Adaptation in Drosophila melanogaster Natural Populations. Fitness Effects and Evolutionary History of a Natural Insertion and Molecular Effects of Several Transposable Elements on Immune-Related Genes

Abstract

A major challenge of modern Biology is elucidating the genetic basis of adaptation. While there are many SNP-based studies trying to elucidate the genetic basis of genotype-phenotype relationships, the role of transposable element (TE)-induced mutations is understudied. Recent evidences demonstrate that TEs are a powerful tool to identify the genetic basis of adaptive phenotypic traits. Drosophila melanogaster is a good model to study adaptation because it is original from subtropical Africa and only recently colonized out-of-Africa environments. To identify and characterize the role of several candidate TEs in D. melanogaster adaptation, we have followed two different strategies: locus-specific and trait-specific. In the first chapter, we have characterized both at the molecular and phenotypic level FBti0019386, a previously identified candidate adaptive TE. We first elucidated the evolutionary history of this natural insertion and provided evidences of genomic signatures of positive selection. We then explored several phenotypes related to known phenotypic effects of nearby genes, and having plausible connections to fitness variation in nature. We found that flies with FBti0019386 insertion had a shorter developmental time and were more sensitive to stress, which are likely to be the adaptive effect and the cost of selection of this mutation, respectively. Interestingly, these phenotypic effects are not consistent with a role of FBti0019386 in temperate adaptation as has been previously suggested. Indeed, a global analysis of the population frequency of FBti0019386 showed that climatic variables explain well the FBti0019386 frequency patterns only in Australia. These results suggest that further functional validation should be gathered before concluding that a candidate loci is under spatially varying selection. Finally, although FBti0019386 insertion could be inducing the formation of heterochromatin by recruiting HP1a (Heterochromatin Protein 1a) protein, the insertion is associated with up-regulation of sra in adult females.

In the second chapter of this thesis, we have studied the impact of several TE insertions in a highly conserved and ecologically relevant trait: the immune response. To do that, we first performed a new genome-wide screening in order to identify a dataset of candidate TEs involved in adaptation. By increasing the number of populations and the number of TEs analyzed compared to similar studies, we were able to increase the number of identified candidate TEs: a total of 121 TEs. Interestingly, we found that genes associated with those TEs are enriched for stress-related functions, specifically we detected a significant enrichment for immune response functions. We combined allele-specific expression (ASE), enhancer assays, and TSS detection experiments to characterize the impact of these TEs in oral immune response to the gram-negative bacteria Pseudomonas entomophila. We were also able to associate the 12 candidate TEs with gene expression changes, and determine some of the molecular mechanisms behind these expression changes. We showed that the allele with the TE was differently expressed in 13 out of the 16 analyzed genes under non-infected and/or infected conditions in at least one of the two genetic backgrounds analyzed. We also show that different TEs alter gene expression by adding promoters and enhancer regulatory sequences to their nearby genes. Although we found evidences pointing to a possible role of TEs in immune response regulation, more experiments should be performed in order to link the identified TEs with a fitness effect in this trait.

Overall, our two integrative approaches allowed us to shed light on the role of TEs in generating genomic natural variation potentially underlying adaptation. The results obtained in this work illustrate that TEs are a good tool to bridge the gap between genotypic and phenotypic evolution.

Un dels reptes actuals en biologia és explicar la base genètica de l’adaptació. Mentre que hi ha molts estudis basats en SNPs intentant trobar les bases genètiques de les relacions genotip-fenotip, no s’ha estudiat tant bé el paper de les mutacions generades pels elements mòbils (TEs, de l’anglès Transposable Elements). Evidències recents demostren que els TEs són una eina potent per identificar les bases genètiques dels fenotips adaptatius. Drosophila melanogaster és un bon model per estudiar l’adaptació, ja que és originària de l’Àfrica subtropical i recentment ha colonitzat altres ambients. Per identificar i caracteritzar el paper de diversos TEs candidats per l’adaptació a D. melanogaster, hem seguit dues estratègies diferents: locus-específica i tret-específica. En el primer capítol hem caracteritzat a nivell molecular i fenotípic el TE FBti0019386, identificat prèviament com a candidat per l’adaptació. Primer hem estudiat la història evolutiva d’aquesta inserció i hem demostrat que està associada a senyals genòmiques de selecció positiva. Després hem explorat diferents fenotips relacionats amb els efectes fenotípics coneguts dels gens del costat, que poguessin tenir connexions plausibles amb la variació de la fitness a la natura. En el segon capítol, hem estudiat l’impacte de diferents TEs en la resposta immune. Per això, hem mostrejat el genoma buscant TEs candidats per l’adaptació en quatre poblacions naturals. Després, hem combinat anàlisis d’expressió específica d’al·lel, assajos d’enhancer i detecció de TSS per caracteritzar l’impacte d’aquests TEs durant la resposta a infecció amb el bacteri gram-negatiu Pseudomonas entomophila. Hem trobat que l’al·lel amb el TE s’expressa de manera diferent en 13 dels 16 gens analitzats en condicions control i/o d’infecció en almenys un dels dos fons genètics analitzats. Hem demostrat que alguns d’aquests TEs alteren l’expressió afegint promotors i enhancers als gens del costat. Tot i que les evidències assenyalen cap a un possible paper dels TEs en la regulació de la resposta immune, es requereixen més experiments per associar els TEs identificats amb un efecte en la fitness. En resum, les dues estratègies integratives seguides ens han permès mostrar el paper dels TEs en la generació de variació natural genòmica potencialment implicada en l’adaptació.