Every semester, EES organise a seminar series, which takes place on Mondays at 16:00 at Biozentrum, Großhaderner Str. 2, 82152 Planegg-Martinsried, Lecture Hall B 01.027
Speakers are invited from mainly around Europe across all three areas (Evolution, Ecology and Systematics), leading to a wide-range of presented research topics.
Winter Semester 2018/2019
David Garfield - Single-cell and population genetic approaches to understand developmental evolution
Humboldt University, Berlin, Germany
Please note: This seminar will exceptionally take place on a Wednesday at 13:00 h!
Abstract: Mutations affecting non-coding, regulatory DNA play an important role in evolution and contribute disproportionately to human disease phenotypes. But identifying functional mutations in non-coding DNA is hard – typically we don’t know where to look, and when we do, we often find redundancy and degeneracy that complicate a simple mapping of genotype to phenotype. New advances in single-cell sequencing technologies, particularly single-cell ATAC-Seq, can help to delineate and identify regulatory elements active in different tissues. We recently used one such approach to construct a cell-type specific atlas of regulatory DNA used during embryonic development in Drosophila. In this talk, I will discuss our efforts to move this atlas one step farther, using population genetic information and allele-specific sequencing to understand how the impacts of selection and functional mutations are distributed across this regulatory landscape, with an eye towards the role that single-cell assays and evolutionary analyses can play in understanding the evolution of development across a range of taxa.
Fritz Sedlazeck - Size matters: accurate detection and phasing of structural variations
Baylor University, Texas, USA
Abstract: In this presentation I will describe our latest work to obtain comprehensive genomes leveraging long and linked reads. The vast majority of NGS whole-genome data covers hundreds of thousands of samples with short illumina reads, which are unable to capture the full spectrum of genetic variation and genomic complexity. Such comprehensive variation is critical to understanding the full heritability and genetic foundations of human disease. In this seminar I will present our novel alignment strategy (NGMLR) for long read data (Oxford Nanopore and PacBio) and our novel Structural Variations (SVs) caller Sniffles. These two methods improved the accuracy for both technologies enabling the accurate and easy detection of SVs. This includes also nested events that we have previously been blind to or linked events connecting genes over multiple regions. We will discuss problems, characteristics and limitations of short reads. In addition, I will discuss the impact of these novel found SVs in cancer and other genomes with respect to RNA seq. In the end, I will highlight our current findings where we combine these long read technologies with linked reads to be able to phase SNV and SVs together to obtain a diploid genome per sample. These phased genomes are the most comprehensive representation of genomes up to date and we can now finally generate them within days.
Kees van Oers - Genomic and epigenetic insights into the heritability of exploratory behaviour
Netherlands Institute for Ecology, Wageningen University
Abstract: For behavioural geneticists, the search for the hereditary mechanisms underlying quantitative traits traditionally focussed on the identification of underlying genomic polymorphisms such as SNPs, but this has not been very fruitful. It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. Non-geneticists found out that these methylation patterns are prone to changes and such changes may be transmitted over generations. DNA methylation may therefore be an potential mechanism linking genetic and non-genetic inheritance. In this presentation, I will focus on exploratory behaviour in great tits (Parus major) as an example to highlight the successes and failures of modern genomic approaches. Furthermore, I will present preliminary results on the relative role of induced- versus genetic variation in DNA methylation for variation in exploratory behaviour. I will however also elaborate on the pitfalls when studying epi-genomics in an ecological model species. The explanation of variation in DNA methylation offers a great opportunity to combine genetic and non-genetic approaches to inheritance of complex traits.
Markus Knaden - Olfactory-guided navigation in a desert ant
Max Planck Institute for Chemical Ecology, Jena, Germany
Abstract: The desert ant Cataglyphis inhabits the arid environment of North Africa where it forages individually for dead arthropods. Because of the ants’ high motivation to find the nest entrance and due to the almost lab-like conditions of their environment — the flat salt pan (where visual information and partly also olfactory information available to a homing ant can be easily manipulated) — Cataglyphis has become an important model for animal navigation. The ants use path integration, i.e. always compute their walking direction and distances and by that calculate their position to the nest entrance. In addition they learn visual and olfactory cues that help them pinpointing the nest entrance. The seminar will describe recent findings on olfactory navigation and will present how Cataglyphis combines the visual and olfactory navigational strategies efficiently.
Krysztof Kozak - Drivers of diversification in Neotropical butterflies and beyond
Smithsonian Tropical Research Institute, Panama
Abstract: The richest diversity of life on Earth is found in the Neotropics, an area characterized by fast and dramatic environmental changes over the last 25 million years. Studies of complex adaptive radiations at the continental scale provide an opportunity to understand how speciation and adaptation have interacted with abiotic factors to produce high species richness. I focus on Heliconiini butterflies (Nymphalidae), a group of 77 species renown for spectacular diversity in aposematic wing patterns and formation of Müllerian mimicry rings. Phylogenetic analyses of entire genomes reveal rampant admixture across the genus Heliconius, with evidence for adaptive introgression at all five loci controlling the color and shape of the mimetic wing patterns. These findings suggest that the radiation ought to be represented as a network and imply that our ability to study traits in a comparative framework may be affected by the imposition of a bifurcating tree model.
To better understand the processes of diversification at the species level, I leverage the natural experiment formed by the radiations of Heliconius erato and H. melpomene, two widely spread species that mimic each other in a continental patchwork of 29 distinct wing pattern forms. Although the matching phenotypes have been used as an example of coevolution ever since Bates, it is unclear if the two species diversified in parallel. Using genomes of 170 H. melpomene and 260 H. erato and cognates collected widely across the Neotropics, I demonstrate substantial differences in the evolutionary history of the two species. Surprisingly, while mountain uplift left a strong signature on the early evolution of the two species, populations across the Amazon basin appear unexpectedly homogenous.
Finally, I will present first insights from a systematic survey of phylogenetic studies of American tropical taxa, highlighting perilously poor accessibility of published data. A re-analysis of a sample of chronograms for a wide spectrum of Neotropical taxa reveals that most extant species formed before Quarternary climatic disturbances. However, contrary to recent proposals, there is limited evidence for response to environmental disturbances in the Miocene, as many groups show surprisingly constant rates of diversification.
Simone Immler - Haploid gametic selection in animals and its evolutionary consequences Cancelled
University of East Anglia, UK
Abstract: Biphasic life cycles with alternating diploid and haploid gametic phases are a traits shared by all sexually reproducing eukaryotes. Selection occurring during - even a short - haploid gametic phase may have substantial consequences for a wide range of biological processes including adaptation, inbreeding depression and sex chromosome evolution. While in plants, selection in haploid gametes is well established, in animals, the idea has remained largely untested. This is somewhat surprising given that particularly male gametes (sperm) are generally produced in large numbers but only few fertilise an egg offering an ideal opportunity for selection to act upon. We tested for selection on the haploid sperm genome in the zebrafish combining selection experiments with transcriptome and genome sequencing. We found clear evidence that the haploid sperm genome is more than just a silenced genome and selection at this stage has major fitness consequences for the following generations.
Sonja Grath - Winter is coming – Cold tolerance in Drosophila
LMU Munich, Germany
Abstract: When organisms are faced with new environmental conditions, such as those caused by climate change or range expansion, they must adapt in order to survive. For evolutionary biologists, studying how species are formed and how they adapt to their environment are central questions. The evolutionary process by which individuals have their highest fitness in their local environment by means of natural selection is called local adaptation. Drosophila vinegar flies have been an important model system for biological studies since the early 1900s and Drosophila species having a worldwide distribution are excellent models for studying local adaptation. One example for local adaptation is adaptation to cold. Here, I will give insight into our work on cold tolerance in Drosophila ananassae. We used chill coma recovery time (CCRT) as proxy for cold tolerance in several fly strains. CCRT is the time required for a fly to recover from a cold-induced chill coma. We performed high-throughput gene expression analysis before and after a cold shock and conducted a quantitative trait loci (QTL) mapping experiment to identify candidate genes involved in cold tolerance. Finally, I will present our preliminary work on functional validation of these candidate genes by the means of CRISPR/Cas9-manipulated flies.
Georg Oberhofer - Cleave and Rescue: a novel selfish genetic element and general strategy for gene drive
University of Göttingen, Germany
Abstract: Gene drive provides an opportunity to spread beneficial traits into a wild population. Here we describe a novel toxin-antidote type of synthetic selfish genetic element, Cleave and Rescue (ClvR), that is simple to build, and can spread a linked gene to high frequency in populations. ClvR is composed of two components. The first, germline expressed Cas9 and gRNAs (the toxin), cleave and disrupt versions of an essential gene located elsewhere in the genome. The second, a version of the essential gene resistant to cleavage, provides essential gene function (the antidote). ClvR spreads by creating conditions in which progeny lacking ClvR die because they have no functional copies of the essential gene. In contrast, those who inherit ClvR survive, resulting in an increase in ClvR frequency.
Konrad Lohse - What determines genetic diversity in butterflies? Lewontin's paradox revisited
University of Edinburgh, UK
Abstract: The amount of genetic diversity segregating within a species is a function of its demographic and selective past and, in turn, determines its future evolutionary potential. Under the neutral theory genetic diversity is expected to be a linear function of population size. However, comparative studies have consistently failed to find any strong correlation between measures of census size and genetic diversity. Instead, a recent comparative study across several animal phyla identified propagule size as the strongest predictor of genetic diversity, suggesting that r-strategist which produce many offspring but invest little in each, have a greater long effective population sizes. I present a comparison of genome-wide levels of genetic diversity across 38 species of European butterflies. Analyses of these data suggest that across Lepidoptera genetic diversity varies over an order of magnitude and that this variation cannot be explained by differences in abundance, fecundity, host or geographic range. Instead, genetic diversity is correlated with genetic map length suggesting that the effect of selection on linked neutral diversity varies substantially between species.
Summer Semester 2018
Martin Kapun - Clines and inversions as evidence for local adaptation in Drosophila melanogaster
University of Fribourg, Switzerland
Abstract: Clines, which are gradual changes of genotypes or phenotypes along environmental transects, are often taken as prima facie evidence for the action of spatially varying selection. However, only due to recent advances in sequencing technology it now becomes possible to compare genome-wide clinal patterns and test for alternative models. We use the Drosophila melanogaster system to study genomic diversity along a latitudinal temperature gradient at the North American east coast. We found evidence for steep and temporally stable clinal variation associated with In(3R)Payne, a common cosmopolitan inversion, that cannot be explained by demography alone. To learn more about the potential adaptive effect of this inversion, we compare karyotype-specific genomic and transcriptomic variation on different continents. We find genomic regions in the center of the inversion that are in strong linkage disequilibrium with the inversion breakpoints possibly as a result of selection for inversion-specific genetic variation. Finally, with the help of a newly founded population genetics consortium, we now expand the genome-wide analysis of clinal genomic variation to the yet largely unexplored European continent and find further evidence for the clinal variation of In(3R)Payne despite complex demographic patterns.
Dieter Heylen - Evolutionary ecological interactions between songbirds, ticks and Borrelia burgdorferi s.l.: a community perspective
University of Antwerp, Belgium
Please note that this seminar will Mutations affecting non-coding, regulatory DNA play an important role in evolution and contribute disproportionately to human disease phenotypes. But identifying functional mutations in non-coding DNA is hard – typically we don’t know where to look, and when we do, we often find redundancy and degeneracy that complicate a simple mapping of genotype to phenotype. New advances in single-cell sequencing technologies, particularly single-cell ATAC-Seq, can help to delineate and identify regulatory elements active in different tissues. We recently used one such approach to construct a cell-type specific atlas of regulatory DNA used during embryonic development in Drosophila. In this talk, I will discuss our efforts to move this atlas one step farther, using population genetic information and allele-specific sequencing to understand how the impacts of selection and functional mutations are distributed across this regulatory landscape, with an eye towards the role that single-cell assays and evolutionary analyses can play in understanding the evolution of development across a range of taxa.
Abstract: Dieter Heylen is postdoctoral at the University of Antwerp (Biology department, Evolutionary Ecology group). He has more than ten years of experience in the study of ticks, songbirds and tick-borne diseases (TBD). He studies how the evolutionary ecology of host-parasites interactions relates to virulence, ecological specialization, adaptation, and spatio-temporal occurrence of ticks and TBD in songbirds. In more recent work, he investigates how ticks and birds contribute in the maintenance and establishment of TBD foci, by studying the reservoir competence of songbird species, and the vector-competence of bird-specialized tick species. He currently investigates how landscape determines TBD transmission flows over urbanisation gradients, and how isotope ratios of ticks can help in
elucidating transmission dynamics in the wild. In his seminar, he will consider the findings on the ecological interactions between ixodid ticks, common European songbirds and the Lyme disease causing bacteria Borrelia burgdorferi s.l..
Chris Jiggins - Understanding porous species boundaries by studying butterfly genomes
University of Cambridge, UK
Abstract: A major undertaking in evolutionary biology is to link genotype to phenotype and understand the evolutionary changes that lead to adaptation and speciation. Here I will give an overview of our work on the brightly coloured Heliconius butterflies, showing that hybridisation makes species boundaries remarkably porous across the genome. Patterns of species relationships are highly variable across the genome, and this can offer insight into the process of speciation. There is little evidence for changes in recombination rate or inversion differences between species during speciation. Despite these loci of large effect, across the genome there is evidence for pervasive polygenic selection maintaining species differences in the face of ongoing gene flow, indicated by a strong association of admixture with regions of high recombination.
Gergely Szollosi - Gene transfers, like fossils, can date the tree of life
University of Budapest, Hungary
Abstract: The geological record provides the only source of absolute time information to date the tree of life. But most life is microbial, and most microbes do not fossilize, leading to major uncertainties about the ages of microbial groups and the timing of some of the earliest and most important events in life's evolutionary history. I discuss our recent results, which show that patterns of lateral gene transfer deduced from analysis of modern genomes encode a novel and highly informative source of information about the temporal coexistence of lineages throughout the history of life. We use new phylogenetic methods to reconstruct the history of thousands of gene families and show that dates implied by gene transfers are strongly correlated with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukaryotes. A comparison with mammalian fossils shows that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.
Rodrigo Medellin - How to do conservation science, implement it, and not die trying.
Instituto de Ecología, UNAM, Mexico
Abstract: Conducting research for conservation is, unfortunately, too often cut short or rarely implemented. I will discuss a few examples of research projects that have become official federal government programs with nation-wide implications. Mexico is the fifth country with the greatest biodiversity in the world. Challenges are thick and plentiful. Recently Mexico became the first country in the world to have an estimate of how many jaguars inhabit the country and the National Jaguar Strategy is fully in place and being implemented today. I will also speak about bighorn sheep and how a sustainable harvest has become the heart and soul of a strong conservation and development program for the Seri indigenous group. Bats represent about one-fourth of Mexico’s mammals and they include critically endangered and endangered species. The lesser long-nosed bat has been a focal species for my research and after 25 years it was recently delisted from Mexico’s Endangered Species List. The recovery implied lots of research, education, and specific conservation actions. The job of conservation professionals must include working with government and public to be effective.
Tuncay Baubec - Function and regulation of mammalian DNA methylation
University of Zurich, Switzerland
Abstract: DNA methylation is a prevalent epigenetic modification involved in transcriptional regulation and essential for mammalian development. In mammalian genomes, DNA methylation is a prevalent modification that decorates the majority of cytosines. It is found at the promoters and enhancers of inactive genes, at repetitive elements, and within transcribed gene bodies. Its presence at promoters is dynamically linked to gene activity, suggesting that it could directly influence gene expression patterns and cellular identity. While the genome-wide distribution of this mark has been studied to great detail, the mechanisms responsible for its correct deposition, as well as the cause for its aberrant localization in cancers, have not been fully elucidated. I will present our recent efforts to elucidate the targeting preferences of DNA methyltransferases to the genome, and how chromatin states, histone modifications and DNA sequence help to guide deposition of DNA methylation to specific genomic sites.
Homa Papoli - The evolution of sex chromosomes and sex-linked sequences in systems with female heterogamety
Uppsala University, Sweden
Abstract: Sex chromosomes evolved from a pair of autosomes between which recombination stopped. We can look at sex chromosome evolution at two levels. The first is looking at a large evolutionary time scale to investigate the steps involved in recombination cessation. In another level, we can look at the consequences of recombination cessation in the evolution of sex linked sequences. We used ostrich, as a representative of a basal clade of birds, together with several avian species to infer the chromosomal inversions involved in the evolution of sex chromosomes. To understand the consequences of recombination suppression on the evolution of DNA sequences, we used multiple avian species and a population level data of ostrich sex chromosomes to infer determinants of genetic diversity.
Thomas Gilbert - Dogs and Wolves in Time and Space
University of Copenhagen, Denmark
Abstract: Despite the key position that dogs hold in the lives of many of us, and the extensive efforts of many previous scientific studies, a surprising amount remains to be learnt about our faithful friends. For example, considerable controversy exists over such basic questions as: When did we first domesticate the dog? Where was the domestication centre? Was there more than one? And perhaps most surprisingly, what was the dog even domesticated from? Given the extent to which we have both moved and shaped dog breeds in recent centuries, and taken a good stab at eradicating their wild relatives, it seems unlikely that analyses of modern genetic material alone will be able to solve these questions. As such deciphering dog domestication represents an exciting frontier on which palaeogenomic approaches stand to make enormous contribution, and indeed, in light of a vastly expanded reference dataset of contemorary genomic material, a number of intriguing findings are already coming to light.