Appendix 1.

Generating Rarefied Matrices in NONA


Rarefied data matrices were created using a batch file executed in NONA

(Goloboff, 1993). Initially, the following options were set: AMBIGUOUS= (support

from ambiguous optimizations considered), RSEED 0 (random number generator seed

set based on the computer’s clock). Characters were randomly removed using the

RESAMPLE N command (where N is the percent probability of removing any

individual character from the matrix), HOLD 10000 (tree buffer set to 10,000),

HOLD/10 (to limit the number of trees kept in each replication of “MULT” to ten),

MULT* 50 (performs TBR branch swapping on a Wagner tree generated using random

taxon addition over 50 replicates). The results were saved using KSV* (save all trees in

memory to a file), KSV/ (closes tree file), KEEP 0 (purges tree file), CCODE [.

(restores all characters to the matrix). This sequence was repeated 100 times for each

value of N. The value of N varied between 2 and 98 in intervals of 2. In total, 4900

rarefied matrices were analyzed for each complete data set.