Can taxon-sampling effects be minimized by using branch supports?

Abstract

Rydin and Källersjö (2002) found that taxon-sampling effects were a strongly disturbing factor in a high-level phylogenetic analysis. I have reanalyzed some of their data to assess whether bootstrap frequencies can be used to predict the stability of clades to taxon sampling, and to compare it with the performance of a stability measure based on taxon resampling ("taxon jackknifing"). High bootstrap frequencies correctly identify a small number of stable clades, but miss many other equally stable clades. When the total error rate is considered, no cut-off level based on bootstrap frequencies performs better than using all clades in the strict consensus, whereas a slight improvement was observed when cut-off levels based on taxon jackknifing frequencies are used. © The Willi Hennig Society 2006.