Identification of loci underlying local adaptation in European Drosophila populations

生物必须科普不断变化的环境。由于对当地生物和非生物条件的适应，种群内和种群之间的个体在基因组和表型水平上存在差异，种群多样化受到选择以及中性事件（如遗传漂变和迁移）的影响。我们目前对种群遗传多样性的理解大多是基于对特定基因或限制性基因组位点的分析。基于下一代测序技术的群体基因组学的出现促进了在全基因组范围内评估遗传分化。例如，种群基因组学分析揭示了世界性人类果蝇的迁徙历史，大约10，000年以来，果蝇已经成功地在世界上大部分地区定居。同样，我们现在有工具来识别选择的特征，局部适应的基因组位点和中性进化的基因组区域。相比之下，生物表型性状的数量群体差异的评估往往受到阻碍，因为高通量筛选是耗时的，他们需要专门的设备和专业知识。因此，受局部适应的基因组位点影响的表型往往仍然难以捉摸。 欧洲果蝇种群基因组学联盟（DrosEU）一直在收集天然D。自2014年以来，欧洲的黑腹果蝇种群和第一个种群基因组学分析揭示了当地适应的模式。2018年，该联盟建立了168个代表9个欧洲D。黑腹果蝇种群进行广泛的表型分析，以量化18个生活史，生理，形态和行为生物特征。该表型数据集的分析揭示了多个性状的倾斜模式，表明在表型水平上的局部适应。因此，这些稳定的同雌系是一个很好的系统，在自然群体中的局部适应的基因组签名的表型变异。我们建议利用这一资源，通过测序所有168 isofemale线的基因组连接观察到的表型变异基因组分歧。为了获得对遗传多样性后果的机制性见解，我们将研究与观察到的成虫表型相关的两种组织的基因组范围内的基因表达模式（RNAseq）和染色质可及性（ATACseq），即肠道和翅膀成虫盘。这些实验的结果将有助于了解自然种群的地方适应性。此外，使用国家的最先进的基因组和表观基因组方法将提供新的机制的见解基因功能的背景下，当地的适应。作为该项目一部分建立的基因组资源、结果和分析管道将代表D. melanogaster和超越，以确定一般和不同的模式，当地的适应。

Organisms must cope with an ever-changing environment. Due to adaptations to local biotic and abiotic conditions, individuals within and between populations differ at the genomic and phenotypic level and population diversification is shaped by selection, as well as neutral events, such as genetic drift and migration. Most of our current understanding of genetic diversity in populations is based on analyses of specific genes or restricted genomic loci. The advent of population genomics based on next generation sequencing technologies facilitated assessing genetic differentiation on a genome-wide scale. For example, population genomics analyses revealed the migration history of the cosmopolitan human commensal Drosophila melanogaster, that has successfully colonized most of the world since ~10,000 years. Similarly, we have now the tools to identify signatures of selection, genomic loci underlying local adaptation and neutrally evolving genomic regions. In contrast, the assessment of quantitative population differences in organismal phenotypic traits is often hampered because high-throughput screens are time consuming, and they require specialized equipment and expertise. Therefore, the phenotypes influenced by locally adapted genomic loci often remain elusive. The European Drosophila Population Genomics Consortium (DrosEU) has been collecting natural D. melanogaster populations across Europe since 2014 and first population genomics analyses revealed patterns of local adaptation. In 2018, the consortium established 168 isofemale lines representing nine European D. melanogaster populations for an extensive phenotyping effort to quantify 18 life history, physiological, morphology and behavioral organismal traits. The analysis of this phenotypic dataset revealed clinal patterns for multiple traits, indicating local adaptation at the phenotypic level. Therefore, these stable isofemale lines are an excellent system to link phenotypic variation to genomic signatures of local adaptation in natural populations. We propose to harness this resource by sequencing the genomes of all 168 isofemale lines to link observed phenotypic variation to genomic divergence. To gain mechanistic insights into the consequences of genetic diversity, we will study genome wide patterns of gene expression (RNAseq) and chromatin accessibility (ATACseq) for two tissues with relevance for observed adult phenotypes, namely the gut and wing imaginal discs. The results of these experiments will shed light on local adaptation of natural populations. In addition, the use of state-of-the-art genomic and epigenomic methods will provide novel mechanistic insights into gene function in the context of local adaptation. The genomic resources, results and analysis pipelines established as part of this project will represent a blueprint for follow-up projects in D. melanogaster and beyond to identify general and divergent patterns of local adaptation.