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

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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?