Comparative plastid genomics and phylogenetics of land plants

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My research program is aimed at generating reliable estimates of major branches of the land plant 'Tree of Life'. Phylogenetic trees have a tremendous impact in diverse fields of biology. They provide evolutionary biologists, systematists and geneticists with historical frameworks for studying plant biodiversity, allowing us to test hypotheses on how plants and their genomes evolved, and to create classification schemes for life on earth that reflect evolutionary history. They also identify groups that were previously unrecognized as deep phylogenetic lineages, flagging them for more detailed study and increased conservation attention. Much of what we know about plant phylogeny comes from the genomes of plastids (chloroplasts), which are the organelles that perform photosynthesis in green plants. We will take advantage of advances in DNA sequencing technology to recover the whole plastid genomes of multiple plant species. These data sets will provide additional power to resolve phylogenies, allowing us to tackle problems that were previously too difficult to address, including problematic root nodes of several major branches of the Tree of Life. In one test case, the water-hyacinth family, we will balance this plastid phylogenetic information with multiple single-copy genes from the nuclear genome. Some plants steal nutrients from fungi involved in an underground food web with green plants, and consequently have lost or reduced their ability to photosynthesize. We will sequence the plastid genomes of these mycoheterotrophic plants and compare them to their green relatives, to examine how this major nutritional shift affects patterns of gene retention and loss, and the rate of molecular evolution. These new data will allow us to test the prediction that some genomic changes precede the evolution of full-blown mycoheterotrophy, and will provide novel insights into the non-photosynthetic functions of plastid genomes.