Using a subset of the Australian species of Hibiscus sect. Furcaria we will survey 2-4 non-coding regions of cpDNA and 2-4 regions of nuclear DNA to reconstruct relationships between species of this group. Both chloroplast and nuclear DNA are used to maximize the potential variability between species. During this process I am growing fresh plant material from seed (National Seed Storage Laboratory, Southern Regional Plant Introduction Station) and take leaf samples to obtain DNA. I PCR-amplify and sequence regions of cpDNA and nDNA (specific regions to be determined based on results of preliminary screens) to obtain highly variable regions for phylogenetic comparison (6 or so). Since these species are hexaploid, part of the challenge is sorting out the sequences from the 3 different genomes present but this process should illuminate what sort of role polyploidization plays for this particular group and will add to the building evidence of the complex relationship between polyploidzation and diversity in plants. Also, the screening process to find primers could be useful for the study of polyploidy species in future studies.
Data analysis includes sequence alignment for the different genetic regions and phylogenetic comparison between copies within individuals and comparison to other species using a variety of analytical approaches (e.g., parsimony, maximum likelihood, Bayesian). Differences in phylogenies inferred from the cpDNA regions and nDNA regions may be present so we will need to compare using all sets of trees to determine the most accurate relationships.
Data analysis includes sequence alignment for the different genetic regions and phylogenetic comparison between copies within individuals and comparison to other species using a variety of analytical approaches (e.g., parsimony, maximum likelihood, Bayesian). Differences in phylogenies inferred from the cpDNA regions and nDNA regions may be present so we will need to compare using all sets of trees to determine the most accurate relationships.