Summer Semester 2017
Kris Murray - "Pathogeography - the biogeography of human infectious diseases"
Imperial College London, UK
Abstract: With infectious diseases having repeatedly altered the course of human history, and still responsible for almost a fifth of the global burden of disease, understanding the distributions of infectious diseases is a central public and global health objective. I will discuss some recent work in which we show that human infectious diseases exhibit striking biogeographic grouping patterns at a global scale, reminiscent of “Wallacean” zoogeographic patterns. This result is surprising, given the global distribution and unprecedented connectivity of humans as hosts and the homogenizing forces of globalization; despite these factors, infectious disease assemblages appear to remain fundamentally constrained in their distributions by ecological barriers to their dispersal or establishment. Biogeographic processes thus appear to provide an overarching context in which other factors promoting infectious disease emergence and spread are set, providing a potentially useful prior with which to evaluate a range of disease risks and potential management interventions.
Robert Whittaker - "Oceanic island biogeography through the lens of the General Dynamic Model"
University of Oxford, UK
Abstract: The general dynamic model of oceanic island biogeography (GDM) provides a theoretical framework incorporating the dynamics of island platforms alongside the key biological drivers of immigration, extinction and speciation. It provides an essentially non-equilibrium framework generating novel predictions for emergent diversity properties of oceanic islands and archipelagos. Based on efforts of the biodynamics of islands workshop group I review progress, both in testing the GDM’s predictions and in developing and enhancing ecological-evolutionary understanding of oceanic island systems, through the lens of the GDM. The presentation considers such themes as: 1, what we have learnt from species-area relationships for remote islands; 2, macroecological tests of the GDM using a space-for-time rationale; 2, extensions of theory to islands following different patterns of ontogeny; 3, the implications of GDM dynamics for lineage diversification and trait evolution; 4, the potential for downscaling GDM dynamics to local-scale ecological patterns and processes within islands; 5, island theory and non-native species.
Justin Crocker - "Decoding evolution and development: from enhancer structure to function"
EMBL Heidelberg, Germany
Abstract: In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox because different Hox proteins bind with high affinity in vitro to similar DNA sequences. Here, I will show that the Hox protein Ultrabithorax (Ubx) binds specifically to clusters of very low-affinity sites in Drosophila. These low-affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture—clusters of low-affinity binding sites—is maintained and required for enhancer function. Natural selection, therefore, works at the level of the enhancer, requiring a particular density of low-affinity Ubx sites to confer both specific and robust expression. Finally, I will discuss results that suggest that low-affinity sites drive efficient transcription by utilizing nuclear microenvironments with high concentrations of transcription factors and cofactors. Mechanisms that generate these microenvironments are likely to be a general feature of eukaryotic transcriptional regulation.
Martin Wikelski - "The ICARUS Project"
Max Planck Institute for Ornithology, Konstanz, Germany
Abstract: The goal of the ICARUS (International Cooperation for Animal Research Using Space) Initiative is to observe global migratory movements of small animals through a satellite system. Global data about animal movements are indispensable in our today international networked world to understand how to safe human health and wildlife simultaneously. To this date scientists are unable to follow small animals and insects on their long journey. Billions of songbirds move every year from continent to continent. Also many bats and numberless species of insects manage long distances and in doing so possibly move from one continent to another. We do not know exactly. However, this knowledge plays a fundamental role to understand the propagation of pathogens through their hosts for instance to preserve ecosystem services or to predict natural disasters through intelligent sensors of animals. To remedy the worldwide lack of knowledge about the distribution and the individual migratory habits of small animals and insects, an international consortium of scientists got the ICARUS project underway in 2002. With the data generated by ICARUS, scientists expect revolutionary new insights about life, behavior, vital functions and death of the animals on our planet. The globally collected data allows us among other things conclusions for the spread of diseases (zoonosis), understanding of climate change and disaster forecast. The research results to be expected here are of invaluable importance for mankind and finally for life on earth.
Susanne Foitzik - “The evolution of division of labor and parasite defense: from the phenotype to changes in gene expression and regulation”
University of Mainz, Germany
Abstract: Social insects show fascinating behaviours, from slavery, over social immunity to an effective division of labour in their societies. In this talk, I will give insights into the evolution and molecular basis of behaviour in ants and present recent results that reveal, which proteins, genes and gene regulatory mechanisms are involved. In most insect societies, division of labour among workers is age dependant and we demonstrate this also for the small Temnothorax ants. Transcriptome analyses allowed us to identify candidate genes, which control the behavioural transition from brood care to foraging behaviour. RNAi-mediated knockdown of a brood care gene, vitellogenin-6, showed that division of labour is indeed controlled via response thresholds to social cues, which shift with gene expression. Inhibition of histone-acetyltransferase revealed that behavioral transitions in ant workers are controlled by histone acetylation via an alteration of gene expression. Parasites can also affect ant behaviour, either by direct manipulation or by selecting for behavioral defense mechanisms. Our study on a cestode parasite and its ant host show, that parasite infection not only affects behaviour (by lowering general activity), but also increases longevity. Proteome analyses of proteins released by the cestode into the host indicate that the parasite directly manipulates the host phenotype. Finally we investigate the evolution of slavery in ants and can show, which genes are differently expressed during slave raids and host defence in three slavemakers and their three hosts. We could functionally characterize some of these candidates using RNAi. Selection analyses reveal that different genes are under selection in independent origins of slavery, suggesting convergent evolution of these fascinating behaviours.
Meike Wittmann - "Fluctuating balancing selection and its effects on neutral genetic diversity”
University of Vienna, Austria
Abstract: For organisms with several generations per year, seasonally fluctuating selection can be a powerful mechanism to maintain genetic polymorphism. For example, an allele favored during summer may stably coexist with an allele favored during winter, a form of balancing selection. Despite intense debate over decades, it is still unclear how much of the variation observed in the genomes of natural populations is due to balancing selection. In recent years, evolutionary biologists have started scanning genomes for genetic footprints of balancing selection (e.g. regions of increased diversity and positive Tajima's D). However, these scans have generally assumed the simplest form of balancing selection where alleles are maintained at constant frequencies over time. There is currently insufficient theory to tell us what genetic footprint to expect under seasonally fluctuating selection, and how to distinguish it from neutrality but also from other forms of balancing selection. In this talk I will present results from coalescent models and stochastic simulations to characterize the impact of fluctuating balancing selection on neutral genetic diversity at various scales: at closely linked sites, at the scale of the chromosome, and at the genomic scale.
Winter Semester 2016/2017
Nico Posnien - "Systems-Evo-Devo: Evolution of developmental gene regulatory networks”
University of Göttingen, Germany
Abstract: The size and shape of an organism and its organs is tightly controlled during embryonic and postembryonic development to ensure proper functionality. However, in the light of the breath-taking diversity of body forms observed in nature, adult features are certainly targets for evolutionary changes. This contradiction suggests that developmental gene regulatory networks (GRNs) are constrained to a certain level, but nodes within this network are prone to change to give rise to morphological divergence.
We have previously shown that the three closely related Drosophila species D. melanogaster, D. simulans and D. mauritiana exhibit natural variation in eye size and overall head morphology. In this survey, D. melanogaster has the smallest eyes and D. mauritiana has the largest eyes. The aim of our research is to identify flexible nodes within the GRN underlying adult head formation in these three Drosophila species. To this end, we combine unbiased genome-wide approaches like quantitative trait loci (QTL) mapping and comparative transcriptomics with developmental genetics and geometric morphometrics to identify genes and developmental processes responsible for the observed differences in head morphology.
Our genome-wide expression analysis of different developmental stages of eye and head development shows that many genes that are differentially expressed between D. melanogaster and D. mauritiana are regulated by the GATA transcription factor Pannier (Pnr). Using interspecific crosses with D. melanogaster pnr deficiency lines, we provide further support for an involvement of the pnr locus. Eventually, we place pnr in the developmental gene regulatory network underlying eye development. All this data strongly suggests that divergence at the pnr locus is likely to be responsible for the morphological differences between D. melanogaster and D. mauritiana.
Qi Zhou - "Evolution of sex chromosomes of flies, birds, snakes and beyond"
University of Vienna, Austria
Abstract: Sex is a nearly universal biological feature, and is determined by sex chromosomes in many, but not all the eukaryotes. After the birth of sex-determining genes, X and Y chromosomes start their separate evolutionary trajectories and form opposite patterns of gene content and epigenomic landscapes. Over the past several years, I have studied birds, snakes and Drosophila species, and will use them as examples to introduce my current and future research. We have studied complete genomes of 50 bird species. We reconstructed complex scenarios of recombination loss between sex chromosomes, caused by Z- or W-chromosome inversions, and uncovered a great diversity of their evolution rate comparing to the mammalian XY systems. In Drosophila, we show Y chromosomes can degenerate very quickly, manifested by increased bindings of heterochromatin modification, and decreased bindings of euchromatin modification together. This process is not random across the Y-linked regions, but constrained by the ancestral chromatin configuration. It is probably triggered by the vulnerability of Y against the transposable element insertions, and further results in the chromosome-wide silencing of Y-linked genes. It also creates an arms-race between the piRNA and TEs, which forms my main topic of research in Vienna for the next five years.
Tom Tregenza - "Ageing in the wild"
University of Exeter, Cornwall, UK
Abstract: In recent years a growing number of field studies have identified senescent declines (age-related degeneration) across a broad range of taxa. However, studies examining changes in behaviour are rare, and insects in their natural context have hardly been studied all, despite their importance as laboratory model systems. I will describe our decade long study of a population of wild crickets which has allowed us to analyse patterns of mortality and the effect of age on a suite of traits including naturally and sexually selected behavioural traits measured at the individual level. We find substantial evidence of actuarial senescence, with the probability of death increasing with individual age. However the nature of these declines varies among years and the key prediction that males should age faster than females is only true in some years. Behavioural traits show a range of patterns, although evidence of senescence is abundant. I will discuss potential explanations for the striking variation we observe.
Patrik Fink - "The challenged consumer - aquatic herbivores’ response to variable resource quantity and quality”
University of Cologne, Zoological Institute, Workgroup Aquatic Chemical Ecology &
Heinrich-Heine-University of Duesseldorf, Institute for Zoology and Cell Biology, Germany
Abstract: Herbivores play a key role in aquatic food webs as they are responsible for the trophic transfer of photosynthetically assimilated carbon into the animal food web, which makes them crucial for the functioning of marine and freshwater ecosystems. It is hence of paramount importance for ecologists to understand the reasons for constrained efficiency of the transfer of matter and energy at the plant-herbivore interface, but also the potential compensation mechanisms that consumers have evolved to cope with such constraints. This relies on a firm understanding of food web structure and the physiological ecology of the respective organisms. In this presentation, I summarize some of my recent research on the structure of aquatic food webs with particular focus on aspects of biodiversity and the impact of invasive species. I highlight some of the nutritional constraints for the efficient transfer of algal biomass to benthic and pelagic herbivores and their consequences for herbivore fitness. I further discuss potential strategies of aquatic herbivores to compensate or overcome nutritional constraints through the evolution of physiological and/or behavioural adaptation strategies and show case studies for such strategies from both marine and freshwater environments.
Siegfried Roth - "The evolution of dorsoventral patterning in insects"
University of Cologne, Germany
Abstract: Toll-dependent patterning of the dorsoventral axis in Drosophila represents one of the best-understood gene regulatory networks. However, its evolutionary origin has remained elusive. Outside the insects Toll is not known for a patterning function, but rather for a role in pathogen defense. I will present our recent findings on the evolution of dorsoventral patterning in insects. In particular, I will describe our work on a hemimetabolous insect, the milkweed bug Oncopeltus fasciatus, whose lineage split from Drosophila’s more than 350 million years ago. In Oncopeltus, Toll is only required to polarize a dynamic BMP signaling network. Modeling of this network reveals that shallow Toll signaling gradients are sufficient to initiate axis formation. Dynamic BMP signaling combined with long-range, shallow Toll signaling gradients can explain the twinning of embryos upon egg fragmentation which has been observed in many insect lineages except the higher dipterans to which Drosophila belongs. Broad Toll signaling during early embryogenesis may also explain the emergence of Toll’s patterning function from a prior role in protecting the egg and embryo against microbial attacks.
Stefan Laurent - "Using population genetics and field experiments to study molecular evolution at Agouti: a gene underlying coat color adaptation in the Nebraskan deer mouse"
University of Lausanne, Switzerland
Abstract: Natural selection is widely accepted as the evolutionary force driving adaptation in natural populations, but in higher organisms, there are only a limited number of adaptive events that have been described not only at the phenotypic but also at the molecular and ecological level. One of these well-described adaptations is the evolution of cryptic coat color in the deer mice (Peromyscus maniculatus) living in the Nebraskan Sand Hills. In this region, a large field of dunes established around 10 to 15 thousand years ago and caused the color of the soil to become significantly lighter than the ancestral (and currently surrounding) darker soils. This change in substrate color is thought to have had dramatic consequences for dark-coated wild-type individuals because they are preys of visually-hunting predators. It has been hypothesized that by increasing their camouflage, light-coated mutants increase their fitness and that strong and recent positive selection, acting on the Agouti gene, is responsible for the correlation between substrate color and coat color observed in populations on and off the Sand Hills. In this talk I will present the results of population genomic analyses that improved our understanding of the selective sweep on Agouti and show that several mutations and recombination events contributed to this adaptive event. I will also present the results of a manipulative field experiment in which survival rates and genome-wide allele frequency changes (before/after predation) have been measured in controlled populations of dark and light populations on and off the Sand Hills. The results of this experiment highlight the reproducibility of positive selection on Agouti in this system. Finally, I will discuss statistical issues related to the analyses of this new type of temporal population genetic data.
Daniel Wegmann - "Inferring evolutionary processes from temporal and ancient data"
University of Fribourg, Switzerland
Abstract: Evolutionary change is the result of both genetic drift and selection, but disentangling these two processes has been proven difficult. Recent technological progress now hold promise to address this by looking at data from many individuals and the entire genomes. I will discuss recent statistical advances to make use of such new data and argue that power is maximized by investing into larger samples or over larger temporal scales, rather than the accuracy of individual samples. I will first discuss the potential of time series data to observe evolutionary change and introduce a novel method to jointly infer demography and selection from such data. As an example I will identify the loci conferring resistance to Influenza viruses that were evolved experimentally in the presence of Oseltamivir. Second, I will discuss statistical challenges along with solutions to include ancient DNA into evolutionary analysis to increase the temporal scale at which we quantify evolution of long-lived organisms such as humans. As an example I will discuss our latest insights into the spread of farming into Europe that we gained from sequences of the very first farmers in both the fertile crescent as well as the Aegean region. Interestingly, these data suggest that while farming spread from the Aegean mainly by the movement of people, it initially reach the shores of Europe by cultural diffusion.
Summer Semester 2016
Katja Räsänen - "Phenomics of maternally mediated adaptive divergence: insight from Rana arvalis and Salvelinus alpinism"
EAWAG Zürich, Switzerland
Abstract: Natural selection acts on the composite phenotype of organisms, meditated through a web of interactions between the external environment and genotype. One important source of phenotypic variation – especially at early life stages - are maternal effects, which can influence speed and direction of evolutionary responses and facilitate rapid local adaptation. Katja will focus on egg coats (maternally derived extra-embryonic membranes) as facilitators of adaptive divergence along an acidification gradient in the moor frog (Rana arvalis), and on egg size as facilitators of resource polymorphism evolution in sympatric arctic charr (Salvelinus alpinus). She will provide insight to the molecular and functional basis of these maternal effects, and emphasize that early life stage traits can play an important role in evolutionary diversification.
Tobias Uller - "Adaptive evolution of inheritance"
Lund University, Sweden
Abstract: Evolution by natural selection requires three conditions: variation between individuals, that some variants leave more descendants than others, and that offspring resemble their parents. The high-fidelity replication of DNA gives the impression that inheritance can be treated as a fixed channel of transmission. However, there is more to heredity than genes. Treating parent-offspring similarity as an evolving feature of life cycles allows us to address how mechanisms of inheritance change under natural selection. This sheds light on the adaptive evolution of a suite of transgenerational phenomena, from environmental maternal effects to incomplete epigenetic resetting. This perspective demonstrates that epigenetic and behavioural mechanisms can play several roles in evolution – from being a cause of phenotypic variation to enabling adaptive transgenerational plasticity and stable transmission of species-typical phenotypes.
Marc Naguib - " The evolution of communication: information flow in territorial animal societies"
Wageningen University, The Netherlands
Abstract: Many animals hold specific social relations to other individuals, like their mates, relatives, other group members, or territorial neighbours. To maintain such relations, communication is essential. Among such signals, advertisement signals are particularly interesting as they attract and repel others and are important in mating decisions and decisions to defend resources. To obtain information from such signals individuals often need move around to be in range of the signals, so that communication and spatial relations are strongly linked. This presentation will provide an overview over signalling, communication networks and spatial behaviour in animals, mainly using our long-term research on nightingales (Luscinia megarhynchos) and great tits (Parus major) as example. This includes also a current large-scale automatized radio-tracking project where we integrate social and communication networks to better understand the functioning on territorial animal societies.
Leonida Fusani - "The interplay between condition, food, and rest in migratory birds"
University of Vienna, Austria
Abstract: During migration, birds experience continuous changes in body condition. During long migratory flights over ecological barriers, such as deserts and seas, they use most of their energy stores. Therefore, birds spend a considerable amount of time at so-called stopover sites to refuel between flights. In the last decade, we studied the mechanisms controlling decision-making at stopover sites, that is, how birds decide whether they are ready to resume migration or not. Our work showed that when controlling for environmental factors, the extent of subcutaneous fat stores is the best predictor of the migratory disposition and in fact of the duration of the stopover. However, food has a strong effect on migratory behaviour, which is not necessarily linked to changes in body mass. As migratory birds literally eat their guts during migration, they need to rebuild their gastrointestinal tract before they can restore their energy reserves. This requires a fine control of activity patterns, because refuel occurs during the day whereas migration is mostly nocturnal. In this talk, I will present some highlights of our recent research on stopover physiology.
Winter Semester 2015/2016
Beatriz Vicoso - "Frequent sex chromosome turnover in dipteran insects"
Abstract: In many species, sex is determined by a pair of sex-chromosomes, such as the X and Y chromosomes of mammals. Although they originally arise from a pair of autosomes, X and Y chromosomes eventually acquire very specialized biologies. This is thought to prevent them from reverting to autosomes, so that the acquisition of differentiated sex chromosomes has been assumed to be an irreversible state.
Dipteran insects (flies, mosquitoes and midges) generally have XY sex chromosomes and a conserved karyotype, consisting of six chromosomal arms (5 large rods and a small dot). The XY pair of Drosophila melanogaster was assumed to be ancestral and shared by most Dipteran insects, an assumption supported by the apparent homology of the mosquito and Drosophila X-chromosomes.
Our genomic analysis of 37 species of Diptera shows that, contrary to this hypothesis, there is tremendous diversity of sex chromosome karyotypes in this group. First, we found that the X of Drosophila is not ancestral to Diptera. Instead, the ancestral X corresponds to the small “dot chromosome”, which then reverted to an autosome in Drosophila, demonstrating that such X to autosome reversals can happen. We also identified species with undifferentiated sex chromosomes, and others where a different chromosome replaced the dot as a sex chromosome, or where up to three chromosomes became incorporated into the sex chromosomes.
While surprising in itself, this diversity also allows us to test theories of sex chromosome evolution more systematically than was previously possible. Our multi-species transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through upregulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner, and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.
Denis Reale - "Pulses resources and the ecology of eastern chipmunks"
UQAM, Montreal, Canada
Abstract: Animal populations have to deal with temporal and spatial availability of resources. Pulsed resources represent an extreme case of resources fluctuation in a way that they are produced in huge amounts during restricted periods and are almost inexistent the rest of the time. Pulsed resources create a challenge to animals exploiting them, as these consumers have to find ways to adjust their life history in response to these fluctuations. This is the case of the eastern chipmunk (Tamia striatus) a small Sciurid commonly found in North-American forests, and that relies mainly on the American beech (Fagus grandifolia) in the northern regions of its distribution range. Once every 2-3 years, beech trees produce massive amounts of seeds, during what is generally called a masting even. Although eastern chipmunks can feed on different plants, small invertebrates, and other sources of food, they rely mostly on beech seeds for their reproduction and winter survival. Chipmunks store seeds into their burrow over the summer and the fall, and use these resources for their winter needs. Here we show the case of a chipmunk population in Southern Quebec that we have followed for 10 years. In this individually marked population we have collected information on individual burrow locations, habitat characteristics, behaviour, physiology, and genetics. Using this long-term data set we show how chipmunks life history and ecology depends strongly on beech seed fluctuations. Chipmunk reproductive cycles and population demography depend on masts; chipmunks do not reproduce every year, but concentrate their reproductive effort around masting events. Masts affect winter torpor, dispersal and the genetic structure of the population. Furthermore, because of the temporal fluctuation of seed production, chipmunks born at different cohorts show different life history strategies and personalities, and our results show cohort-dependent personality types fitted with specific life histories. Our results shed light on how fluctuation in ecological conditions may maintain personality differences and relationships between animal personality and life history.
Angela Hay - "Morphomechanical innovation drives explosive seed dispersal"
Abstract: How mechanical and biological processes are integrated across different scales to create complex traits is largely unknown. In this work, we combine biological, mathematical, and computational approaches to understand the mechanical basis for explosive seed dispersal - a key life history trait underpinning invasive behavior in the common weed Cardamine hirsuta. We have exploited the experimental tractability of C. hirsuta - a close relative of the model organism Arabidopsis thaliana – to understand the mechanism of explosive pod shatter and provide insights into the origin of this striking trait.
Krushnamegh Kunte - "Speciation and morphological diversification in Papilio swallowtail butterflies"
Abstract: The hallmark of life on earth is morphological diversity, which is often represented in spectacular sexually dimorphic and polymorphic phenotypes across species. I will address ecological pressures and genetic mechanisms that shape the evolution of morphological diversity with three stories of the iconic PapilioSwallowtail Butterflies. First, I will discuss the species radiation of Papilio in the geologically complex Indo-Australian Region, which has shaped reproductive isolation and speciation in Papilio as a function of biogeographic separation. Second, I will show how Batesian mimicry has driven wing pattern diversification, sexual dimorphism and polymorphism in Papilio. I will show that frequency dependent natural selection (predation) and sex-specific advantages of mimicry appear to have driven most of the wing pattern diversification in Papilio and related tropical butterflies. Finally, I will present the remarkable wing pattern polymorphism in Papilio polytes, which is an emerging genetic model system. Earlier I showed that doublesex, a transcription factor that regulates sexual differentiation in insects, also controls this female-limited mimetic polymorphism. I will present some recent work on the genetics of this polymorphism, which is beginning to characterize molecular variation in doublesex in nature. Thus, in this talk I will present a broad picture of the evolution of morphological diversification with respect to ecological and biogeographic processes, and its genetic and developmental regulation.
Amanda Bretman - "No fly is an island: how Drosophila respond to socio-sexual environments"
University of Leeds, UK
Abstract: We all modify our behaviour in different social situations to adapt, fit in or to become more competitive. Fruit flies also have complex social lives, aggregating independently of any resources, engaging in social learning, forming social networks and having a genetic propensity for different types of social environments. Using Drosophila melanogaster fruit flies as a model, we can investigate both the fitness consequences of changes of social environment and the mechanisms by which individuals can respond to such changes.
One aspect of the social environment that has a particular impact on males is how much mating competition (both before and after mating) they encounter. Theory predicts that if males can mate more than once they need to trade-off current and future mating opportunities, hence they should modify their mating effort at a particular mating depending on the amount of competition they face. Males of many species use plastic strategies to cope with this uncertainty, taking cues from the presence of other males or the mating status of females, and making adjustments to behaviour and ejaculate content accordingly. In D. melanogaster, after being exposed to a potential competitor, males mate for longer and transfer a higher quality ejaculate. This is has fitness benefits, at least in the short term, but is costly. By combining behavioural and life history data with transgenics and transcriptomics, we can investigate how such responses are coordinated and regulated, an important step in understanding how sophisticated, flexible social behaviours evolve. We are also starting to use this paradigm to investigate other consequences of social contact on traits such as ageing, immunity and cognition.
Jochen Blath - "On the role of dormancy in population genetics"
TU Berlin, Germany
Abstract: We analyse patterns of genetic variability of populations in the presence of a large seed bank with the help of a new coalescentstructure called the seed bank coalescent. This ancestral process appears naturally as scaling limit of the genealogy of large populations that sustain seed banks if the seed bank size and individual dormancy times are of the same order as the size of the active population. Mutations appear as Poisson processes on the active lineages, and potentially at reduced rate also on the dormant lineages. The presence of 'dormant' lineages leads to qualitatively altered times to the most recent common ancestor and non-classical patterns of genetic diversity. To illustrate this we provide a Wright-Fisher model with seed bank component and mutation, motivated from recent models of microbial dormancy, whose genealogy can be described by the seed bank coalescent. Based on our coalescent model, we derive recursions for the expectation and variance of the time to most recent common ancestor, number of segregating sites, pairwise differences, and singletons. The effect of a seed bank on the expected site-frequency spectrum is also investigated using simulations. Our results indicate that the presence of a large seed bank considerably alters the distribution of the site-frequency spectrum. Thus, one should be able to detect the presence of a large seed bank in genetic data.
Summer Semester 2015
Maria Anisimova-"Disentangling tandem repeats with computational prediction"
ETH Zürich, Switzerland
Abstract: Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions, and can be associated with virulence, resistance and infectious/ neurodegenerative diseases. Genome-scale systematic studies of TRs have the potential to unveil core mechanisms governing TR evolution and TR roles in shaping genomes. However, TR-related studies are often non-trivial due to heterogeneous and sometimes fast evolving TR regions. In this talk I will discuss our recent contributions to computational and statistical approaches for TR annotation, TR-aware sequence alignment, and phylogenetic analyses of TR conservation. All these methods explicitly rely on the evolutionary definition of a tandem repeat as a sequence of adjacent repeat units stemming from a common ancestor. The discussed work has a focus on protein TRs, yet is generally applicable to nucleic acid TRs, sharing similar features.
Frank Oliver Glöckner - Environmental Bioinformatics - with a focus on “Marine”
Max Planck Institute for Marine Microbiology & Jacobs University Bremen gGmbH
Abstract: Investigations in molecular biology have transitioned from single experiments to high-throughput “big data” endeavours spearheaded by genomic sciences. New integrative approaches are needed to transform the wealth of environmental sequences and contextual (meta)data into biological knowledge on microbial diversity and function.
The talk will elaborate on the goals and perspectives of bioinformatics capacity building in the EU 7FP “Ocean of Tomorrow Project” Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology, www.microb3.eu). It will explain the concept, standards and implementation of the community driven Ocean Sampling Day (OSD, www.oceansamplingday.org). The first OSD took place worldwide on 21st of June (summer solstice) 2014, mobilizing over 190 marine sampling sites. The next OSD is planned for June 2015 with a strong involvement of citizen scientists (www.my-osd.org). These cumulative samples, fixed in time and space supplemented with a broad set of geo-referenced environmental parameters will provide new insights into the relationships between organisms, their genomic repertoire, and the environment surrounding them. Since most of the sampling sites are coastal, OSD provides the unique opportunity to study the effect of human pressure on the unseen majority in our ocean.
Jose Jimenez-Gomez- "Natural variation in circadian rhythms suggests effect of domestication on the circadian clock of tomato"
MPI Cologne, Germany
Abstract: The circadian clock controls many important aspects of plant physiology and development, including several traits of agronomical significance. Variation in circadian rhythms appears to be important for adaptation to specific environments. Domestication in tomato (Solanum lycopersicum) has drastically affected its geographical distribution and many characters of agricultural interest. I will show our work using tomato as a model system to study the importance of circadian rhythms during domestication.
Julian Glos - "Species and functional diversity of amphibian assemblages in a rainforest in Madagascar"
University of Hamburg, Germany
Abstract: Functional diversity illustrates the range of ecological functions in a community, and it allows revealing the appearance of functional redundancy in communities and processes of community assembly. Functional redundancy illustrates the overlap in ecological functions of community members which may be an indicator of community resilience. I will present patterns of species richness and species turnover, and of functional diversity and functional redundancy, in tadpole and frog communities in a rainforest of Eastern Madagascar. This habitat harbours one of the world's most species-rich amphibian communities. It is characterized by environmental changes and steep environmental gradients that are due to either natural changes (i.e., between two seasons) or anthropogenic impact (i.e., habitat fragmentation, disturbances). Accordingly, I will show how the patterns of species and functional diversity in amphibian assemblages vary along these environmental changes.
Ivan Gomez-Mestre- "Micro- and Macroevolution of Life Histories in Anurans:
Can Developmental Plasticity help Connect the Dots?"
Donana Biological Station, Spain
Abstract: Developmental plasticity allows populations to withstand rapid environmental changes and confers an overall faster rate of adaptation. However, selection in stable environments can result in genetic assimilation, potentially leading to trait divergence and species diversification. In that case, we would expect ancestral plasticity to mirror differences among taxa. Thus in that light, we are studying mechanisms of plasticity behind the evolutionary divergence of spadefoot toads. By studying the mechanisms of developmental acceleration in response to pond drying and comparing them across species, we have found that Pelobates tadpoles, which reflect the ancestral state of the group, increase their metabolic rate, and thyroid hormone and corticosterone concentrations in response to decreased water levels. All these parameters, however, seem to have been canalized in the descendant-state group Scaphiopus, leading support to the hypothesis of genetic accommodation.
Holger Goerlitz - "Auditory interactions in the night sky: bats, moths, and global warming"
Abstract: Echolocating bats and moths with bat-detecting ears interact in a predator-prey-relationship that is solely based on acoustic information. Bats use echolocation, an active-sensing strategy, to detect their insect prey. In turn, ears and evasive flight evolved in many insect taxa to prevent being captured by bats. We study these auditory-guided interactions between echolocating bats and eared moths in the field and lab, using neurophysiological recordings from moth ears, molecular diet analysis, flight path tracking in the field and acoustic modelling. This talk will present auditory adaptations in the prey to their sympatric predator ensemble, counter-measures in predators to avoid being heard by the prey, and additionally how external factors such as global warming might affect auditory interactions.
Winter Semester 2014/15
Clelia Gasparini - "Sex in the tank: what guppies can tell us about sexual selection and sexual conflict before and after mating"
The University of Western Australia, Perth, Australia
Abstract: Sex is rarely a harmonious process, and males and females often have conflicting evolutionary interests over reproduction. In most species such conflict rarely ends at mating because females typically mate with multiple males (polyandry), thus extending the opportunities for sexual selection to include sperm competition (where ejaculates from different males compete for fertilization) and cryptic female choice (where females moderate this competition). Using a small livebearing fish, the guppy, I study pre- and post- copulatory sexual selection to unravel strategies used by males and females to maximize their own reproductive success. In this seminar I will present results from my ongoing research that explores how these reproductive conflicts of interest play out across the sexual selection continuum (pre- and postcopulatory sexual selection). Insights from this work reveal how the females’ choice of attractive mates can be undermined by male behavioural strategies, how males make faster sperm to win the (sperm competition) race while ‘fussy’ females potentially counteract these effects by slowing them down, and ultimately why choosing the most popular male may yet pay off for females.
Robert Ptacnik - "Fresh and salty: Spatial pattern in plankton diversity along natural stress gradients"
WasserCluster Lunz, Austria
Abstract: Salinity represents about the strongest selective gradient in aquatic habitats, which is reflected in the distinctive biotas of freshwater and marine habitats. In estuaries, the transition from freshwater to marine conditions is populated by a few tolerant freshwater and marine taxa forming opposing ends of the gradient, plus a limited number of specialized brackish taxa. The brackish taxa, however, do not compensate for the species loss of other taxa. As a result, communities of most higher taxa exhibit a characteristic diversity minimum at intermediate salinities ('Artenminimum', Remane 1934).
This relationship can be understood regarding the limited connectivity among estuaries. It implies that the total species pool available for colonizing this intermediate zone is considerably smaller than the species pools populating its end points. Microscopic organisms are assumed to be highly mobile and at the same time expected to evolve rapidly. Salinity gradients therefore represent a test ground for the assumptions that biogeography of microbes differs fundamentally from higher organisms. I will show data on the spatial pattern of phytoplankton diversity in the Baltic Sea with a focus on the species pools and their origin that populate different salinities in the Baltic Sea.
Michal Kucera - "Cryptic diversity in marine plankton"
MARUM & Fachbereich Geowissenschaften, University of Bremen, Germany
Abstract: Species of marine eukaryotic plankton have numerically enormous populations, exposed to constant passive dispersal by currents that is not limited by physical barrier. Intuitively, these factors can be expected to inhibit speciation. Yet, marine plankton is highly diverse and, paradoxically, genetic fingerprinting has revealed that its biological diversity has been severely underestimated due to the abundance of cryptic speciation. Our research seeks to understand the nature and origin of cryptic species in the plankton and unravel the consequences for the study of biodiversity and evolution in the largest environment on the surface of the Earth. We use planktonic foraminifera, which produce one of the best fossil records available to study, allowing us to combine present-day phylogeography with the evolutionary history of the group. I will present the results from extensive global surveys of single-cell sequence data in three clades that revealed unexpected patterns of geographical and ecological structure in what previously seemed to be cosmopolitan species. Using well constrained molecular clocks, I will show that cryptic divergences are ancient and their existence reflects a fundamental de-coupling of morphological evolution from genetic divergence.
Marie Manceau - "Morphogenesis and Molecular Regulation of Colour Patterning in Natural Populations"
College de France, Paris, France
Abstract: The distribution of color across the body (i.e., color pattern) is a crucial morphological trait involved in survival and reproductive success which varies tremendously both within and between species. Despite their ecological importance, the genetic and developmental mechanisms responsible for the formation and variation of naturally-occurring color patterns have remained a black box. We showed that in deer mice (genus Peromyscus), the formation of a simple bicolor pattern typical of most vertebrates relies on the establishment of an embryonic “pre-pattern” (i.e., the spatial restriction of pigmentation genes) causing regional differences in pigment cell behavior. Moreover, we showed that large adaptive changes in the adult color pattern seen in a derived Peromyscus population are provoked by small accumulating changes in the pre-pattern. These findings laid the groundwork for studying (1) the embryonic origin of pre-patterns in the skin, (2) the molecular control of their formation and (3) the genetic basis of their evolution in other vertebrates groups. To this end, we propose to use analyses of gene expression and function in natural populations of birds displaying a vast array of skin patterns.
Julien Gagneur - "Insights from genetics of gene expression into mutational robustness and causal inference."
LMU Genzentrum, Munich, Germany
Abstract: I will present two of our systems genetics studies.
1. Mechanisms conferring robustness against regulatory variants have been controversial. Previous data suggested widespread buffering of RNA misexpression on protein levels during translation. We do not find evidence that translational buffering is common. Instead, we find extensive buffering at the level of RNA expression, exerted through negative feedback regulation acting in trans, which reduces the effect of regulatory variants on gene expression.
2. We show how non-additive effects between genotype and environment can be exploited for causal inference in molecular networks. Using genome-wide perturbation assays in yeast, we experimentally demonstrate the validity of the approach.
Andrea Betancourt - "Transposable element dynamics in Drosophila”
VedMedUni Vienna, Austria
Abstract: Transposable elements are genomic parasites with an evolutionary strategy of increasing their copy number; the success of this strategy can be seen in many eukaryotic genomes, which contain large fractions of transposon derived DNA. Recently, we have begun to acquire an in-depth picture of the population dynamics of transposable elements in Drosophila, with both bursts of transposition and purifying selection against new insertions appear to affect population frequencies of insertions. However, another important process in transposable element evolution -- horizontal transmission between species -- is less wellunderstood. The classic example of a horizontally transmitted element is that of the P-element in D. melanogaster. Recently, we have found that the P-element appears to have recently spread from D. melanogaster into a sister species, D. simulans. P-element appears to have spread quickly in D. simulans, with strains from the same geographic region showing P-element to have increased from low to high frequency within a decade.
Brian Hollis - "Adaptation and antagonism in populations evolving without sexual selection"
University of Lausanne, Switzerland
Abstract: Sexual selection may accelerate adaptation, as "good genes" theory predicts, or act as a load upon populations because of conflict between the sexes. We investigate these possibilities with fly populations that have evolved in the laboratory for over 150 generations either with sexual selection (a polygamous mating system) or without sexual selection (a monogamous mating system). Monogamous populations benefit from the evolution of reduced sexually antagonistic interactions, which can be detected in the female post-mating transcriptional response. Male selection pressures are also greatly relaxed under monogamy. This has resulted in the evolution of feminized patterns of gene expression, suggesting strong constraints on sexually dimorphic gene expression in nature.
Wolfgang Stephan - "Population genomics of adaptation in Drosophila melanogaster"
Abstract: In several organisms (whose genome has been sequenced) scans of DNA sequence variation have been carried out to elucidate the recent demographic and adaptive histories of these species. Using selective sweeps, it is possible to identify adaptive events in the genome. I will present results from our work on Drosophila melanogaster. I show that selective sweep analysis can be used to accurately map targets of positive selection in the genome. Furthermore, I will discuss whether selective sweep mapping can be combined with QTL mapping to determine the phenotype selection has been operating on. Two case studies will be highlighted: (1) the divergence of the tandemly duplicated polyhomeotic (ph) genes under positive selection, and (2) the localization of candidate genes for cold tolerance.
Summer Semester 2014
Miltos Tsiantis - "From genes to geometry: towards understanding development and diversification of leaf form"
MPI for Plant Breeding Research, Cologne, Germany
Abstract: A key challenge in biology is to understand how diversity in organismal form is generated. Genetic analyses in model systems have identified key regulators that sculpt the body plans of metazoa and seed plants. However, less is known about how the action of such regulators produces particular organ shapes, or how the balance of conservation versus divergence of such form regulating pathways generated the tremendous morphological diversity of multicellular eukaryotes. One impediment to answering these questions is the relative paucity of experimental platforms where genetic tools can be utilized to unambiguously study morphogenesis and its evolution in a genome-wide, unbiased fashion. To circumvent this problem we developed the Arabidopsis thaliana relative Cardamine hirsuta into a versatile system for studying morphological evolution. We aim to understand the molecular mechanisms through which leaf morphology evolved in these species, resulting in simple, undivided leaves in A. thaliana and dissected leaves with distinct leaflets in C. hirsuta. This presentation will discuss our progress towards understanding the genetic pathways that specify dissected versus entire leaf shapes and that regulate the number, position and timing of leaflet production.
Jonathan Jeschke - "What we know and don’t know about invasive species and other novel organisms"
Technical University of Munich, Germany
Abstract: The talk will consist of two parts, the first one focusing on invasive species and the second one on other types of novel organisms, e.g. range-expanding species, GMOs, or emerging pathogens. I will start with an overview of current understanding, and lack thereof, about invasive species. The focus will be on animals, but comparisons to plants and other organisms will be made as well. I will address the following fundamental questions about biological invasions: (1) How many species become invasive in a given region? (2) Which ecosystems are especially susceptible to invaders? And (3) What are the long-term effects of invaders? In the second part of the talk, I will present a framework that compares invasive species with other types of novel organisms, e.g. emerging pathogens, and allows knowledge transfer among researchers and managers working on different novel organisms.
Gerald Wilkinson - "Sexual selection, genomic conflict and speciation in stalk-eyed flies"
University of Maryland, USA, and Wissenschaftskolleg zu Berlin, Germany
Abstract: Speciation occurs when isolated populations diverge sufficiently to cause reproductive isolation. The processes that drive such divergence remain poorly understood. One possibility is sexual selection, which can cause rapid evolution of traits that influence precopulatory or postcopulatory success, but should only cause divergence if populations exhibit differences in mating preferences. An alternative is some type of genomic conflict, such as that responsible for biased transmission of X or Y-bearing sperm, that leads to an arms race between driving and suppressing elements. If coevolution among elements proceeds independently in isolated populations, then heterogametic hybrid sterility or inviability could occur. In this talk, I will present results from a series of studies on stalk-eyed flies that show how sexual selection and genomic conflict operate and interact to cause rapid evolution of reproductive isolation among allopatric populations in southeast Asia. I will also discuss recent genome and transcriptome studies that provide insight into the genetic causes and consequences of the ongoing sex chromosome conflict. The results suggest the genomic landscape, especially of the sex chromosomes, is remarkably dynamic in this extraordinary group of flies.
Gerald Schneeweiss - "Phylogeny and evolution of the non-photosynthetic parasitic broomrapes (Orobanchaceae)"
University of Vienna, Austria
Abstract: A hallmark of plants is their ability to utilize light as the primary energy source for producing complex organic compounds. Some plants, however, developed deviating nutritional modes including parasitism, which within angiosperms has independently evolved about twelve times. A major lineage of parasitic angiosperms is the family Orobanchaceae, containing c. 2000 species, where the full range of nutritional modes from non-parasitic via facultative and obligate photosynthetic parasites (hemiparasites) to non-photosynthetic parasites (holoparasites) is realized, rendering Orobanchaceae the model group for studying genetic, genomic, physiological and morphological adaptations and changes associated with the shift to and the intensification of parasitism. Here, I will focus on the exclusively holoparasitic clade containing Orobanche and related genera to address phylogenetic-taxonomic and evolutionary questions with respect to, for instance, genome or life history evolution.
Christian Sturmbauer - "Adaptive evolution and phenotypic plasticity in the context of adaptive radiation"
Department of Zoology, University of Graz, Graz, Austria
Abstract: Allopatric speciation often yields ecologically equivalent sister species, so that their secondary admixis enforces competition under sympatry. The rocky shores of Lake Tanganyika harbor more than 100 distinct populations and sister species of the cichlid genus Tropheus, but only some are sympatric. When alone Tropheus occupies a relatively broad depth zone, but in sympatry fish segregate by depth. To assess the effects of competition we studied the partial co-occurrence of Tropheus moorii “Kaiser” and “Kirschfleck” with Tropheus polli along a section of the central eastern shores of the lake. Hybridization experiments demonstrated that some observed differences between Tropheus “Kaiser” living alone and in sympatry to T. polli have a genetic basis despite large-scale phenotypic plasticity. Using geometric morphometrics and neutral genetic markers, we investigated whether sympatric populations differ consistently in body shape from populations living alone and if the differences are adaptive. We found significant differences in mean shape between non-sympatric and sympatric populations, whereas all sympatric populations of both color morphs clustered together in shape space. Sympatric populations had a relatively smaller head, smaller eyes, and a more anterior insertion of the pectoral fin than non-sympatric populations. Genetically, however, non-sympatric and sympatric “Kaiser” populations clustered together to the exclusion of “Kirschfleck”. Genetic distances, but not morphological distances, were correlated with geographic distances. Within- and between-population covariance matrices for T. moorii populations deviated from proportionality. We conclude that natural selection acts on both phenotypic plasticity and heritable traits, and that both factors contribute to the observed shape differences. The consistency of the pattern in five populations suggests ecological character displacement.
Fabian Staubach - "Approaches to better understand the role of microbes in the adaptation of metazoans"
University of Freiburg, Germany
Abstract: Almost all organisms on earth are associated with microorganisms. These microorganisms are important for the evolution of their hosts. However, the role they play for the evolution of their hosts can be very different. On the one hand, disease causing pathogens can exert strong selection pressures on the host that are reflected by fast evolution of host immune genes. On the other hand, microbes that are beneficial for the host have facilitated major adaptations of their host. A prominent example of an adaptation through microorganisms is the protistan microbiota in the gut of termites that facilitates the digestion of wood. I will present approaches to better understand the role of microbes in adaptation using Drosophila and termites as models.
Gerton Lunter - "Inferring demography from whole-genome data"
University of Oxford, UK
Abstract: Genetic data is informative about demography, and holds for instance evidence of past population bottlenecks, admixture and migration. Inferring these from genetic data is however not trivial. Most existing approaches rely on summary statistics, such as site-frequency spectra. More recently, approaches that directly model the process of recombination and coalescence along the sequence have succeeded in inferring past population changes from a single diploid genome. However, extending this approach to multiple samples is not straightforward.
In the talk I will discuss an approach we have been taken, using a fairly recent statistical technique known as particle filters. This approach has the promise to scale to high-dimensional models, and is well suited to this particular inference problem.
Detlev Arendt - "Evolution of the central nervous system in Bilateria"
EMBL Heidelberg, Germany
Abstract: We are intrigued by one of the great remaining mysteries in animal evolution: how did our central nervous system (CNS) come into existence? What did it look like at first and how did it function? We are especially interested in the CNS of an extinct animal known as Urbilateria, the last common ancestor of humans, flies and most other ‘higher’ animals that live today, which lived some 600 million years ago in the ocean. Our lab has chosen to investigate a new molecular animal model, the marine annelid Platynereis dumerilii. As a ‘living fossil’, Platynereis represents an ideal connecting link between vertebrates and the fast evolving protostome models, Drosophila and Caenorhabditis. Genomic resources and molecular techniques have been generated that make it a model marine invertebrate for ocean biology and for organismal systems biology. As characteristic for the Platynereis life cycle with different stages exploring different ecological niches, environmental influences impact directly on the organismal state (eco-devo) or are sensed via the nervous system (organismal neurobiology) and are reflected by the variation on genome, transcriptome or any other level of the cellome.
Miguel Gallach - "Recurrent turnover of chromosome-specific satellites in Drosophila"
Abstract: Non-coding repetitive DNA has the ability to adopt specific folding structures that may help cells identify chromosomes. In addition, repetitive DNA elements have also become a major interest among evolutionary biologists since species-specific interactions between chromatin remodeling proteins and repetitive DNA elements are disrupted in hybrids. Remarkably, in Drosophila, the X and dot chromosomes are identified by chromosome-specific binding proteins and they are particularly involved in genetic incompatibilities between closely related species. I found that these two chromosomes are overpopulated by certain repetitive elements that undergo recurrent turnover in Drosophila species. The biology and evolutionary patterns of the characterized satellites suggest that they provide both chromosomes with some kind of structural identity and are exposed to natural selection. The rapid satellite turnover fits some speciation models and may explain why these two chromosomes are typically involved in hybrid incompatibilities
Winter Semester 2013/14
John Colbourne - "How Genomic Responses to the Environment Vary"
Environmental Genomics Group, School of Biosciences, University of Birmingham, UK
Abstract: Daphnia, or the water flea, is a sentinel species of freshwater ecosystems. Their populations are defined by the boundaries of ponds and lakes, are sensitive to modern toxicants in the environment, and thus are used to assess the ecological impact of environmental change. Their short generation time, large brood sizes, and ease of laboratory and field manipulation have assured Daphnia’s importance for setting regulatory standards by environmental protection agencies, testing chemical safety, monitoring water quality, and as a model for environmental genomics research. In this study, we take advantage of the animal’s clonality and mature genomics tools to dissect the sources of gene expression variation in the stress response of genetic isolates to six environmentally relevant pollutants, and their binary mixtures. One isolate originates from a natural population that has faced severe chemical challenges for over a century of industrial iron/ore smelting and thus demonstrates evolved tolerance to toxic levels of certain metals. Another isolate originates from a population that has no history of chemical stress and is clearly harmed by metal exposure. By interrogating differential expression of 31,000 annotated genes from 50 comparisons across conditions and between isolates, the current study provides new insights into the functional interactions among genes and environment.
The research was conducted during hands-on training in “Environmental Genomics” – an annual summer course offered at the Mount Desert Island Biological Laboratory.
Alexandre Courtiol - "What can humans tell us about mate choice in other species?"
Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
Summary: My talk aims at demonstrating that anthropocentrism is a flaw that can be turned into an asset. Keeping humans in mind can indeed help us to better understand animal behaviour and working on humans allows researcher to gather data that are difficult to collect in other organisms. I will rely on the work I performed on mate choice in humans to illustrate this claim. I will show you how some trivial observations of our everyday life has lead me to rethink the theory of sexual selection. In short, I will explain why humans could be considered as a model organism for the study of mate choice.
Winter Semester 2013/14
Masaru Iizuka - "A Model of Compensatory Molecular Evolution with Indirect Compensation"
Division of Mathematics, Kyushu Dental University, Japan
Abstract: Consider two sites under compensatory fitness interaction. If there is an extra pair of sites that can reduce the deleterious effects of single mutants at the original sites, this reduction is called indirect compensation. We develop a mathematical model of indirect compensation and discuss the effects of indirect compensation on the rate of compensatory molecular evolution.
Rosemary G. Gillespie - "Community assembly through adaptive radiation: Spiders on islands"
University Of California, Berkeley, USA
Abstract: Remote islands are heralded as “natural laboratories”, with communities largely comprising species that have evolved within the islands as a result of adaptive radiation. I have been examining commonalities underlying patterns of adaptive radiation and how communities are filled in such situations, focusing on spiders in conjunction with other lineages of both animals and plants. Here, I examine patterns of morphological and ecological differentiation across the Pacific and how diversity can arise from a small sample of colonists. Specific topics will include: (1) Patterns of diversification and species accumulation within an adaptive radiation. What are the relative roles of colonization or dispersal versus parallel or convergent evolution and associated niche shifts, in shaping ecologically similar sets of species on different islands of the Hawaiian chain? (2) Integrating population genetics and macroecological metrics to assess biodiversity dynamics. How can we use the dynamic geology of the Hawaiian Islands to understand feedbacks between adaptation, population divergence, and associated community succession? Overall, this research promises insights into the interplay between selection and the biotic environment in the evolution of species within a community, and the nature and timing of species accumulation and equilibrium.
Ines Hellmann - "Evidence for local selection in northern Swedish Arabidopsis thaliana"
Section of Anthropology and Human Biology, LMU Munich, Germany
Abstract: Arabidopsis thaliana is the model organism for plant genetics and that is at least partially due to the wealth in natural phenotypic variation. Moreover, there is accumulating evidence that some of the phenotypes represent adaptations to local environments. Keeping this in mind, the lack of genetic evidence for positive selection is surprising. Here, we investigate signatures of selection more closely in southern and northern Swedish A. thaliana. After characterizing the demographic history of Swedish A. thaliana, we find evidence for hard selective sweeps in the northern and southern population, although selection in the south appears to be weaker. Further, characterizing synonymous and non-synonymous polymorphisms suggest that this difference in selection strength is due to a more heterogeneous environment in the south.
Kavita Jain - "Fixation of beneficial mutations in finite asexual populations"
J Nehru Centre for Advanced Scientific Research, Bangalore, India
Abstract: I will discuss the adaptive evolution of finite asexual populations on simple and complex fitness landscapes.
In the first part of the talk, I will describe a model in which deleterious and beneficial back mutations occur and fitnesses are multiplicative. As a result of reversible mutations, the population reaches an equilibrium at large times and I will explain how the number of deleterious mutations in the stationary state depend on various population genetic parameters. Our results are relevant to an understanding of the bias in codon usage and halting the Muller's ratchet.
In the second part of the talk, I will describe the adaptive walk performed by a population under strong selection-weak mutation conditions on a fitness landscape with many local fitness peaks. We find a simple relationship between the trends in the fitness gain during successive steps of the adaptive walk and the extreme value domain of the distribution of beneficial fitness effects (DBFE). This result may be useful in the experimental determination of DBFE using adaptation dynamics .
Nicolas Gompel - "The genetics underlying the emergence and diversification of a wing decoration”
Evolutionary Ecology, LMU Munich, Germany
Abstract: The typical pattern of morphological evolution associated with the radiation of a group of related species is the emergence of a novel trait and its subsequent diversification. From butterfly eyespots and their various colorful rings to the diversity of shapes assumed by vertebrate teeth, seashells or horn beetles, this pattern of emergence-diversification holds for countless characters across most animal groups. Yet the genetic mechanisms associated with these two evolutionary steps are poorly characterized. We're studying the evolution of wing pigmentation patterns in flies to address from a gene regulatory perspective how morphological novelties (rarely) emerge and how they (often) diversify. We're also studying the function of wing pigmentation patterns in mating behavior to identify the possible selective mechanisms underlying the evolution of this morphological trait.
Francesco Catania - "Networks, competition, trade-offs, and the evolution of genes in eukaryotes"
Institute for Evolution and Biodiversity (IEB), University of Münster, Germany
Abstract: The instructions for the synthesis of proteins are stored within genes in sequences called exons. In eukaryotes, genes contain additional DNA sequences, known as spliceosomal introns, which neither inform nor regulate the assemblage of amino acid chains. Why do eukaryotic genes have introns, and where do introns come from are still open questions in biology. In this talk, I will revisit one mechanism for the origin of spliceosomal introns, the intronization of exonic sequences, which describes the physical establishment and distribution of spliceosomal introns along transcripts. I will then discuss some ramifications that result when the model is applied to a scenario that accounts for 1) the extensive network of interactions between mRNA-associated processes and 2) the antagonistic relationships between molecules mediating the co-transcriptional processes of mRNA splicing and mRNA 3-end formation. The simple and logical connections that result from this molecular scenario suggest that a number of gene properties may be the byproduct of structural molecular constraints rather than adaptive selection.
Philipp Assmy - "Thick-shelled, grazer-protected diatoms decouple ocean carbon and silicon cycles in the iron-limited Antarctic Circumpolar Current"
Norwegian Polar Institute, Tromsoe, Norway
Abstract: Diatoms of the iron-replete continental margins and North Atlantic are key exporters of organic carbon. In contrast, diatoms of the iron-limited Antarctic Circumpolar Current sequester silicon, but comparatively little carbon, in the underlying deep ocean and sediments. Because the Southern Ocean is the major hub of oceanic nutrient distribution, selective silicon sequestration there limits diatom blooms elsewhere and consequently the biotic carbon sequestration potential of the entire ocean. We investigated this paradox in an in situ iron fertilization experiment by comparing accumulation and sinking of diatom populations inside and outside the iron-fertilized patch over 5 weeks. A bloom comprising various thin- and thick-shelled diatom species developed inside the patch despite the presence of large grazer populations. After the third week, most of the thinner-shelled diatom species underwent mass mortality, formed large, mucous aggregates, and sank out en masse (carbon sinkers). In contrast, thicker-shelled species, in particular Fragilariopsis kerguelensis, persisted in the surface layers, sank mainly empty shells continuously, and reduced silicate concentrations to similar levels both inside and outside the patch (silica sinkers). These patterns imply that thick-shelled, hence grazer-protected, diatom species evolved in response to heavy copepod grazing pressure in the presence of an abundant silicate supply. The ecology of these silica-sinking species decouples silicon and carbon cycles in the iron-limited Southern Ocean, whereas carbon-sinking species, when stimulated by iron fertilization, export more carbon per silicon. Our results suggest that large-scale iron fertilization of the silicate-rich Southern Ocean will not change silicon sequestration but will add carbon to the sinking silica flux. Significance statement: Silica-shelled diatoms dominate marine phytoplankton blooms and play a key role in ocean ecology and the global carbon cycle. I will show how differences in ecological traits of dominant Southern Ocean diatom species, observed during the in situ European Iron Fertilization Experiment (EIFEX), can influence ocean carbon and silicon cycles. I argue that the ecology of thick-shelled diatom species, selected for by heavy copepod grazing, sequesters silicon relative to other nutrients in the deep Southern Ocean and underlying sediments to the detriment of diatom growth elsewhere. This evolutionary arms race provides a framework to link ecology with biogeochemistry of the ocean.
Rita Adrian - "Windows of opportunity: The role of extremes and thresholds in ecological research"
IGB Berlin, Germany
Abstract: We use Long-Term Ecological Research to understand lake ecosystem dynamics with a focus on plankton communities. The value of long-term ecological research is that the observed pattern and temporal dynamics incorporate the entire complexity of internal and external driving forces, which cannot by mimicked in experimental or modelling exercises. I will present a couple of case studies showing responses of lakes to environmental change such as climate warming. The case studies encompass the role of critical time windows, the quantification of critical thresholds, the impact of heat wave events, etc. Moreover, I will provide an example documenting- how long-term ecological research can help to test and combine ecological theory – and by that help to understand the complex nature of driving forces.
Summer Semester 2013
Julia Schroeder - "Indirect genetic effects through social interactions - a case study"
Max Planck Institute for Ornithology, Seewiesen, Germany
Abstract: The social environment - the presence and behaviour of conspecifics - can influence the expression of phenotypes i.e., individuals other than the one expressing the focal trait can explain some of the phenotypic variation. The genetic part of this indirect effect represents an indirect genetic effect (IGE). Not accounting for IGEs can considerably under- or over-estimate the total heritable variation available for selection to act on, and thus predict misleading evolutionary trajectories. Yet, empirical studies on wild populations often ignore IGEs. I will present a quantitative genetic analysis of biparental care in a wild bird population. My results suggests that the female trait could evolve through indirect selection by her mating partner, which most theoretical models explaining the evolution of biparental care do not assume. Notably, the within-individual repeatability of female parental care was lower than the total heritable variation. This shows that the assumption that repeatability is the upper limit of heritability should be used cautiously when applying to socially interactive traits, and highlights the importance of accounting for social effects.
Daniel Wegmann - "Model based inference of evolutionary histories"
Swiss Federal Institute of Technology (EPFL) Lausanne, Switzerland
Abstract: A detailed understanding of the evolutionary history of a species or population is crucial when identifying the targets of selection, inferring modes and tempo of speciation or designing appropriate management efforts in conservation. However, inferring evolutionary histories has been proven difficult, mainly because neutral processes are extremely stochastic and analytical solutions are difficult to obtain expect for the most simple models. This situation only recently changed with the advent of ever more powerful sequencing technologies allowing us to generate enormous data sets to overcome the stochastic nature of neutral processes, and numerical approaches that allow us to side-step or facilitate the calculation of likelihood functions. In this talk, I will make the case for model based inference in an evolutionary context and illustrate various numerical strategies, focusing on a composite likelihood approach and, in particular, Approximate Bayesian Computation (ABC). I will then discuss ideas on how to render ABC fit for complex models and large data sets, and illustrate them by inferring aspects of the evolutionary history of humans, rose finches and the clade of all carnivora.
Wolfgang Weisser - "Ten years of the Jena Biodiversity Experiment – a selective review"
Department of Ecology and Ecosystem Management, Technische Universität München & The Jena Experiment Consortium, Germany
Abstract: The Jena Experiment was set up in 2002 to investigate the effects of plant diversity on closed element cycling and trophic interactions and presents today one of the largest and longest-running functional biodiversity experiments. In the talk I will review the results of the almost 10 years of research in the experiment. I will review which ecosystem variables are more strongly affected by biodiversity and which ones are less affected, including measurements of element cycling and biotic interactions. A main conclusion that emerges from the work is that the future of biodiversity research lies in understanding why the magnitude of biodiversity effects differs between processes. Future studies need to concentrate on the identification of the mechanisms underlying the observed patterns, in particular on how ecosystem variables are driven by species interactions and how these interactions are affected by diversity.
Michael Monaghan – "Large-scale evolution and local adaptation in aquatic insects"
Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Germany
Abstract: Large-scale sequencing projects of communities in nature (DNA barcoding, next-generation "meta-barcoding") are increasingly applied to species delineation and identification in biodiversity research and bio-monitoring applications. These same methods also provide novel insights into large-scale patterns of evolution across taxa, which in turn lead to interesting interface of basic and applied biodiversity research is whether and how the nature of the evolutionary process makes the observed patterns scale-dependent. Here I present ongoing work on how the evolutionary process makes the application of sequence-based inventorying scale-dependent for a group of aquatic insects in Europe. In contrast to this large-scale work (100s - 1000s km) using neutral markers, ongoing work in natural populations using genome scans (AFLP) shows consistent patterns of local adaptation (1-10 km) in aquatic insect populations in nature.
Piet Spaak - "Daphnia hybridization in peri-alpine lakes over space and time"
EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Switzerland
Abstract: The three Daphnia species of the D. longispina complex (D. galeata, D. longispina and D. cucullata) and their hybrids can be found in lakes all over Europe. Many factors (e.g. food quality and quantity, predation, diseases, competition) have been studied to explain why parentals and hybrids co-occur. We reconstructed some of the Daphnia populations North of the Alps over time, using sediment cores, and showed that eutrophication is an important factor in determining the composition of Daphnia populations over time.
To study on a spatial scale the composition of Daphnia populations we surveyed Daphnia populations north and south of the Swiss Alps. We found that Lakes North of the Alps were invaded with one species (D. galeata) and hypothesize that lakes south of the Alps were invaded with D. longispina. A first life history experiment shows some evidence for this hypothesis. Further, testing of this hypothesis needs to come from sediment cores from lakes from the south side of the alps. I will present recent data about these studies.
Urban Friberg - "Genetics of sexual dimorphism"
Evolutionary Biology Centre, Uppsala University, Sweden
Abstract: Evolution of sexual dimorphism (SD) is a paradox. On the one hand it shouldbe constrained, because it is restricted to occur only through geneexpression and because it relies on gene expression having a sex-specificgenetic architecture. On the other hand SD is common and SD traits are amongthose that evolve the fastest. How is this possible? Is evolution of SDreally constrained, or is SD evolving rapidly despite constraints? Previousstudies have given inconsistent answers to this question, when applied totraits at a high level of phenotypic organization (morphological, behavioraland physiological). We addressed this question at the lowest level ofphenotypic organization – gene expression – and found substantial evidencefor constraints hindering evolution of SD in the Drosophila genus. I willpresent results from this study, as well as preliminary data which indicatesthat the X-chromosome may play a key role in mediating evolution of SD. Iwill also present data from a study on the genetics of SD for lifespan inDrosophila. Lifespan turns out to have a surprisingly decoupled geneticarchitecture between the sexes, which results in large differences in theheritability of this trait within and across the sexes and points to thatdisease genetics in fruit flies is vastly different in males and females.
Volker Sommer - "Neither Good Nor Bad. Morality And Evolution"
Department of Anthropology, University College London, UK
Abstract: Many people judge a behaviour as morally wrong, because it is allegedly "unnatural". A prominent example is the condemnation of homosexual conduct as directed "against nature". Such arguments are typically ill-informed. For example, same-sex sexual contacts are quite common in non-human animals. Still, this doesn't imply that one should condone such behaviour either. Virtually all conceivable human behaviours are also shown by animals - be it cannibalism, cooperation, incest, infant-killing, empathy, masturbation, food-sharing, sex with immatures, polyandry, sacrifice for one's group or war. Whether or not we judge such traits as reprehensible, acceptable or desirable, depends on our cultural background. Nevertheless, solid natural history can certainly be helpful in debates about how societal norms should be constructed.
Vasilis Promponas - "Genome evolution and large-scale protein function prediction"
Department of Biological Sciences, University of Cyprus, Cyprus
Abstract: Since the first complete genome sequences of free-living organisms became available, a number of computational methods –collectively known as "genome-aware methods"– were proposed for the inference of protein function, structure and interactions. Such methods (including gene clusters, gene fusions and phylogenetic profiles) have proved invaluable for the in silico functional characterization of proteins, especially in cases where no identifiable sequence similarity exists to proteins of known function.
In this presentation, I will describe the basic principles behind these genome-aware methods, using as examples applications to real-world complete genome data. I will try to highlight specific success stories and pitfalls, elaborating on how genome-aware methods (in particular gene-fusion analysis) are confounded by genome sequence quality, including gene prediction accuracy and assembly validation. Finally, I will conclude with a discussion on how such limitations can be addressed in the context of automated function prediction methods, while we are rapidly approaching the $1000 genome era.
Adam Petrusek - "Diversity and impact of invasive crayfish and the crayfish plague: old menace is back with new surprises"
Charles University, Prague, Czech Republic
Abstract: Crayfish plague, caused by an oomycete Aphanomyces astaci, is a well-studied invasive disease of wildlife with substantial conservationaland economic impact. Having stricken Europe already in the second half of 19th century, it has been substantially studied in the past, and became one of the best known diseases of aquatic invertebrates. Still, many aspects of its ecology and host-pathogen interactions are only being discovered in recent years. Original hosts of the crayfish plague pathogen are North American freshwater crayfish that are usually able to resist the infection without major symptoms or mortalities. Crayfish from other biogeographicregions are susceptible to the disease, which remains one of the key threats to native European populations. Several North American invasive crayfish species are found in European waters, three of these crayfish plague carriers being very widespread. In the talk, I will first summarise the history and present status of invasive crayfish in Europe, and their ecology and diversity. Afterwards, I will discuss the crayfish plague, its life cycle and impact, and some of the most interesting recent discoveries facilitated by development of molecular tools.
Fani Papagiannouli - "Close contacts in the Drosophila testis: Crosstalk of germline and somatic cells promotes stem cell niche and testis homeostasis"
Centre for Organismal Studies (COS) Heidelberg, Germany
This seminar will take place on a special day and time: Friday at 14:00 at Biozentrum, Großhaderner Str. 2, 82152 Planegg-Martinsried. Also, it is in a different room than usual (B01.015)!
Abstract: Stem cells reside in microenvironments, known as the stem cells niches, that play an important role in stem cell behavior. The Drosophila testis provides a powerful system to study stem cell behavior. Stem cell niche and testis morphogenesis is achieved through the physical contact and diffusible signals exchanged between the germline and somatic cell populations. The cytoskeletal proteins Dlg, Lgl and Scrib are required in the somatic lineage for testis development and homeostasis with Dlg acting on survival, growth and membrane proliferation of the somatic cyst cells. On the other hand, the Hox gene Abd-B in the testis spermatocytes provides upstream positional cues to maintain niche architecture and localization, and ensure proper niche function and germline stem cell activity. Identification of Abd-B binding regions throughout the genome, revealed that Abd-B mediates its effects by directly controlling at multiple levels the localization, recycling and thus signaling activity of the Sevenless (Sev) ligand, Bride of Sevenless (Boss), via its direct targets src42A and sec63. Using genomic, genetic and molecular techniques combined with the related microscopy, I am interested in understanding the fundamental regulation of testis cell communication. In particular, my focus is to elucidate how testis-specific gene regulation and cytoskeletal components affect endocytosis, membrane trafficking as well as the signaling events that shape the germline-soma microenvironment and promote testis homeostasis.
Winter Semester 2012/13
Katja Nowick - "Changes in transcription factor genes and gene regulatory networks during primate evolution"
TFome and Transcriptome Evolution, Bioinformatics, University of Leipzig, Germany
Aurelien Tellier - "Ecological and evolutionary importance of soil seed banks for plant species"
Population Genetics Group, Center of Life and Food Sciences Weihenstephan, TU München, Germany
Felicity Jones - "The genetics and genomics of stickleback adaptive diversity"
Molecular Mechanisms of Adaptation and Speciation, MPI for Developmental Biology, Tübingen, Germany
Julien Dutheil - "Ancestral population genomics: sequencing the present to infer the past"
Evolutionary Bioinformatics, Institut des Sciences de l'Evolution de Montpellier, France
Nicole Kammerer / Bernhard Busch - "Multiplatform-based sequencing: combining libraries, sequencing technologies and software tools"
DNA Sequencing and Bioinformatics, GATC Biotech, Konstanz, Germany
Johannes Söding - "Protein structure prediction, transcriptional regulation, and core promoters"
Soeding Lab, Gene Center, Munich, Germany
Harold P. de Vladar - "The different facets of evolutionary genetics: from bean-bag genetics to statistical mechanics & computer science"
Barton Group, Institute for Science and Technology Austria, Vienna, Austria