Rooting the tree of life (ToL): an exercise for “tree-thinkers.” (a) A node-based tree representation of the ToL focuses on taxa (sampled or inferred vertices illustrated with open circles) and models edges as ancestry relationships. The unrooted tree describes taxa as conglomerates of extant species for each domain of life, Archaea (A), Bacteria (B), and Eukarya (E) (abbreviations are used throughout the paper). Adding a universal ancestor vertex (rooting the ToL) implies adding a reconstructed entity (urancestor) that roots the tree but does not model ancestry relationships. The vertex is either a “most recent universal ancestor” if one defines it from an ingroup perspective or a “last universal common ancestor” (LUCA) if the definition relates to an outgroup perspective. Rooting the tree enables defining “total lineages,” which are lists of ancestors spanning from the ancestral taxon to the domain taxa. (b) A stem-based view focuses on edges (branches), which are sampled, and inferred ancestral taxa are viewed as lineages under the paradigm of descent with modification. Vertices correspond to speciation events. Terminal edges represent conglomerates of lineages leading to domains of life (the terminal nodes of node-based trees) and the ancestral stem represents the lineage of the urancestor (U) (double arrowhead line). Total lineages are simply a chain of edges that goes back in time and ends in the ancestral stem. Both node-based and stem-based tree representations are mathematically isomorphic but they are not equal [154]. They change the concept of monophyletic and paraphyletic relationships. A node-based clade starts with a lineage at the instant of the splitting event, incorporating the ancestor into the makeup of the clade. In contrast, a stem-based clade originates with a planted branch on the tree, where the branch represents a lineage between two lineage splitting events. Planting an ancestral stem defines an origin of lineages and the first speciation event in the record of life. This delimits a crown clade of two domain lineages in the stem-based tree (labeled with black lines) that includes the ancestor of the sister groups, a, and a stem domain group at its base. (c) The three possible rootings of the ToL depicted with stem-based tree representations. Terminal edges are labeled with thin lines and these conglomerate lineages can include stem and crown groups.
