Handledare: Bengt Oxelman
Dating of divergence times is an important issue which recently has become tractable due to biotechnological advances enabling access to large amounts of DNA sequence data and from methodological advances. Chloroplasts are usually inherited through the maternal line only, and the genome usually behaves as a haploid non-rcombined unit. These properties have made it popular as a marker for phylogenetic inference. However, recent work by our research group has demonstrated gross incongruencies to gene trees inferred from nuclear genes. There are a number of possible explanations to these. The chronological order of split events in different gene trees provides information that may be useful for these purposes. Reliable dating is dependent on a good calibration of the tree, and of the robustness of the toplogy and branch lengths of the inferred tree. A previous study has used a single fossil to calibrate the Caryophyllaceae chloroplast tree, based on the matK gene. Your task will be to increase the sequence length from the chlorplast genome by adding sequences from the rps16, trnL/F, psbE/petG, and rpoC1 regions. The results will be used to test previous hypotheses about phylogenetic relationships among the major groups of
Caryophyllaceae, provide novel information about the major phylogenetic patterns of the tribe Caryophylleae (Dianthus and relatives) for which very little phylogenetic information is available, and check robustness of calibration prior distributions defined from previous dated phylogenies based on matK data only are robust to the addition of sequence data.