Project acronym AdaptoSCOPE
Project Using cis-regulatory mutations to highlight polygenic adaptation in natural plant systems
Researcher (PI) Juliette de Meaux
Host Institution (HI) UNIVERSITAET ZU KOELN
Call Details Consolidator Grant (CoG), LS8, ERC-2014-CoG
Summary The goal of this project is to demonstrate that novel aspects of the molecular basis of Darwinian adaptation can be discovered if the polygenic basis of adaptation is taken into account. This project will use the genome-wide distribution of cis-regulatory variants to discover the molecular pathways that are optimized during adaptation via accumulation of small effect mutations. Current approaches include scans for outlier genes with strong population genetics signatures of selection, or large effect QTL associating with fitness. They can only reveal a small subset of the molecular changes recruited along adaptive paths. Here, instead, the distribution of small effect mutations will be used to make inferences on the targets of polygenic adaptation across divergent populations in each of the two closely related species, A. thaliana and A. lyrata. These species are both found at diverse latitudes and show sign of local adaptation to climatic differences. Mutations affecting cis-regulation will be identified in leaves of plants exposed to various temperature regimes triggering phenotypic responses of adaptive relevance. Their distribution in clusters of functionally connected genes will be quantified. The phylogeographic differences in the distribution of the mutations will be used to disentangle neutral from adaptive clusters of functionally connected genes in each of the two species. This project will identify the molecular pathways subjected collectively to natural selection and provide a completely novel view on adaptive landscapes. It will further examine whether local adaptation occurs by convergent evolution of molecular systems in plants. This approach has the potential to find broad applications in ecology and agriculture.
Summary
The goal of this project is to demonstrate that novel aspects of the molecular basis of Darwinian adaptation can be discovered if the polygenic basis of adaptation is taken into account. This project will use the genome-wide distribution of cis-regulatory variants to discover the molecular pathways that are optimized during adaptation via accumulation of small effect mutations. Current approaches include scans for outlier genes with strong population genetics signatures of selection, or large effect QTL associating with fitness. They can only reveal a small subset of the molecular changes recruited along adaptive paths. Here, instead, the distribution of small effect mutations will be used to make inferences on the targets of polygenic adaptation across divergent populations in each of the two closely related species, A. thaliana and A. lyrata. These species are both found at diverse latitudes and show sign of local adaptation to climatic differences. Mutations affecting cis-regulation will be identified in leaves of plants exposed to various temperature regimes triggering phenotypic responses of adaptive relevance. Their distribution in clusters of functionally connected genes will be quantified. The phylogeographic differences in the distribution of the mutations will be used to disentangle neutral from adaptive clusters of functionally connected genes in each of the two species. This project will identify the molecular pathways subjected collectively to natural selection and provide a completely novel view on adaptive landscapes. It will further examine whether local adaptation occurs by convergent evolution of molecular systems in plants. This approach has the potential to find broad applications in ecology and agriculture.
Max ERC Funding
1 683 120 €
Duration
Start date: 2015-09-01, End date: 2020-08-31
Project acronym EVOLRECOMBADAPT
Project Recombination in Adaptive Evolution
Researcher (PI) Felicity Clare Jones
Host Institution (HI) MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Call Details Consolidator Grant (CoG), LS8, ERC-2013-CoG
Summary Meiotic recombination is a key source of genetic diversity with considerable implications for the genomic landscape and evolutionary process. By shuffling parental alleles to produce novel haplotypes, recombination impacts the strength of selection on nearby polymorphisms, and can increase the rate of adaptation in natural populations. Recombination defects can have serious phenotypic consequences: inviable gametes, miscarriages and developmental abnormalities. Strikingly, recombination rate differs by orders of magnitude across the genome, among individuals, sexes, populations and species. Despite recent progress, we know little about how molecular constraints and evolutionary forces interact to shape recombination in natural populations. We will close this knowledge gap using threespine stickleback fish—an exceptional evolutionary model system that bridges molecular genetic studies and adaptive evolution in the wild. This research program combines next-generation genomics with cutting-edge molecular biology and transgenics. We will 1) create kilobase-scale maps of the recombination landscape in adaptively diverging populations; 2) genetically dissect factors cis- and trans-acting factors that cause recombination variation; 3) characterize molecular mechanisms of recombination modifiers using cutting-edge techniques; and 4) test evolutionary theory that predicts natural selection favours recombination suppression in hybrids. This will significantly improve our understanding of recombination and introduce sophisticated genetic engineering techniques that further cement sticklebacks as an evolutionary model organism. Our ultimate goal is to understand how molecular mechanisms and natural selection shape and constrain recombination during adaptive divergence. This research connects a fundamental biological process that underlies severe human diseases with the tempo of adaptation in natural populations
Summary
Meiotic recombination is a key source of genetic diversity with considerable implications for the genomic landscape and evolutionary process. By shuffling parental alleles to produce novel haplotypes, recombination impacts the strength of selection on nearby polymorphisms, and can increase the rate of adaptation in natural populations. Recombination defects can have serious phenotypic consequences: inviable gametes, miscarriages and developmental abnormalities. Strikingly, recombination rate differs by orders of magnitude across the genome, among individuals, sexes, populations and species. Despite recent progress, we know little about how molecular constraints and evolutionary forces interact to shape recombination in natural populations. We will close this knowledge gap using threespine stickleback fish—an exceptional evolutionary model system that bridges molecular genetic studies and adaptive evolution in the wild. This research program combines next-generation genomics with cutting-edge molecular biology and transgenics. We will 1) create kilobase-scale maps of the recombination landscape in adaptively diverging populations; 2) genetically dissect factors cis- and trans-acting factors that cause recombination variation; 3) characterize molecular mechanisms of recombination modifiers using cutting-edge techniques; and 4) test evolutionary theory that predicts natural selection favours recombination suppression in hybrids. This will significantly improve our understanding of recombination and introduce sophisticated genetic engineering techniques that further cement sticklebacks as an evolutionary model organism. Our ultimate goal is to understand how molecular mechanisms and natural selection shape and constrain recombination during adaptive divergence. This research connects a fundamental biological process that underlies severe human diseases with the tempo of adaptation in natural populations
Max ERC Funding
1 998 704 €
Duration
Start date: 2014-08-01, End date: 2020-07-31
Project acronym OntoTransEvol
Project Ontogenetic transcriptome evolution in tetrapods
Researcher (PI) Henrik Kaessmann
Host Institution (HI) RUPRECHT-KARLS-UNIVERSITAET HEIDELBERG
Call Details Consolidator Grant (CoG), LS8, ERC-2013-CoG
Summary A central goal in evolutionary biology is to understand the molecular changes responsible for phenotypic differences between species, in particular those that have arisen among mammals. Phenotypic evolution is thought to be largely founded on developmental gene regulatory changes, which determine species-specific tissue morphologies and thus lay the foundation for their typical physiological properties. We recently performed the first cross-mammalian transcriptome comparisons for adult organs, providing many insights into the molecular evolution of organ physiologies, but the evolution of developmental transcriptomes remains largely unstudied. I propose to generate comprehensive RNA sequencing data for a collection of adult tissues and developmental precursors from many mammals and tetrapod outgroup species (birds, reptiles, amphibians). The data will include dense ontogenetic time courses for key reference species, covering embryonic stages and, for mammals, placental tissues. We will identify coding and noncoding genes constituting core ancestral tissue transcriptomes and assess relative contributions of gene expression changes and the emergence of new genes to the evolution of phenotypically relevant expression patterns. We will also empirically evaluate global models of evolutionary conservation patterns during embryogenesis and placentation. To understand the dynamics of functional and regulatory interactions of different gene types and their evolutionary relevance, we will reconstruct evolutionary transcription networks and assess associated regulatory mechanisms. Overall, this inter-disciplinary “evo-devo” project will unveil ontogenetic and adult gene expression programs underlying shared (ancestral) and lineage-specific morphological and physiological phenotypes. It will thus substantially advance our understanding of the molecular basis of phenotypic evolution.
Summary
A central goal in evolutionary biology is to understand the molecular changes responsible for phenotypic differences between species, in particular those that have arisen among mammals. Phenotypic evolution is thought to be largely founded on developmental gene regulatory changes, which determine species-specific tissue morphologies and thus lay the foundation for their typical physiological properties. We recently performed the first cross-mammalian transcriptome comparisons for adult organs, providing many insights into the molecular evolution of organ physiologies, but the evolution of developmental transcriptomes remains largely unstudied. I propose to generate comprehensive RNA sequencing data for a collection of adult tissues and developmental precursors from many mammals and tetrapod outgroup species (birds, reptiles, amphibians). The data will include dense ontogenetic time courses for key reference species, covering embryonic stages and, for mammals, placental tissues. We will identify coding and noncoding genes constituting core ancestral tissue transcriptomes and assess relative contributions of gene expression changes and the emergence of new genes to the evolution of phenotypically relevant expression patterns. We will also empirically evaluate global models of evolutionary conservation patterns during embryogenesis and placentation. To understand the dynamics of functional and regulatory interactions of different gene types and their evolutionary relevance, we will reconstruct evolutionary transcription networks and assess associated regulatory mechanisms. Overall, this inter-disciplinary “evo-devo” project will unveil ontogenetic and adult gene expression programs underlying shared (ancestral) and lineage-specific morphological and physiological phenotypes. It will thus substantially advance our understanding of the molecular basis of phenotypic evolution.
Max ERC Funding
1 998 632 €
Duration
Start date: 2015-02-01, End date: 2020-01-31
Project acronym SESyP
Project Identifying Social-Ecological System Properties Benefiting Biodiversity and Food Security
Researcher (PI) Jörn Fischer
Host Institution (HI) LEUPHANA UNIVERSITAT LUNEBURG
Call Details Consolidator Grant (CoG), SH3, ERC-2013-CoG
Summary Ensuring food security and halting biodiversity decline are urgent, interconnected challenges. Drawing on the natural and social sciences, I propose an interdisciplinary research agenda to address these challenges. My goal is to develop a global theory that explains which properties of social-ecological systems benefit both biodiversity conservation and food security (and which benefit one but not the other). This holistic, systems-oriented approach radically differs from existing work: The most high-profile framing at present focuses on the question how to increase agricultural yields without compromising biodiversity. By contrast, a systems-oriented approach recognizes yield as just one variable alongside others that also influence biodiversity and food security. I will use a multi-scale approach that balances the likely trade-offs between depth and generality. Using a specifically developed typology of social-ecological system properties, I will investigate rural landscapes as social-ecological systems at three levels of detail. First, drawing on expert knowledge, I will develop a global database of at least 50 relevant systems, relating general system properties to indicators of food security and biodiversity. Second, I will conduct in-depth workshops on 15-20 social-ecological systems worldwide to reveal in more detail the causal linkages between system properties, food security and biodiversity. Third, I will conduct an in-depth empirical case study on food security and biodiversity in Ethiopia. This will complement the other components by highlighting the nature of potentially important regional subtleties. My multi-scale approach effectively combines high ambition and high feasibility. SESyP will produce new tools and a holistic theory of relevance to researchers, policy makers, supra-national bodies and non-governmental organizations worldwide.
Summary
Ensuring food security and halting biodiversity decline are urgent, interconnected challenges. Drawing on the natural and social sciences, I propose an interdisciplinary research agenda to address these challenges. My goal is to develop a global theory that explains which properties of social-ecological systems benefit both biodiversity conservation and food security (and which benefit one but not the other). This holistic, systems-oriented approach radically differs from existing work: The most high-profile framing at present focuses on the question how to increase agricultural yields without compromising biodiversity. By contrast, a systems-oriented approach recognizes yield as just one variable alongside others that also influence biodiversity and food security. I will use a multi-scale approach that balances the likely trade-offs between depth and generality. Using a specifically developed typology of social-ecological system properties, I will investigate rural landscapes as social-ecological systems at three levels of detail. First, drawing on expert knowledge, I will develop a global database of at least 50 relevant systems, relating general system properties to indicators of food security and biodiversity. Second, I will conduct in-depth workshops on 15-20 social-ecological systems worldwide to reveal in more detail the causal linkages between system properties, food security and biodiversity. Third, I will conduct an in-depth empirical case study on food security and biodiversity in Ethiopia. This will complement the other components by highlighting the nature of potentially important regional subtleties. My multi-scale approach effectively combines high ambition and high feasibility. SESyP will produce new tools and a holistic theory of relevance to researchers, policy makers, supra-national bodies and non-governmental organizations worldwide.
Max ERC Funding
1 788 724 €
Duration
Start date: 2014-06-01, End date: 2019-05-31
Project acronym SYMBeetle
Project Symbiont-assisted cuticle biosynthesis as a key innovation contributing to the evolutionary success of beetles
Researcher (PI) Martin Kaltenpoth
Host Institution (HI) JOHANNES GUTENBERG-UNIVERSITAT MAINZ
Call Details Consolidator Grant (CoG), LS8, ERC-2018-COG
Summary To elucidate the key adaptations underlying evolutionary success remains one of the central challenges in evolution and ecology. However, rigorous experimental tests are usually hampered by the lack of replicate evolutionary events or the inability to manipulate a candidate trait of importance. SYMBeetle exploits the naturally replicated evolution of an experimentally tractable, symbiont-assisted key adaptation in beetles to understand its impact on niche expansion and diversification. Recent evidence indicates that beetles across at least seven different families associate with microbial symbionts that provision their host with tyrosine, an aromatic amino acid necessary for cuticle biosynthesis, hardening, and tanning. SYMBeetle addresses the hypothesis that the acquisition of tyrosine-supplementing microbes constituted a key innovation across phylogenetically distinct beetles that allowed them to expand into novel ecological niches, by relaxing the dependence on nitrogen-rich diets for successful formation of the rigid exoskeleton and protective front wings. Specifically, tyrosine supplementation may facilitate the transition to herbivory and allow for subsisting at very low ambient humidity, by facilitating the production of a thick cuticular barrier to desiccation. To test this, SYMBeetle will uniquely combine experimental manipulation of symbiotic associations to assess the symbionts’ contribution to cuticle biosynthesis and its fitness consequences (desiccation resistance and defense) with large-scale comparative approaches aimed at elucidating the taxonomic distribution, ecological contexts, and evolutionary origins of cuticle-supplementing symbioses. The results are expected to transform our understanding of microbes as important facilitators for the evolution of herbivory and the colonization of dry habitats in beetles, two factors of major relevance for the emergence of economically relevant insect pests of agricultural crops and stored products.
Summary
To elucidate the key adaptations underlying evolutionary success remains one of the central challenges in evolution and ecology. However, rigorous experimental tests are usually hampered by the lack of replicate evolutionary events or the inability to manipulate a candidate trait of importance. SYMBeetle exploits the naturally replicated evolution of an experimentally tractable, symbiont-assisted key adaptation in beetles to understand its impact on niche expansion and diversification. Recent evidence indicates that beetles across at least seven different families associate with microbial symbionts that provision their host with tyrosine, an aromatic amino acid necessary for cuticle biosynthesis, hardening, and tanning. SYMBeetle addresses the hypothesis that the acquisition of tyrosine-supplementing microbes constituted a key innovation across phylogenetically distinct beetles that allowed them to expand into novel ecological niches, by relaxing the dependence on nitrogen-rich diets for successful formation of the rigid exoskeleton and protective front wings. Specifically, tyrosine supplementation may facilitate the transition to herbivory and allow for subsisting at very low ambient humidity, by facilitating the production of a thick cuticular barrier to desiccation. To test this, SYMBeetle will uniquely combine experimental manipulation of symbiotic associations to assess the symbionts’ contribution to cuticle biosynthesis and its fitness consequences (desiccation resistance and defense) with large-scale comparative approaches aimed at elucidating the taxonomic distribution, ecological contexts, and evolutionary origins of cuticle-supplementing symbioses. The results are expected to transform our understanding of microbes as important facilitators for the evolution of herbivory and the colonization of dry habitats in beetles, two factors of major relevance for the emergence of economically relevant insect pests of agricultural crops and stored products.
Max ERC Funding
1 997 750 €
Duration
Start date: 2019-06-01, End date: 2024-05-31
Project acronym VOCO
Project Biochemical link between plant volatile organic compound (VOC) emissions and CO2 metabolism - from sub-molecular to ecosystem scales
Researcher (PI) Christiane Werner Pinto
Host Institution (HI) ALBERT-LUDWIGS-UNIVERSITAET FREIBURG
Call Details Consolidator Grant (CoG), LS8, ERC-2014-CoG
Summary Plant metabolic processes exert a large influence on global climate and air quality through the emission of the greenhouse gas CO2 and volatile organic compounds (VOCs). Despite the enormous importance, processes controlling plant carbon allocation into primary and secondary metabolism, such as respiratory CO2 emission and VOC synthesis, remain unclear.
This project (VOCO2) develops a novel technological and theoretical basis to couple CO2 fluxes with VOC emissions and establish a mechanistic link between primary and secondary carbon metabolism. This radically new approach uses stable isotope fractionation of central metabolites (glucose, pyruvate) to trace carbon partitioning at metabolic branching points. A unique combination of cutting-edge technology (δ13CO2 laser spectroscopy, high sensitivity PTR-TOF-MS and isotope NMR spectroscopy) will allow an unprecedented assessment of carbon partitioning, bridging scales from sub-molecular to whole-plant and ecosystem processes in an interdisciplinary approach. Innovative positional 13C-labelling will break new ground quantifying real-time sub-molecular carbon investment into VOCs and CO2, enabling mechanistic descriptions of the underlying biochemical pathways coupling anabolic and catabolic processes, particularly the long overlooked link between secondary compound synthesis and CO2 emission in the light. This approach will permit the development of a novel mechanistic leaf model and its integration into a state-of-the-art ecosystem flux model.
VOCO2 will set a new dimension with a world-wide first ecosystem positional labelling experiment in the unique Biosphere 2 enclosure (Arizona, US). Jointly with the novel process-based ecosystem model, VOCO2 will open new frontiers for assessing biogenic emissions of greenhouse gases at the ecosystem scale. This will deliver important information for global change related aspects, as these greenhouse gases can impact atmospheric chemistry and enhance global warming.
Summary
Plant metabolic processes exert a large influence on global climate and air quality through the emission of the greenhouse gas CO2 and volatile organic compounds (VOCs). Despite the enormous importance, processes controlling plant carbon allocation into primary and secondary metabolism, such as respiratory CO2 emission and VOC synthesis, remain unclear.
This project (VOCO2) develops a novel technological and theoretical basis to couple CO2 fluxes with VOC emissions and establish a mechanistic link between primary and secondary carbon metabolism. This radically new approach uses stable isotope fractionation of central metabolites (glucose, pyruvate) to trace carbon partitioning at metabolic branching points. A unique combination of cutting-edge technology (δ13CO2 laser spectroscopy, high sensitivity PTR-TOF-MS and isotope NMR spectroscopy) will allow an unprecedented assessment of carbon partitioning, bridging scales from sub-molecular to whole-plant and ecosystem processes in an interdisciplinary approach. Innovative positional 13C-labelling will break new ground quantifying real-time sub-molecular carbon investment into VOCs and CO2, enabling mechanistic descriptions of the underlying biochemical pathways coupling anabolic and catabolic processes, particularly the long overlooked link between secondary compound synthesis and CO2 emission in the light. This approach will permit the development of a novel mechanistic leaf model and its integration into a state-of-the-art ecosystem flux model.
VOCO2 will set a new dimension with a world-wide first ecosystem positional labelling experiment in the unique Biosphere 2 enclosure (Arizona, US). Jointly with the novel process-based ecosystem model, VOCO2 will open new frontiers for assessing biogenic emissions of greenhouse gases at the ecosystem scale. This will deliver important information for global change related aspects, as these greenhouse gases can impact atmospheric chemistry and enhance global warming.
Max ERC Funding
1 895 245 €
Duration
Start date: 2015-10-01, End date: 2020-09-30
