Interesting paper. In “The Trouble with Topology: Phylogenies without Fossils Provide a Revisionist Perspective
of Evolutionary History in Topological Analyses of Diversity”(Syst. Biol. 60(5):700–712, 2011),
James E. Tarver and Philip C. J. Donoghue explain,
Topology-based methods provide a means of describing tree shape and determining whether or not the shape of a particular phylogenetic tree deviates from the kind of shape that would be produced by a homogenous process of random branching. Inevitably, where differences in the diversity of sister lineages deviate significantly from random chance, causal drivers are sought. However, phylogenetic tree topology is the sum of multiple rounds of speciation and extinction, resulting in tree symmetry within the topology of the tree. To determine the material basis of tree asymmetries, it is necessary to discriminate between those that occur as a result of contemporaneous changes in diversification rates versus tree asymmetries that occur through extinction-driven loss of phylogenetic history. This cannot be achieved using topological data from extant species alone. Fossil taxa incorporated into phylogenies of their extant relatives provide a means of temporally constraining and discriminating between the relative contributions of speciation and extinction in effecting diversification.
More.