Christian Schlotterer

..Plasmids are an important component of the bacterial genome, but the crosstalk between genes encoded on the chromosome and on the plasmid is still poorly understood...

..Until now, such composite microsatellites have not been investigated in a comprehensive manner...

..Sequencing of cDNA does not only provide an estimate of the absolute expression level, it can also be used for the identification of allele specific gene expression...

..The allele-specific mutation rate of 3.0 x 10(-4) per generation is within the range of mammalian mutation rates. Future microsatellite analyses will have to account for the dramatic differences in allele-specific mutation rates...

..As the latter are notoriously difficult to obtain for experimental data, we suggest that other statistics, such as lnRV, may be better suited to the identification of microsatellite loci subject to selection...

..We propose that the availability of D. melanogaster populations with high and low population structure provides a novel tool for the identification of ecologically important adaptations by hitchhiking mapping...

..This result provides a possible explanation for the genome-wide low density of microsatellites in E. coli. Furthermore, we show that the F-plasmid induced microsatellite instability is independent of the mismatch repair pathway...

..Furthermore, this 'hitchhiking mapping' could also help in the functional characterization of genomes...

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..7 repeats vs. 12.2 repeats). Characterization of 11 microsatellite loci mapping to division 40-49 on the fourth chromosome of D. virilis indicated that D. virilis microsatellites are more variable than those of D. melanogaster...

..This result suggests that diversity estimates based on SNPs from ancestral populations could provide a general strategy to avoid biased SNP diversity estimates. Finally, the potential of SNPs for nonmodel organisms is discussed...

..g., fragile X and Huntington's disease). A detailed understanding of the processes underlying microsatellite instability is therefore an important contribution toward a better understanding of these human neurodegenerative diseases...

..melanogaster populations was low (F(ST) = 0.0012). Also a tree of individuals based on the proportion of shared alleles and a model-based clustering method provided no evidence for population substructuring...

..a. americana and D. a. texana as well as between the neo-X and neo-Y chromosomes in D. a. americana. Nevertheless, levels of variability were similar among the neo-sex chromosomes, indicating a very recent origin...

..The ln RV test statistic is applied to a data set of 94 loci typed in eight non-African and two African human populations...

..Our results imply that the population structure and demographic past of African D. melanogaster populations need to be considered for the inference of footprints of selection in non-African populations...

..In the light of the well-established African origin of D. melanogaster, our results cast severe doubts about the suitability of mtDNA for biogeographic inference in this model organism...

..Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects...

..Finally, we also identified several transcripts with a noncanonical structure, suggesting that processing of mitochondrial transcripts may be more complex than previously assumed...

..Pairwise F(ST) analysis, however, indicated significant population differentiation between all eight populations surveyed. A significant signal for population reduction in cosmopolitan populations was found only for X-linked loci...

..simulans. We conclude that our data are not compatible with a neutral scenario. Thus, the reduced variability at X-linked loci is most likely caused by selective sweeps associated with the out-of-Africa habitat expansion of D. simulans...

..Our study suggests that hitchhiking mapping is a universal approach for the identification of ecologically important mutations...

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..The origin of functional innovation is among the key questions in biology. Recently, it has been shown that new genes could arise from non-coding DNA and that such novel genes are often involved in male reproduction...

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..simulans. Our observation of similar levels of variability of both species will have important implications for the interpretation of patterns of molecular evolution...

..Although it is difficult to identify the evolutionary forces causing the global increase of wMel, the parallel sweep of Wolbachia and an mtDNA haplotype suggests a fitness advantage of the Wolbachia infection...

..In the case of population bottlenecks, however, our methods frequently showed fewer false positives...

..We scrutinized the evolutionary dynamics of retroposition by focusing on retrogenes for which the parental copy has degenerated...

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..simulans and D. mauritiana. Our results suggest that these species are exchanging genes more frequently than previously thought...

..Consequently temporal sampling is basic for adequate diversity and species richness estimates...

..This mechanism reduces the sequence requirement imposed on novel introns and implies that the capacity of the spliceosome to recognize weak splice sites was a prerequisite for intron gain during eukaryotic evolution...

..The remating parameter alpha was similar in both populations (a = 1.3-1.4). No more than two distinct paternal genotypes per family were detected in each population...

..Recent studies have shown that multilocus scans that compare different populations for several loci can identify genomic regions carrying a mutation that results in a local adaptation...

..Furthermore, the thermosensitivity of this network may be related to the high evolvability of several secondary sexual characters in the genus Drosophila...

..Our analyses suggest that the 454 technology has a large potential for expression profiling, and the high mapping accuracy indicates that it should be possible to compare expression profiles across species...

..google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data...

..In addition, we show that pad interacts synergistically with the repressor hairy and with Dpp signaling in posterior and anterior regions of the notum, respectively...

..Since this adaptive evolution is continuing after the split of D. mauritiana and Drosophila simulans, we conclude that genomic conflict is not restricted to short episodes, but rather an ongoing process in Drosophila...

..Finally, we identified 99 additional new genes that are not represented in the current genome contigs of D. pseudoobscura, probably due to location in genomic regions that are difficult to assemble (e.g. heterochromatic regions)...

..Phylogenetic analyses provided insights about the evolution of fiber genes in avian adenoviruses and their genetic relationships...

..Together with an analysis of intron length and splice site strength, we observe that the genomic signature of splicing-coupled selection differs between long and short introns...

..abstract:..

..This is consistent with the view that morphology can evolve by coding changes that can subtly modulate protein activity as well as cis-regulatory changes that alter expression patterns...

..melanogaster. When compared to other species, D. melanogaster has significantly shorter microsatellites. Our results suggest that the mismatch repair system may have an important role in shaping genome composition...

..Reliable expression profiling by massively parallel sequencing depends crucially on the accuracy to which the reads could be mapped to the corresponding genes...

..simulans, and artificial infections have been reported from several Drosophila species and other insects, it remains unclear to date whether DCV infections also occur naturally in other Drosophila species...

..A user-friendly software utility that carries out these steps is still lacking...