of red-handed howler monkey populations in the fragmented landscape of Eastern Brazilian Amazonia

    Directory of Open Access Journals (Sweden)

    Heitor B. Bastos

    2010-01-01

    Full Text Available We genotyped 15 microsatellite loci in order to evaluate the effects of habitat fragmentation, caused by flooding of the Tucuruí reservoir, on the genetic structure of Alouatta belzebul in eastern Amazonia. The analysis included two populations sampled in 1984, representing both margins of the Tocantins river, and three populations sampled 18 years later. Minimal differences in the diversity levels between present-day (Ho = 0.62-0.69 and A R = 6.07-7.21 and pre-flooding (Ho = 0.60-0.62 and A R = 6.27-6.77 populations indicated there was no significant loss of genetic variability, possibly because of successful management strategies applied during the flooding. The changes observed were limited to shifts in the composition of alleles, which presumably reflect the admixture of subpopulations during flooding. Given this, there were significant differences in the Rst values (p = 0.05 in all but one between-site comparison. Both present-day and original populations showed a deficit of heterozygotes, which suggests that this may be typical of the species, at least at a local level, perhaps because of specific ecological characteristics. The relatively large number of private alleles recorded in all populations may be a consequence of the Wahlund effect resulting from population admixture or a process of expansion rather than the loss of rare alleles through genetic drift. Additionally, the levels of genetic variability observed in this study were higher than those reported for other species of Neotropical primates, suggesting good fitness levels in these A. belzebul populations. Regular genetic monitoring of remnant populations, especially on islands, should nevertheless be an integral component of long-term management strategies.

  5. The role of the Vlax Roma in shaping the European Romani maternal genetic history.

    Science.gov (United States)

    Salihović, Marijana Peričić; Barešić, Ana; Klarić, Irena Martinović; Cukrov, Slavena; Lauc, Lovorka Barać; Janićijević, Branka

    2011-10-01

    The Roma are comprised of many founder groups of common Indian origins but different socio-cultural characteristics. The Vlax Roma are one of the founder Roma populations characterized by a period of bondage in the historic Romanian principalities, and by the archaic Romanian language. Demographic history suggests different migration routes of Roma populations, especially after their arrival in Mesopotamia and the eastern boundary of the Byzantine Empire. Although various genetic studies of uniparental genetic markers showed a connection between Roma genetic legacy and their migration routes, precise sampling of Roma populations elucidates this relationship in more detail. In this study, we analyzed mitochondrial DNA of 384 Croatian Vlax Roma from two geographic locations in the context of 734 European Roma samples. Our results show that Roma migration routes are marked with two Near-Eastern haplogroups, X2 and U3, whose inverse proportional incidence clearly separates the Balkan and the Vlax Roma from other Roma populations that reached Europe as part of the first migration wave. Spatial and temporal characteristics of these haplogroups indicate a possibility of their admixture with Roma populations before arrival in Europe. Distribution of haplogroup M35 indicates that all Vlax Roma populations descend from one single founder population that might even reach back to the original ancestral Indian population. Founder effects followed by strict endogamy rules can be traced from India to contemporary small, local communities, as in the case of two Croatian Vlax Roma populations that show clear population differentiation despite similar origins and shared demographic history.

  6. Assessing Patterns of Admixture and Ancestry in Canadian Honey Bees

    Science.gov (United States)

    Canada has a large beekeeping industry comprised of 8483 beekeepers managing 672094 23 colonies. Canadian honey bees, like all honey bees in the New World, originate from centuries of importation of predominately European honey bees, but their precise ancestry remains unknown. There have been no i...

  7. 含掺合料混凝土水化产物体积分数计算及其影响因素%Calculation of concrete with mineral admixture hydration products volume fraction and its influential factors

    Institute of Scientific and Technical Information of China (English)

    吴福飞; 董双快; 宫经伟; 陈亮亮; 李东生; 侍克斌

    2016-01-01

    and the same mineral admixture content, the hydration extent of cement-based materials with lithium slag was maximal, followed by fly ash, steel slag was minimal, and it could be improved when curing period was extended. The calculated volume fractions of composite cementitious material, CSH, aluminates phase AF and CH in composite cementitious material were lower than cement paste, the volume fraction of unhydrated particles and pores were higher than cement slurry. The volume fraction of unhydrated particles, CSH, CH, aluminates phase AF and pores in lithium slag-cement based was 36.64%, 37.01%, 9.48%, 17.45% and 8.68%, respectively. The volume fraction of unhydrated particles, CSH, CH, aluminates phase AF and pores of fly ash and steel slag-cement based was 100.93%, 91.49%, 101.79%, 102.81%, 131.80% and 97.59%, 91.38%, 106.33%, 97.71%, 170.16% that of lithium slag-cement based. The volume of the pores and CSH gel increased because of the secondary reactions between CH in cement and SiO2 and Al2O3 in mineral admixture when lithium slag, fly ash and slag were incorporated. But the volume fraction of CSH in cement-lithium slag slurry and the volume fraction of AF in cement- fly ash slurry were larger than others, even if the water-cement ratio was from 0.30 to 0.40. Mineral admixtures was different because of chemical composition of mineral admixtures, pozzolanic activity, particle morphology and origin and processing techniques was different, therefore, the volume fraction of unhydrated particles, pores, CSH, CH and aluminates phase were affected by water-cement ratio with content and admixture species, water-cement ratio, water-cement ratio and admixture species and content, respectively. On the whole, the performance of cement-lithium slag slurry was the best, followed by cement-fly ash slurry, and cement-steel slag was the minimum. This study can provide valuble information for lithium slag, fly ash and steel slag to use in cement and concrete, and to reduce

  8. Race, Interracial Admixture and Genetic Differentiation of Avocado (Persea americana Mill)

    Science.gov (United States)

    Avocado (Persea americana Mill.) is a major tropical fruit crop native to Mesoamerica and domesticated around 8000 to 7000 BC. It is a member of the Laureace family and currently classified into three subspecies or races: Guatemalan (G), Mexican (M) and West Indian (WI) according to their ecological...

  9. Genetic affinity among five different population groups in India reflecting a Y-chromosome gene flow.

    Science.gov (United States)

    Saha, Anjana; Sharma, Swarkar; Bhat, Audesh; Pandit, Awadesh; Bamezai, Ramesh

    2005-01-01

    Four binary polymorphisms and four multiallelic short tandem repeat (STR) loci from the nonrecombining region of the human Y-chromosome were typed in different Indian population groups from Uttar Pradeh (UP), Bihar (BI), Punjab (PUNJ), and Bengal (WB) speaking the Indo-Aryan dialects and from South India (SI) with the root in the Dravidian language. We identified four