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Abstract

The genome contains an organism's complete set of instructions for development, survival and reproduction. “Decoding” these instructions, particularly the functional effects of naturally occurring genomic variation under a range of environmental conditions, remains one of the biggest challenges in biology with enormous implications for medicine, agriculture, and conservation. The adaptation of natural populations to changing environments is often driven by numerous genetic loci predominantly found in non-coding regions with likely gene regulatory roles. Using adaptively diverging marine and freshwater stickleback fish ecotypes as a model, we have previously identified more than 81 predominantly intergenic loci across the genome that have alleles consistently divergent between marine and freshwater ecotypes. In my talk I am going to discuss two linked aspects of this research programme: defining the components of chromatin and transcription regulation underlying adaptive divergence using functional genomics approaches like allele-specific RNAseq, ChIPseq, ATACseq, and transgenic assays, and investigations into how meiotic recombination and standing genetic variation facilitate and constrain the shuffling and reassembly of adaptive variation. These approaches highlight how cis-acting changes are particularly important for divergent adaptation with on-going gene flow because they are closely linked to the genomic elements they regulate. Together these approaches provide insight into how natural selection shapes genome function, and how molecular mechanisms can facilitate rapid adaptation in the wild.