While the latitudinal diversity gradient is one of the rare patterns that might be considered general and widely accepted in ecology, the latitudinal specialisation gradient remains controversial. Ecological specialisation varies greatly across the tree of life, with clades that depend on a host organism for survival being among the most specialised. Understanding the processes that produce the global pattern of increasing host specialisation with decreasing latitude would be a breakthrough in the field of evolutionary ecology. This project will investigate the causes and consequences of higher host specialisation in the tropics, focusing on fundamental repertoires (expressed and non-expressed host use abilities). First, we will test if tropical species are genetically more specialised to their hosts by identifying host-associated gene modules and reconstructing their evolution across tropical and temperate species in the tribe Nymphalini. Then, we will test if higher specialisation is an artifact of data scarcity in the tropics. For that, we will develop an efficient approach for data collection based on interaction prediction, and produce a comprehensive dataset of fundamental and realised host repertoires for tropical Melitaeini butterflies. Then, including the entire Nymphalidae family, we will test if evolution of species interactions in the tropics favours specialisation. We will apply a combination of phylogenetic and network analyses to existing global datasets (augmented with all data produced in this project) to unravel how fundamental host repertoires evolve and whether current theory is able to explain tropical interactions equally well as the better-studied temperate interactions. Finally, we will quantify the consequences of host specialisation in a changing world in terms of risk of coextinction. The frameworks developed here can be easily expanded to other symbiont-host systems, increasing the significance of this research far beyond butterflies.

Plants lack a nervous system and central decision-making organ like a brain, but can nevertheless sense and respond to environmental cues that play crucial roles in regulating their growth, through poorly understood mechanisms. The aim of DECORE is to elucidate these mechanisms, particularly those underlying the low temperature-mediated control of bud dormancy in the model tree hybrid aspen. A recent discovery in the host lab, pinpointing AGL8 as a low temperature responsive transcription factor involved in bud dormancy release, has lead us to hypothesize that AGL8-mediated transcriptional control of the plant hormone gibberellin, mobile signaling component FT1 (a tree ortholog of Arabidopsis FLOWERING LOCUS T) and cell-cell communication together orchestrate bud dormancy release. In DECORE, Dr. Pandey will test this hypothesis by deciphering the interplay between gene expression, hormonal regulation and cell-cell communication during dormancy release, and simultaneously acquire skills in cutting-edge techniques like transmission electron microscopy, immunocytochemistry and mass spectrometry in leading environments at the host SLU/UPSC (Umeå, Sweden) and via secondment to CNRS (Bordeaux, France). Synergistically complementing the skills in biochemistry and genomics gained during his PhD, this training will provide Dr. Pandey with a unique opportunity to broaden his technical and theoretical expertise, which will promote a successful achievement of the project’s goals, open new vistas in developmental adaptation, and support his ambition of becoming a research leader. Dr. Pandey will follow a personalized career development plan to enhance his skills in communication, grant writing, public engagement and student mentoring. Thus, DECORE will contribute fundamental knowledge on a key process in seasonal adaptation, critical for mitigating the effects of climate change on seasonal growth in trees, and career advancement of a scientist with outstanding potential.

Adaptive Radiation of Aquatic MIcrobial Species (ARAMIS). The action aims to understand the causes, mechanisms and consequences of adaptive radiation (i.e. the process in which organisms diversify rapidly to occupy ecological niches) in freshwater microbial communities. This will help solve several of the outstanding questions in the field of microbial ecology, such as how shifts in environmental conditions impact the trajectory of microbial evolution, the relative importance of horizontal versus vertical gene transfer in microbial ecosystems, or the definition of microbial ‘species’. As diversity is linked with stability, elucidating the factors driving diversification in freshwater taxa will also help us predict how such ecosystems may respond to future change. ARAMIS proposes the novel hypothesis that, while every freshwater clade has a unique evolutionary history, the environmental forces driving such evolution are fundamentally the same, both in nature and in relative importance. If validated, this simple paradigm would push the state of the art and allow the development of powerful conceptual models integrating environmental constraints, microbial diversification, and community stability. The hypothesis will be tested by combining metagenomics, metatranscriptomics and enrichment cultures over a set of more than 200 lake samples. This will contribute to a conceptual synthesis between community ecology and evolutionary biology by closing the gap between theoretical work and data-driven studies. ARAMIS has a high academic potential but, since it deals with the stability of freswater microbial populations, can also have social and public policy impact by bringing an ecoevolutionary perspective to the management of aquatic resources.

Ash trees (Fraxinus spp.) in Europe are threatened by two alien invasive organisms; a deadly fungal pathogen Hymenoscyphus fraxineus that has been causing a slow, steady decline in Europe’s ash population, and emerald ash borer (EAB; Agrilus planipennis), a buprestid beetle that is quickly killing trees in eastern Europe, and moving west. There are fears that EAB will follow the same path as it did recently in USA – killing millions of ash trees, unless active research is undertaken to prevent the spread of EAB and protect the ash resource. EMERALD is a multidisciplinary and innovative project that approaches this invasion through the combination of molecular biology, analytical chemistry, sensor technology, insect ecology, and tree physiology to understand host-pest interactions and improve the options for integrated pest management in European forests. In this project, naïve and a co-evolved ash species will be investigated to understand their attractive volatile chemistry and influence on EAB’s behaviour and host preference (antixenosis), differences in host chemical defenses that either promote or deter EAB performance (antibiosis), and the confounding effect of H. fraxineus in relation to both interactions. Novel early detection tools will be developed including new lure traps and molecular assays based on optimized environmental DNA protocols of samples filtered from stem flow and canopy foliage, and portable loop mediated isothermal amplification (LAMP) to achieve point-of-use and real-time detection of EAB. The training-through-research will diversify and expand the skillset of the applicant, while also providing reciprocal teaching and new insights for the host unit. The results of this project will have tremendous value for European stakeholders and the general public for those concerned with saving the economically and ecological valuable ash in urban and rural forested environments by developing an arsenal of tools to manage the impending EAB invasion.

This proposal aims to explore the precise mechanism, overall impact and complete population of the small RNAs derived of transfer RNAs (tsRNAs) in plants. The proposed research would be carried out in a laboratory that specializes in RNA regulation and that made substantial contributions to the plant tRNA-derived sRNA field (Dr. German Martinez). Although it has been described that these molecules are highly expressed in stress conditions, we still lack a clear understanding of the biogenesis pathways that lead to tsRNA accumulation, as well as of the array of biological processes they influence and their mechanism of action. Additionally, because of the widespread presence of RNA modifications in these molecules, the unbiased genome-wide quantification is not possible with the conventional sequencing technologies. Therefore, these molecules represent a largely uncharacterized stress-responsive regulatory network in plants, and thus an exciting source of potential applications for agriculture. The experimental approach of this project will use a model plant (Arabidopsis thaliana) in order to characterize the tsRNA population and evaluate the importance of this regulatory layer under viral stress. First, a method to compare the accumulation profiles of tsRNAs based on the enzymatic removal of RNA modifications will be implemented. Second, the biogenesis pathway of tRNA-derived sRNAs will be studied using mutant plants, and how this affects viral infection will be evaluated with these mutant plants. Third, the genes targeted by tRNA-derived sRNAs will be identified using a combined approach based on the immunoprecipitation of crosslinked AGO proteins and ribosome profiling that determines the translation rate. Overall, the data that this project would obtain has the potential to shift our understanding of tsRNAs and provide cutting-edge applications for agriculture. Thus, the completion of this project would provide me a considerable professional maturity.