EES seminars SoSe 2012
From EESwiki
EES and Forschergruppe seminars take place on Mondays at 17:00h in the Biozentrum.
23.04.2012 Magnus Nordborg - "Elucidating the genotype-phenotype map using Arabidopsis"
Website: Gregor Mendel Institute of Molecular Plant Biology, Vienna
Contact: Aurelien Tellier
Abstract: Making sense of natural variation remains one of the greatest challenges in biology. Understanding how genetic variation translates into phenotypic variation, and how this translation depends on the environment is fundamental to our understanding of evolution, and has enormous practical implications for medicine, agriculture and energy production.
We are attempting to tackle this problem using Arabidopsis thaliana as a model. Because it is highly self-fertilizing and naturally exists as inbred lines, A. thaliana can be brought into the laboratory and grown, in replicate, under different environmental conditions, in order to explore how the genotype-phenotype map works and has been molded by evolution. The presence of inbred lines, coupled with its compact, 120 Mb genome, also makes A. thaliana useful as a model for genomic approaches that will soon be possible in others organisms. As part of the 1,001 Genomes Project, we are sequencing well over 1,000 inbred lines, and are complementing these data with other kinds of “-omic” information, such as DNA methylation patterns and transcriptome measurements in large numbers of lines under multiple environmental conditions. For example, we are currently analyzing the data from a study that involved flowering time and multiple other phenotypes in a sample of 200 Swedish lines grown at two different temperatures. These data have been complemented with transcriptome (via mRNA-seq) and DNA methylation (via bisulfite sequencing) measurements of all lines under both temperatures. By supplementing the genome-wide associations between genotype and phenotype with the “in-between-ome”, we hope to gain insight not only in which genetic polymorphisms are associated with phenotypic variation, but why.
By carrying out these kinds of studies in A. thaliana, which can be grown in replicate under controlled conditions, we also hope to gain insight into the limitations of these “brute force” genomic approaches, which are rapidly becoming economically feasible for a broad range of species, but may not be practicable from a biological point of view. In particular, we have learned much about the difficulties involved in identifying causal genetic polymorphisms through genome-wide association studies.
10.05.2012 Charles Godfray - "Ecological and co-evolutionary interactions between insects and their endosymbionts."
Website: Department of Zoology, University of Oxford
Contact: Francesco Paparazzo <paparazzo@bio.lmu.de>
Please note: this seminar will be held during the LSM seminar series (room G00.031) at 17:00 and is not an official part of the EES seminar series!
21.05.2012 Eva Stukenbrock - "Unravelling patterns of speciation and specialization in fungal plant pathogens using comparative population genomics."
Website: MPI for Terrestrial Microbiology, Marburg
Contact: Wolfgang Stephan
Abstract: The fungus Mycosphaerella graminicola emerged as a new pathogen of cultivated wheat during its domestication about 11000 years ago. We assembled 12 high quality full genome sequences to investigate the genetic footprints of selection in this wheat pathogen and closely related species that infect wild grasses.
Current levels of genetic diversity measured through statistics such as PN / PS and π were not significantly different in M. graminicola relative to its wild sister species. Furthermore M. graminicola still contains a significant amount of “ancestral” polymorphisms shared with its wild sister species suggesting that the loss of variation in M. graminicola was not severe during its specialization to wheat.
Recent divergence between pathogen sister species is attested by the high degree of incomplete lineage sorting (ILS) in their genomes. We exploit ILS to generate an ancestral recombination map of the species without any crossing data, document recent times of species divergence relative to genome divergence and show that gene rich regions or regions with low recombination experiences stronger effects of natural selection on neutral diversity.
It is clear that while domesticated plant species have become restricted in their evolutionary potential through loss of variation, “domesticated” pathogens such as M. graminicola seem readily able to maintain ancestral variation, regenerate lost diversity and evolve new specificities.
11.06.2012 Dan Graur - "The compositional architecture of mammalian genomes"
Website: Theoretical Molecular Evolution and Bioinformatics, University of Houston
Contact: John Parsch
18.06.2012 Patrick Mardulyn - "Genetic variation and evolutionary history of cold-adapted European leaf beetles."
Website: Evolutionary Biology and Ecology, Université Libre de Bruxelles
Contact: Adrián Troya
Abstract: The geographic distribution of genetic diversity in many organisms is thought to have been strongly influenced by Pleistocene climate fluctuations. We focus on the genetic variation found in cold-adapted leaf beetles, by collecting multi locus DNA sequence data in several European species that share a similar geographic distribution. Among others, these molecular data allow us to highlight hybridization among species, to compare phylogeographic patterns among related organisms that share a similar habitat, to contrast genetic variation in these cold-adapted species with that found in temperate climate species, and to gain information of the evolutionary history of host-plant shifts in these specialized herbivorous insects. Several historical hypotheses regarding the influence of past climatic changes on these organisms are compared under a coalescence framework.
25.06.2012 Eckhard Heymann -"Evolutionary ecology of tamarin interspecific associations."
Website: Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen
Contact: Monika Poxleitner
Abstract: Group living is known to be beneficial in terms of increased safety from predators or foraging efficiency, amongst other benefits. While groups are usually composed of conspecifics, they may also be formed by individuals from different species. Although such mixed-species groups or interspecific associations may occur randomly or context-dependent (e.g. through simultaneous attraction to a resource) there are also examples for consistent, long-term and context-independent associations, e.g. in Neotropical primates of the genus Saguinus (tamarins). This talk will present information on the patterns of association between different tamarin species, the supposed benefits and costs of such associations, and mechanisms of niche differentiation between associated species. Based on recent phylogenetic analyses, a scenario for the evolutionary origin of tamarin interspecific associations is presented.
02.07.2012 Stephan Greiner - "Oenothera - A model for cytoplasmic speciation barriers and functional asexuality."
Website: MPI for Molecular Plant Physiology, Potsdam
Contact: Wolfgang Stephan
Abstract: The genus Oenothera Oenothera displays a unique combination of non-Mendelian genetic features, like permanent translocation heterozygosity and biparental transmission of plastids. They allow the exchange of plastids between species, which often results in plastome-genome incompatibility (PGI) - a hybridization barrier according to the Dobzhansky-Muller model. In turn, PGI provides molecular access to speciation forces acting on photosynthesis. Furthermore, Oenothera exhibits over 20 transitions between sexual and functionally asexual reproduction, caused by chromosomal translocations. Both features make Oenothera an ideal model for examining hypotheses regarding the evolutionary advantages of sex, as well as of speciation. To address these questions we established Oenothera as a molecular model over the past decade. We could indentify two plastid candidate loci for PGI, both involved in plastid gene regulation. Moreover, the first genetic map of sexual Oenothera species has been generated assigning more than 1,700 dominant and co-dominant molecular markers to seven coupling groups. Remarkably, homologous recombination (HR) was almost completely suppressed in F2 segregants and, if it occurred at all, was restricted to the telomeric regions of the chromosomes. These data shade a new light on the role of HR in sexual reproduction.
09.07.2012 Dirk Schmeller - "Chytridiomycosis and the risks for European amphibians."
Website: Station d'Ecologie Experimentale du CNRS, Moulis, France
Contact: Michelle Guevara Nieto
Abstract: Europe´s amphibians are threatened by a new emerging infectious disease, Chytridiomycosis, caused by the pathogen Batrachochytrium dendrobatidis (Bd). This disease is known to be a proximate driver of rapid species declines and extinctions in five continents. It is now clear that Bd infects populations and species widely across Europe. It is also clear that, in some regions, populations and possibly species are undergoing rapid catastrophic declines as a result of the infection, and that the infection has caused local extirpations. However, the extent that this invasive infectious disease is impacting on amphibian biodiversity across Europe is almost completely unrecognised, despite clear signs that there is a widespread and urgent problem.
16.07.2012 Alexander Kirschel - "Competitive interactions in tropical birds and their role in phenotypic evolution and community structure."
Website: Edward Grey Institute of Field Ornithology, Oxford
Contact: Alfonso Rojas
Abstract: When related species come into contact they might character displace and coexist, they might converge and coexist, or they might exclude each other completely from their ranges. Much theoretical work has described how each of these outcomes could be predicted to occur. Yet, little work has examined when you might expect convergence versus divergence, and empirical evidence is lacking of examples comparing when related species might on some occasions coexist and others exclude each other. I show how two related species of tinkerbird coexist in Central and East Africa, facilitated by character displacement in their song and morphology, while in West Africa there is competitive and/or reproductive exclusion. I also describe the interaction between two further tinkerbird species that are largely excluded from one another’s ranges and relate those patterns to the molecular phylogeny. I then show an example of character convergence and discuss how it also facilitates coexistence in Amazonian antbirds.
30.07.2012 Haipeng Li - "A New Test for Detecting Recent Positive Selection that is Free from the Confounding Impacts of Demography."
Website: Evolutionary Genomics Lab, CAS-MPG Partner Institute for Computational Biology, China
Contact: Wolfgang Stephan
Abstract: It has been a long-standing interest in evolutionary biology to search for the traces of recent positive Darwinian selection in organisms. However, such efforts have been severely hindered by the confounding signatures of demography. As a consequence neutrality tests often lead to false inference of positive selection since they detect the deviation from the standard neutral model. Here, using the maximum frequency of derived mutations (MFDM) to examine the unbalanceness of the tree of a locus, I propose a statistical test that is analytically free from the confounding effects of varying population size and has a high statistical power (up to 90.5%) to detect recent positive selection. When compared with five well-known neutrality tests for detecting selection (i.e., Tajima’s D-test, Fu & Li’s D-test, Fay & Wu’s H-test, the E-test and the joint DH test), the MFDM test is indeed the only one free from the confounding impacts of bottlenecks and size expansions. Simulations based on wide-range parameters demonstrated that the MFDM test is robust to background selection, population subdivision and admixture (including hidden population structure). Moreover, when two high-frequency mutations are introduced, the MFDM test is robust to the misinference of derived and ancestral variants of segregating sites due to multiple hits. Finally, the sensitivity of the MFDM test in detecting balancing selection is also discussed. In summary, it is demonstrated that summary statistics based on tree topology can be used to detect selection, and this work provides a reliable method that can distinguish selection from demography even when DNA polymorphism data from only one locus is available. The software is available at http://www.picb.ac.cn/evolgen/softwares/.
