Me:

If these pores [...] are retained ancestral characters that have been lost in some but retained by others, then the genus Pogona may well be polyphyletic.



WW:

"Actually, in that case, it would be paraphyletic."



Me:

Not quite. If the defining characters of Pogona are retained ancestral characters, but they are treated erroneously as shared derived characters, then Pogona would indeed be polyphyletic.



It would be best if you refer to fig. 3.71 of S.J. Gould's Wonderful Life: The Burgess Shale and the Nature of History. In this figure, suppose the genus Pogona is represented by the species 1, 2, 3 and 4. This genus is polyphyletic because the stem group (all those species below the dotted line) is excluded. You may ask why these species from the stem group are excluded. That is because the character defining the genus Pogona is thought (albeit erroneously) to be a shared derived character (or synapomorphy) even though it is in reality a symplesiomorph (or shared ancestral character). A systematist who mistook a symplesiomorph as a synapomorph therefore treats the genus Pogona, comprising species 1, 2, 3 and 4, as a crown group that shares a recent common ancestor. To illustrate that erroneous assumption, simply draw a set of dotted lines connecting species 1, 2, 3, and 4 to a single ancestor. Of course this set of dotted lines represent a false phylogeny, but a false phylogeny is exactly what one gets if one mistook symplesiomorphs as synapomorphs. If a systematist is cognizant of the fact that a character is a symplesiomorph, then all the stem species would be included, and the resultant group would be paraphyletic instead of polyphyletic.



WW:

Interesting to see that you are objecting to taxa defined by ancestral features. Can we now expect your campaign against the continued use of "Reptilia", traditional "Elaphe", etc.?



Me:

As I explained above, I do not object to paraphyletic groups. I only object to polyphyletic groups. Pogona can indeed be a polyphyletic group even if the similarities defining this genus genus are shared ancestral characters instead.



That said, not all paraphyletic groups should be recognized. It depends on whether such groups are homogeneous. For example, one can certainly recognize a paraphyletic group of tetrapods which retain the ancestral character of all 4 limbs. That means all species that have lost some or all of their limbs would be excluded from this taxon. Such a group would be very heterogeneous since it would exclude the caecilians, snakes, amphisbaenians, whales and many legless lizards while including frogs, salamanders, most lizards, the tuatara, turtles, crocodilians, birds, and most mammals.



Fortunately, the genus Elaphe and the traditional Reptilia, while paraphyletic, is also quite homogeneous, unlike the hypothetical paraphyletic tetrapod group above. Hence it would be wise to continue recognizing Elaphe and Reptilia instead of the inane alternatives proposed by Utiger et al. and Gauthier, respectively.

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