The seed plants include two living groups of plants, the gymnosperms and angiosperms. Traditionally, it was believed that the angiosperms, or flowering plants, were derived directly from some gymnosperm ancestor. Numerous analyses, both morphological and molecular, have supported this traditional view. However, recently, several molecular studies have produced results in which the extant gymnosperms form a monophyletic group that is a sister group of the angiosperms. It remains to be seen whether these new studies will be corroborated by additional analyses.
"Zilla" is the original 500-taxon rbcL matrix for seed plants that was originally analyzed by Chase et al. (1993). It has been the basis of many subsequent papers. Chase et al. found trees of length 16225 (the corrected length without autapomorphies, as PAUP reported an incorrect length for the original analyses). The Chase et al. analysis was performed on a Macintosh running PAUP and let run for approximately one month. Later, Rice et al. "reanalyzed" the matrix using PAUP on Sun Workstations, and after 11.6 months of computer time discovered trees that were 5 steps shorter, or length 16220 (corrected) for this matrix. Soon after the publication of the Rice et al. paper in October 1997, Goloboff, Nixon and Davis (unpublished) discovered trees of length of 16218, or two steps shorter than Rice et al., while analyzing the matrix with existing versions of NONA. Using a reasonable strategy (unlike Rice et al.) it is possible to find trees of length 16218 ca. Every 7 days or so on a 200 MHz Pentium class computer running NONA. Trees of the length reported by Rice et al. after 11.6 months are found every 48 hours or so, again with existing versions of NONA and no special strategies.
The parsimony ratchet (Nixon, 1998, 1999) generally will find shortest trees for zilla within 2-4 hours on a 200 MHz Pentium, and has a greater than 95% probability of finding such trees within 22 hours of analysis with the parameters set correctly.
We present here the consensus of ca. 100,000 trees of length 16218 that have been found by various means, including traditional searches with NONA and various analyses with the parsimony ratchet. This consensus has 398 resolved nodes, ca. 30 nodes less than the tree presented by Rice et al., and we are fairly confident that all islands have been adequately sampled - in other words, the consensus will not change with the addition of more trees.
The tree has been broken into parts for convenience of viewing, and the parts are appropriately labeled as to the groups that are included.
Chase, M. W., D. E. Soltis, R. G. Olmstead, D. Morgan, D. H. Les, B. D. Mishler, M. R. Duvall, R. A. Price, H. G. Hills, Yin-Long Qiu, et al. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Annals Missouri Bot. Gard. 80: 528-580.
Horovitz, I. 1999. A report on "One Day Symposium on Numerical Cladistics." Cladistics 15: 177-182.
Nixon, K. C. 1998. The parsimony ratchet. Numerical Cladistics Symposium. American Museum of Natural History, New York, May 1998 (see Horovitz, 1999).
-------. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414.
Rice, K. A., M. J. Donoghue, and R. G. Olmstead. 1997. Analyzing large data sets: rbcL 500 revisited. Syst. Biol. 46: 554-563.