One of the more remarkable ancient invertebrate clades revealed by morphological and molecular animal phylogenies is Gnathifera, constituting Rotifera, Micrognathozoa, Gnathostomulida, and most recently thanks to phylotranscriptomics, Chaetognatha. Various Cambrian Lagerstaetten fossils have also been suggested as members of the stem group of Gnathifera or its constituent phyla. Unfortunately, despite the evident importance of this clade for animal evolution, few genomic and molecular developmental data have been collected from gnathiferans, and some uncertainty remains over both their internal phylogeny and their putative position as the sister group to the remaining Spiralia.
In this project, the student will lead chromosome-scale, long-read derived de novo genome assemblies of representatives of the deepest branches of Gnathifera, from existing material (including 9 of 11 families of Gnathostomulida) and material the student will newly collect from the field, using recently developed low-input ‘omics protocols. With the wide taxon sampling of these efforts, we will precisely resolve the internal phylogeny of Gnathifera, and test their overall position within Protostomia. Excitingly, these data will also allow us to interrogate the history of genome evolution within Gnathifera, using phylostratigraphic approaches to assess the de novo origin of taxon-restricted genes, as well as loss or expansion of ancestral orthologs including developmental transcription factors, and using whole-genome alignments and ortholog painting to reconstruct ancestral karyotype evolution in this group. Genome data could also help clarify taxon-specific issues, such as the relationship of Chaetognatha to the giant viruses that have been recently discovered to infect them. Potentially, the project could also include a single-cell genomics dimension, data which could be used to evaluate homology of morphological character systems such as the iconic jaw elements that give this clade its name