Project acronym ARCHADAPT
Project The architecture of adaptation to novel environments
Researcher (PI) Christian Werner Schlötterer
Host Institution (HI) VETERINAERMEDIZINISCHE UNIVERSITAET WIEN
Call Details Advanced Grant (AdG), LS8, ERC-2011-ADG_20110310
Summary One of the central goals in evolutionary biology is to understand adaptation. Experimental evolution represents a highly promising approach to study adaptation. In this proposal, a freshly collected D. simulans population will be allowed to adapt to laboratory conditions under two different temperature regimes: hot (27°C) and cold (18°C). The trajectories of adaptation to these novel environments will be monitored on three levels: 1) genomic, 2) transcriptomic, 3) phenotypic. Allele frequency changes during the experiment will be measured by next generation sequencing of DNA pools (Pool-Seq) to identify targets of selection. RNA-Seq will be used to trace adaptation on the transcriptomic level during three developmental stages. Eight different phenotypes will be scored to measure the phenotypic consequences of adaptation. Combining the adaptive trajectories on these three levels will provide a picture of adaptation for a multicellular, outcrossing organism that is far more detailed than any previous results.
Furthermore, the proposal addresses the question of how adaptation on these three levels is reversible if the environment reverts to ancestral conditions. The third aspect of adaptation covered in the proposal is the question of repeatability of adaptation. Again, this question will be addressed on the three levels: genomic, transcriptomic and phenotypic. Using replicates with different degrees of genetic similarity, as well as closely related species, we will test how similar the adaptive response is.
This large-scale study will provide new insights into the importance of standing variation for the adaptation to novel environments. Hence, apart from providing significant evolutionary insights on the trajectories of adaptation, the results we will obtain will have important implications for conservation genetics and commercial breeding.
Summary
One of the central goals in evolutionary biology is to understand adaptation. Experimental evolution represents a highly promising approach to study adaptation. In this proposal, a freshly collected D. simulans population will be allowed to adapt to laboratory conditions under two different temperature regimes: hot (27°C) and cold (18°C). The trajectories of adaptation to these novel environments will be monitored on three levels: 1) genomic, 2) transcriptomic, 3) phenotypic. Allele frequency changes during the experiment will be measured by next generation sequencing of DNA pools (Pool-Seq) to identify targets of selection. RNA-Seq will be used to trace adaptation on the transcriptomic level during three developmental stages. Eight different phenotypes will be scored to measure the phenotypic consequences of adaptation. Combining the adaptive trajectories on these three levels will provide a picture of adaptation for a multicellular, outcrossing organism that is far more detailed than any previous results.
Furthermore, the proposal addresses the question of how adaptation on these three levels is reversible if the environment reverts to ancestral conditions. The third aspect of adaptation covered in the proposal is the question of repeatability of adaptation. Again, this question will be addressed on the three levels: genomic, transcriptomic and phenotypic. Using replicates with different degrees of genetic similarity, as well as closely related species, we will test how similar the adaptive response is.
This large-scale study will provide new insights into the importance of standing variation for the adaptation to novel environments. Hence, apart from providing significant evolutionary insights on the trajectories of adaptation, the results we will obtain will have important implications for conservation genetics and commercial breeding.
Max ERC Funding
2 452 084 €
Duration
Start date: 2012-07-01, End date: 2018-06-30
Project acronym EVOCHLAMY
Project The Evolution of the Chlamydiae - an Experimental Approach
Researcher (PI) Matthias Horn
Host Institution (HI) UNIVERSITAT WIEN
Call Details Starting Grant (StG), LS8, ERC-2011-StG_20101109
Summary Chlamydiae are a unique group of obligate intracellular bacteria that comprises symbionts of protozoa as well as important pathogens of humans and a wide range of animals. The intracellular life style and the obligate association with a eukaryotic host was established early in chlamydial evolution and possibly also contributed to the origin of the primary phototrophic eukaryote. While much has been learned during the past decade with respect to chlamydial diversity, their evolutionary history, pathogenesis and mechanisms for host cell interaction, very little is known about genome dynamics, genome evolution, and adaptation in this important group of microorganisms. This project aims to fill this gap by three complementary work packages using experimental evolution approaches and state-of-the-art genome sequencing techniques.
Chlamydiae that naturally infect free-living amoebae, namely Protochlamydia amoebophila and Simkania negevensis, will be established as model systems for studying genome evolution of obligate intracellular bacteria (living in protozoa). Due to their larger, less reduced genomes compared to chlamydial pathogens, amoeba-associated Chlamydiae are ideally suited for these investigations. Experimental evolution approaches – among the prokaryotes so far almost exclusively used for studying free-living bacteria – will be applied to understand the genomic and molecular basis of the intracellular life style of Chlamydiae with respect to host adaptation, host interaction, and the character of the symbioses (mutualism versus parasitism). In addition, the role of amoebae for horizontal gene transfer among intracellular bacteria will be investigated experimentally. Taken together, this project will break new ground with respect to evolution experiments with intracellular bacteria, and it will provide unprecedented insights into the evolution and adaptive processes of intracellular bacteria in general, and the Chlamydiae in particular.
Summary
Chlamydiae are a unique group of obligate intracellular bacteria that comprises symbionts of protozoa as well as important pathogens of humans and a wide range of animals. The intracellular life style and the obligate association with a eukaryotic host was established early in chlamydial evolution and possibly also contributed to the origin of the primary phototrophic eukaryote. While much has been learned during the past decade with respect to chlamydial diversity, their evolutionary history, pathogenesis and mechanisms for host cell interaction, very little is known about genome dynamics, genome evolution, and adaptation in this important group of microorganisms. This project aims to fill this gap by three complementary work packages using experimental evolution approaches and state-of-the-art genome sequencing techniques.
Chlamydiae that naturally infect free-living amoebae, namely Protochlamydia amoebophila and Simkania negevensis, will be established as model systems for studying genome evolution of obligate intracellular bacteria (living in protozoa). Due to their larger, less reduced genomes compared to chlamydial pathogens, amoeba-associated Chlamydiae are ideally suited for these investigations. Experimental evolution approaches – among the prokaryotes so far almost exclusively used for studying free-living bacteria – will be applied to understand the genomic and molecular basis of the intracellular life style of Chlamydiae with respect to host adaptation, host interaction, and the character of the symbioses (mutualism versus parasitism). In addition, the role of amoebae for horizontal gene transfer among intracellular bacteria will be investigated experimentally. Taken together, this project will break new ground with respect to evolution experiments with intracellular bacteria, and it will provide unprecedented insights into the evolution and adaptive processes of intracellular bacteria in general, and the Chlamydiae in particular.
Max ERC Funding
1 499 621 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
Project acronym FLORSIGNALS
Project Evolution and consequences of floral signaling in plants
Researcher (PI) Florian Paul Schiestl
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Starting Grant (StG), LS8, ERC-2011-StG_20101109
Summary Most angiosperms plants use animals as vector for their gametes, and the interaction of plants with their pollinators represents a key mutualism for ecosystem functioning as well as for human nutrition. For maintaining interactions with pollinators, plants have evolved floral signals, such as color and fragrance. In the proposed research, functions and evolution of floral signals will be investigated in model systems representing key components of ecosystems and agriculture. In the first part, functions of floral signals will be investigated in the context of a plant’s dilemma arising through the need of attracting pollinators, but at the same time deterring herbivores. Fitness effects of herbivore-induced floral volatiles in different biotic environments, synergistic effect with visual cues, and the molecular bases will be analyzed. In the second topic, the maintenance of mutualistic associations will be studied in a so-called open nursery pollination system, where plant-pollinator associations can vary between mutualisms and antagonism. Cost/benefit ratios of this association and thus selection for/against nursery pollinators will be quantified in different populations, and corresponding floral adaptations, such as signals attracting/deterring pollinators/parasitoids as well as oviposition cues for pollinators will be analyzed. The third part will focus on pollinator/herbivore-induced selection on floral traits, adaptations to specific pollinators, and plant speciation. In an experimental approach, the evolution of floral traits under selection will be directly quantified, by imposing plants over several generations to mutualist/antagonist-driven selection. Diversification through adaptation to different pollinators will be investigated in a second experiment. In a highly specialized pollination system, floral signals mediating specific pollinator attraction and thus delivering reproductive isolation and their genetic basis will be studied.
Summary
Most angiosperms plants use animals as vector for their gametes, and the interaction of plants with their pollinators represents a key mutualism for ecosystem functioning as well as for human nutrition. For maintaining interactions with pollinators, plants have evolved floral signals, such as color and fragrance. In the proposed research, functions and evolution of floral signals will be investigated in model systems representing key components of ecosystems and agriculture. In the first part, functions of floral signals will be investigated in the context of a plant’s dilemma arising through the need of attracting pollinators, but at the same time deterring herbivores. Fitness effects of herbivore-induced floral volatiles in different biotic environments, synergistic effect with visual cues, and the molecular bases will be analyzed. In the second topic, the maintenance of mutualistic associations will be studied in a so-called open nursery pollination system, where plant-pollinator associations can vary between mutualisms and antagonism. Cost/benefit ratios of this association and thus selection for/against nursery pollinators will be quantified in different populations, and corresponding floral adaptations, such as signals attracting/deterring pollinators/parasitoids as well as oviposition cues for pollinators will be analyzed. The third part will focus on pollinator/herbivore-induced selection on floral traits, adaptations to specific pollinators, and plant speciation. In an experimental approach, the evolution of floral traits under selection will be directly quantified, by imposing plants over several generations to mutualist/antagonist-driven selection. Diversification through adaptation to different pollinators will be investigated in a second experiment. In a highly specialized pollination system, floral signals mediating specific pollinator attraction and thus delivering reproductive isolation and their genetic basis will be studied.
Max ERC Funding
1 395 640 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
Project acronym NITRICARE
Project Nitrification Reloaded - a Single Cell Approach
Researcher (PI) Michael Wagner
Host Institution (HI) UNIVERSITAT WIEN
Call Details Advanced Grant (AdG), LS8, ERC-2011-ADG_20110310
Summary "Nitrification is a central component of the Earth’s biogeochemical nitrogen cycle. This process is driven by two groups of microorganisms, which oxidize ammonia via nitrite to nitrate. Their activities are of major ecological and economic importance and affect global warming, agriculture, wastewater treatment, and eutrophication. Despite the importance of nitrification for the health of our planet, there are surprisingly large gaps in our fundamental understanding of the microbiology of this process. Nitrifiers are difficult to isolate and thus most of our current knowledge stems from a few cultured model organisms that are hardly representative of the microbes driving nitrification in the environment. The overarching objective of NITRICARE is to close some of these knowledge gaps and obtain a comprehensive basic understanding of the identity, evolution, metabolism and ecological importance of those bacteria and archaea that actually catalyze nitrification in nature. For this purpose innovative single cell technologies like Raman-microspectroscopy, NanoSIMS and single cell genomics will be combined in novel ways and a Raman microfluidic device for high-throughput cell sorting will be developed. Application of these approaches will reveal the evolutionary history and metabolic versatility of uncultured ammonia oxidizing archaea and will provide important insights into their population structure. Furthermore, the proposed experiments will allow us to efficiently search for unknown nitrifiers, evaluate their ecological importance and test the hypothesis that organisms catalyzing both steps of nitrification may exist. For non-model nitrifiers we will develop a unique genetic approach to reveal the genetic basis of key metabolic features. Together, the genomic, metabolic, ecophysiological and genetic data will provide unprecedented insights into the biology of nitrifying microbes and open new conceptual horizons for the study of microbes in their natural environments."
Summary
"Nitrification is a central component of the Earth’s biogeochemical nitrogen cycle. This process is driven by two groups of microorganisms, which oxidize ammonia via nitrite to nitrate. Their activities are of major ecological and economic importance and affect global warming, agriculture, wastewater treatment, and eutrophication. Despite the importance of nitrification for the health of our planet, there are surprisingly large gaps in our fundamental understanding of the microbiology of this process. Nitrifiers are difficult to isolate and thus most of our current knowledge stems from a few cultured model organisms that are hardly representative of the microbes driving nitrification in the environment. The overarching objective of NITRICARE is to close some of these knowledge gaps and obtain a comprehensive basic understanding of the identity, evolution, metabolism and ecological importance of those bacteria and archaea that actually catalyze nitrification in nature. For this purpose innovative single cell technologies like Raman-microspectroscopy, NanoSIMS and single cell genomics will be combined in novel ways and a Raman microfluidic device for high-throughput cell sorting will be developed. Application of these approaches will reveal the evolutionary history and metabolic versatility of uncultured ammonia oxidizing archaea and will provide important insights into their population structure. Furthermore, the proposed experiments will allow us to efficiently search for unknown nitrifiers, evaluate their ecological importance and test the hypothesis that organisms catalyzing both steps of nitrification may exist. For non-model nitrifiers we will develop a unique genetic approach to reveal the genetic basis of key metabolic features. Together, the genomic, metabolic, ecophysiological and genetic data will provide unprecedented insights into the biology of nitrifying microbes and open new conceptual horizons for the study of microbes in their natural environments."
Max ERC Funding
2 499 107 €
Duration
Start date: 2012-05-01, End date: 2017-04-30
Project acronym VIRMUT
Project Variability in the mutation rate of RNA viruses
Researcher (PI) Rafael Sanjuán Verdeguer
Host Institution (HI) UNIVERSITAT DE VALENCIA
Call Details Starting Grant (StG), LS8, ERC-2011-StG_20101109
Summary RNA viruses are the fastest evolving entities in nature. Such rapid evolution is explained by their mutation rates, which are orders of magnitude higher than those of DNA organisms. The error-prone replication of RNA viruses also has public-health implications related to pathogenesis, antiviral research, or viral emergence. However, current mutation rate estimates vary by more than 100-fold across different RNA viruses and sometimes over one order of magnitude for the same virus, and the causes of this variation remain poorly understood. Here, we plan to investigate variability in the mutation rate of RNA viruses at different levels. First, polymorphic sites in viral polymerases could produce populations with heterogeneous mutation rates, and the spread of genotypes with altered mutation rates might influence viral fitness and disease progression. Second, spontaneous mutations might occur preferentially at some regions of the viral genome, and these mutational hotspots could match genome regions where the selective pressure imposed by the host is strongest, thereby increasing viral adaptability. Third, RNA viruses with different types of genomes, such as single-stranded versus double-stranded RNA or sense versus anti-sense genome polarity might differ in their susceptibility to nucleic-acid damage or host-mediated editing and thus, in their mutation rate. Fourth, RNA viruses with larger genomes might have evolved increased replication fidelity to compensate for their greater genetic load. To address these issues, we will use several biomedically relevant and/or model viruses, including HIV-1, hepatitis C virus, a rotavirus, a coronavirus and a bacteriophage. The experimental procedures will include in vitro replication fidelity assays, ex vivo infections using cell cultures, and analysis of patient samples by next-generation sequencing. This thorough and multilevel approach may reveal previously unrecognized mechanisms for generating diversity in RNA viruses.
Summary
RNA viruses are the fastest evolving entities in nature. Such rapid evolution is explained by their mutation rates, which are orders of magnitude higher than those of DNA organisms. The error-prone replication of RNA viruses also has public-health implications related to pathogenesis, antiviral research, or viral emergence. However, current mutation rate estimates vary by more than 100-fold across different RNA viruses and sometimes over one order of magnitude for the same virus, and the causes of this variation remain poorly understood. Here, we plan to investigate variability in the mutation rate of RNA viruses at different levels. First, polymorphic sites in viral polymerases could produce populations with heterogeneous mutation rates, and the spread of genotypes with altered mutation rates might influence viral fitness and disease progression. Second, spontaneous mutations might occur preferentially at some regions of the viral genome, and these mutational hotspots could match genome regions where the selective pressure imposed by the host is strongest, thereby increasing viral adaptability. Third, RNA viruses with different types of genomes, such as single-stranded versus double-stranded RNA or sense versus anti-sense genome polarity might differ in their susceptibility to nucleic-acid damage or host-mediated editing and thus, in their mutation rate. Fourth, RNA viruses with larger genomes might have evolved increased replication fidelity to compensate for their greater genetic load. To address these issues, we will use several biomedically relevant and/or model viruses, including HIV-1, hepatitis C virus, a rotavirus, a coronavirus and a bacteriophage. The experimental procedures will include in vitro replication fidelity assays, ex vivo infections using cell cultures, and analysis of patient samples by next-generation sequencing. This thorough and multilevel approach may reveal previously unrecognized mechanisms for generating diversity in RNA viruses.
Max ERC Funding
1 432 021 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
