Most DNA sequences are expected to be selectively neutral. Genes which are expressed in the phenotype are however typically negatively selected. A small proportion of genes are subject to positive (Darwinian) selection which can be identified by elevated non-synonymous substitution rates. Gene duplications are thought to promote positive selection, because new gene copies are expected to either become silenced or evolve novel function. It has recently been demonstrated that positive selection at the whole-gene level has been switched on in the plastid clpP1 gene at least four different lineages within the tribe Sileneae (Caryophyllaceae). With various degree of confirmation, these events are associated with gene duplication, elevated synonymous rates (!), inserts of multiplied short amino acid motifs, and intron loss. Your task will be to determine the onset of positive selection in Silenesection Silene, and how it correlates to the associated phenonema. The phylogenetic relationships within this group of a large number (around a hundred) of species is largely undetermined. Therefore, you will sample sequence information from the negatively selected or neutral parts of the chloroplast genome to infer the plastid phylogeny and to identify where positive selection of the clpP gene has occurred. The results can then be used to test hypotheses that positively selected clpP genes, and therefore entire chloroplast genomes, have crossed species borders.