In a recent letter, Storer (2006) criticized a study in which I presented morphological characters in support of a flamingo-grebe clade (Mayr 2004). Because many of his claims are incorrect, I would like to address some of his arguments.
A sister-group relationship between flamingos (Phoenicopteriformes) and grebes (Podicipediformes) was first proposed by van Tuinen et al. (2001), who analyzed mitochondrial and nuclear DNA sequences as well as DNA-DNA hybridization data. A clade (Phoenicopteridae and Podicipedidae) was supported by independent and combined analyses of these different kinds of molecular data. Although my study provided the first evidence of shared derived morphological similarities, additional morphological synapomorphies of flamingos and grebes were described by Manegold (2006).
In my 2004 study, I discussed 11 characters as potential apomorphies of a clade including Podicipedidae and Phoenicopteridae. Storer discussed only two of these, the presence of a notarium and the chalky covering of the eggshell. He noted that the presence of a notarium is likely to be convergent because this feature also occurs in several other avian groups. However, there is no way to recognize convergence a priori. If there were, there would be no controversies on the phylogeny of birds at all. To show that the notarium of flamingos and grebes evolved convergently, Storer would have had to present more convincing evidence for alternative phylogenetic hypotheses, which he did not.
Storer (2006) admitted that the eggshell character was unique to flamingos and grebes. However, he then (Storer 2006:1184) made the curious comment that an “analysis omitting this structure and the notarium would, ipso facto, diminish support for a sister-group relationship between the flamingos and grebes.” I completely concur with this statement, but see little reason why one should leave out potential synapomorphies from phylogenetic analyses. Anyway, in bootstrap analyses, which I also performed in my study, the robustness of the tree is evaluated by randomly omitting characters from the analysis.
I also listed other characters that were not mentioned by Storer, most notably that flamingos and grebes have 11 primaries, which are otherwise found only in storks (and, in fact, are one of the characters used to support a flamingo-stork alliance). Instead, Storer (2006) discussed in detail the parasitological evidence for a flamingo-grebe clade, which I merely noted as further evidence but deliberately excluded from the phylogenetic analysis (Storer's note that this character was also mentioned by van Tuinen et al.  is incorrect).
Storer further listed some purported technical inaccuracies in my manuscript. However, I do not understand what he intended to express with his comment that “in figure 3 [of Mayr 2004], the tubercle on the cnemial crest of the grebe is not clearly depicted, and the structure connected to the tubercles in the three species should be identified to confirm that it is the same in all groups” (Storer 2006:1184). Storer appears to have misinterpreted the figure that I used to illustrate the length of the cnemial crests in the figured species, and in which I did not indicate any particular tubercle. His notes on the hypotarsus structure (i.e., that I was “unaware that the hypotarsal canal for M. flexor perforatus digiti II is present in the primitive genera of grebes” [Storer 2006:1184]) are irrelevant, because this character was not included in my analysis. Storer (2006:1184) noted “other inaccurate representations of skeletal characters,” but in regard to the only example he provided, he was mistaken. In the illustration of the grebe's foot, the longest toe is indeed the fourth (in any case, this figure does not illustrate the relative length of the foretoes but that of the hallux, which is clearly visible).
Storer (2006:1183) dismissed my morphological analysis and noted my “failure to use the mass of basic natural-history information relevant to the subject.” He then noted my “inability to explain how the structure of the feet could change from webbed in flamingos to the far more complex structure of grebes, or vice versa” (Storer 2006:1184). Apart from the fact that his considerations on the evolution of the foot morphology of grebes are speculation, there is no reason to assume that the foot of any of these extant taxa evolved from a morphology that is represented by its extant sister group, and the foot morphologies of extant grebes and flamingos may represent autapomorphic specializations of these taxa.
In addition to van Tuinen et al.'s (2001) study, the sister-group relationship between flamingos and grebes resulted from analyses of various different gene sequences, such as the nuclear ZENK gene (Chubb 2004), RAG-2 exon (Cracraft et al. 2004), and RAG-1 exon and myoglobin intron 2 (Ericson et al. 2006; their figs. ESM-2 and ESM-3, respectively). Recent comments to the contrary by Livezey and Zusi (2007) notwithstanding, the flamingo-grebe clade is one of the best-supported higher-level clades of birds.
Storer (2006:1183) introduced his note by remarking that information “on phylogeny is obtainable from at least two present sources: the whole-animal biology of the organisms and molecular biology. The most accurate phylogenies will result from those sets of data in which there is the closest agreement.” There is nothing to add to these statements, except that I find it difficult to understand why in this case he did not follow his own advice.