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Berlin Brandenburg

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  • 1
    In: Molecular Ecology, August 2011, Vol.20(15), pp.3128-3143
    Description: Admixed populations represent attractive biological models to study adaptive selection. Originating from several waves of recent introduction from European (EUT), African (AFT) and zebus (ZEB) cattle, New World Creole cattle allow investigating the response to tropical environmental challenges of these three ancestries. We here provide a detailed assessment of their genetic contributions to the Creole breed from Guadeloupe (CGU). We subsequently look for footprints of selection by combining results from tests based on the extent of haplotype homozygosity and the identification of excess/deficiency of local ancestry. To tackle these issues, 140 CGU individuals and 25 Brahman zebus from Martinique were genotyped at 44 057 SNPs. These data were combined to those available on 23 populations representative of EUT, AFT or ZEB. We found average proportions of 26.1%, 36.0% and 37.9% of EUT, AFT and ZEB ancestries in the CGU genome indicating a higher level of African and zebu ancestries than suggested by historical records. We further identified 23 genomic regions displaying strong signal of selection, most of them being characterized by an excess of ZEB local ancestry. Among the candidate gene underlying these regions, several are associated with reproductive functions (RXFP2, PMEPA1, IGFBP3, KDR, PPP1R8, TBXA2R and SLC7A5) and metabolism (PDE1B and CYP46A1). Finally, two genes (CENTD3 and SAMD12) are involved in cellular signalization of immune response. This study illustrates the relevance of admixed populations to identify footprints of selection by combining several tests straightforward to implement on large data sets.
    Keywords: Admixture ; Creole Cattle ; Footprints Of Selection ; Snps
    ISSN: 0962-1083
    E-ISSN: 1365-294X
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  • 2
    In: Molecular Ecology, June 2013, Vol.22(11), pp.3165-3178
    Description: Inexpensive short‐read sequencing technologies applied to reduced representation genomes is revolutionizing genetic research, especially population genetics analysis, by allowing the genotyping of massive numbers of single‐nucleotide polymorphisms () for large numbers of individuals and populations. Restriction site–associated () sequencing is a recent technique based on the characterization of genomic regions flanking restriction sites. One of its potential drawbacks is the presence of polymorphism within the restriction site, which makes it impossible to observe the associated allele (i.e. allele dropout, ). To investigate the effect of on genetic variation estimated from markers, we first mathematically derived measures of the effect of on allele frequencies as a function of different parameters within a single population. We then used data sets simulated using a coalescence model to investigate the magnitude of biases induced by on the estimation of expected heterozygosity and under a simple demographic model of divergence between two populations. We found that tends to overestimate genetic variation both within and between populations. Assuming a mutation rate per nucleotide between 10 and 10, this bias remained low for most studied combinations of divergence time and effective population size, except for large effective population sizes. Averaging values over multiple s, for example, by sliding window analysis, did not correct biases. We briefly discuss possible solutions to filter the most problematic cases of using read coverage to detect markers with a large excess of null alleles.
    Keywords: Allele Dropout ; Allele Frequency ; F St ; Heterozygosity ; Next‐Generation Sequencing ; Markers ; Single‐Nucleotide Polymorphisms
    ISSN: 0962-1083
    E-ISSN: 1365-294X
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  • 3
    Language: English
    In: Genetics, 2015, Vol.201(4), pp.1555-1579
    Description: In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations.
    Keywords: Population Genetics – Analysis ; Single Nucleotide Polymorphisms – Research ; Genome-Wide Association Studies – Analysis ; Genetic Variation – Research
    ISSN: 0016-6731
    Source: Cengage Learning, Inc.
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  • 4
    Language: English
    In: Molecular Ecology, 2017
    Description: A model-based approach to characterize individual inbreeding at both global and local genomic scales
    Keywords: Life Sciences ; Inbreeding ; Runs of Homozygosity ; Hidden Markov Models ; Identity-By-Descent ; Homozygosity-By-Descent ; Biology ; Ecology
    ISSN: 0962-1083
    E-ISSN: 1365-294X
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  • 5
    Language: English
    In: Genetics, 2014, Vol.196(2), pp.799-817
    Description: The recent advent of high-throughput sequencing and genotyping technologies makes it possible to produce, easily and cost effectively, large amounts of detailed data on the genotype composition of populations. Detecting locus-specific effects may help identify those genes that have been, or are currently, targeted by natural selection. How best to identify these selected regions, loci, or single nucleotides remains a challenging issue. Here, we introduce a new model-based method, called SelEstim, to distinguish putative selected polymorphisms from the background of neutral (or nearly neutral) ones and to estimate the intensity of selection at the former. The underlying population genetic model is a diffusion approximation for the distribution of allele frequency in a population subdivided into a number of demes that exchange migrants. We use a Markov chain Monte Carlo algorithm for sampling from the joint posterior distribution of the model parameters, in a hierarchical Bayesian framework. We present evidence from stochastic simulations, which demonstrates the good power of SelEstim to identify loci targeted by selection and to estimate the strength of selection acting on these loci, within each deme. We also reanalyze a subset of SNP data from the Stanford HGDP-CEPH Human Genome Diversity Cell Line Panel to illustrate the performance of SelEstim on real data. In agreement with previous studies, our analyses point to a very strong signal of positive selection upstream of the LCT gene, which encodes for the enzyme lactase-phlorizin hydrolase and is associated with adult-type hypolactasia. The geographical distribution of the strength of positive selection across the Old World matches the interpolated map of lactase persistence phenotype frequencies, with the strongest selection coefficients in Europe and in the Indus Valley.
    Keywords: Genomes – Research ; Nucleotides – Usage ; Diffusion of Innovations – Analysis ; Markov Processes – Analysis
    ISSN: 0016-6731
    Source: Cengage Learning, Inc.
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  • 6
    In: Molecular Ecology Resources, November 2014, Vol.14(6), pp.1141-1159
    Description: The recent democratization of next‐generation‐sequencing‐based approaches towards nonmodel species has made it cost‐effective to produce large genotyping data sets for a wider range of species. However, when no detailed genome assembly is available, poor knowledge about the organization of the markers within the genome might hamper the optimal use of this abundant information. At the most basic level of genomic organization, the type of chromosome (autosomes, sex chromosomes, mitochondria or chloroplast in plants) may remain unknown for most markers which might be limiting or even misleading in some applications, particularly in population genetics. Conversely, the characterization of sex‐linked markers allows molecular sexing of the individuals. In this study, we propose a Bayesian model‐based classifier named , to assign markers to their chromosome type and/or to perform sexing of individuals based on genotyping data. The performance of is further evaluated by a comprehensive simulation study and by the analysis of real data sets from various origins (microsatellite and SNP data derived from genotyping assay designs and NGS experiments). Irrespective of the origin of the markers or the size of the data set, was proved efficient (i) to identify the sex‐linked markers, (ii) to perform molecular sexing of the individuals and (iii) to perform basic quality check of the genotyping data sets. The underlying structure of the model also allows to consider each of these potential applications either separately or jointly.
    Keywords: Bayesian Models ; Genotyping Data ; Molecular Sexing ; Ngs ; Sex Chromosome
    ISSN: 1755-098X
    E-ISSN: 1755-0998
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  • 7
    Language: English
    In: PLoS ONE, 2010, Vol.5(9), p.e13038
    Description: Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time. ; This study gives a detailed assessment of cattle genetic diversity based on 1,121 individuals sampled in 47 populations from different parts of the world (with a special focus on French cattle) genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of new genotypes for 296 individuals representing 14 French cattle breeds which were combined to those available from three previously published studies. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. We further searched for spatial patterns of genetic diversity among 23 European populations, most of them being of French origin, under the recently developed spatial Principal Component analysis framework. ; Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. In addition, patterns of differentiation among the three main groups of populations—the African taurine, the European taurine and zebus—may provide some additional support for three distinct domestication centres. Finally, among the European cattle breeds investigated, spatial patterns of genetic diversity were found in good agreement with the two main migration routes towards France, initially postulated based on archeological evidence.
    Keywords: Research Article ; Genetics And Genomics ; Genetics And Genomics -- Animal Genetics ; Genetics And Genomics -- Population Genetics
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: Journal of Environmental Management, May 2017, Vol.193, pp.567-575
    Keywords: Environmental Sciences ; Environmental Engineering ; Chemical Sciences ; Analytical Chemistry ; Chemical Sciences ; Inorganic Chemistry ; Sciences of the Universe ; Earth Sciences ; Mineralogy ; Sciences of the Universe ; Earth Sciences ; Geochemistry ; Sciences of the Universe ; Earth Sciences ; Applied Geology ; Sciences of the Universe ; Continental Interfaces, Environment ; Environmental Sciences ; Economics
    ISSN: 0301-4797
    E-ISSN: 1095-8630
    Source: Hyper Article en Ligne (CCSd)
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  • 9
    Language: English
    In: Water Science and Technology, 17 January 2018, Vol.77(1), pp.79-90
    Description: French vertical flow constructed wetlands (French VFCWs) are widely used for the treatment of wastewaters from small communities. In the system, unsettled wastewater is percolated through two successive stages of filter-cells planted with reeds. This causes the formation of a surface sludge...
    Keywords: Chemical Sciences ; Inorganic Chemistry ; Chemical Sciences ; Analytical Chemistry ; Environmental Sciences ; Environmental Engineering ; Sciences of the Universe ; Earth Sciences ; Geochemistry ; Deposit ; Humification ; Organic Matter ; Sludge ; Treatment Wetland ; Vertical Flow Constructed Wetland ; Engineering ; Environmental Sciences
    ISSN: 0273-1223
    E-ISSN: 1996-9732
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  • 10
    Language: English
    In: International Journal of Mineral Processing, Sept 10, 2013, Vol.123, p.94(8)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.minpro.2013.05.002 Byline: Mathieu Gautier, Jacques Poirier, Francoise Bodenan, Gilles Franceschini, Emmanuel Veron Abstract: The recycling of basic oxygen furnace (BOF) slag is largely limited by its free lime and free magnesia content leading to highly problematic swelling, preventing civil engineering applications. Moreover the presence of phosphorus is a limited factor for their reuse in iron and steel industrial processes. The results of thermodynamic calculations coupled with cooling laboratory experiments and mineralogical characterisation are presented. The aim of this study was to follow slag crystallization with time and temperature from 1600[degrees]C to ambient temperature using standard tools but also in-situ methods. The predominance of dicalcium silicate (50wt.%) was highlighted for each type of cooling conditions then calcium ferrites with various proportions. Less total free lime/magnesia is observed for slow cooling conditions (4.5 against 14.9wt.% in the industrial sample), which is an interesting result for recycling. Experiments are in good agreement with the calculations concerning the nature of the main phases depending on the influence of oxygen. The sequence of crystallisation, the variations in the nature of silicate phases depending on the temperature and the evolution of the phosphorus content are documented. Proportions of low and high phosphorus-bearing calcium silicates are evolving with cooling, which will have to be considered when optimising phosphorus retrieval. Article History: Received 9 January 2013; Revised 29 April 2013; Accepted 20 May 2013
    Keywords: Hvac Industry -- Production Processes ; Furnaces ; Calcium Silicate
    ISSN: 0301-7516
    Source: Cengage Learning, Inc.
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