Title: Looking down in the ancestral selection graph: A probabilistic approach to the common ancestor type distribution
Abstract: In a (two-type) Wright-Fisher diffusion with directional selection and two-way mutation, let x denote today’s frequency of the beneficial type, and given x, let h(x) be the probability that, among all individuals of today’s population, the individual whose progeny will eventually take over in the population is of the beneficial type. Fearnhead (2002) and Taylor (2007) obtained a series representation for h(x). We develop a construction that contains elements of both the ancestral selection graph and the lookdown construction and includes pruning of certain lines upon mutation. Besides interest in its own right, this construction allows a transparent derivation of the series coefficients of h(x) and gives them a probabilistic meaning. Joint work with Ute Lenz, Sandra Kluth, and Anton Wakolbinger.
Title: A framework to infer fitness landscapes from experimental evolution data
Abstract: The process of adaptation results from natural selection acting on existing genetic variation and many fundamental features of this process depend on the fitness landscape, i.e. the mapping between genotypes and fitness. These properties of fitness landscapes can now be determined empirically in microbial species thanks to the rise of experimental evolution and increasingly sophisticated molecular techniques. Yet, no generic method has been proposed to link more directly the growing amount of experimental data to theoretical models of fitness landscapes. (Read more).
Title: Estimating and disentangling weak selection on codon usage and GC-biased gene conversion using sequence polymorphism data.
Abstract: Beyond mutation and drift, nucleotide composition in a genome can be affected by weak selection, like selection on codon usage (SCU), or selective-like process, like GC-biased gene conversion (gBGC). In principle, the strength of selection or gBGC can be measured from the analysis of derived allele frequency spectra. However, this approach is sensitive to a number of confounding factors. In particular, we show by simulations that the inference is pervasively affected by polymorphism polarization errors, especially at hypermutable sites, and spatial heterogeneity in selection/gBGC strength. Here we propose a new method to quantify gBGC from DAF spectra, incorporating polarization errors and taking genomic heterogeneity into account. This method is very general in that it does not require any prior knowledge about the source of polarization errors and also provides information about mutation patterns. (Read more).
Title: Recombination rate variation and recombination hot spots in fungal plant pathogens
Abstract: We study a species complex of plant pathogenic fungi including the wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola). Speciation of Z. tritici was associated with wheat domestication and dates back to 10-12000 ya. Several closely related species of Z. tritici exist in natural grasslands in the Middle East. We have taken a comparative population genomics approach to study the underlying evolutionary processes that drive adaptive evolution of Zymoseptoria in managed and natural ecosystems. (Read more).
Title: Modeling allele frequency data under a Wright-Fisher model of drift, mutation and selection: the Beta distribution approach
Abstract: Advances in sequencing technologies have revolutionized the collection of genomic data. These data contain information about mutation rates and selection coefficients, but also demographic history of populations. Researchers have been successfully applying the coalescent process to infer these, but such approaches are limited to a rather small number of individuals. More recently, the Wright-Fisher model has been increasingly used for data analysis. However, exact results for the behavior of the allele frequency as a function of time are not available in closed analytic form. (Read more).
Title: Quantifying the effects of selection and mutation rate heterogeneity on patterns of parallel evolution
Abstract: Parallel evolution is often attributed to similar selective pressures favoring the fixation of similar evolutionary changes across multiple populations. However, parallel evolutionary changes may also be driven by selectively neutral processes when mutation rates are heterogeneous across regions of the genome, genes, and even from nucleotide to nucleotide. I discuss our work attempting to quantify the contributions of these two processes to patterns of parallel evolution observed in experimentally evolved populations of Saccromyces cervisiae (from Lang et al Nature 2013). Read more.
Title: Transition between commensalism and pathogenesis: an experimental evolution study of pathoadaptation in E. coli
Abstract: Members of the E. coli species can either be commensals, assume the form of different pathovars or of deadly pathogens. Importantly, it is thought that many pathogenic E. coli strains have a commensal ancestor. Thus, understanding evolutionary changes that lead to the commensal-to-pathogen transition is a key task. The success of such transition will partially depend on E. coli’s ability to adapt to the immune system. We hypothesized that the ability of evolved bacteria to escape specific components of host innate immunity, such as phagocytosis and killing by macrophages (MΦ), is an important trait relevant in the acquisition of bacterial virulence. Read more.
Title: Fisher’s model realism and theories of adaptation.
Abstract: Mutations and their diversity of effects is the fuel of Evolution. Yet, most population genetics models ignore this statement and its consequences. It is extremely frequent in these models to consider a single class of mutations (e.g. deleterious recessive mutations). Of course all types of mutations occur simultaneously and it is difficult to ignore this reality if we want to make quantitative predictions in evolution. The difficulty is to describe in a general and realistic way how the effect of mutations varies. Read more.
Title: Estimating Allele Age and Selection Coefficient from Time-Serial Data
Abstract: Recent advances in sequencing technologies have made available an ever-increasing amount of ancient genomic data. In particular, it is now possible to sequence whole genome data from extinct species at different time points. Such time-series data are also available in the context of experimental or viral evolution. Time-series data should allow for a more precise inference of population genetic parameters and to test hypotheses about the recent action of natural selection. We develop a likelihood method to jointly estimate the selection coefficient and the age of an allele from time-serial data. Our method can be used for allele frequencies sampled from a single diallelic locus. The transition probabilities are calculated by approximating the standard diffusion equation of the Wright–Fisher model with a one-step process. We test the accuracy of the method via simulations and discuss its performance compared to recently published methods based on time-series data. Finally, the utility of the method is illustrated with applications to two datasets collected at several time points: coat color encoding loci in horses, and whole genomes of influenza viruses.
Title: Strong selective sweeps on the X chromosomes of the great apes
Abstract: Disproportionate inheritance pattern of X chromosomes may leave stronger signature of adaptive evolution because recessive alleles are exposed to natural selection in males. We perform a comparative study on the diversity pattern of X chromosomes in all great ape species. Strikingly, the X chromosomes exhibit regions up to several megabase in size where diversity is reduced more than five fold. These regions overlap significantly among species and shows higher proportions of singleton polymorphisms, higher levels of population differentiation, and a higher non-synonymous to synonymous substitution ratio than the rest of X chromosomes. Simulations show that background selection and soft sweep along cannot explain these patterns. Thus, we conclude that strong selective sweeps target specific regions of X chromosome recurrently.
Title: The repeatability of Escherichia coli evolution in its natural environment
Abstract: Classic examples of experiments where evolution is studied in real time make use of model organisms (such as bacteria, bacteriophages or yeast) that typically evolve under a strong selective pressure a priori determined. The typical design involves following adaptive changes in multiple replicates and has revealed an impressive level of parallelism in the genetic basis of adaptation. Usually the parallelism is observed at the level of gene or operon and much more rarely at the nucleotide level. An interesting exception to the lack of parallelism at the nucleotide level are the adaptations caused by transposable elements (TE), which are known to have strong preference for particular insertion sites (hotspots). Read more.
