At 5% nucleotide substitution, there was no difference between the input and output topologies in all simulations, but, at substitution rates of 7.5% and 10% the input tree was recovered in no more than 8 of 100 simulations.
Approximately 40% of the input DNA was recovered, except for TK103D, which exhibited 15% recovery.
With NJ using Euclidean distances, the input topology was recovered in 100% of simulations when the most derived taxon was the reference taxon, but almost never when either an internal (S6) or basal (S12) taxon was designated as reference.
With parsimony analysis, the input topology was recovered in all simulations when the most derived taxon was the reference, but never when an internal or basal taxon was so designated.
With parsimony, again the input tree was recovered only when the most basal taxon, N. discreta, was reference and then only 22% of the time at 5% nucleotide substitution and only 3% of the time at 7.5% nucleotide substitution.
For example, with NJ using Pearson's correlation distances, the input tree was recovered at least 95% of the time when the most basal (S12) or the most derived taxon (S1) were used as reference, but never when an interior taxon (S6) was designated as reference.
For each round of selection, the GuHCl concentration was gradually increased from 1.5 M to 3 M in an effort to ensure that less than 10% of the input to each round of selection was recovered in the elution step.
The supernatant (soluble chromatin) was recovered and 10 μl were kept as input sample.
A qualitatively nearly identical topology (not shown) was recovered using bootstrap majority rule consensus trees as input.
Using an input of 100 ng of unamplified RNA, 20 100 μg of amplified RNA was recovered.
