- 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.
Have the assumptions underlying cladism been empirically falsified?
The abstract of the present paper claimed that the "biologically unrealistic assumptions on which cladism is based ... have been empirically falsified". I was curious what this would be about. As far as I can tell, the only subsection of the paper dealing with the claim is 10.4., Unformitarianism and Punctualism.
There are two separate arguments, the first of which is based on a very selective perception of phylogenetic systematics. A lot of text is spent saying that cladists assumed phenetic similarity to be strongly correlated with relatedness because they assumed that evolutionary change was uniform along all lineages; thus they concluded that a classification by relatedness would maximise phenetic similarity within and dissimilarity between groups. Now Punctuated Equilibrium demonstrates that "the pace of evolution can greatly vary", consequently cladism doesn't maximise phenetic information content, consequently cladism is pining for the fjords.
It is not at all clear to me how varying rates of change mean that a phylogenetic classification isn't predictive of morphological traits. Unless we are talking about regular violations of Dollo's Law, okay, but I would not find that plausible.
But set that aside for the moment. To the best of my understanding, the cladist project was never primarily about maximising phenetic information content anyway, even if some cladists might argue that a phylogenetic classification fortuitously also happens to do that.
There are considerably more important arguments for phylogenetic systematics. For example:
- The understanding that a clade is what an ancestral species has turned into, and that consequently a clade is just as natural as a species while part of a clade isn't.
- The realisation that meaningful groups should be defined based on shared traits and not based on the traits that non-members of the group have.
- Logical consistency with the tree of life.
- Not wanting to supply the end users of a classification with groups that are evolutionarily and biogeographically misleading.
- The insight that it merely thinks to its logical conclusion what systematists have always done, i.e. classifying specimens by their relatedness even if they are as morphologically divergent as a butterfly and its caterpillar stage. In other words, intellectual consistency.
- Perhaps that nobody has ever come up with an alternative testable, objective and universal criterion for the delimitation of taxa. Etc.
As an aside, if one were to examine the phenetic information content of a phylogenetic system, one would first have to contemplate very carefully what a cladist of the 1970ies would have meant with that as opposed, for example, to a pheneticist from 1960 or a molecular phylogeneticist from 2016. For example, one would have to discuss similarity arising from a shared plesiomorphy, which an 'evolutionary' systematist would count but which a cladist would exclude from consideration as misleading. One would also have to discuss homoplasy, which a pheneticist might perhaps just throw into the mix but which a cladist would have to consider a character state coding error. (E.g. absence of legs in caecilians and in snakes is not homologous.) Finally, a taxonomist of the 1970ies would, when saying something like "overall similarity", be thinking in terms of morphology and anatomy, but not in terms of DNA sequence data as seen in the light of coalescent theory.
Taking into account what a cladist a generation ago would have actually meant with phenetic information content, it is easy to see how the argument could indeed be made that a phylogenetic system represents it best, and I do not see how varying rates of evolution or anything evolutionary biologists have learned since then would change that. Although I guess a pheneticist might consider the treatment of homoplasies to be circular, but that just shows that they would have a different understanding of similarity.
But again, maximising phenetic information content is unlikely to be among the arguments for phylogenetic systematics that any significant number of contemporary systematists would come up with if queried, and it is certainly not an assumption on which the current mainstream practice of classification is based. So it wouldn't even matter if it was true that phylogenetic classifications are only, say, the third best option in terms of phenetic information content. And that was that.
However, there may also be a misunderstanding of Punctuated Equilibrium behind the first argument, because that theory is here somehow used as an explanation for the superficial similarity of crocodiles to squamates as opposed to the more closely related birds. A proper discussion of P.E. would be leading too far now, but it just doesn't have anything to do with differences or similarity between such distant groups. The claim underlying Punctuated Equilibrium is that species are pretty much in morphological stasis most of the time and undergo change only at speciation events, which then appears "fast" (on a geological scale).
To the best of my knowledge it doesn't say anything about generation-to-generation changes being anything but minuscule, gradual and slow. And it doesn't say anything about massive acceleration along some branches of the tree of life either, rather it envisions something like a constant beat along all branches. Even if assumed to be true, P.E. just does not postulate evolutionary patterns that would be a problem for the morphological information content of clades in the first place.
Long Branch Attraction
The second argument implies that cladism (classification by relatedness) is empirically wrong because cladistics (parsimony analysis) suffers from long-branch attraction if data are used that are too homoplasious. Ignore for the moment that other phylogenetic criteria apart from parsimony also suffer the same problem. Doesn't matter for present purposes.
What matters is that this is a conflation of two totally different issues that only share a similar name. And as discussed in the last post, the paper is arguing against the monophyly requirement as such and thus also against all the phylogenetic systematists today who consider parsimony analysis to be outdated and use Likelihood or Bayesian phylogenetics instead. Choice of tree inference method is irrelevant for discussing the merits of rejecting non-monophyletic groups.