"Darwin in the Origin of Species laid the foundations of modern evolutionary biology on two central ideas: (i) all species are related to each other through a history of common descent, and (ii) the delicate match between a species and its environment is explained by natural selection. These two ideas embody the duality of pattern and process that is a fundamental feature of the evolution of life on earth: the unique historic pattern of descent and the interplay of population genetic and genomic processes that have generated it.In the proposed research I plan to undertake the reconstruction of the historic pattern of genome evolution across a broad phylogenetic range encompassing the three domains of life. I aim to reconstruct the prevailing trend of genomic descent (the tree of genomes) together with inference of the genomic process that relate it to the histories of its constituent parts (the forest of gene trees). Explicitly considering these processes, i.e. the history of gene transfers, duplications and losses will permit the use of complete genomes, instead of a handful of genes. The proposed large scale reconstruction will also enable the development of a valuable database of gene transfer, duplication and loss events that could potentially benefit a wide range of biological research. I will use this database to investigate the role of horizontal gene transfer (HGT) in genomic innovation, and ask questions about the biochemical, regulatory and ecological opportunities and constraints that govern the process of gene acquisition and loss that gave rise to the observed phylogenetic pattern of HGT.During the course of the fellowships I will be able to use my experience in developing quantitative evolutionary models and preforming Monte Carlo simulations in an entirely new setting. I expect to obtain extensive experience at both the theoretical level, in evolutionary genomics and phylogenetic inference, as well as at the methodological level, in handling la"