After Stian, we had another Master student, Pia, who concentrated on a purely bioinformatic topic in our group. She successfully defend here thesis with the title “Evaluating the Applicability of Macrosynteny as a Phylogenetic Trait Based on an Exploration of Spiralia” yesterday. Like Stian, Pia is also moving on to a PhD. There she will do genomics of very small animals. Hence, she can bring her skills learned as being part of our group to a new project as Pia did not only do her Master thesis with us but also two UiO Summer internships as a Bachelor students. This provided her with a broad experience in different topics including field work.
In her thesis, Pia addressed the topic of genome evolution and if it can be used as marker for deciphering the phylogeny of Spiralia (also known as Lophotrochozoa). In recent years, it has been found that the chromosomes in animals can be surprisingly stable with essentially more or less the same chromosomes occurring in the lancelet and the great scallop. Moreover, while chromosomes fuse and mix, these events are rare in some parts of the tree. Hence, it has the potential to be a strong marker to resolve phylogenies as the fusion with mixing cannot be unmixed and separated to the old condition. On the other hand, it has be shown that other parts of the tree the chromosomes fuse and mix substantially, in effect scrambling up the genomes like eggs in a scrambled egg. This is known to have occurred in some taxa of Spiralia as well.
Pia used now all genomes that were publicly available and with an completeness at the chromosome-level. This means that the entire chromosomes of a species have been sequenced and the different parts of a chromosome put together as one chromosome (or also called linkage groups). Pia worked thereby from scratch establishing the so-called ancestral linkage groups and tested if they could be used to reconstruct the phylogeny of the investigated groups. She thereby worked from low levels of taxonomy like the genus to higher levels like phyla and beyond.
Pia found that the number of recovered single-copy genes, which are needed to conduct this kind of macrosynyteny analyses, varies dramatically depending on annotation methodology, taxonomic depth, and number of species in any given analysis. In turn, the number of single-copy genes affects the robustness of the macrosyntenic patterns found and in accordance the resultant phylogenetic hypothesis based on this pattern. More such genes resulting in more robustly supported patterns and hypotheses. Pia also determined that phylogenetic macrosynteny is not informative in the case of two extremes – highly divergent genomic landscapes, and highly conserved genomic landscapes, with respect to recovered numbers of genes, the ability to recover ancestral linkage groups, and the interpretations of patterns among the linkage groups. The former might result in low numbers of genes, but independent of the number of genes it resulted in scrambled patterns mentioned above hindering the ability to recover ancestral groups. The latter has the opposite effect, ancestral groups can be easily detected but are the same across all investigated species and hence to not provide any phylogenetic signal.
