Identification of loci underlying local adaptation in European Drosophila populations

有机体必须应对不断变化的环境。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，种群多样性是由选择以及遗传漂移和迁徙等中性事件形成的。我们目前对种群遗传多样性的大多数理解都是基于对特定基因或限制性基因组座位的分析。基于下一代测序技术的种群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，种群基因组分析揭示了世界性人类共生果蝇的迁徙历史，自约10,000年来，黑腹果蝇成功地在世界大部分地区定居。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置和中性进化的基因组区域。相比之下，对生物表型性状的数量种群差异的评估往往受到阻碍，因为高通量筛选非常耗时，而且需要专门的设备和专业知识。因此，受局部适应的基因组基因座影响的表型通常仍然难以捉摸。自2014年以来，欧洲果蝇种群基因组联盟(DrosEU)一直在收集欧洲各地的天然黑腹果蝇种群，第一批种群基因组分析揭示了当地适应的模式。2018年，该联盟建立了168个等雌系，代表9个欧洲黑腹果蝇种群，进行了广泛的表型工作，以量化18个生活史、生理、形态和行为的有机特征。对这个表型数据集的分析揭示了多个性状的克隆模式，表明在表型水平上的局部适应。因此，这些稳定的雌株系是一个很好的系统，可以将表型变异与自然种群中局部适应的基因组特征联系起来。我们建议通过对所有168个雌雄异株系的基因组测序来利用这一资源，将观察到的表型变异与基因组差异联系起来。为了从机制上深入了解遗传多样性的后果，我们将研究两种组织的全基因组基因表达模式(RNAseq)和染色质可及性(ATACseq)，这两种组织与观察到的成体表型相关，即肠道和翅膀想象盘。这些实验的结果将有助于揭示自然种群的局部适应情况。此外，使用最先进的基因组和表观基因组学方法将在局部适应的背景下提供对基因功能的新的机械性见解。作为该项目的一部分而建立的基因组资源、结果和分析管道，将为黑腹隐翅虫及以后的后续项目提供蓝图，以确定当地适应的一般和不同模式。

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.