Evolutionary genomic approaches to understand the origin and maintenance biodiversity in forest and agricultural landscapes

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Majority of plant species are considered to have derived from past hybridization events and the present hybridization may have positive or negative influence on the maintenance of biodiversity. Despite widespread occurrence of hybridization, its role in the origin and maintenance of biodiversity remains controversial. A detailed understanding of the past and present hybridization patterns in selected groups of plants is essential for gaining insights into the origin and maintenance of biodiversity. Phylogenetic analyses provide a means to infer past hybridization and reticulate evolution, and parentage analyses of selected plant populations using genotypic data are invaluable to infer the present hybridization levels. Therefore, it is crucial to have a robust phylogeny of an ecologically and morphologically diverse group of forest trees as a framework onto which morphological, biogeographical, ecological and genetic data can be super-imposed to elucidate evolutionary patterns and reticulate evolution. The forest tree genus Populus, the emerging model organism of tree biology research, with its wide geographic distribution, extensive hybridization, adaptability to a variety of habitats, many industrial applications and economic importance as a major source of wood, and the availability of extensive genetic, genomic and biochemical tools provides an ideal system to investigate the role of hybridization in evolution of biodiversity. We will i) reconstruct robust phylogenetic tree(s) of the genus Populus based on DNA sequences of nearly complete chloroplast and nuclear genomes, ii) develop species diagnostic molecular markers to identify the parentage of hybrids, and iii) determine the levels of hybridization and introgression in natural hybrid zones of selected Populus species. This research will capitalize on recent advances in high throughput genomics techniques to generate nearly complete sequences of the nuclear and chloroplast genomes to reconstruct phylogenetic trees, and high throughput genotyping technologies to genotype genome-wide single nucleotide polymorphism to determine the parentage of inter-specific hybrids at an unprecedented level of resolution. The resulting phylogenetic tree(s) will be used a) to test evolutionary hypotheses and reticulate evolution in poplars, and b) as a framework for systematic classification of taxa within the genus Populus. The resulting knowledge of the levels and directionality of introgression and parentage of hybrids will be valuable for a) understanding the genetic architecture and evolutionary dynamics of hybrid zones, and b) developing models to predict genetic consequences of hybridization between native and potentially invasive, non-native species. In addition, resulting species diagnostic molecular markers will serve as a tool for genome mapping and parentage identification in poplar breeding programs geared to address challenges in meeting wood and energy demands of the forest, paper pulp and biofuel industries under changing climatic conditions.