About
169
Publications
37,297
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,921
Citations
Introduction
Additional affiliations
August 2014 - present
May 2011 - July 2014
September 2006 - September 2007
Publications
Publications (169)
De novo evolved genes emerge from random parts of noncoding sequences and have, therefore, no homologs from which a function could be inferred. While expression analysis and knockout experiments can provide insights into the function, they do not directly test whether the gene is beneficial for its carrier. Here, we have used a seminatural environm...
The rate at which recombination events occur in a population is an indicator of its effective population size and the organism’s reproduction mode. It determines the extent of linkage disequilibrium along the genome and, thereby, the efficacy of both purifying and positive selection. The population recombination rate can be inferred using models of...
Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying the primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, and Cry4a from a migratory songbird seems to show enhanced magn...
Comparative sequence analysis permits unravelling the molecular processes underlying gene evolution. Many statistical methods generate candidate positions within genes, such as fast or slowly-evolving sites, coevolving groups of residues, sites undergoing positive selection or changes in evolutionary rates. Understanding the functional causes of th...
De novo evolved genes emerge from random non-coding sequences and have, therefore, no homologs from which a function could be inferred. While expression analysis and knockout experiments can provide insights into the function, they do not directly test whether the gene is beneficial for its carrier. Here, we have used a seminatural environment expe...
Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This...
The variability of gene expression levels, also known as gene expression noise, is an evolvable trait subject to selection. While gene expression noise is detrimental in constant environments where the expression level is under stabilizing selection, it may be beneficial in changing environments when the phenotype is far from the optimum. However,...
Comparative sequence analysis permits unravelling the molecular processes underlying gene evolution. Many statistical methods generate candidate positions within genes, such as fast or slowly-evolving sites, coevolving groups or residues, sites undergoing positive selection or changes in evolutionary rates. Understanding the functional causes of th...
The rate at which recombination events occur in a population is an indicator of its effective population size and the organism's reproduction mode. It determines the extent of linkage disequilibrium along the genome and, thereby, the efficacy of both purifying and positive selection. The population recombination rate can be inferred using models of...
Incomplete lineage sorting (ILS) causes the phylogeny of some parts of the genome to differ from the species tree. In this work, we investigate the frequencies and determinants of ILS in 29 major ancestral nodes across the entire primate phylogeny. We find up to 64% of the genome affected by ILS at individual nodes. We exploit ILS to reconstruct sp...
Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilisation during the Neolithic period, and the yeast remains of importance in industry and biotechnology, giving rise to bona fide domesticated populations. Here, we conduct a population genomic study of domesticated and wild populations of S. cerevis...
What shapes the distribution of nucleotide diversity along the genome? Attempts to answer this question have sparked debate about the roles of neutral stochastic processes and natural selection in molecular evolution. However, the mechanisms of evolution do not act in isolation, and integrative models that simultaneously consider the influence of m...
Expression noise, the variability of the amount of gene product among isogenic cells grown in identical conditions, originates from the inherent stochasticity of diffusion and binding of the molecular players involved in transcription and translation. It has been shown that expression noise is an evolvable trait and that central genes exhibit less...
Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying the primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, specifically Cry4 shows enhanced magnetic sensitivity in migrat...
Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilization during the Neolithic period, and the yeast remains of importance in industry and biotechnology giving rise to bona fide domesticated lineages. Here, we conduct a population genomic study of both domesticated and wild lineages of S. cerevisia...
Understanding the dynamics of species adaptation to their environments has long been a central focus of the study of evolution. Theories of adaptation propose that populations evolve by “walking” in a fitness landscape. This “adaptive walk” is characterised by a pattern of diminishing returns, where populations further away from their fitness optim...
Expression noise, the variability of the amount of gene product among isogenic cells grown in identical conditions, originates from the inherent stochasticity of diffusion and binding of the molecular players involved in transcription and translation. It has been shown that expression noise is an evolvable trait and that central genes exhibit less...
À l’origine de la diversité du vivant, l’évolution biologique est le phénomène par lequel les espèces naissent, se transforment ou disparaissent au cours du temps. Son étude fait intervenir des méthodes d’analyse sophistiquées qui reposent à la fois sur la modélisation mathématique des processus biologiques qui interviennent et sur la conception d’...
White-nose syndrome has killed millions of bats, yet both the origins and infection strategy of the causative fungus, Pseudogymnoascus destructans, remain elusive. We provide evidence for a novel hypothesis that P. destructans emerged from plant-associated fungi and retained invasion strategies affiliated with fungal pathogens of plants. We demonst...
Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PRDM9, a key determinant of recombination dynamics in most metazoans. The historical recombination maps in birds show an apparent stasis in the positioning of recombination events. This highly conser...
Compensating substitutions happen when one mutation is advantageously selected because it restores the loss of fitness induced by a previous deleterious mutation. How frequent such mutations occur in evolution and what is the structural and functional context permitting their emergence remain open questions. We built an atlas of intra-protein compe...
Compensating substitutions happen when one mutation is advantageously selected because it restores the loss of fitness induced by a previous deleterious mutation. How frequent such mutations occur in evolution and what is the structural and functional context permitting their emergence remain open questions. We built an atlas of intra-protein compe...
What shapes the distribution of nucleotide diversity along the genome? Attempts to answer this question have sparked debate about the roles of neutral stochastic processes and natural selection in molecular evolution. However, the mechanisms of evolution do not act in isolation, and integrative models that simultaneously consider the influence of m...
Understanding the dynamics of species adaptation to their environments has long been a central focus of the study of evolution. Theories of adaptation propose that populations evolve by "walking" in a fitness landscape. This "adaptive walk" is characterised by a pattern of diminishing returns, where populations further away from their fitness optim...
The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns o...
In this article, we review the different models and methods to understand and estimate correlated evolution within the same genome, individual or species. We describe correlated evolution among traits, among genetic components and finally between traits and genetics.
The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns o...
The development of coalescent theory paved the way to statistical inference from population genetic data. In the genomic era, however, coalescent models are limited due to the complexity of the underlying ancestral recombination graph. The sequentially Markov coalescent (SMC) is a heuristic that enables the modelling of complete genomes under the c...
Homing endonucleases (HE) are enzymes capable of cutting DNA at highly specific target sequences, the repair of the generated double‐strand break resulting in the insertion of the HE‐encoding gene (“homing” mechanism). HEs are present in all three domains of life and viruses; in eukaryotes, they are mostly found in the genomes of mitochondria and c...
Comparative genome analyses of eukaryotic pathogens including fungi and oomycetes have revealed extensive variability in genome composition and structure. The genomes of individuals from the same population can exhibit different numbers of chromosomes and different organization of chromosomal segments, defining so-called accessory compartments that...
As the number of available genome sequences from both closely related species and individuals within species increased, theoretical and methodological convergences between the fields of phylogenomics and population genomics emerged. Population genomics typically focuses on the analysis of variants, while phylogenomics heavily relies on genome align...
Population genomics is a growing field stemming from soon a 100 years of developments in population genetics. Here, we summarize the main concepts and terminology underlying both theoretical and empirical statistical population genomics studies. We provide the reader with pointers toward the original literature as well as methodological and histori...
This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demog...
Chapter 2, “Processing and Analyzing Multiple Genomes Alignments with MafFilter,” was previously published without including the Electronic Supplementary Material. This has now been included in the revised version of this book.
The importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness effects to the observed patterns of polymorphism and divergence at sites under selection and sites assumed to evolve neutrally. Here, we summa...
Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datas...
Homing endonucleases (HE) are enzymes capable of excising their encoding gene and inserting it in a highly specific target sequence. As such, they act both as intronic sequences (type-I introns) and selfish invasive elements. HEs are present in all three kingdoms of life and viruses; in eukaryotes, they are mostly found in the genomes of mitochondr...
Borrowing both from population genetics and phylogenetics, the field of population genomics emerged as full genomes of several closely related species were available. Providing we can properly model sequence evolution within populations undergoing speciation events, this resource enables us to estimate key population genetics parameters such as anc...
Adaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intra-molecular level is poorly understood. To address this, we analysed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation...
Unravelling the strength, frequency, and distribution of selective variants along the genome as well as the underlying factors shaping this distribution are fundamental goals of evolutionary biology. Antagonistic host‐pathogen coevolution is thought to be a major driver of genome evolution between interacting species. While rapid evolution of patho...
Adaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intra-molecular level is poorly understood. To address this, we analysed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation...
Understanding the causes and consequences of recombination rate evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Since statistical inference of recombination maps typically depends on large samples, reaching out studies to non-model organisms requires alternative tools. Here we extend the se...
Antagonistic host-pathogen co-evolution is a determining factor in the outcome of infection and shapes genetic diversity at the population level of both partners. Little is known about the overall genomic rate of evolution in pathogens or the molecular bases of rapid adaptation. Here we apply a population genomic approach to infer genome-wide patte...
Plants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example are secreted fungal effector proteins and their host targets, which play an important role in...
Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation and rates of adaptation. In many organisms recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate an...
Plants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example are secreted fungal effector proteins and their host targets, which play an important role in...
Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation and rates of adaptation. In many organisms recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate an...
Gene expression is a noisy process: in constant environment and genotype, cell to cell variability occurs because of randomness of biochemical reactions...
Biochemical reactions within individual cells result from the interactions of molecules, typically in small numbers. Consequently, the inherent stochasticity of binding and diffusion processes g...
Because biochemical processes within individual cells involve a small number of molecules, they are subject to random fluctuations. As a result, isogenic cell populations show different concentrations of the same mRNA and protein, even in homogeneous conditions. The extent and consequences of this stochastic gene expression have only recently been...
With the advent of sequencing techniques population genomics took a major shift. The structure of data sets has evolved from a sample of a few loci in the genome, sequenced in dozens of individuals, to collections of complete genomes, virtually comprising all available loci. Initially sequenced in a few individuals, such genomic data sets are now r...
The biotrophic basidiomycete fungus Ustilago maydis causes smut disease in maize. Hallmarks of the disease are large tumors that develop on all aerial parts of the host in which dark pigmented teliospores are formed. We have identified a member of the WOPR family of transcription factors, Ros1, as major regulator of spore formation in U. maydis. ro...
Ros1 belongs to the WOPR family of transcriptional regulators.
(A) Schematic representation of the domain structure of U. maydis Ros1 protein (UmRos1, XP_011392215) and other members of the WOPR family including all WOPR proteins which have been experimentally characterized: Zymoseptoria tritici Wor1 (ZmWor1, AHH91582), Cladosporium fulvum Wor1 (Cf...
Virulence of mutants lacking either UMAG_02775 or UMAG_01390.
Wild type strains FB1 and FB2 and the corresponding UMAG_02775 and UMAG_01390 deletion and complementation strains were mixed in the indicated combinations and injected into maize seedlings. Disease symptoms were scored 12 days after infection according to Kämper et al. (2006) [10]. Colo...
List of potential direct Ros1 targets in U. maydis.
(XLSX)
Occurence of motifs related to the Wor1 binding site in the ChIP peak sequences.
(XLSX)
In vitro binding of Ros1WOPR-His to several target promoters identified by ChIP.
Ros1WOPR-His expressed and purified from E. coli was used in EMSA assays with probes corresponding to target sequences identified by ChIP in the promoters of the transcription factor gene UMAG_02775 (A), the downregulated effector genes UMAG_02854, UMAG_04040, UMAG_025...
ros1 mutants are able to mate and filament.
Strains FB1, FB2, FB1Δros1 and FB2Δros1 were grown in YEPSL to an OD600 of 1.0, washed and resuspended in water. The strains indicated on top were spotted alone and in combinations with the strains indicated on the left side on charcoal-containing PD plates and incubated at room temperature for 48h. White...
Ros1 is involved in the regulation of rum1, ust1 and hgl1.
qRT-PCR analysis of rum1, ust1, hgl1 and tup1 expression during plant infection by the wild type strains FB1 x FB2 or the corresponding ros1 deletion strains. Infected plant samples were collected at the time-points indicated below. qRT-PCR analysis was performed using the constitutively ex...
ros1-dependently regulated U. maydis genes 8 days after infection determined by RNA-seq.
(XLSX)
Validation of putative Ros1 targets identified by RNA-seq results through RT-qPCR.
The expression of genes encoding glycoside hydrolases (UMAG_05550, UMAG_04503), a trehalase: (UMAG_02212), a cyclopropane fatty acid synthase (UMAG_01070), a polyketide synthase (pks1), transcription factors (UMAG_04101, biz1, rbf1, fox1, UMAG_02775) and secreted eff...
Ros1 induces the expression of the transcription factor genes UMAG_01390 and UMAG_02775 late during infection.
qRT-PCR analysis of UMAG_02775 and UMAG_01390 expression during plant infection by the wild type strains FB1 x FB2 (grey bars) or the corresponding ros1 deletion strains (white bars). Infected plant samples were collected at the time-point...
List of genomic regions bound by Ros1 determined by ChIP-seq analysis.
(XLSX)
U. maydis strain list.
(DOCX)
Motivation:
In many organisms, including humans, recombination clusters within recombination hotspots. The standard method for de novo detection of recombinants at hotspots is sperm typing. This relies on allele-specific PCR at single nucleotide polymorphisms. Designing allele-specific primers by hand is time-consuming. We have therefore written a...
