- The various definitions provided in the paper are in some way better than the ones that are currently accepted.
- There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)
- A strictly phylogenetic classification is formally impossible.
- Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".
- Cladism is built on biologically unrealistic assumptions that have been empirically falsified.
- There exists an objective approach to delimiting paraphyletic groups.
- It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.
Is there an objective approach to delimiting paraphyletic groups?
In Aubert's paper, this is apparently dealt with in section 10.7., "Evolutionist Solution". However it remains unclear to me where the actual objectivity comes in. After mentioning that colleagues who promote paraphyletic taxa can use Bayesian phylogenetics, which is true but irrelevant for principles of classification, it continues with "progress has also been made in the field of taxonomy". Three examples are provided:
- Richard Zander's Framework. As I have discussed before, and unless I severely misunderstood something, it starts with a taxonomist's personal intuition and then does not appear to contain any step where falsification of the original hunch is even possible.
- Stuessy et al.'s recent (2014) suggestion to use what appears to amount to a phenetic clustering analysis to justify paraphyletic groups. Approximate values for considering something different enough are suggested, but it remains unclear what they are based on. What is more, any character-based clustering is open to somebody coming along and suggesting a slightly different character set. That is not a problem if we based taxonomic decisions on relatedness and if we have clear handle on what kinds of characters are important (synapomorphies).
- Stuessy and Koenig's patrocladistics. I should really do a dedicated post on it, but its clustering by phylogenetic distance does not appear to have any biological and/or theoretical justification. More importantly for present purposes, in the original paper it is presented as a new tool that people can try to use if they want, with whatever weighting they personally find helpful, to justify paraphyletic taxa.
I just don't see how any of the three approaches listed above provide an answer to the question how significantly a cluster needs to be separated or supported to be acceptable as a taxon or, even more importantly, for the question how much isn't enough. And unless we assume saltationism to be true, no such criterion is possible even in principle, because all life forms throughout the history of the planet are connected by a smooth morphological and genetic gradient, generation to generation along the branches of the tree of life.
One might wonder, by the way, if cladists do not face the same problem. After all, they also need to circumscribe taxa, right? But the situation is different, precisely because a cladist thinks in terms of nested clades. The smooth gradient leads from the ancestral species of a group into new subgroups of that group. If we say: this is still the same group, but now a new, nested subgroup of it has evolved, we do not have to demand a massive jump in morphology. I think most people would agree that one new trait can be enough for a mere subgroup.
The paraphylist, on the other hand, has to argue that there is such a significant difference between the subgroup and the rest of the group that it should not just be a subgroup, it should be another group at the same level, perhaps at a very high level. Perhaps this is the case where, from one ancestral species to the scarcely different immediate descendant, the lineage shifts suddenly between two different orders of insects! Because... the descendant species has one antenna segment more and a slightly different colour pattern on the wings! And to do science, we need to have an objective and universal criterion to separate this situation from the ones where there isn't enough difference for the transition from one order to another. (Or class, or phylum.)
Once more: With evolution being gradual, this is doomed from the start.