Dr Tim Littlewood (T.Littlewood@nhm.ac.uk) and Dr Max Telford (University College of London)
Over the last 5 years my group has been characterizing mitochondrial genomes of numerous parasitic flatworms. Results show that obligate parasites (Neodermata) show a shared gene arrangement. In addition there is a unique change within the digenean genus Schistosoma. Additionally, amongst the predominantly free-living, paraphyletic "Turbellaria" we have completed mitochondrial genomes from a polyclad and triclad, and a partial genome from a macrostomid. Each of these groups shows a different arrangement from each other and from the Neodermata. We have established laboratory protocols for characterizing mt genomes of flatworms and key evolutionary/systematic questions may now be addressed with this approach. I wish to pursue mitogenomics as a tool for resolving the interrelationships of the major flatworm lineages relevant to flatworm and wider animal systematics through a programme of research and training for a PhD student. The project will be a phylogenomic study on a small and do-able scale for a PhD candidate offering opportunities to generate primary data, analyse new and published data and test a variety of hypotheses of wide interest. The phylogenomics will be complemented by a small scale EST sequencing based approach to the same groups. Results will be of use in addressing the following questions:
6-12 mitochondrial genomes will be characterized: from the Catenulida, Macrostomida, Polycladida, Proseriata, Fecampiida, Temnocephalida. Completion of the mt genome of an acoelomorph flatworm will also be done. In addition, five sets of 3,000 ESTs will be characterized for each of these key lineages (adding to one on-going project being undertaken offsite). In addition to giving valuable information on the interelationships of these taxa, these data will effectively reduce the problematic long branches of the flatworms in the EST based Tree of Life as found recently with neodermatan representatives (see Rokas et al., Science 2005, 310: 1933-1938 and Philippe et al, Mol. Biol. Evol. 2005, 22 (5): 1246-1253).
Training and skills to be learned and developed:
Molecular - basic molecular systematic skills (PCR, cloning, sequencing) and additional specialist skills (longPCR, cloning of long fragments, transposon-mediated sequencing EST library preparation).
Bioinformatic - contig assembly, genome annotation, trn secondary structure prediction, sliding window-analysis
Phylogenetic - nucleotide, amino acid and gene order (breakpoint etc) analyses within a phylum and across the Metazoa (in particular the Lophotrochozoa, employing existing and forthcoming data on GenBank); single gene and combined evidence analysis (including additional genes when considering the lophotrochozoan question; ESTs etc).