Three Gene Tree:
rbcL, atpB, 18s...
- The "three gene" tree includes 567 taxa, mostly angiosperms, with a carefully
selected group of gymnosperms. For some reason, Cycads were not included.
- The shortest trees for this data set were first found with the parsimony ratchet.
The Soltises approached Kevin Nixon after several months of anlayzing this data set with
PAUP* on very fast Macs. They were concerned that they were not finding the shortest
tree(s). The first night of running the ratchet (with DADA and NONA) on this data
set (on a much slower PC), trees 12 steps shorter than had previously found were
discovered. The next day, trees one additional step shorter (13 steps shorter) were
found. These are almost certainly THE shortest trees for this data set. They
have been verified (hit several times) with Pablo Goloboff's new methods, sectorial
searches, drift, etc., using TNT.
- We provide here a WINC file that can be loaded directly into Winclada that contains the
data file (stripped of uninformative characters) and the consensus tree. Anyone
wishing to have sets of individual shortest trees can send an email to the address on the
- The data/tree is stored in a single self-extracting executable. After downloading,
run the executable and the file threegen.winc will be extracted. Open this file with
Winclada to see/edit/play with the tree...
DOWNLOAD SELF-EXTRACTING THREEGEN.WINC
The tree you are about to link to is the REAL consensus of the shortest trees for the
500-taxon rbcL data set for seed plants that was originally published by Chase et al.
(1993) and later reanalyzed by Rice et al. (1997) who was still not able to find the
shortest trees for this data set.
The tree you are about to view is the ONLY public posting I am aware of (April
2002) in ANY form of the most parsimonious trees for this data set. Strangely,
other sites have not acknowledged the existence of these shorter trees.
- The trees from which this consensus tree are derived are in excess of 50,000 trees
- Found with NONA using traditional searches (usually in 1-3 weeks on a 200 mhz
- Found with the ratchet (usually in 3-6 hours on a 200 mhz machine)
- These trees have a length of 16218 when uninformative characters are removed, 2
steps shorter than those found by Rice et al. (the Rice et al. trees have been verified to
have 16220 steps when uninformative characters are removed, although massive confusion
persists because of incorrect values reported by PAUP).
VIEW ZILLA TREE
If you want to read more about the ratchet, see:
Nixon, K. C. 1999. The parsimony ratchet, a new method for rapid parsimony
analysis. Cladistics 15: 407-414.
This page and tree were first posted on the web on 4 February 2000 A.D., and updated in