Ancestral state reconstructions for genomes

The recent expansion of phylogenetic analysis from the traditional field of molecular evolution, analyzing histories of genes, to the nascent field of 'genomic evolution', analyzing histories of entire genomes, enables the construction of trees based on genome information, the quantification of the key processes that shape genome content and, ultimately, plausible parsimony reconstructions of ancestral genomes. Thus, when genomes are considered as phylogenetic characters, it is possible to reconstruct not only the history of species but also the ancestral states in terms of genome structure or function. In the future, we might be able to accurately reconstruct - or retrodict - a chain of events that led to the emergence of a specific genome sequence and, ultimately, to synthesize ancestral genomes at will, creating a 'Jurassic database' of genomes.