Abstract Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

Elucidating the fitness effects of natural genetic variants is one of the current major challenges in evolutionary biology. Understanding the interplay between genotype, phenotype and environment is necessary to make accurate predictions of important biological outcomes such as stress resistance or yield in economically important plants and animals, and disease in humans. Based on population frequency patterns and footprints of selection at the DNA level, the transposable element Bari-Jheh, inserted in the intergenic region of Juvenile Hormone Epoxy Hydrolase (Jheh) genes, was previously identified as putatively adaptive. However, the adaptive effect of this mutation remained elusive. In this work, we integrate information on transcription factor binding sites, available ChIP-Seq data, gene expression analyses and phenotypic assays to identify the functional and the mechanistic underpinnings of Bari-Jheh. We show that Bari-Jheh adds extra antioxidant response elements upstream of Jheh1 and Jheh2 genes. Accordingly, we find that Bari-Jheh is associated with upregulation of Jheh1 and Jheh2 and with resistance to oxidative stress induced by two different compounds relevant for natural D. melanogaster populations. We further show that TEs other than Bari-Jheh might be playing a role in the D. melanogaster response to oxidative stress. Overall our results contribute to the understanding of resistance to oxidative stress in natural populations and highlight the role of transposable elements in environmental adaptation. The replicability of fitness effects on different genetic backgrounds also suggests that epistatic interactions do not seem to dominate the genetic architecture of oxidative stress resistance.

79Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamics in 80 natural populations is challenging, sequencing of entire populations remains costly and 81 comprehensive sampling logistically difficult.

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

One contribution of 15 to a discussion meeting issue 'Crossroads between transposons and gene regulation'.

Transposable elements are emerging as an important source of cis-acting regulatory sequences and epigenetic marks that could influence gene expression. However, few studies have dissected the role of specific transposable element insertions on epigenetic gene regulation. Bari-Jheh is a natural transposon that mediates resistance to oxidative stress by adding cis-regulatory sequences that affect expression of nearby genes. In this work, we integrated publicly available ChIP-seq and piRNA data with chromatin immunoprecipitation experiments to get a more comprehensive picture of Bari-Jheh molecular effects. We showed that Bari-Jheh was enriched for H3K9me3 in nonstress conditions, and for H3K9me3, H3K4me3 and H3K27me3 in oxidative stress conditions, which is consistent with expression changes in adjacent genes. We further showed that under oxidative stress conditions, H3K4me3 and H3K9me3 spread to the promoter region of Jheh1 gene. Finally, another insertion of the Bari1 family was associated with increased H3K27me3 in oxidative stress conditions suggesting that Bari1 histone marks are copy-specific. We concluded that besides adding cis-regulatory sequences, Bari-Jheh influences gene expression by affecting the local chromatin state.

Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.

Although adaptive mutations are often considered to be dominant, it has been recently shown that a substantial proportion of adaptive mutations should display heterozygote advantage. In this work, we take advantage of a recently characterized transposable element insertion mediating oxidative stress response in Drosophila melanogaster to test the dominance effect of an adaptive mutation. The comparison of the survival curves of heterozygous and the two corresponding homozygous flies indicated that the dominance effect of Bari-Jheh depends on the genetic background. Both in homozygous and in heterozygous flies, Bari-Jheh was associated with upregulation of Jheh1 (Juvenile Hormone Epoxyde Hydrolase 1) and/or Jheh2 genes. Our results add to the limited number of studies in which the dominance effect of adaptive mutations has been empirically estimated and highlights the complexity of their inheritance.