Evolution & Development Group

Scientific overview

Knowledge of evolutionary principles is essential for the understanding of both, the function of an organism and its relationship with its environment. In this respect, it is fundamental for the comprehension of human biology and disease. Evolutionary questions such as how species are formed and how environmental influences lead to the development of a range of phenotypes from a single genotype are very relevant for understanding the origin of phenotypic variation between individuals and how individuals might respond to environmental chal- lenge. Whole genome duplications (WGD) are a recurrent feature of eukaryotic evolution, and the frequency of polyploid species suggests that WGD can confer selective advantages. WGD simultaneously generate a large amount of redundant genetic material, which when exploited can lead to functional novelty. Our group has contributed to the understanding of the impact of WGDs in genomic order, the evolution of regulatory elements and duplicate gene function. We also study the above issues within an applied context, using medically relevant examples and additional animal model systems. Thus, we search for copy number variations (CNVs) and rearrangements linked to autism in whole genome and exome by next generation sequencing of autism families. We then functionally analyse SNPs and CNVs via in vivo assays in human cultures and in zebrafish embryos. As an example, we have analysed the expression patterns and the morpholino knockout phenotypes of the zebrafish orthologs of the human genes within the 16p11.2 600Kb region. One fifth of the patients carrying this deletion develop autism.

Taking advantage of the advance in sequencing technologies, we investigated the phylogenetic position of three marine worms, the Xenoturbellida, Acoelomorpha, and Nemertodermatida. Together with others, we have recently published a paper in Nature making use of the first draft assembly of the genome sequence of the enigmatic worm Xenoturbella bocki. We suggested that in contrast to previous studies acoelomorph flatworms (acoels and nemertodermatids) form a new phylum of deuterostomes together with Xenoturbella, which we have named the Xenacoelomorpha. Meanwhile, we have sequenced the complete genome and made the first draft assemblies of 5 members of Xenacoelomorpha. We also organised the first international Xenacoelomorpha genome sequencing project meeting in November 2011 in Berlin.

In another project recently completed, we have characterized via mass spectrometry the proteomes of several sea urchin skeletal elements.

Finally, in a recent DFG funded project and in collaboration with Dr. J. Ploetner (Natural History Museum, Berlin), we have sequenced the brain and testis transcriptomes of the European water frog Pelophylax ridibunda. The hybrid Pelophylax esculenta can only produce viable offspring by interbreeding with one of its parent species P. ridibunda or P. lessonae through a process called Hybridogenesis, where via an unknown mechanism during meiosis one parental genome is excluded.

Evolution of regulatory elements

Using a computational method developed in our lab, we identified phylogenetically conserved noncoding elements (PCNEs) in a manner that is not biased by rearrangement and duplication. We identified more than a thousand PCNEs that have been conserved between vertebrates and the basal chordate amphioxus. Via transgenic zebrafish assays we found that the majority of the computationally identified elements are functional enhancers. We could show that PCNEs are enriched around genes with ancient synteny conservation and that this association is strongest for extragenic PCNEs, suggesting that cis-regulatory interdigitation plays a key role in repressing genome rearrangement. Our results also demonstrate that subfunctionalization of conserved cis-regulation has not been the primary determinate of gene duplicate retention in vertebrates. Instead, the data supports the gene balance hypothesis, which proposes that duplicate retention has been driven by selection against dosage imbalances in genes with many protein connections.