E. coli Microcosms Indicate a Tight Link between Predictability of Ecosystem Dynamics and Diversity

The diversity-stability hypothesis proposes that ecosystem diversity is positively correlated with stability. The impact of ecosystem diversity is, however, still debated. In a microcosm experiment using diverged Escherichia coli cells, we show that the fitness of community members depends on the complexity (number of participants) of the system. Interestingly, the spread of a community member with a superior genotype is mostly stochastic in low-complexity systems, but highly deterministic in a more complex environment. We conclude that system complexity provides a buffer against stochastic effects

Non-random genomic integration - an intrinsic property of retrogenes in Drosophila?

ABSTRACT: BACKGROUND: The Drosophila X-chromosome shows a significant underrepresentation of genes with male-biased gene expression (demasculinization). This trend is matched by retrogenes, which typically have a male biased gene expression pattern and show a significant movement bias from X-chromosomes to autosomes. It is currently assumed that these patterns are best explained by selection, either mediated by male meiotic sex chromosome inactivation (MSCI) or sexually antagonistic forces. We scrutinized the evolutionary dynamics of retroposition by focusing on retrogenes for which the parental copy has degenerated. RESULTS: Consistent with a functional substitution of the degenerated gene by the retrogene, patterns of sequence evolution and gene expression were similar between retroposed and parental genes. Like previous studies, our set of retrogenes showed a significant movement off the X-chromosome. In contrast to data sets where retroposition caused gene duplication, the genes in our study showed primarily female-biased or unbiased gene expression. CONCLUSIONS: Based on our results, the biased transposition pattern cannot be explained by MSCI and probably not by sexual antagonism. Rather, we propose that the movement away from the X-chromosome represents a general property of retroposition in Drosophila

Gene expression analysis indicates extensive genotype-specific crosstalk between the conjugative F-plasmid and the E. coli chromosome

BACKGROUND: 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. RESULTS: We performed a large-scale survey for genes on the E. coli chromosome that are affected by the presence of the conjugative F-plasmid (crosstalk). The expression pattern of about 4% (107 genes) of the genes encoded by the chromosome was affected by the presence of the F-plasmid. Comparing two different Escherichia coli strains, MG1655 and DH5α, we found a strong host genotype-specific crosstalk of the host chromosome with the F-plasmid. About 88% of the genes affected by the presence of the F-plasmid showed a significant plasmid by host genotype interaction, i.e. the presence of the F-plasmid resulted in a different gene expression in the two host genotypes. Less than 12% of the genes showed an additive effect of gene expression, i.e. host genotype independent crosstalk between plasmid and host chromosome. CONCLUSION: We propose that epistatic effects also contribute to the maintenance of F-plasmids in natural populations

The life cycle of Drosophila orphan genes

Funding: Austrian Science Funds (FWF) (P22834).Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements.Publisher PDFPeer reviewe

Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling

BACKGROUND:Massively parallel sequencing offers an enormous potential for expression profiling, in particular for interspecific comparisons. Currently, different platforms for massively parallel sequencing are available, which differ in read length and sequencing costs. The 454-technology offers the highest read length. The other sequencing technologies are more cost effective, on the expense of shorter reads. Reliable expression profiling by massively parallel sequencing depends crucially on the accuracy to which the reads could be mapped to the corresponding genes. METHODOLOGY/PRINCIPAL FINDINGS:We performed an in silico analysis to evaluate whether incorrect mapping of the sequence reads results in a biased expression pattern. A comparison of six available mapping software tools indicated a considerable heterogeneity in mapping speed and accuracy. Independently of the software used to map the reads, we found that for compact genomes both short (35 bp, 50 bp) and long sequence reads (100 bp) result in an almost unbiased expression pattern. In contrast, for species with a larger genome containing more gene families and repetitive DNA, shorter reads (35-50 bp) produced a considerable bias in gene expression. In humans, about 10% of the genes had fewer than 50% of the sequence reads correctly mapped. Sequence polymorphism up to 9% had almost no effect on the mapping accuracy of 100 bp reads. For 35 bp reads up to 3% sequence divergence did not affect the mapping accuracy strongly. The effect of indels on the mapping efficiency strongly depends on the mapping software. CONCLUSIONS/SIGNIFICANCE:In complex genomes, expression profiling by massively parallel sequencing could introduce a considerable bias due to incorrectly mapped sequence reads if the read length is short. Nevertheless, this bias could be accounted for if the genomic sequence is known. Furthermore, sequence polymorphisms and indels also affect the mapping accuracy and may cause a biased gene expression measurement. The choice of the mapping software is highly critical and the reliability depends on the presence/absence of indels and the divergence between reads and the reference genome. Overall, we found SSAHA2 and CLC to produce the most reliable mapping results

Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models

The genomes of related species contain valuable information on the history of the considered taxa. Great apes in particular exhibit variation of evolutionary patterns along their genomes. However, the great ape data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms. Previous methods for genome-scale analysis are restricted to very few individuals or cannot disentangle the contribution of mutation rates and fixation biases. This represents a limitation both for the understanding of these forces as well as for the detection of regions affected by selection. Here, we present a new model designed to estimate mutation rates and fixation biases from genetic variation within and between species. We relax the assumption of instantaneous substitutions, modeling substitutions as mutational events followed by a gradual fixation. Hence, we straightforwardly account for shared ancestral polymorphisms and incomplete lineage sorting. We analyze genome-wide synonymous site alignments of human, chimpanzee, and two orangutan species. From each taxon, we include data from several individuals. We estimate mutation rates and GC-biased gene conversion intensity. We find that both mutation rates and biased gene conversion vary with GC content. We also find lineage-specific differences, with weaker fixation biases in orangutan species, suggesting a reduced historical effective population size. Finally, our results are consistent with directional selection acting on coding sequences in relation to exonic splicing enhancers.Publisher PDFPeer reviewe

Genealogical lineage sorting leads to significant, but incorrect Bayesian multilocus inference of population structure

Over the past decades, the use of molecular markers has revolutionized biology and led to the foundation of a new research discipline—phylogeography. Of particular interest has been the inference of population structure and biogeography. While initial studies focused on mtDNA as a molecular marker, it has become apparent that selection and genealogical lineage sorting could lead to erroneous inferences. As it is not clear to what extent these forces affect a given marker, it has become common practice to use the combined evidence from a set of molecular markers as an attempt to recover the signals that approximate the true underlying demography. Typically, the number of markers used is determined by either budget constraints or by statistical power required to recognize significant population differentiation. Using microsatellite markers from Drosophila and humans, we show that even large numbers of loci (>50) can frequently result in statistically well-supported, but incorrect inference of population structure using the software baps. Most importantly, genomic features, such as chromosomal location, variability of the markers, or recombination rate, cannot explain this observation. Instead, it can be attributed to sampling variation among loci with different realizations of the stochastic lineage sorting. This phenomenon is particularly pronounced for low levels of population differentiation. Our results have important implications for ongoing studies of population differentiation, as we unambiguously demonstrate that statistical significance of population structure inferred from a random set of genetic markers cannot necessarily be taken as evidence for a reliable demographic inference

CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing (NGS) technologies have substantially increased the sequence output while the costs were dramatically reduced. In addition to the use in whole genome sequencing, the 454 GS-FLX platform is becoming a widely used tool for biodiversity surveys based on amplicon sequencing. In order to use NGS for biodiversity surveys, software tools are required, which perform quality control, trimming of the sequence reads, removal of PCR primers, and generation of input files for downstream analyses. A user-friendly software utility that carries out these steps is still lacking.</p> <p>Findings</p> <p>We developed CANGS (<b>C</b>leaning and <b>A</b>nalyzing <b>N</b>ext <b>G</b>eneration <b>S</b>equences) a flexible and user-friendly integrated software utility: CANGS is designed for amplicon based biodiversity surveys using the 454 sequencing platform. CANGS filters low quality sequences, removes PCR primers, filters singletons, identifies barcodes, and generates input files for downstream analyses. The downstream analyses rely either on third party software (e.g.: rarefaction analyses) or CANGS-specific scripts. The latter include modules linking 454 sequences with the name of the closest taxonomic reference retrieved from the NCBI database and the sequence divergence between them. Our software can be easily adapted to handle sequencing projects with different amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians.</p> <p>Conclusion</p> <p>CANGS performs PCR primer clipping, filtering of low quality sequences, links sequences to NCBI taxonomy and provides input files for common rarefaction analysis software programs. CANGS is written in Perl and runs on Mac OS X/Linux and is available at <url>http://i122server.vu-wien.ac.at/pop/software.html</url></p