The Experts below are selected from a list of 306 Experts worldwide ranked by ideXlab platform
Michael G B Blum - One of the best experts on this subject based on the ideXlab platform.
-
NONSTATIONARY PATTERNS OF ISOLATION-BY-DISTANCE: INFERRING MEASURES OF LOCAL Genetic Differentiation WITH BAYESIAN KRIGING.
Evolution - International Journal of Organic Evolution, 2014Co-Authors: Nicolas Duforet-frebourg, Michael G B BlumAbstract:: Patterns of isolation-by-distance (IBD) arise when population Differentiation increases with increasing geographic distances. Patterns of IBD are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial variations of demographic parameters such as migration rate or population density can generate nonstationary patterns of IBD where the rate at which Genetic Differentiation accumulates varies across space. To characterize nonstationary patterns of IBD, we infer local Genetic Differentiation based on Bayesian kriging. Local Genetic Differentiation for a sampled population is defined as the average Genetic Differentiation between the sampled population and fictive neighboring populations. To avoid defining populations in advance, the method can also be applied at the scale of individuals making it relevant for landscape Genetics. Inference of local Genetic Differentiation relies on a matrix of pairwise similarity or dissimilarity between populations or individuals such as matrices of FST between pairs of populations. Simulation studies show that maps of local Genetic Differentiation can reveal barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with two datasets: single nucleotide polymorphisms from human Swedish populations and dominant markers for alpine plant species.
-
Anisotropic Isolation by Distance: The Main Orientations of Human Genetic Differentiation.
Molecular Biology and Evolution, 2012Co-Authors: Flora Jay, Per Sjödin, Mattias Jakobsson, Michael G B BlumAbstract:Genetic Differentiation among human populations is greatly influenced by geography due to the accumulation of local allele frequency differences. However, little is known about the possibly different increment of Genetic Differentiation along the different geographical axes (north-south, east-west, etc.). Here, we provide new methods to examine the asymmetrical patterns of Genetic Differentiation. We analyzed genome-wide polymorphism data from populations in Africa (n = 29), Asia (n = 26), America (n = 9), and Europe (n = 38), and we found that the major orientations of Genetic Differentiation are north-south in Europe and Africa, and east-west in Asia, but no preferential orientation was found in the Americas. Additionally, we showed that the localization of the individual geographic origins based on single nucleotide polymorphism data was not equally precise along all orientations. Confirming our findings, we obtained that, in each continent, the orientation along which the precision is maximal corresponds to the orientation of maximum Differentiation. Our results have implications for interpreting human Genetic variation in terms of isolation by distance and spatial range expansion processes. In Europe, for instance, the precise northnorthwest-southsoutheast axis of main European Differentiation cannot be explained by a simple Neolithic demic diffusion model without admixture with the local populations because in that case the orientation of greatest Differentiation should be perpendicular to the direction of expansion. In addition to humans, anisotropic analyses can guide the description of Genetic Differentiation for other organisms and provide information on expansions of invasive species or the processes of plant dispersal.
-
Research article Anisotropic Isolation by Distance: The Main Orientations of Human Genetic Differentiation
2012Co-Authors: Flora Jay, Mattias Jakobsson, Michael G B BlumAbstract:Genetic Differentiation among human populations is greatly influenced by geography due to the accumulation of local allele frequency differences. However, little is known about the possibly different increment of Genetic Differentiation along the different geographical axes (north–south, east–we st, etc.). Here, we provide new methods t o examine the asymmetrical patterns of Genetic Differentiation. We analyzed genome-wide polymorphism data from populations in Africa (n = 29), Asia (n = 26), America (n =9 ), and Europe (n = 38), and we found that the major orientations of Genetic Differentiation are north–south in Europe and Africa, and east–west in Asia, but no preferential orientation was found in the Americas. Additionally, we showed that the localization of the individual geographic origins based on single nucleotide polymorphism data was not equally precise along all orientations. Confirming our findings, we obtained that, in each continent, the orientation along which the precision is maximal corresponds to the orientation of maximum Differentiation. Our results have implications for interpreting human Genetic variation in terms of isolation by distance and spatial range expansion processes. In Europe, for instance, the precise northnorthwest–southsoutheast axis of main European Differentiation cannot be explained by a simple Neolithic demic diffusion model without admixture with the local populations because in that case the orientation of greatest Differentiation should be perpendicular to the direction of expansion. In addition to humans, anisotropic analyses can guide the description of Genetic Differentiation for other organisms and provide information on expansions of invasive species or the processes of plant dispersal.
Bao-rong Lu - One of the best experts on this subject based on the ideXlab platform.
-
Introgression from cultivated rice influences Genetic Differentiation of weedy rice populations at a local spatial scale.
Theoretical and Applied Genetics, 2011Co-Authors: Zhuxi Jiang, Barbara Basso, Bao-rong LuAbstract:Hybridization and introgression can play an important role in Genetic Differentiation and adaptive evolution of plant species. For example, a conspecific feral species may frequently acquire new alleles from its coexisting crops via introgression. However, little is known about this process. We analyzed 24 weedy rice (Oryza sativa f. spontanea) populations and their coexisting rice cultivars from northern Italy to study their Genetic Differentiation, outcrossing, and introgression based on microsatellite polymorphisms. A total of 576 maternal plants representing 24 weedy populations were used to estimate their Genetic Differentiation, and 5,395 progeny (seedlings) derived from 299 families of 15 selected populations were included to measure outcrossing rates. Considerable Genetic Differentiation (Fst = 0.26) was detected among weedy rice populations, although the Differentiation was not associated with the spatial pattern of the populations. Private alleles (28%) were identified in most populations that exhibited a multiple cluster assignments, indicating stronger Genetic affinities of some weedy populations. Outcrossing rates were greatly variable and positively correlated (R2 = 0.34, P = 0.02) with the private alleles of the corresponding populations. Paternity analysis suggested that ~15% of paternal specific alleles, a considerable portion of which was found to be crop-specific, were acquired from the introgression of the coexisting rice cultivars. Frequent allelic introgression into weedy populations resulting from outcrossing with nearby cultivars determines the private alleles of local feral populations, possibly leading to their Genetic Differentiation. Introgression from a crop may play an important role in the adaptive evolution of feral populations.
Jun Rong - One of the best experts on this subject based on the ideXlab platform.
-
Low Genetic Differentiation among altitudes in wild Camellia oleifera , a subtropical evergreen hexaploid plant
Tree Genetics & Genomes, 2018Co-Authors: Xiaomao Huang, Jiaming Chen, Xiaoqiang Yang, Shihua Duan, Chuan Long, Jun RongAbstract:Camellia oleifera is a subtropical evergreen plant. Cultivated C. oleifera is the most important woody oil crop in China. Wild C. oleifera is an essential Genetic resource for breeding. The patterns of Genetic Differentiation among altitudes/latitudes in wild C. oleifera are still unknown. Camellia oleifera may be predominantly hexaploid. The characteristics of polyploidy may lead to considerable biases in estimates of Genetic diversity and Differentiation. Our study used C. oleifera as a case study for analysing Genetic diversity, structure and Differentiation in polyploid plants using simple sequence repeats (SSRs). Wild C. oleifera samples were collected at different altitudes on the Jinggang and Lu mountains of China. The ploidy levels were determined with flow cytometry analysis. Eight highly polymorphic SSRs were used to genotype the samples. Genetic diversity and structure were analysed. Various estimates of Genetic Differentiation were compared. The flow cytometry results indicated that wild C. oleifera samples were all hexaploid at various altitudes of the Jinggang and Lu mountains. High levels of Genetic diversity were found on both the Jinggang and Lu mountains. Genetic structure analyses indicated clear Genetic Differentiation between the Jinggang and Lu mountains and lower Genetic Differentiation among altitudes within each mountain. Classical Genetic Differentiation estimates of Fst failed to discriminate Genetic Differentiation between and within mountains. The Rho statistic showed a moderate level of Genetic Differentiation between mountains and lower levels of Genetic Differentiation within each mountain. Our study demonstrates that Rho is the statistic of choice for estimating Genetic Differentiation in polyploids.
Dongfa Sun - One of the best experts on this subject based on the ideXlab platform.
-
solar radiation associated adaptive snp Genetic Differentiation in wild emmer wheat triticum dicoccoides
Frontiers in Plant Science, 2017Co-Authors: Jing Ren, Eviatar Nevo, Liang Chen, Xiaoli Jin, Miaomiao Zhang, Frank M You, Jirui Wang, Vladimir Frenkel, Xuegui Yin, Dongfa SunAbstract:Abstract: Whole-genome scans with large number of Genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation Genetic Differentiation causassociated by with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 meters. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable Genetic Differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05≤ FST ≤ 0.15) or high Genetic Differentiation (FST > 0.15). A total of 18 21 outlier loci under positive selection were identified by using a four different FST-outlier methodtesting algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that Genetic Differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP Genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.
Tiejun Bao - One of the best experts on this subject based on the ideXlab platform.
-
Effects of climatic gradients on Genetic Differentiation of Caragana on the Ordos Plateau, China
Landscape Ecology, 2013Co-Authors: Jiuyan Yang, Samuel A Cushman, Jie Yang, Mingbo Yang, Tiejun BaoAbstract:The genus Caragana (Fabr.) in the Ordos Plateau of Inner Mongolia, China, provides a strong opportunity to investigate patterns of Genetic Differentiation along steep climatic gradients, and to identify the environmental factors most likely to be responsible for driving the radiation. This study used a factorial, multi-model approach to evaluate alternative hypotheses and identify the combination of environmental factors that appear to drive Genetic divergence of Caragana in the Ordos Plateau. We had three specific hypotheses. First, we expected that gradients of changing climate would act as resistant factors limiting gene flow, and would provide stronger prediction of Genetic Differentiation than isolation by distance. Second, we expected that variation in precipitation would be a stronger predictor of Genetic Differentiation among populations than variation in temperature. Third, we expected that the pattern of phyloGenetic differences, in terms of derived versus ancestral states of rachis and leaf shape, would be highly correlated with these gradients of changing precipitation, reflecting adaptive radiation along gradients of changing precipitation driven by reduced gene flow and differential patterns of directional selection. As we expected, variation in precipitation was a much stronger predictor of Genetic Differentiation than were other climatic variables or isolation by distance. The pattern of phyloGenetic Differentiation among Caragana species is also closely associated with gradients of changing patterns of precipitation, suggesting that differential precipitation plays a major role in driving the Genetic Differentiation and adaptive radiation of the Caragana genus in the region of the Ordos Plateau.