My research program examines the evolution of tree populations to their local environment as the outcome of gene flow, natural selection and their demographic history. I have selected trees as a focus of my research for many reasons?they are key determinants of their ecosystem; their long lifespan and typically high population sizes provides an interesting context for studying evolution; and their conservation not only preserves the tree species of interest by multiple trophic levels of biodiversity from the soil microbiome to the wildlife that feed on their fruit. Oaks (Quercus) in general, and valley oak (Quercus lobata Née) in particular, are an excellent study system for investigating the molecular basis of local adaptation of trees. The genus Quercus has many species through the Northern Hemisphere that are important economically and ecologically; in North American oaks have more biomass and species than pine.
Our lab has long used genetic markers as a valuable tool for studying gene flow and demographic history and in the last five years we have switched our emphasis to genomic tools for studying adaptive genetic variation. With that transition, we have increasingly focused on oaks as a model system, in particular valley oak (Quercus lobata). Below are some topics currently under investigation:
1) Valley oak as an emerging model system. To support research on valley oak, we have created a high quality, well annotated genome of valley oak and two common gardens containing over 600 families derived from throughout the species range. The genome provides an essential too
2) Evolution of local adaptation. For this research theme, we are conducting studies on landscape and ecological genomics of trees, transcriptomic studies of gene expression in response to water stress, and epigenetic studies of DNA methylation patterns across environments.
3) Molecular ecology of pollen- and seed-mediate gene movement. For many years, our lab has used genetic markers to study pollen and seed dispersal to understand how these processes affect genetic diversity within populations and and connectivity among populations. With new genomic tools, we can now study how these processes affects patterns of adaptive genetic variation that may be critical for survival.
4) Phylogeography and geographic patterns of genetic variation. Phylogeography is the study of geographic patterns of genetic lineages with the goal of understanding how the physical landscape (e.g. mountains, valleys, water bodies) and climate cycles shape the evolutionary history of species, the emergence of new species, and the extinction of others.
5) Hybridization and introgression. Interspecific gene flow is a potential source of genetic variation, including favorable variants that may allow plants to survive better locally. My research program explores hybridization and ancient introgression in California oaks from a population and phylogenetic perspective.
6) Conservation science of trees. Through the integration of genomic studies and the analysis of phenotypic variation observed in the two common gardens, we are developing models of how valley oak will respond to climate change. Such information will be critical in developing specific management strategies for this species, and rules of thumb for tree species in general.
In all these topics, my research integrates genetic patterns across scales that range from a single nucleotide base in a DNA sequence of plant to the landscape to the species' range. This work addresses fundamental questions about the evolutionary ecology of tree species and utilizes that information to inform policies about reserve networks that will optimize their survival in constantly changing landscapes and rapidly changing environment.
