Taxon Sampling Affects Inferences of Macroevolutionary Processes from Phylogenetic Trees

Abstract

Phylogenetic relationships across the Tree of Life form the basis for comparing and organizing the Earth's biodiversity. In addition to providing information about the evolution of individual genes, populations, or species, phylogenetic trees are often used to study broader evolutionary patterns. In particular, the shape of phylogenetic trees (e.g., the distribution of cladogenic events across the tree) has been used to understand broad speciation and extinction patterns (Raup et al., 1973; Gould et al., 1977; Rosen, 1978; Savage, 1983; Mitter et al., 1988; Heard, 1992; Guyer and Slowinski, 1993; Mooers and Heard, 1997; Dodd et al., 1999; Good-Avila et al., 2006; Ricklefs, 2006). The results of many studies on phylogenetic tree shape suggest that variation in the rates of speciation and extinction has played an important role in shaping the Tree of Life. However, it remains to be determined to what extent we can detect the patterns resulting from the evolutionary processes that shape trees. These patterns can be obscured by nonbiological factors that can bias tree shape, such as incomplete taxon sampling (Mooers, 1995; Rannala et al., 1998; Pybus and Harvey, 2000; Purvis and Agapow, 2002; Huelsenbeck and Lander, 2003), phylogenetic reconstruction methods (Heard and Mooers, 1996; Huelsenbeck and Kirkpatrick, 1996), or phylogenetic noise (Mooers et al., 1995; Heard and Mooers, 1996; Stam, 2002). Therefore, it is important to understand how estimates of tree shapes might be biased as a result of nonbiological factors.