The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony. Systematic Biology

Abstract.—The effect of taxonomic sampling on phylogenetic accuracy under parsimony is examined by simulating nu-cleotide sequence evolution. Random error is minimized by using very large numbers of simulated characters. This allows estimation of the consistency behavior of parsimony, even for trees with up to 100 taxa. Data were simulated on 8 distinct 100-taxon model trees and analyzed as stratified subsets containing either 25 or 50 taxa, in addition to the full 100-taxon data set. Overall accuracy decreased in a majority of cases when taxa were added. However, the magnitude of change in the cases in which accuracy increased was larger than the magnitude of change in the cases in which accuracy decreased, so, on average, overall accuracy increased as more taxa were included. A stratified sampling scheme was used to assess accuracy for an initial subsample of 25 taxa. The 25-taxon analyses were compared to 50- and 100-taxon analyses that were pruned to include only the original 25 taxa. On average, accuracy for the 25 taxa was improved by taxon addition, but there was considerable variation in the degree of improvement among the model trees and across different rates of substitution. [Parsimony; phylogenetic accuracy; phylogenetic error; taxon sampling.] Finding optimal phylogenetic trees using parsimony is extremely difficult when there are many taxa. As the number of taxa grows, the number of possible bifurcating trees grows such that it rapidly becomes impossible t