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

在一个不断变化的世界中，适应新的或变化的环境条件是最基本和最重要的生物过程之一。尽管我们有很多关于栖息地适应在表型和种群结构水平上的后果的数据，但除了少数例外，我们目前缺乏对栖息地依赖适应的遗传结构的更深层次的洞察。并行自适应进化的研究可以揭示潜在的进化过程和机制。与任何其他脊椎动物不同，两栖动物物种可以显示出令人着迷的广度，以适应水生和陆地栖息地。这项提案的研究小组研究了两种不同种类的火蜥蜴--德国的火蜥蜴和以色列的无斑火蜥蜴--对幼虫繁殖栖息地的平行生态适应。通过将强大的生态背景与基因组方法相结合，本研究方案旨在将平行栖息地适应的生态-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、分化模式。我们将根据每个物种的幼虫转录本的EST序列设计特定物种的寡核苷酸微阵列。然后，这些微阵列可以用来在完全自然的条件下和在实验装置中分析基因表达模式，从而分析受到分析火蜥蜴幼虫生态的实地研究的启发。由于火蜥蜴幼虫可以大量接触，并且在普通环境实验中易于操作，因此该研究系统适合于在反映不同幼虫栖息地类型和生态参数的专用实验中探索基因表达对特定栖息地线索或选择压力的反应。由此产生的数据将揭示塑料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，我们将使用一种新开发的以个体为中心的方法，使用一种新的载体相关性度量来识别在个体中共同表达的基因，而不是跨种群的基因差异表达。通过这种方法，我们将能够解决以下主题/问题：识别每个物种内不同栖息地类型之间差异表达的基因。两个物种的并行栖息地适应是相同的一组基因还是涉及不同的一组基因？基因的差异表达是因为环境因素(干燥、食物短缺、捕食者的存在等)？基于联合的共同环境/基因表达分析，我们将能够推断对特定环境条件或选择压力的表型或行为反应在多大程度上是可塑性的，或者在每个物种系统中已经遗传固定。火蜥蜴的可塑性反应和平行进化分化是由相同的一组基因、途径和功能促进的，还是由独立的调控变化促进的？

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?