Frigatebirds, tropicbirds, and Ciconiida: Excesses of confidence probability

Because it is based on a significance test that takes the shape of the tree as given, the Rzhetsky/Nei Confidence Probability (CP) can attribute high 'confidence' to groups with little or even literally no support. CP further overestimates confidence in that it takes no account of reliability of alignment, and it shows instability in that drastic changes in results can be produced by small changes in data. Instability can arise when alignment is uncertain, since different alignment strategies can lead to slightly different matrices. Parsimony jackknifing offers a more reliable and stable way of assessing support. To take ambiguities of alignment into account with parsimony jackknifing, we suggest 'consensus' and 'average' methods of summarizing jackknife results from several alignments. Reanalyzing 12S and 16S rRNA data on pelecaniform birds, we find that CP has overestimated support for the Ciconiida, for placing frigatebirds with condors, and for placing tropicbirds with cormorants.