1. Ureotelism/uricotelism is a relatively conservative character, maybe not an absolutely infallible one. Are you so certain it couldn't have changed twice istead of once? (No need to answer that, surely)



2. Rest et al's assumption that mammals (Synapsida) represent an outgroup to other amniotes (Reptilia) is based not on any particular dogma but on analyses of large data sets by authors such as Gauthier et al. (several papers in 1988) and Laurin and Reisz (1995), references easy to find on the web.



3. The 'unresolved polytomy' at the base of the cladogram is not an anomaly. All standard phylogenetic analyses produce unrooted dendrograms, which are converted to cladograms (or phylogenetic hypotheses) by choosing the position of the root. There is no way that the analysis could identify common ancestry of the two furthest outgroup taxa (unless a different, arbitrary, method of placing the root was used), and hence it is correct that the figure doesn't show it.



4. Adding another, more distant outgroup (any non-amniote, such as an amphibian and/or fish) would let the mammalian group be resolved. And it would, as you say, further test the accepted view that Synapsida and Reptilia are sister groups. We would then be assuming (based on cladistic dogma, or whatever) that Amniota is monophyletic. I wonder where the fish-amphibian outgroup would attach to the cladogram in Rest et al's Fig. 3?



5. Of course, in theory the addition of new 'outgroup' taxa (or new characters) could also change the ingroup relationships. Bayesian analysis produces a lot of high numbers inspiring high confidence that this is the best result for the particular data matrix analysed, but addition of new (independent, e.g. nuclear, morphological etc.) data and new (e.g. fossil) taxa could still overturn the result, particularly at places where internal branches are much shorter than terminal ones.



6. Darwin would have been a cladist if he'd thought of it. T.H. Huxley came pretty close, he had a good eye for patterns of relationship (e.g. trumping Owen on Gorilla brains, and realising that birds were dinosaurs), while Darwin was looking for the process.



7. Many scientists behave badly, but Feduccia has always been wrong about bird origins and by now he must surely know it. The cladists were right again: birds are theropod dinosaurs.
-----
John D. Scanlon

Riversleigh Fossil Centre

Outback at Isa

Mount Isa, Queensland, Australia

riversleigh@outbackatisa.com.au

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