The tree of life (TOL), as an organizing metaphor and concept, has been greatly challenged by the discovery of extensive horizontal gene transfer. While various attempts have been made to preserve the traditional TOL, other efforts are now focused on phylogenetic analysis and evolutionary reconstruction beyond the TOL. The articles in this special thematic series ofBiology Direct demonstrate methodologically and conceptually new and constructive ways of working with and thinking about the TOL and its phylogenetic legacy. Whether these approaches modify or ultimately reject the TOL, they show the wealth of insight gained by thinking beyond a central icon of evolutionary biology. Image courtesy of Mandy Budan.