Genomes conceal a vast intricate record of their carriers' descent and evolution. To disclose this information, biologists need phylogenetic models that integrate various levels of organization, ranging from nucleotide sequences to ecological interactions. Rates of duplication and horizontal gene transfer, organism trees and ancestral population sizes can all be inferred through statistical models of gene family evolution and population genetics. Similarly, phylogenomics combined with other fields of natural sciences can reveal the nature of ancient phenotypes and paleoenvironments. These computationally intensive approaches now benefit from progress in statistics and algorithmics. In this article, we review the recent advances and discuss possible developments towards a comprehensive reconstruction of the history of life.
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