Periodic Reporting for period 4 - DROSADAPTATION (New approaches to long-standing questions: adaptation in Drosophila)
Reporting period: 2020-07-01 to 2021-12-31
How organisms adapt to the environment is a key question in evolutionary biology. Because adaptation affects the ability of species to survive in changing environments, host-pathogen interactions, and resistance to pesticides and drugs, answering this question has also implications for conservation biology, medicine, and agriculture. The overall objective of DROSADAPTATION is to understand how organisms adapt to a wide-range of environments. To do this, (i) we systematically identify adaptive mutations and the most relevant environmental variables associated with them; (ii) we investigate the molecular mechanisms, both genetic and epigenetic, underlying the effect of the mutations identified; and (iii) we identify the relevant organismal traits affected by the adaptive mutations. We focus on the analysis of transposable element induced mutations that despite their crucial role in genome function, genome structure and genome evolution remained understudied mainly due to technical limitations. We take advantage of the wealth of knowledge and research tools available for the model species Drosophila melanogaster, that together with its recent colonization of a wide-range of environments makes it the ideal species to pinpoint the genetic, epigenetic, environmental and phenotypic basis of adaptive evolution.
To accomplish DROSADAPTATION objectives, we have used an integrative approach that combines -omics methodologies, such as long-read DNA sequencing, transcriptomics, and chromatin analysis (ATAC-seq, ChIP-seq, Hi-C), with in depth individual characterization of adaptive mutations, using RT-qPCR, allele-specific expression, in vivo reporter gene assays, and CRISPR/Cas9 genome editing. We have generated 32 new reference Drosophila melanogaster genomes that have allowed us to identify 58% more transposable element insertions than previously described. We have identified hundreds of transposable element insertions that affect the expression of their nearby genes. We have showed that environmental variables related with wind are relevant for adaptation in Drosophila. Regarding the molecular mechanisms of adaptive mutations, we have showed that transposable elements contribute to the regulation of stress-response genes by adding transcription factor binding sites, and that the effect that transposable elements have on gene expression through epigenetic changes is body part specific. Finally, stress response, development, behaviour, morphogenesis and pigmentation are the phenotypic traits most often shaped by transposable elements, and their role in oxidative stress and insecticide resistance appears to be more prevalent than in other stress responses. The DROSADAPTATION results have been shared with the scientific community through research, review, protocol, and commentary articles and through conference, workshop, and seminar presentations across the world. All the datasets and scripts generated during the project are publicly available.
Overall, the results obtained in DROSADAPTATION go beyond the state of the art as they provide unequivocal quantitative evidence for the need to generate and analyze multiple genomes per species, and integrate different types of genetic variants, if we are to understand the genetic basis of phenotypic traits such as those relevant for the ability of species to adapt to changing climatic conditions, but also traits associated with livestock production or disease. We prove that beyond the well-studied temperature and precipitation, other environmental variables are also relevant for adaptation and should be included in the analysis aimed at identifying the environmental pressures shaping the evolution of natural populations. We also show that transposable elements are complex mutations that can provide regulatory regions (transcription factor binding sites) and epigenetic marks that affect the expression of nearby genes, and that can modulate gene expression depending on the environmental condition and the developmental stage. Finally, we have successfully involved citizens across Europe in a citizen science project tightly linked to the scientific objectives of DROSADAPTATION. As such, DROSADAPTATION has increased science literacy, and has contributed to increase the trust of citizens in science as they have been part of the scientific process, as exemplified by their co-authorship in publications.