The Trouble with Topology: Phylogenies without Fossils Provide a Revisionist Perspective of Evolutionary History in Topological Analyses of Diversity
James E. Tarver1,2,* and Philip C. J. Donoghue1,*
1School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
2Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
*Correspondence to be sent to: School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK;
Received February 10, 2010.
Revision received May 7, 2010.
Accepted January 7, 2011.
The decidedly asymmetrical architecture of the Tree of Life betrays the fact that some evolutionary lineages have diversified to a greater or lesser extent than have others. It has been a goal of evolutionary ecology to identify shifts in diversification rate (speciation rate minus extinction rate) and their causal bases. Historically, the question of relative diversity was addressed in terms of phylogenies of fossils (Simpson 1944) with focus shifting to taxonomies in the 1970s (Raup et al. 1973, Gould et al. 1977). The dramatic rise in the availability of molecular sequence data in the 1990s led to renewed interest in phylogenies and diversity from evolutionary biologists and attempts to explain patterns of diversity returned to phylogenies. For the first time, however, historical events inferred to have shaped current diversity were identified without recourse to palaeontological data (Harvey et al. 1994).
Two principal approaches have been developed– “distance” and “topological” methods. Distance (aka “temporal”) methods represent a natural development of taxonomic methods that were initially aphylogenetic. They exploit branch length data or the temporal spacing of branching events within phylogenetic trees and while distance methods remain popular for analyzing rates of evolution, they have lost out in favor of topological methods for the analysis of the history of clade diversity.
Topological (aka “tree shape”) methods were developed in parallel with distance methods but are distinguished in that they exploit only tree balance as a record of evolutionary history (Slowinski and Guyer 1989). They have been adopted widely because they eschew temporal and distance data and so they can be applied readily to phylogenetic trees, such as supertrees, where distance data are lacking (Moore et al. 2004). The purpose of these methods is to determine 1) if lineages within a given phylogenetic tree diversified under different rates and 2) which particular …