The Experts below are selected from a list of 60 Experts worldwide ranked by ideXlab platform
Svante Paabo - One of the best experts on this subject based on the ideXlab platform.
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x chromosome as a marker for population history linkage disequilibrium and haplotype study in eurasian populations
European Journal of Human Genetics, 2005Co-Authors: Maris Laan, Victor Wiebe, Elza Khusnutdinova, Maido Remm, Svante PaaboAbstract:Linkage disequilibrium (LD) structure is still unpredictable because the interplay of regional recombination rate and Demographic history is poorly understood. We have compared the distribution of LD across two genomic regions differing in crossing-over activity – Xq13 (0.166 cM/Mb) and Xp22 (1.3 cM/Mb) – in 15 Eurasian populations. Demographic Events predicted to increase the LD level – genetic drift, bottleneck and admixture – had a very strong impact on extent and patterns of regional LD across Xq13 compared to Xp22. The haplotype distribution of the DXS1225–DXS8082 microsatellites from Xq13 exhibiting strong association in all populations was remarkably influenced by population history. European populations shared one common haplotype with a frequency of 25–40%. The Volga-Ural populations studied, living at the geographic borderline of Europe, showed elevated LD as well as harboring a significant fraction of haplotypes originating from East Asia, thus reflecting their past migrations and admixture. In the young Kuusamo isolate from Finland, a bottleneck has led to allelic associations between loci and shifted the haplotype distribution, but has much less affected single microsatellite allele frequencies compared to the main Finnish population. The data show that the footprint of a Demographic Event is longer preserved in haplotype distribution within a region of low crossing-over rate, than in the information content of a single marker, or between actively recombining markers. As the knowledge of LD patterns is often chosen to assist association mapping of common disease, our conclusions emphasize the importance of understanding the history, structure and variation of a study population.
Ryk Ward - One of the best experts on this subject based on the ideXlab platform.
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Linkage disequilibrium in the human genome
Nature, 2001Co-Authors: David E. Reich, Michele Cargill, Stacey Bolk, James Ireland, Pardis C. Sabeti, Daniel J. Richter, Thomas Lavery, Rose Kouyoumjian, Shelli F. Farhadian, Ryk WardAbstract:With the availability of a dense genome-wide map of single nucleotide polymorphisms (SNPs)^ 1 , a central issue in human genetics is whether it is now possible to use linkage disequilibrium (LD) to map genes that cause disease. LD refers to correlations among neighbouring alleles, reflecting ‘haplotypes’ descended from single, ancestral chromosomes. The size of LD blocks has been the subject of considerable debate. Computer simulations^ 2 and empirical data^ 3 have suggested that LD extends only a few kilobases (kb) around common SNPs, whereas other data have suggested that it can extend much further, in some cases greater than 100 kb^ 4 , 5 , 6 . It has been difficult to obtain a systematic picture of LD because past studies have been based on only a few (1–3) loci and different populations. Here, we report a large-scale experiment using a uniform protocol to examine 19 randomly selected genomic regions. LD in a United States population of north-European descent typically extends 60 kb from common alleles, implying that LD mapping is likely to be practical in this population. By contrast, LD in a Nigerian population extends markedly less far. The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked Demographic Event about 27,000–53,000 years ago.
Maris Laan - One of the best experts on this subject based on the ideXlab platform.
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x chromosome as a marker for population history linkage disequilibrium and haplotype study in eurasian populations
European Journal of Human Genetics, 2005Co-Authors: Maris Laan, Victor Wiebe, Elza Khusnutdinova, Maido Remm, Svante PaaboAbstract:Linkage disequilibrium (LD) structure is still unpredictable because the interplay of regional recombination rate and Demographic history is poorly understood. We have compared the distribution of LD across two genomic regions differing in crossing-over activity – Xq13 (0.166 cM/Mb) and Xp22 (1.3 cM/Mb) – in 15 Eurasian populations. Demographic Events predicted to increase the LD level – genetic drift, bottleneck and admixture – had a very strong impact on extent and patterns of regional LD across Xq13 compared to Xp22. The haplotype distribution of the DXS1225–DXS8082 microsatellites from Xq13 exhibiting strong association in all populations was remarkably influenced by population history. European populations shared one common haplotype with a frequency of 25–40%. The Volga-Ural populations studied, living at the geographic borderline of Europe, showed elevated LD as well as harboring a significant fraction of haplotypes originating from East Asia, thus reflecting their past migrations and admixture. In the young Kuusamo isolate from Finland, a bottleneck has led to allelic associations between loci and shifted the haplotype distribution, but has much less affected single microsatellite allele frequencies compared to the main Finnish population. The data show that the footprint of a Demographic Event is longer preserved in haplotype distribution within a region of low crossing-over rate, than in the information content of a single marker, or between actively recombining markers. As the knowledge of LD patterns is often chosen to assist association mapping of common disease, our conclusions emphasize the importance of understanding the history, structure and variation of a study population.
Celso Omoto - One of the best experts on this subject based on the ideXlab platform.
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genetic variability and Demographic history of heliothis virescens lepidoptera noctuidae populations from brazil inferred by mtdna sequences
Bulletin of Entomological Research, 2012Co-Authors: K C Albernaz, Karina L Silvabrandao, P Fresia, Fernando L Consoli, Celso OmotoAbstract:Intra- and inter-population genetic variability and the Demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent Demographic expansion. The recent expansion was supported by other Demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima’s D and Fu’s FS parameters. In addition, high values of haplotype diversity (^ H) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ< θW, suggested a recent Demographic expansion of H. virescens populations in Brazil. This Demographic Event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.
Christian Schlotterer - One of the best experts on this subject based on the ideXlab platform.
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Patterns of Microsatellite Variability Among X Chromosomes and Autosomes Indicate a High Frequency of Beneficial Mutations in Non-African D. simulans
Molecular Biology and Evolution, 2004Co-Authors: Gerhard Schöfl, Christian SchlottererAbstract:We analyzed microsatellite variability at 42 X-linked and 39 autosomal loci from African and European populations of Drosophila simulans. The African D. simulans harbored significantly more microsatellite variability than the European flies. In the European population, X-linked polymorphism was more reduced than autosomal variation, whereas there was no significant difference between chromosomes in the African population. Previous studies also observed a similar pattern but failed to distinguish between a Demographic Event and a selection scenario. We performed extensive computer simulations using a wide range of Demographic scenarios to distinguish between the two hypotheses. Approximate summary likelihood estimates differed dramatically among X chromosomes and autosomes. Furthermore, our experimental data showed a surplus of X-linked microsatellites with a significantly reduced variability in non-African D. simulans. We conclude that our data are not compatible with a neutral scenario. Thus, the reduced variability at Xlinked loci is most likely caused by selective sweeps associated with the out-of-Africa habitat expansion of D. simulans.