InvertOmics - Phylogeny and evolution of lophotrochozoan invertebrates based on genomic data

How the last common ancestor of animals like humans, fishes, insects, roundworms, snails and earthworms looked and how evolution proceeded within this large group of animals is discussed in biology. One hypothesis suggests that evolution advanced from a simple organization similar to flatworms towards more complex forms several times independently, while another one favors the opposite direction from a complex, bristle worm-like ancestor to simple organizations by several separate reductions. Support for one or the other hypothesis depends on how the phyla in the group Lophotrochozoa, comprises 16 of the 32 animal phyla, are related to each other. This is presently unknown, and one of the major reasons for this are that only very few genomes have been sequenced for this group, and that the genomic data are heavily affected biases, which can mislead analyses trying to resolve their relationships. In this project, we will generate high-quality genomes for 50 species covering all lophotrochozoan phyla using modern sequencing technology. Several lophotrochozoan species have very small body sizes (smaller than 0.5 mm), but we will address this challenge by adapting existing single-cell genomic protocols from cancer research. High-quality genomes will be determined for the first time for such species. We will also develop new bioinformatic tools. They will allow us to ameliorate the effects of the misleading biases. Moreover, this will also include a new support measurement, which is entirely different from all recent measurements. Due to both these new genomes and tools, we will be able find out how the different lophotrochozoan phyla are related to each other and how the last common ancestor of animals like humans, insects, and earthworms looked and how evolution proceeded within this large group. Thus far, we were able to submit a paper on different biases in phylogenomic studies, conducted first detailed studies on specific bioinformatic approaches and generate genomic data for a few different species of these groups. We are on our way to assemble the first genomes for some these species to understand their genomic evolution better, for example, with respect to toxins and developmental genes.

The origin and evolution of Bilateria is controversially discussed in several biological disciplines such as systematics or evolutionary developmental biology. In one hypothesis, evolution in Bilateria advances from a simple body organization similar to flatworms towards more complex forms several times independently. In the other one, the evolution progresses in the opposite direction from a complex ancestor more like an annelid to simple organizations by several separate reductions. Support for one or the other depends on the phylogeny and evolution of Lophotrochozoa, one of the major bilaterian taxa, but a robust phylogeny is still lacking despite recent phylogenomic studies. This is due to both low coverage by genomic data and misleading biases in data of lophotrochozoan taxa. In this project, high-quality reference genomes shall be generated for 50 species covering all 16 lophotrochozoan phyla using high-throughput sequencing. As several lophotrochozoan species have very small body sizes (< 500 µm length) this is challenging, but adapting existing protocols of single-cell genomics these problems can be circumvented and genomic data derived from single small-sized individuals be used for phylogenomic studies for the first time. Using simulation studies tailored towards the problem at hand we will establish both best procedures ameliorating negative effects of biases and a new measurement of support, which is entirely different from all recent measurements of support. Due to both the large genomic dataset and these thorough analyses, a robust phylogeny of Lophotrochozoa will be provided allowing contributions to discussions about the origin and evolution of Bilateria as well as of lophotrochozoan taxa and character traits. The project will generate deep genomic resources for several non-model organisms providing, e.g., new opportunities for studies in functional genome evolution, developmental biology, ecology or discovery of new medicinal drugs