A5054617014- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- Plant Reproductive Biology
- Plant and animal studies
- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Animal Behavior and Reproduction
- Parasitic Infections and Diagnostics
- Genetic and phenotypic traits in livestock
- Chromosomal and Genetic Variations
- Genetic and Environmental Crop Studies
- Agricultural Systems and Practices
- Isotope Analysis in Ecology
- Machine Learning in Bioinformatics
- Animal Ecology and Behavior Studies
- Wildlife Ecology and Conservation
- Plant Virus Research Studies
- Genomics and Chromatin Dynamics
- Plant-Microbe Interactions and Immunity
- Plant nutrient uptake and metabolism
- Mathematical and Theoretical Epidemiology and Ecology Models
- Marine Biology and Ecology Research
- RNA Research and Splicing
- Plant Gene Expression Analysis
Max Planck Institute for Plant Breeding Research
2018-2024
BioNTech (Germany)
2023-2024
Max Planck Society
2024
École Polytechnique Fédérale de Lausanne
2015-2019
SIB Swiss Institute of Bioinformatics
2015-2016
Ludwig-Maximilians-Universität München
2009-2014
Urologische Klinik München
2012
Irvine University
2011
Université de Montpellier
2010
Institut des Sciences de l'Evolution de Montpellier
2010
How natural selection affects mouse coat color Evolution, at its core, involves changes in the frequency of alleles subject to selection. But identifying target can be difficult. Barrett et al. investigated how allele frequencies affecting pigmentation change over time (see Perspective by Pelletier). Wild-caught mice ( Peromyscus maniculatus ) were exposed avian predators against naturally occurring dark or light backgrounds. Natural yielded shifts coloration owing genetic variants Agouti...
How is time encoded into organ growth and morphogenesis? We address this question by investigating heteroblasty, where leaf development form are modified with progressing plant age. By combining morphometric analyses, fate-mapping through live-imaging, computational genetics, we identify age-dependent changes in cell-cycle-associated histogenesis that underpin heteroblasty. show juvenile leaves, cell proliferation competence rapidly released a "proliferation burst" coupled fast growth,...
Abstract Drosophila melanogaster spread from sub-Saharan Africa to the rest of world colonizing new environments. Here, we modeled joint demography African (Zimbabwe), European (The Netherlands), and North American (North Carolina) populations using an approximate Bayesian computation (ABC) approach. By testing different models (including scenarios with continuous migration), found that admixture between Europe most likely generated population, estimated proportion ancestry 15%. We also...
With the availability of whole-genome sequence data biologists are able to test hypotheses regarding demography populations. Furthermore, advancement Approximate Bayesian Computation (ABC) methodology allows demographic inference be performed in a simple framework using summary statistics. We present here msABC, coalescent-based software that facilitates simulation multi-locus data, suitable for an ABC analysis. msABC is based on Hudson's ms algorithm, which used extensively simulating...
Seed and egg dormancy is a prevalent life-history trait in plants invertebrates whose storage effect buffers against environmental variability, modulates species extinction fragmented habitats, increases genetic variation. Experimental evidence for reliable differences over evolutionary scales (e.g., seed banks between sister species) scarce because complex ecological experiments the field are needed to measure them. To cope with these difficulties, we developed an approximate Bayesian...
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from theoretical perspective over the last century. Wright Haldane laid foundation for expectations under an island-continent model, demonstrating island-specific beneficial allele may be maintained locally if selection coefficient larger than rate migration ancestral continent. Subsequent extensions this model have provided considerably more insight. Yet, connecting...
The cohabitation of Drosophila melanogaster with humans is nearly ubiquitous. Though it has been well established that this fly species originated in sub-Saharan Africa, and only recently spread globally, many details its swift expansion remain unclear. Elucidating the demographic history D. provides a unique opportunity to investigate how human movement might have impacted patterns genetic diversity commensal species, as providing neutral null models for studies aimed at identifying genomic...
Foundation models have achieved remarkable success in several fields such as natural language processing, computer vision and more recently biology. DNA foundation particular are emerging a promising approach for genomics. However, so far no model has delivered granular, nucleotide-level predictions across wide range of genomic regulatory elements, limiting their practical usefulness. In this paper, we build on our previous work the Nucleotide Transformer (NT) to develop segmentation model,...
Language models are thriving, powering conversational agents that assist and empower humans to solve a number of tasks. Recently, these were extended support additional modalities including vision, audio video, demonstrating impressive capabilities across multiple domains healthcare. Still, remain limited in biology as they cannot yet fully comprehend biological sequences. On the other hand, high-performance foundation for sequences have been built through self-supervision over sequencing...
Self-fertilization is hypothesized to be an evolutionary dead end because reversion outcrossing can rarely happen, and selfing lineages are thought rapidly become extinct of limited potential for adaptation and/or accumulation deleterious mutations. We tested these two assumptions by combining morphological characters molecular-evolution analyses in a tribe hermaphroditic grasses (Triticeae). First, we determined the mating system 19 studied species. Then, sequenced 27 protein-coding loci...
Southeast Asian populations of the fruit fly Drosophila melanogaster differ from ancestral African and derived European by several morphological characteristics. It has been argued that this differentiation could be result an early colonization Asia predated migration D. to Europe after last glacial period (around 10,000 years ago). To investigate process Asia, we collected nucleotide polymorphism data for more than 200 X-linked fragments 50 autosomal loci a population Malaysia. We analyzed...
Abstract Understanding the process of adaptation during rapid environmental change remains one central focal points evolutionary biology. The recently formed White Sands system southern New Mexico offers an outstanding example adaptation, with a variety species having rapidly evolved blanched forms on dunes that contrast their close relatives in surrounding dark soil habitat. In this study, we focus two lizard species, Sceloporus cowlesi and Aspidoscelis inornata , for which previous...
Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, employing comparative transcriptomics six Arabidopsis thaliana accessions and three additional Brassicaceae species investigate responses, we identified a set genes that commonly respond MAMP flg22 exhibit species-specific expression...
We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta . observed strong genetic differentiation among several ancestry groups broader distribution of Iberian relict strains European C compared to Arabidopsis. found synchronization between vegetative reproductive development a pervasive role for heterochronic pathways shaping variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia,...
The evolution from outcrossing to selfing occurred recently across the eukaryote tree of life in plants, animals, fungi, and algae. Despite short-term advantages, is hypothetically an evolutionary dead-end reproductive strategy. tippy distribution on phylogenies suggests that most species are recent origin. However, dating such transitions challenging yet central for testing this hypothesis. We build previous theories disentangle differential effect past changes rate or population size...
A transition to selfing can be beneficial when mating partners are scarce, for example, due ploidy changes or at species range edges. Here, we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and it contributed the establishment of allotetraploid kamchatica. First, provide chromosome-level genome assemblies two self-fertilizing A. lyrata accessions, one from North America Siberia, including a fully assembled S-locus latter. We then propose sequence events...
How tissue-level information encoded by fields of regulatory gene activity is translated into the patterns cell polarity and growth that generate diverse shapes different species remains poorly understood. Here, we investigate this problem in case leaf shape differences between
Mechanisms through which the evolution of gene regulation causes morphological diversity are largely unclear. The tremendous shape variation among plant leaves offers attractive opportunities to address this question. In cruciferous plants, REDUCED COMPLEXITY (RCO) homeodomain protein evolved via duplication and acquired a novel expression domain that contributed leaf diversity. However, molecular pathways RCO regulates growth unknown. A key question is identify genome-wide transcriptional...
Communities in spatially fragmented deep-sea hydrothermal vents rich polymetallic sulfides could soon face major disturbance events due to mineral mining, such that unraveling patterns of gene flow between vent populations will be an important step the development conservation policies. Indeed, time required by recover following habitat perturbations depends both on direction and number migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod...
During his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for observed change in allele frequencies. This model has since been invoked number analyses, focus discussion centering mainly on random or oscillatory fluctuations intensities. Here, we present novel method to consider nonrandom changes intensities using Wright-Fisher approximate Bayesian (ABC)-based approaches, order detect and...
Drosophila melanogaster as a cosmopolitan species has successfully adapted to wide range of different environments. Variation in temperature is one important environmental factor that influences the distribution nature. In particular for insects, which are mostly ectotherms, ambient plays major role their ability colonize new habitats. Chromatin-based gene regulation known be sensitive temperature. Ambient leads changes activation genes regulated this manner. One such regulatory system...