On quality of evidence in phylogeny reconstruction: a reply to Zrzavy's defence of the 'Ecdysozoa' hypothesis

Zrzavy's arguments against the critical analyses of data supporting the Ecd ysozoa hypothesis (Wagele et al., J. Zool. Syst. Evol. Res. 37, 211-223, 19 99) are discussed. Zrzavy does not understand that the same basic principle of a priori weighting can be applied to sequence data as well as to morpho logical characters. Quality of evidence is the same as probability of homol ogy, which is estimated from the number of discernible identical details. I n sequences it is the number of identical nucleotides. Spectral analyses, d ismissed by Zrzavy, visualize patterns of putative homologies present in al ignments and also the number of positions supporting splits by chance alone . In cases in which old phylogenetic signals for a given monophylum are ero ded in a gene, plesiomorphies and chance patterns will have strong influenc e on tree topologies and spectra. If plesiomorphies are a cause of errors, the addition of taxa that shorten internal branches is a remedy, although, in many cases such taxa may be extinct. The place of a priori estimations o f data quality in a sequence of steps necessary for a phylogenetic analysis is shown. Morphological complexity is used as a proxy for a complex geneti c basis and is used as a major criterion to compare characters of the Ecdys ozoa and the Articulata. The details associated with the character 'complex cuticle' are discussed. Neither moulting nor the known components of the c uticle are novelties occurring only in Ecdysozoa. A published total evidenc e analysis is used to show that the number of coded characters does not nec essarily reflect the quality of the data set. Zrzavy's misunderstanding of the role of evolutionary scenarios is clarified and the importance of the u se of additional biological data for plausibility arguments is explained. P lausibility arguments in favour of the Articulata hypothesis rely on facts found in functional morphology and in the fossil record. Zrzavy's critique follows the actual mainstream but does not uncover logical mistakes or erro neous data analyses in the work of Wagele et al. (1999). It is concluded th at the Articulata hypothesis is a well-founded alternative to the Ecdysozoa ; it is based on much better morphological evidence and supported by plausi bility arguments that currently do not exist for the Ecdysozoa.