Analyzing Large Data Sets: rbcL 500 Revisited

In 1993, Mark Chase and 41 coauthors published phylogenetic analyses of two very large data sets of nucleotide sequenc? es of the chloroplast gene rbcL, which en? codes the large subunit of ribulose 1,5-bisphosphate carboxylase. Their paper was important for several reasons. These anal? yses were (and still are) among the largest ever attempted using parsimony. The as? sembly of such a large number of sequenc? es clearly demonstrated a high level of co? operation on the part of the botanical systematics community. Furthermore, a number of important new hypotheses re? garding seed plant phylogeny emerged from this study, and it has helped to orient many subsequent phylogenetic analyses. Increasingly, the Chase et al. trees are be? ing used in quantitative comparative anal? yses (e.g., Barraclough et al., 1996; also see Donoghue and Ackerly, 1996, and associ? ated papers). We reanalyzed one of the Chase et al. data sets for two reasons. First, we wanted to explore the general methodological and theoretical issues raised by very large data sets. It is critical that these issues be ad?