Hybridization and genome doubling are both frequent and ubiquitous across the entire evolutionary history of flowering plants and they regularly stimulate plant diversification and speciation. Immediately following a polyploidization event, a genome generally suffers adjustments in organization and function at the genetic and epigenetic level. These alterations have the potential to induce novel expression patterns, which together with permanent heterozygosity and gene redundancy, might result in significant phenotypic shifts and elevated evolutionary flexibility. Recurrent allopolyploidy can result in substantially different lineages, and it is interesting how such species can maintain distinctiveness while sharing the same genetic heritage and ploidy level. Here we aim to screen genome-wide natural diversity in gene expression rates among sibling species in order to identify genes that may drive adaptation to different environments and lead to isolation. By taking advantage of the most recent advances in genomic technologies we will test the theoretical predictions that only a few genetic loci controlling key traits are necessary for rapid ecological diversification. We will use a sophisticated model system, represented by ecologically divergent sibling species of Dactylorhiza in their native environmental context. The project will provide one of the most comprehensive studies of natural variation within an allopolyploid group and will lead to an enhanced appreciation of the effects of polyploidy on the evolution of metabolic pathways that are significant to adaptation and speciation. Finally, it has the potential to provide a drastically new perspective on the links between polyploidy and functional diversity and it will contribute toward a better understanding and hence prediction of the spectrum of genetic and epigenetic mechanisms active at the intraspecific (population) level.
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