Assessing and Improving the Accuracy of Detecting Molecular Adaptation with the TreeSAAP Analytical Software
The TreeSAAP software has been successfully used in
a variety of protein studies for identifying and characterizing
adaptation in terms of shifts in the physicochemical properties of
amino acid replacements. It differentiates adaptive replacements
from those that may have resulted from random mutation. The
accuracy of TreeSAAP was tested using simulated protein-coding
DNA data that was randomly generated using a bifurcating
phylogeny to reflect a random pattern of mutation constrained
only by the structure of the genetic code. A sampling of 1402
simulated amino acid replacements resulted in a default accuracy
of 80.6%. More than 50% of the false-positive results were traced
to just 11 of the possible single–step amino acid exchanges,
each of which exhibited less than 50% accuracy. When these
11 exchanges are eliminated from the subsequent analysis, the
accuracy of TreeSAAP is increased to nearly 90%. Further testing
of this modified approach for adverse implications with empirical
data is warranted.
Index Terms
Simulated protein-coding DNA sequences, TreeSAAP, analytical results, accuracy.
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