Michael Hiller, Max Planck Institute, Dresden
Linking phenotypic differences between species to differences in genes and cis-regulatory elements
Identifying the DNA changes that underlie phenotypic adaptations is a key challenge in genomics and evolutionary biology. In the first part of the talk, I will address the fate of cis-regulatory elements in snakes that lost limbs and in subterranean mammals that have degenerated eyes. By combining genome sequencing and functional genomics with comparative analyses, we identified thousands of non-coding genomic regions that exhibit higher sequence divergence specifically in these lineages. We found that these diverged genomic regions often correspond to limb- and eye-specific regulatory elements and that sequence divergence resulted in an extensive loss of relevant transcription factor binding sites. Overall this reveals a genome-wide picture of the non-coding genomic changes involved in limb loss and eye degeneration. In the second part, I will present our work on investigating the role of gene inactivation (loss) for adaptive evolution in mammals. By developing a genomics approach to accurately detect gene-inactivating mutations and applying it to the genomes of 60 mammals, we discovered a number of lineage-specific as well as convergent gene losses that likely contribute to adaptations of different mammals to life in water or dietary specializations.