- 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.
Why not have parallel phylogenetic and 'evolutionary' classifications?
Damien Aubert ends his paper with the suggestion to have two parallel classifications: The official system of living organisms should allow paraphyletic taxa, and all the mainstream systematists who want to make groups monophyletic should go away and build up a new, separate system of nested clades.
At this moment one might wonder how this suggestion can be consistent with earlier arguments that (a) a strictly cladistic classification is formally impossible and (b) clades can't be taxa, that is named groups of organisms, anyway. If Aubert believes his own arguments, the separate phylogenetic classification he suggests is not possible. If he believes his solution to be possible, those other arguments must be wrong. Presumably the idea would be that the cladistic system should not be called a classification, and that named groups of organisms are not necessarily taxa, but only if they are paraphyletic. Which doesn't make sense to me because even 'evolutionary' taxonomists have to recognise some monophyletic taxa.
Anyway, let's assume that a phylogenetic classification is possible, and let's also disregard for the moment that Aubert would like to reserve the official, widely used classification for what is currently a non-mainstream, minority position. Why not have two parallel classifications?
Of course we do already use parallel classifications all the time. We classify organisms by the food they eat into predators, herbivores, parasites and carrion eaters. We classify them by their life cycle into annuals and perennials. We classify them by their growth form into trees, shrubs, and herbs. We classify them by pollination syndrome into melittophilous, ornithophilous, anemophilous or myophilous. We classify them by dispersal syndrome into myrmecochorous, endozoochorous, exozoochorous or ballistochorous. We classify them by our interactions with them into pests, weeds, ornamentals, crops, lifestock, game, etc. We recognise other polyphyletic groups such as lichens. And, since Darwin, we understand that the one official, natural system of life should be organised by relatedness, which despite not having the concept of synapomorphies available Darwin himself already argued natural to mean in this context, and which is what phylogenetic systematists are working towards.
So if we can have just one phylogenetic classification next to all the non-phylogenetic ones, fine, count me in; that's all that phylogenetic systematists ever wanted.
But the problem I have is that the so-called 'evolutionary' classification that allows monophyletic and paraphyletic taxa does not appear to be good for anything. It does not appear to have any information content, and thus it doesn't have any use case. The classification would sometimes group by relatedness. But sometimes - if the difference in morphology is intuitively large enough (leaving open what large enough means) or, as Aubert argues, if there was a large enough shift in diversification rates (ditto), it would not group by relatedness. It would be inconsistent and unreliable.
If we want to know about groups of close relatives, for example for bioprospecting or to design a biogeographic study, we could not rely on Veronica to be an inclusive group of close relatives, because who knows if in that case the last monographer used the criterion of Hebe being shrubby to separate that subgroup out. So in that case a phylogenetic system would serve us better.
Aubert's paper constantly returns to phenetic information content ("naturalness means maximizing the overall similarity of organisms withing grous"), but if that was our concern we could not trust the 'evolutionary' classification either, because who knows if Veronica wasn't circumscribed as monophyletic by somebody who doesn't consider shrubbyness to be all that impressive a difference, given indistinguishable flowers and fruits? And who gets to say what counts into "overall", and how to weigh the different traits? So in that case several single-character phenetic systems that contain groups like 'herbs' or 'shrubs' would serve us better.
Yes, we could look up if Veronica is paraphyletic in the 'evolutionary' classification and to what other genera, or if the shrubs are included or not. But as I have argued before, the whole point of having a classification is that you do not have to look up the details. The whole point of having a category name is that it alone will already reliably and consistently provide some information on the content of the category. The whole point of the natural system is that a layperson can learn a genus name and assume that it refers to an evolutionarily meaningful unit instead of part of an evolutionarily meaningful unit.
Shrub has direct information content in a single-character phenetic classification based on growth form. Veronica has direct information content in a phylogenetic classification. But Veronica does not have any reliable information content in a so-called 'evolutionary' classification.
So even if the entire scientific mainstream were happy to leave the official classification to a small movement that appears to have lost the argument sometime in the 1970ies, I would still have no idea what an official classification with paraphyletic taxa would be good for. One idea might be to uphold a tradition, on the lines of making it easier to refer back to classifications from 1920. But that is not strong enough an argument to outweigh other considerations, nor is it what science is supposed to do. We don't uphold the traditions of using blood-letting or assuming special creation either.
Another argument appears to be the one advanced by Richard Zander and now Damien Aubert himself, that paraphyletic taxa are necessary to study macroevolution. Most evolutionary biologists, however, seem to do fine with only species and clades, and so I cannot help but wonder if the argument is not a bit circular: Macroevolution is first defined as one supraspecific taxon producing another such taxon at the same level, and then by definition there is no macroevolution if paraphyletic taxa aren't allowed.
None of the research topics listed here, for example (accessed 27 Jan 2016), - adaptive radiations, changes in biodiversity through time, genome evolution, mass extinctions, estimating diversification rates, change in rates of evolution, and the role of development in evolution, have anything to do with or require paraphyletic taxa. In fact in some cases any taxon above the species level that isn't a clade would be positively misleading.
Again, I personally don't see a use case for 'evolutionary' classification, and thus I have no idea why such a system needs to exist.
This concludes my series of posts on the paper. As always I am doing this because I am personally interested in the paraphyly discussion, hope to understand the arguments of the other side, and remain curious if I will ever come across that shows phylogenetic systematics to be undesirable or impossible.
In this case the most novel aspect, at least to me, was the idea of basing the delimitation of a paraphyletic taxon from a clade nested within it on an acceleration of the rate of evolution and/or the diversification rate in the nested clade. Unfortunately I still think that this makes the mistake of defining a group artifiically based on not having something that another group has (non-Russians are not a group equivalent to Russians), and in addition the idea seems like a non sequitur to me (WHY should such a shift define a taxon?). But it was a new idea, and so I found the reading rewarding.