Finding an upper limit for gap costs in direct optimization parsimony

Exploring a large number of parameter sets in sensitivity analyses of direct optimization parsimony can be costly in terms of time and computing resources, and there is little a priori guidance available for reasonable limits to these search parameters. For this reason, we sought a general-purpose upper limit for gap costs in the direct optimization program POY to streamline this process. To test the performance of POY as gap costs increase, we simulated data onto a pre-set topology using a GTR + I + G model modified to include gaps by adding them according to a negative-binomial model. Gaps were then removed and the data were analysed in POY at increasing gap costs. Increasing gap costs consistently resulted in reduced phylogenetic accuracy across trees of different relative branch lengths. Decoupling gap insertion and gap extension costs recovered a fraction of the accuracy lost by having both high gap insertion and gap extension costs, but only in trees with long internal nodes. To determine whether loss of phylogenetic accuracy was node-specific, we designed a small dataset with a constrained node, where all possible combinations of cost substitution and different percentages of gap versus nucleotide changes were explored. These analyses showed that the effects of gap insertion and extension are node-specific, and the minimum threshold for convergence on gap-supported nodes is similar to the threshold for accuracy loss found in the larger simulated datasets. Subsequent analyses of empirical data revealed that a similar pattern of loss with gap cost increase can occur with ribosomal genes (18S, 28S, 16S and 12S) but this pattern was not seen in the intron data (myoglobin II) examined. In conjunction with previously published congruence-based studies, the results suggest that POY sensitivity analyses can be streamlined and made more accurate if gap insertion and extension costs follow, as a guideline, a limit of four times the highest base-transformation cost. (C) The Willi Hennig Society 2008.