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Inferring Geographic Coordinates of Origin for Europeans Using Small Panels of Ancestry Informative Markers  [PDF]
Petros Drineas,Jamey Lewis,Peristera Paschou
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011892
Abstract: Recent large-scale studies of European populations have demonstrated the existence of population genetic structure within Europe and the potential to accurately infer individual ancestry when information from hundreds of thousands of genetic markers is used. In fact, when genomewide genetic variation of European populations is projected down to a two-dimensional Principal Components Analysis plot, a surprising correlation with actual geographic coordinates of self-reported ancestry has been reported. This substructure can hamper the search of susceptibility genes for common complex disorders leading to spurious correlations. The identification of genetic markers that can correct for population stratification becomes therefore of paramount importance. Analyzing 1,200 individuals from 11 populations genotyped for more than 500,000 SNPs (Population Reference Sample), we present a systematic exploration of the extent to which geographic coordinates of origin within Europe can be predicted, with small panels of SNPs. Markers are selected to correlate with the top principal components of the dataset, as we have previously demonstrated. Performing thorough cross-validation experiments we show that it is indeed possible to predict individual ancestry within Europe down to a few hundred kilometers from actual individual origin, using information from carefully selected panels of 500 or 1,000 SNPs. Furthermore, we show that these panels can be used to correctly assign the HapMap Phase 3 European populations to their geographic origin. The SNPs that we propose can prove extremely useful in a variety of different settings, such as stratification correction or genetic ancestry testing, and the study of the history of European populations.
Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals  [PDF]
Andrés Ruiz-Linares ,Kaustubh Adhikari,Victor Acu?a-Alonzo,Mirsha Quinto-Sanchez,Claudia Jaramillo,William Arias,Macarena Fuentes,María Pizarro,Paola Everardo,Francisco de Avila,Jorge Gómez-Valdés,Paola León-Mimila,Tábita Hunemeier,Virginia Ramallo,Caio C. Silva de Cerqueira,Mari-Wyn Burley,Esra Konca,Marcelo Zagonel de Oliveira,Mauricio Roberto Veronez,Marta Rubio-Codina,Orazio Attanasio,Sahra Gibbon,Nicolas Ray,Carla Gallo,Giovanni Poletti,Javier Rosique,Lavinia Schuler-Faccini,Francisco M. Salzano,Maria-Cátira Bortolini,Samuel Canizales-Quinteros,Francisco Rothhammer,Gabriel Bedoya,David Balding,Rolando Gonzalez-José
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004572
Abstract: 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.
Generalizing the GAGA Principle  [PDF]
Jack Hall
Mathematics , 2011,
Abstract: This paper generalizes the fundamental GAGA results of Serre cite{MR0082175} in three ways---to the non-separated setting, to stacks, and to families. As an application of these results, we show that analytic compactifications of $\mathcal{M}_{g,n}$ possessing modular interpretations are algebraizable.
Formal GAGA for good moduli spaces  [PDF]
Anton Geraschenko,David Zureick-Brown
Mathematics , 2012,
Abstract: We prove formal GAGA for good moduli space morphisms under an assumption of "enough vector bundles" (which holds for instance for quotient stacks). This supports the philosophy that though they are non-separated, good moduli space morphisms largely behave like proper morphisms.
Higher analytic stacks and GAGA theorems  [PDF]
Mauro Porta,Tony Yue Yu
Mathematics , 2014,
Abstract: We develop the foundations of higher geometric stacks in complex analytic geometry and in non-archimedean analytic geometry. We study coherent sheaves and prove the analog of Grauert's theorem for derived direct images under proper morphisms. We define analytification functors and prove the analog of Serre's GAGA theorems for higher stacks. We use the language of $\infty$-categories to simplify the theory. Our constructions and theorems cover the classical notion of 1-stacks as a special case.
Remote homologue identification of Drosophila GAGA factor in mouse  [cached]
Suresh Kumar
Bioinformation , 2011,
Abstract: GAGA factor (GAF) is involved in both gene activation and gene repression and plays a role in the modulation of chromatin structure. In Drosophila, Trithroax like (Trl) gene encodes the DNA binding protein called GAGA factor (GAF). Trl-GAF binds to GAGA sites through its C2H2 zinc finger domain and has an N-terminal BTB/POZ domain. Identification of Trl-GAF homologue in mouse helps in deeper understanding of the mechanism and function. Conventional alignment tools such as BLAST and FASTA cannot identify homologues in mouse genome as their sequence identity is below 30%. In the present study, various sequence and structure analyses were followed for the detection of remote homologues of Drosophila GAGA FACTOR in mouse to identify as Zbtb3. Through homology modeling and docking approach, the zinc finger region of mouse Zbtb3 showed conserved residues and favorable DNA binding sites with GAGA sites similar to that of Drosophila GAGA FACTOR.
The geography of recent genetic ancestry across Europe  [PDF]
Peter Ralph,Graham Coop
Quantitative Biology , 2012, DOI: 10.1371/journal.pbio.1001555
Abstract: The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.
The History of African Gene Flow into Southern Europeans, Levantines, and Jews  [PDF]
Priya Moorjani ,Nick Patterson,Joel N. Hirschhorn,Alon Keinan,Li Hao,Gil Atzmon,Edward Burns,Harry Ostrer,Alkes L. Price,David Reich
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1001373
Abstract: Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. However, there has been no accurate characterization of the proportion of mixture, or of its date. We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%–3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. Levantine groups harbor 4%–15% African ancestry with an average mixture date of about 32 generations ago, consistent with close political, economic, and cultural links with Egypt in the late middle ages. We also detect 3%–5% sub-Saharan African ancestry in all eight of the diverse Jewish populations that we analyzed. For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas.
The common ancestry of life
Eugene V Koonin, Yuri I Wolf
Biology Direct , 2010, DOI: 10.1186/1745-6150-5-64
Abstract: We devised a computational experiment on a concatenated alignment of universally conserved proteins which shows that the purported demonstration of the universal common ancestry is a trivial consequence of significant sequence similarity between the analyzed proteins. The nature and origin of this similarity are irrelevant for the prediction of "common ancestry" of by the model-comparison approach. Thus, homology (common origin) of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis.A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming.this article was reviewed by William Martin, Ivan Iossifov (nominated by Andrey Rzhetsky) and Arcady Mushegian. For the complete reviews, see the Reviewers' Report section.In the Origin of Species, Charles Darwin famously proposed what we may now call the Universal Common Ancestry (UCA) hypothesis: "I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed." [1]. For a century after the publication of Darwin's bold proposition, before the advent of molecular biology, the UCA hypothesis remained an untested and hardly testable speculation. However, first the universality of the genetic code and later the demonstration of the (near) universal conservation of approximately 100 RNA and protein-coding genes among cellular life forms provided ample evidence in support of the UCA [2,3]. Although generally considered compelling, this evidence fell short of a rigorous, formal test of the UCA hypothesis.In a recent, remarkable Letter to Nature, Theobald applied an information-theoretical approach to offer just that: a formal, homology-independent tes
Sunspots and Blindspots in The Europeans  [cached]
T. J. LUSTIG
E-rea : Revue électronique d’études sur le Monde Anglophone , 2005, DOI: 10.4000/erea.538
Abstract: In July 1878, when the first number of The Europeans appeared in the Atlantic Monthly, Henry James could hardly be said to be at the beginning of his career. Nor yet had he reached the middle of it. He was, let’s say, at the end of the beginning. It was at this juncture, I’ll argue — after the trials and occasional false starts of the early work, before the more firmly established commitments of the mature phase — that the representational cross-currents which played through his work as a who...
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