The qualitative TOL: integrating trees, networks, and organismal biology

Abstract The tree of life (TOL) was, for almost 150 years, conceived as the representation of the history of life. Since the discovery of lateral gene transfer (LGT) and its relevant evolutionary implications, the TOL has been questioned as a correct representation and several researchers have proposed networks of life as a suitable replacement. Nevertheless, these depictions pose important epistemological problems, such as historicity and resolutions levels. This paper problematizes on such subject and sustains that both representations, the TOL and networks, necessarily collide and correspond to different types of inheritance that require distinct levels of resolution. I argue in favor of doing such a differentiation for understanding and modeling diverse biological processes. I analyze here different representations of the history of life, their meanings, and several inherent problems to some of them. Substituting the TOL by networks of life as the correct representations, or sustaining the TOL notwithstanding the amount of LGT evidence, obliterates important data. This paper proposes a qualitative TOL, a TOL produced by core and essential genes and organismic information, that serves as a necessary scaffolding for anchoring LGT networks and pivotal for providing a historical dimension in our representations. An important part of the paper is the historical parameter of the different representations. An argument about why networks without the TOL fail to retrieve historicity is made. Finally, the qualitative TOL serves as a tool that gives orientation through the entangled data in order to understand the webbed history of life.