Members

Why:

Sensory systems are critical for an organism’s survival and display remarkable diversity—as different species inhabit different environments and occupy diverse niches, sensory systems rapidly evolve to detect the cues relevant for a particular species. Examining these sensory changes in a comparative context yields insight into the evolution of the nervous system and animal behavior, and into broad questions about basic evolutionary processes such as the extent of convergence, the role of epistasis and contingency, and how novel protein functions arise. Current projects in our lab investigate the evolution of taste receptors and digestive enzymes in birds, as well as in other vertebrates.

What:

Functional evolution of sensory receptors and digestive enzymes (from diverse birds, reptiles, and fish); comparative genomics.

How:

cell-based assays, ancestral reconstruction, selection tests, comparative methods, field-based behavior.

Publications

Why:

We study under which circumstances and at what rate epigenetic diversity emerges in plant genomes, and if and how epiallelic variants are transmitted from one generation to the next. We are also interested in the phenotypic expression of such epialleles. In another line of research, we study the evolution and diversification of biosynthetic gene clusters in grasses. Lastly, we are interested in host genotypic diversity driving plant-microbe interactions.

What:

Comparative genomics in plants; comparative epigenomics; genome-wide and epigenome-wide association studies; metagenomics.

How:

We use whole-genome-bisulfite sequencing and long-read sequencing to determine epigenetic variation in plant genomes; we build machine-learning algorithms to identify epiallelic loci and large-scale phenotyping to link epigenotype/genotype to phenotype via genome-wide association. In our parallel line of research, we use synteny analysis to study the evolution and functional diversification of biosynthetic gene clusters, combining metabolomics and comparative genomics. Lastly, we use rDNA and metagenomic profiling to determine the qualitative and quantitative composition of plant-associated microbial communities to understand the impact of plant genotype on colonization and community dynamics.

Publications

Why:

Sequence data have become the main tool in evolution research. We provide a collaborative platform for generation of sequence data with short-read and long-read technologies. As a technology platform we aim to grant access to cutting-edge sequencing methods, dealing with all kinds of challenging samples and providing optimized solutions for the generation of high-quality datasets.

What:

DNA and RNA sequencing from all kingdoms of life.

How:

broad method spectrum on ONT PromethION P24 and Illumina NextSeq2000/.

Publications

Why:

We are interested in understanding the causes and consequences of individuality in behavior and life-history. Essentially, we’d like to know why it is that individuals are not just plastic but also very different from each other and whether this inter-individual variation within single populations has knock-on effects on eco-evolutionary dynamics.

What:

Behavioral ecology, population ecology, quantitative genetics (both classic and social evolution work), educational packages for unbiased study designs and data analyses.

How:

We monitor long-term populations of nest box breeding birds (blue and great tits), in which we perform longitudinal experiments of social environments. We also perform laboratory based experiments to estimate quantitative genetics underpinning of behavior.

Publications

Why:

We are interested in the molecular basis of human evolution and study it using a comparative molecular approach. We investigate brain size evolution, the evolution of speech and the evolution of regulatory networks during early development.

What:

primate iPSCs and mouse models

How:

iPSC technologies, (sc)RNA-seq, massively parallel reporter assays

Publications

Why:

Our group is broadly interested in evolutionary genomics, archaeology, conservation biology and sustainable agriculture. We exploit the power of ancient and modern genomics to contrast current patterns of genetic diversity to those in the past: this allows us to track evolutionary processes including artificial selection, extinction, speciation and domestication through time. WHAT: domestic and wild species such as dogs/wolves, pigs/wild boar, chickens/jungle fowl, (wild) cats, cattle and sheep. Epidemic vectors affecting canids, bovids and suids. HOW: mostly (palaeo)genomics, a bit of transcriptomics and methylomics

What:

domestic and wild species such as dogs/wolves, pigs/wild boar, chickens/jungle fowl, (wild) cats, cattle and sheep. Epidemic vectors affecting canids, bovids and suids.

How:

mostly (palaeo)genomics, a bit of transcriptomics and methylomics

Publications

Why:

Our goal is an improved understanding of the genetic basis of gene regulation and its implication in diseases. To this end, we employ statistical modeling of ‘omic data and work in close collaboration with experimentalists.

What:

omic data

How:

statistical modeling, machine learning

Publications

Why:

We want to understand how gene regulation evolves and thus get a better understanding of the rules behind the regulatory code.

What:

single cell and bulk omics data from closely related species, mainly primates.

How:

Computational pipelines for quantitative evolutionary analyses of single cell expression data.

Publications

Why:

We are interested in the process that has shaped biodiversity across different time-scales. Our primary goal is to understand how evolution works from a macroevolutionary perspective, e.g., how rates of speciation and extinction have changed over time and across lineages. Our secondary goal is to understand the evolutionary processes over different time-scales by bridging phylogenetics and population genetics. There we look at both demographic histories, species delimitation and gene-tree species-tree discordance. WHAT: Phylogenetics and population genetics in a broad but theoretical and computation sense. HOW: We develop software (RevBayes and prev. MrBayes; some R packages) and statistical models based on birth-death process, coalescent theory, Moran process but also substitution process.

What:

Phylogenetics and population genetics in a broad but theoretical and computation sense.

How:

We develop software (RevBayes and prev. MrBayes; some R packages) and statistical models based on birth-death process, coalescent theory, Moran process but also substitution process.

Publications

Why:

In plants, it is becoming increasingly clear that heritable changes in gene function can also be caused by meiotically stable ‘epimutations’, which arise independently of DNA mutations. A well-known example of an epimutation is the accidental gain or loss of cytosine methylation. We have previously shown that experimentally-induced as well as spontaneously occurring epimutations can be remarkably stable across generations, and can in some cases even contribute to the heritability of important plant traits. Because of these, and similar, observations, epigenetic modifications have emerged as potentially important factors in plant evolution, and as possible molecular targets for the improvement of commercial crops. A major focus of our group is to infer the sources, stability and phenotypic impact of induced- and spontaneous epimutations in plants, either by direct observation of multi-generational data, or indirectly by using inference methods from evolutionary genetics. In this context, we are also actively developing computational/bioinformatic methods for the high-throughput analysis of epigenomic data.

What:

Arabidopsis, crops, trees

How:

Epigenomics, transcriptomics, computational biology, modeling

Publications

Why:

We study the diversification of plant lineages in time and space and investigate causes and consequences of evolutionary shifts, dispersal and colonization, adaptation and hybridization. We are interested in the evolution of complex traits and the role of hybridization in speciation. We discover and describe new taxa.

What:

Phylogenomics, systematics and taxonomy, biogeography, trait evolution, ecology, ecophysiology, transcriptomics; flowering plants.

How:

We assess or measure various trait data (including anatomical, ecophysiological and morphological and biochemical traits, distribution and niche modeling, RNA profiles), built phylogenetic trees (partly using historical material) based on genomic data (ddRAD, HybSeq, deep genome skimming, transcriptomes) and use sister group comparisons, biogeographical analyses, ancestral character reconstruction and analyses of reticulate evolution.

Publications

Why:

We are interested in understanding how genetic variation relates to phenotypic variation, particularly behavioural diversity. We investigate molecular mechanisms that lead to variation in mating and parental care strategies within species. We examine ultimate mechanisms that maintain genetic and phenotypic polymorphisms.

What:

currently Birds>Waders>Ruffs|Plovers

How:

Genomics, Transcriptomics, Long-term studies

Publications

Why:

We aim to gain insights into speciation processes primarily through phylogenomic analyses. These allow us to estimate when – and in some cases where – speciation events took place, which can then lead to clues about the underlying causes. We also use genomic analyses to study the frequency of past hybridization among species, and compare these frequencies to speciation rates.

WHAT:

Adaptive radiations (African cichlid fishes, Antarctic fishes, maybe soon Hawaiian honey creepers)

HOW:

Phylogenomics

Publications

Why:

We study genomes, their composition, similarities and differences in structural, compositional, functional and systemic context. Besides description and study of individual plant -crop and non-crop/model plants- genomes, functional output and modular organisation is being studied. We aim to gain insight into similarities and dissimilarities as well as evolutionary forces/drivers that underlie the molecular and modular differences among different species.

What:

crop and non-crop plants; cereal genomes and polyploids as well as legumes

How:

genome assembly, analysis and comparison; transcriptional analysis and system-centric analysis and comparison of composition and regulatory interactions.

Publications

Why:

We mainly study neutral and functional genomic diversity in domestic animals. To gain a deeper insight into the demography and evolution of the variance studied in specific livestock breeds, we usually place them in the context of the whole species (i.e. breeds across continent) and in relation to their wild relatives.

What:

Genomic variations associated with Mendelian traits in domestic animals and their ancestor species. These traits are mostly related to fitness, welfare, development, adaptive introgression, micro-evolutionary history (demography, population structure, migration, and selection) of livestock species.

How:

QTL mapping, population genomics, coalescence, biostatistics, bioinformatics

Publications

Why:

Our research focuses on the ecological, genetic and developmental basis of sensory, neural and behavioural variation, and especially that which contributes to speciation. We are interested in how behavioural isolation evolves, and how genetic architecture and other factors may influence this process. We are increasingly interested in the evolutionary genetics of sensory structures.

What:

Tropical butterflies (mostly Heliconius, but emerging projects/collaborations on other groups)

How:

Field and insectary based behavioural experiments, QTL, transcriptomics, population genomics, neuroanatomy.

Publications

Why:

We develop theoretical models of evolutionary processes and methods for data analyses that are based on these explicit models.

What:

population genetics, hybrid zone dynamics, selection on behavioral traits, models of DNA methylation dynamics. We make implementations of some of our methods available as R packages or other open-source software.

How:

stochastic models, computer simulations and mathematical analyses of model scenarios, computational-statistical approaches like MCMC and ABC.

Publications

Why:

The group is interested in several aspects of evolutionary theory: One is (in close collaborations with Aurélien Tellier’s group) the effect of life history traits, as seedbanks or quiescence, on evolutionary processes. Furthermore, social traits as cooperation, and the related problems of the stability of cooperation are investigated. Here, we also aim to understand the possibilities to use mathematical tools from evolutionary theory to analyze social/political systems.

What:

Mathematical models – they are more patient than living beings 🙂 .

How:

Stochastic processes, coalescence, ODE’s, adaptive dynamics, only little statistics.

Publications

Why:

Microorganisms influence the composition of the atmosphere, the cycling of elements within and through ecosystems, and the functioning of ecosystems. Microorganisms are also the most metabolically flexible, and the most taxonomically and evolutionarily diverse organisms on Earth. Yet deciphering how that diversity influences biogeochemical processes at larger scales is a challenge, because of the overwhelming complexity of microbial communities makes it difficult to quantify how microbial taxa assimilate and transform elements in the environment.

What:

Our research is primarily focused on the biological and biochemical mechanisms underlying microbial food webs, and explaining this through the lens of evolutionary genetics.

How:

We use a combination of methods that blend traditions from microbial ecology including stable isotope probing, genomic, and gene expression tools.

Publications

Why:

In general, we are interested in understanding the molecular basis of adaptation. We study the molecular evolution of genes and gene regulatory elements, the origin and evolution of de novo genes, and the evolution and expression of sex chromosomes.

What:

natural populations of Drosophila melanogaster, other Drosophila species

How:

genomics, transcriptomics, transgenesis, genome editing

Publications

Why:

We have a long-standing interest in the evolution of bacteria that cause diseases of the gastrointestinal tract. We are interested both in global phylogeographic population structure as well as within host evolution and adaptation to different ecological niches and the relative contributions of mutation and recombination to bacterial diversification. Lately, we have also become interested in „bacterial epigenetics“, the diverse methylation patterns generated by highly variable portfolios of methyl transferases and the functional implications of this added layer of diversity.

What:

Helicobacter pylori and related Helicobacter spp., Campylobacterales, other GI pathogens and the GI microbiota.

How:

Bacterial genomics, transcriptomics, „methylomics“. Combination of wet lab (Illumina/PacBio/Nanopore sequencing, mutagenesis and mutant/complementant phenotypical characterization, genetic and biochemical approaches) and computational methods in the field of bacterial genomics.

Publications

Why:

We study patterns and processes of speciation in plants and the anthropogenic effects on those processes. We develop methods and pipelines to speed up discovery of new species and make crop wild relatives available to plant breeders.

What:

gourd family (Cucurbitaceae) and the flora of the Azores archipelago (North Atlantic).

How:

field work, herbarium work, Nanopore, phylogenetics, phylogenomics, molecular clock, biogeographic models

Publications

Why:

DNA is the carrier of heritable information. But despite the high stability of DNA, genomes change over time. Changes in the DNA can occur uncontrolled (i.e., through mutations) or controlled (i.e., through recombination). We are interested in how, why and to what degree genomes change over time and how these changes influence the phenotype of an organism.

What:

Plants including potato, fruit tree, A. thaliana and its relatives

How:

(comparative, single-cell) genomics

Publications

Why:

We are interested in the evolutionary processes underlying plant adaptation to their biotic and abiotic environment, focusing mainly on 1) host-pathogen coevolution and disease epidemiology, and 2) seed dormancy as a bet-hedging strategy. We develop mathematical models and statistical inference methods to leverage information from genomic data.

What:

wild tomato species from South-America, various plant and human parasites.

How:

coalescent theory, statistical inference methods, genomics

Publications

Why:

We investigate the stress responses of free-living and symbiotic organisms in order to understand whether and how they can tolerate changing environmental conditions. Secondly, we study dispersal and gene flow to understand genetic connectivity and evolutionary history of populations. Third, we investigate the factors determining the species diversity of biological communities and how human disturbances impact biota.

What:

natural populations of lichen fungi and their photobionts; higher plants (Myricaria); communities of epiphytic and terricolous lichens.

How:

population genetics, genomics, transcriptomics, community ecology

Publications

Why:

We have a long-standing interest in the evolutionary processes governing adaptation and speciation at early stages of divergence. We also study the role of epigenetic variation for evolution and sometimes look into genome evolution across larger timescales.

What:

natural populations of birds, marine mammals, frogs, yeasts and biodiversity grassland experiments

How:

genomics, transcriptomics, experimental evolution

Publications

Why:

Our research focuses on the (molecular) biodiversity and evolution of primarily marine (coral reef) organisms and their symbionts, and on the evolution of biomineralization. We also investigate the impact of changing environmental conditions on these organisms. Another topic of our interest is deep metazoan phylogeny to understand early animal evolution.

What:

coral reefs: sponges, corals, echinoderms

How:

transcriptomics, genomics, DNA barcoding, experiments in marine research aquaria

Publications