Ecological genomics: Analysis of gene expression underlying parallel habitat adaptation in distinct salamander species

生态基因组学：不同蝾螈物种平行栖息地适应的基因表达分析

• 批准号: 228320886
• 负责人: Professor Dr. Leon Blaustein
• 金额: --
• 依托单位: AG Molekulare Evolution und Systematik der Tiere
• 依托单位国家: 德国
• 项目类别: DIP Programme
• 财政年份: 2013
• 资助国家: 德国
• 起止时间: 2012-12-31 至 2019-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/228320886?language=en
• 关键词: Ecological; genomics; Analysis; gene; expression

In a continuously changing world, adaptation to new or altering environmental conditions is one of the most elementary and important biological processes. Although we have much data on the consequences of habitat adaptation at the phenotypic and population structure levels, we are currently missing, with a few exceptions, deeper insights into the genetic architecture of habitat-dependent adaptation. The study of parallel adaptive evolution can illuminate underlying processes and mechanisms. Unlike any other vertebrate group, amphibian species can show a fascinating breadth ofhabitat-specific adaptations to aquatic and terrestrial habitats. The research teams of this proposal have studied parallel ecological adaptation to larval reproductive habitats in two distinct species of fire salamanders - Salamandra salamandra in Germany and Salamandra infraimmaculata in Israel. By integrating a strong ecological context with genomic approaches, this research proposal aims at extending the ecological-genetic framework of parallel habitat adaptation to the level of the transcriptome in order to simultaneously screen a large number of genes for patterns of evolutionary,divergence. We will design species-specific oligonucleotide microarrays based on EST sequences of the larval transcriptomes for each species. These microarrays can then be used to analyze gene expression patterns under fully natural conditions and in experimental setups, whereby analyses are inspired by field studies that analyze the ecology of salamander larvae. As salamander larvae are accessible in large numbers and can be easily manipulated in common environment experiments, this study system is suited to explore gene-expression responses to habitat-specific cues or selection pressures in dedicated experiments reflecting distinct larval habitat types and ecological parameters. The resulting data will reveal whether plastic phenotypes contribute to adaptive phenotypic change and whether they are enhanced by the emergence of genetically fixed traits. In addition to traditional computational methods, we shall use a newly developed individual-centered approach, using a new vector-correlation measure to identify genes that are co-expressed in individuals as opposed to differential expression of genes across populations. Following this approach we will be able to address the following topics/questions:Identification of genes that are differentially expressed between different habitat types within each species.Does the same set of genes underlie parallel habitat adaptation in both species or are different sets of genes involved?Are genes differentially expressed because of environmental factors that reveal selective pressures (desiccation, food shortage, presence of predators, etc.)? Based on combined common environment/gene expression analysis, we will be able to infer how far phenotypic or behavioral responses to specific environmental conditions or selection pressures are plastic or already genetically fixed in each species system. Are plastic responses and parallel evolutionary divergence in salamanders facilitated by the same sets of genes, pathways and functions or rather by independent regulatory changes?

在一个不断变化的世界中，适应新的或不断变化的环境条件是最基本和最重要的生物过程之一。虽然我们有很多的数据在表型和种群结构水平的栖息地适应的后果，我们目前缺少的，除了少数例外，更深入地了解栖息地依赖适应的遗传结构。并行自适应进化的研究可以阐明其内在的过程和机制。与其他脊椎动物不同的是，两栖动物物种可以对水生和陆生栖息地表现出令人着迷的广泛的栖息地适应性。该提案的研究小组研究了两种不同火蝾螈-德国的Salamandra salamandra和以色列的Salamandra infraimmaculata-对幼虫生殖生境的平行生态适应。通过将强大的生态背景与基因组方法相结合，这项研究计划旨在将平行生境适应的生态遗传框架扩展到转录组水平，以便同时筛选大量基因的进化模式，分歧。我们将根据每个物种的幼虫转录组的EST序列设计物种特异性寡核苷酸微阵列。然后，这些微阵列可以用于在完全自然的条件下和实验设置中分析基因表达模式，其中分析的灵感来自分析蝾螈幼虫生态的实地研究。由于蝾螈幼虫是在大量访问，可以很容易地操纵在共同的环境实验中，本研究系统是适合探索基因表达反应的栖息地特定的线索或选择压力，在专门的实验，反映不同的幼虫栖息地类型和生态参数。由此产生的数据将揭示塑性表型是否有助于适应性表型变化，以及它们是否因遗传固定性状的出现而增强。除了传统的计算方法，我们将使用一个新开发的以个人为中心的方法，使用一个新的向量相关性措施，以确定基因的共同表达的个人，而不是不同的基因在人群中的表达。按照这种方法，我们将能够解决以下主题/问题：识别基因的差异表达在不同的栖息地类型之间的每一个物种。是否相同的一组基因的基础上平行的栖息地适应在两个物种或涉及不同的基因组？基因的差异表达是否是因为环境因素揭示了选择压力（干燥、食物短缺、捕食者的存在等）？基于共同的环境/基因表达分析相结合，我们将能够推断出多远的表型或行为的反应，特定的环境条件或选择压力是塑料或已经在每个物种系统的遗传固定。蝾螈的可塑性反应和平行进化分歧是由相同的基因、通路和功能促成的，还是由独立的调控变化促成的？