Evolutionary dynamics of the natural Drosophila microbiome

天然果蝇微生物组的进化动力学

• 批准号: 433035363
• 负责人: Professorin Dr. Judith Korb, since 6/2022
• 金额: --
• 依托单位: Abteilung Evolutionsbiologie und Ökologie
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/433035363?language=en
• 关键词: Evolutionary; dynamics; natural; Drosophila; microbiome

All known organisms on earth are associated with microorganisms. Pathogenic microorganisms can exert strong selection pressures on their hosts. As a consequence genes involved in pathogen defense often take part in an evolutionary arms race with pathogens, and hence are among the fastest evolving genes. On the other hand, microbes have facilitated a plethora of major adaptive evolutionary innovations of their metazoan hosts. Nonetheless, studies that aim at understanding how organisms adapt to the environment often neglect the role of the microbiome in the adaptive process. D. melanogaster lives in a microbe rich environment, rotting fruit. Its phenotype and fitness are strongly microbiome dependent. This suggests that D. melanogaster is under selection to evolve mechanisms to control its associated microbiome. This means to shape the microbiome for its benefit. In order for selection pressure to result in adaptive evolution of host control, the selected traits have to be variable and have to have a heritable genetic component. We hypothesize that in the only evolutionary relevant setting, under natural conditions, (i) the D. melanogaster associated microbiome varies, (ii) there is a component of this variation that depends on host genotype, (iii) the variation in the underlying loci is shaped by natural selection. We address these hypotheses in a work program including two major project parts. In the first part, we will perform a microbiome Genome Wide Association Study (mGWAS) using 1000 samples collected in Europe, leveraging the resources of the European Drosophila Population Genomics Consortium (DrosEU). This will allow us to quantify the contribution of host genetic factors to microbiome variation and to identify the underpinning loci (mQTL). Drosophila is exceptionally well suited for such a study because it has (i) low levels of linkage disequilibrium that allows to pinpoint mQTLs to the SNP level, (ii) low levels of populations structure that could interfere with GWAS, (iii) a relatively simple microbiome that facilitates a cost effective and detailed assessment, (iv) an almost unrivaled genetic tractability for experimental assessment of mGWAS results. In a second step, we will analyze the mGWAS results in an evolutionary framework, to understand the ultimate forces that shape the variation at microbiome-interacting loci on a genomic level. Therefore, we will use state of the art population genomic methods including, but not limited to novel tests to detect polygenic selection on complex traits. In addition to analyzing potentially varying selective pressures across Europe, we will leverage publicly available population genetic data from the ancestral range of flies to test whether the expansion from Africa and colonization of temperate climates was accompanied by selection on microbiome interacting loci.

地球上所有已知的生物都与微生物有关。病原微生物对寄主有很强的选择压力。因此，参与病原体防御的基因经常参与与病原体的进化军备竞赛，因此是进化最快的基因之一。另一方面，微生物促进了后生动物宿主的大量重大适应性进化创新。尽管如此，旨在了解生物体如何适应环境的研究往往忽视了微生物群在适应过程中的作用。D.黑腹蛇生活在微生物丰富的环境中，腐烂的水果。它的表型和适合性强烈依赖于微生物组。这表明黑腹盘藻正在被选择来进化控制其相关微生物群的机制。这意味着为了它的利益而塑造微生物群。为了使选择压力导致寄主控制的适应性进化，所选择的性状必须是可变的，并且必须具有可遗传的遗传成分。我们假设，在唯一与进化相关的环境中，在自然条件下，(I)与黑腹葡萄球菌相关的微生物群是不同的，(Ii)这种变异的一个组成部分取决于宿主的基因型，(Iii)潜在基因座的变异是由自然选择决定的。我们在包括两个主要项目部分的工作计划中解决这些假设。在第一部分中，我们将利用欧洲果蝇种群基因组联盟(DrosEU)的资源，使用在欧洲收集的1000个样本进行微生物组基因组广泛关联研究(MGwas)。这将使我们能够量化宿主遗传因素对微生物组变异的贡献，并确定支撑基因座(MQTL)。果蝇特别适合于这样的研究，因为它具有(I)低水平的连锁不平衡，使mQTL能够精确地定位到SNP水平，(Ii)低水平的种群结构，可能干扰GWAS，(Iii)相对简单的微生物组，便于进行成本效益和详细的评估，(Iv)几乎无与伦比的遗传易感性，用于实验评估mGWAS的结果。在第二步中，我们将在进化框架中分析mGWAS的结果，以了解在基因组水平上塑造微生物组相互作用基因座变异的终极力量。因此，我们将使用最先进的群体基因组学方法，包括但不限于新的测试来检测复杂性状的多基因选择。除了分析整个欧洲潜在的不同选择压力外，我们还将利用来自苍蝇祖先范围的公开可用种群遗传数据来测试来自非洲的扩张和温带气候的殖民是否伴随着微生物组相互作用基因座的选择。