Aubert's analysis of phylogenetic terminology, part 1: abstract

As always the following is my personal opinion and does not necessarily represent the opinion of any of my friends and relations, of my employer or colleagues, or of anybody whosoever except me.

I have recently set an alert with the key word evolutionary systematics (or similar), and today it delivered the first noteworthy catch: Damien Aubert, A formal analysis of phylogenetic terminology: Towards a reconsideration of the current paradigm in systematics. Published in Phytoneuron, an online journal that has peer review "if deemed appropriate or necessary by the editor, or if requested by the author", this piece of criticism of phylogenetic systematics runs over an astonishing 54 pages. It will certainly have to be tackled in homoeopathic doses.

So for the moment, let's just have a look at the abstract and table of contents.

BACKGROUND: For too many years the practice of systematics has been impeded by profound disagreements about the very foundations of this discipline, that is to say the type of information that should or should not be incorporated into a proper classification of life.

Note here that Aubert writes "information ... incorporated", not "information content". There is no doubt that phylogenetic and 'evolutionary' systematists build their classifications taking different pieces of information into account. The problem is that this is then often transformed into the claim that we can get more information out of 'evolutionary' classifications than out of phylogenetic ones (see especially various publications by Elvira Hörandl).

I, on the other hand, consider 'evolutionary' classifications to be useless because the end user would have to check for each individual taxon with what kind of rationale it was circumscribed. (Similarity or relatedness? And if the former, similarity in what traits?) In contrast, a system incorporating only one type of information is truly informative: in a phylogenetic classification, all the members of one group are each others' closest relatives, and that is that. I am looking forward to seeing how that issue is handled in the present contribution.

Two main schools of systematics, both recognizing evolution, oppose each other: cladism states that the classification should only reflect the branching order of the lineages on the tree of life whereas evolutionism states that the length of the branches, that is the degree of modification, should also be taken into account so as to reflect macroevolutionary leaps. The first one forbids the exclusion of any descendant from a group that contain its ancestors, while the second one explicitly requires that the descendants too much different [sic] from their ancestors must be classified separately.

This is the first time I have ever seen 'evolutionism' used in this sense; it sounds more like an insult made up by creationists. I will continue to scare quote this and related terms because the classification that best reflects evolution is the phylogenetic (= cladist) one.

I am also looking forward to seeing how the present paper handles the problem that the morphological gaps between an ancestor and a descendant are merely the result of our ignorance of the intermediates that must have existed (and might still turn up as newly found species or fossils), given that evolution is the gradual change of allele frequencies in populations. The use of the term "leap" here in the paper abstract might imply that the author is a saltationist, i.e. perhaps he believes that evolution is not gradual but proceeds in rare, big jumps on the lines of a cow suddenly giving birth to a whale. If that were the case, then at least one of the many problems for 'evolutionary' classifications would be solved, but unfortunately saltationism appears to be discredited.

Moreover, both schools often use the same words, such as "monophyly," to designate different ideas. This prevents proper communication between the proponents of either side.

This is the first part of the paper that starts to annoy me. As far as I can tell, the situation is this: Thousands of taxonomists, systematists and phylogenetists working on all groups of organisms across the planet use terminology in the sense of Hennig in papers, in conference presentations, in textbooks, and in lectures. About, I guess?, five to ten people in botany, perhaps a few more in zoology, who promote the acceptance of non-monophyletic supraspecific taxa and thus have a vested interest in blurring the distinction between monophyly and non-monophyly, publish the odd paper here or there in which they use terminology in the sense of Haeckel or Ashlock, or sometimes they invent their own definitions Humpty Dumpty style. And then the same five to ten people turn around, as in this case, and say that everything is now so confusing and complicated, and the other thousands of systematists had better accept their fringe view to make things clear again.

So it seems a bit like that story of the boy who murdered his own parents and then pleaded for leniency on the basis of being an orphan: it is an entirely self-created problem.

Consequently, the research in phylogenetics is globally erratic and the taxonomic classification is highly unstable.

Classifications will remain unstable as long as new data come in, or they are not scientific. That is how science works: we get new insights, we change the conclusions.

RESULTS: I rigorously define the terms which designate the phyletic relationships and explore their properties through use of graph theory. I criticize a similar work (Kwok 2011) that was unable to properly catch these notions.

When I read words like these, I always wonder: Does the author in question really think they alone understand what is going on in a way that nobody else did when these matters were discussed over and over again in the 1960s, in the 1970s, in the 1980s, in the 1990s, in the 2000s, and just again in the last few years?

Well, we shall see what the rest of the paper delivers, but it seems rather... odd ... to believe that all the world's experts would have missed some critical detail that will suddenly bring phylogenetic systematics crashing down, especially one that can be discovered by drawing a bunch of diamonds connected with arrows. (I peeked ahead, that is what the figures in this paper look like.)

This leads me to provide three independent arguments -- one historical, one utilitarian, and one morphosemantic -- in order to retain the original Haeckelian meaning of the term "monophyly" rather than the redefined Hennigian one.

No surprise. Here is a utilitarian and historical counter-argument: >99.9% of all systematists use the words in Hennig's sense, and changing it now would cause precisely the confusion that currently only exists in the imagination of a handful of die-hard opponents of phylogenetic systematics.

I identify some polysemy regarding the term "clade," and that is why I define two new words, "holoclady" and "heteroclady," to contrast respectively with "holophyly" and "heterophyly."

Podani and later Vanderlaan et al. have in recent years undertaken similar efforts especially with regard to the distinction between asynchronous and synchronous classifications. We shall see if this is really new or the same. At any rate, I have my doubts that such distinctions are really necessary in practice.

I also show that a strictly holocladic or holophyletic classification advocated by cladists is formally impossible.

This is another aspect that I am looking forward to. In the past, 'evolutionary' systematists have taken three main approaches to demonstrate that empirical reality forces us to accept paraphyletic taxa: (1) claiming that there is too much hybridisation or introgression, so that we don't really have monophyletic groups anyway, (2) claiming that taxa are just paraphyletic, so there, and (3) Brummitt's observation that there is a tension between phylogenetic systematics and Linnaean ranks when classifying ancestors. The first is self-defeating because if there is no phylogenetic structure then there is no paraphyly either, the second argument is clearly circular, and the third ... depends.

Brummitt's argument is correct if we have positively identified ancestral species, if we want to treat them as ancestral as opposed to side branches, if we want to build one classification of all life that has ever existed as opposed to one per time-slice, and if we insist on using Linnaean ranks, all at the same time. That is a lot of "ifs", and it could be added that the paraphylist ('evolutionary') approach causes even more problems when classifying ancestral species, because the ancestors break the morphological divergence between the extant species down into smooth gradients. Just think of all the feathered dinosaurs, and what that does to the idea that birds should be classified as separate from dinosaurs.

I therefore review and criticize the philosophical postulates subtending such an illogical paradigm. I show that cladism is part of a more general philosophical movement named structuralism, which is mainly characterized by anti-realism and a metaphysical way of thinking.

The charge of cladism being equivalent to structuralism has previously been advanced by Richard Zander. It is fascinating how these colleagues claim to know better than cladists what cladists believe. Why, I am a cladist and I have no idea what structuralism even is! (At least to me, Zander's explanation was about as clear as Minoan Linear A script, but maybe that is a failing on my part.)

And to the degree that the above quotation allows any inferences to be made, I would suspect that I am not a structuralist. In fact I am wondering whether this might be a case of projection; in my experience it is usually the pro-paraphyly people who have extremely formulaic views of how things should be while rarely grounding their thoughts in a clear mental model of how alleles evolve in meta-populations, how sexually reproducing individuals are related to other such individuals, how species are related to other species, and how evolution actually happens in real life.

Not all of them of course, but the ones who do try to visualise what is going on then have an unfortunate tendency to conflate gene trees with species trees, and tokogeny with phylogeny.

I identify the biologically unrealistic assumptions on which cladism is based and argue that they have been empirically falsified.

This has also been tried in the past, but unfortunately it always relied on a complete misunderstanding of the assumptions of cladism. If this has anything to do with "paraphyletic species" I am going to be very disappointed, because that is like telling a mathematician that they are doing circles wrong when they are drawing them without corners. Circles are defined as not having corners, and similarly all the words ending in -phyletic and -phyly are defined in a way that they cannot possibly apply to a group of sexually reproducing individuals forming a single meta-population species.

I therefore defend the use of paraphyletic groups in the scientific classification of life and review the main arguments that have been opposed to this solution. Some of them, such as anthropocentrism or the lack of an objective manner to determine paraphyletic groups, are grossly outdated, while others simply rest upon the difficulty in conceptualizing emergent phenomena.

This is then what interests me most about this paper, because it sounds as if it will rebut some arguments that I published myself, and indeed the reference list features three of my own papers. At the moment I don't get the relevance of emergence - it is generally the pro-paraphylists who have great difficulty understanding that different approaches to classification emerge above the species-lineage level than below, but again, let's see.

CONCLUSION: Since clades are still useful for methodological reasons,

Clades are "still useful"? What is next, the insight that the concept of the population is still useful to population genetics?

I offer a compromise that should make possible the coexistence of the two main opposing schools of systematics by eliminating competition between clades and taxa for the same names. I propose therefore that in a future revision, the BioCode should approve a dual system by recognizing both a "phyletic arrangement" made of clades and a "phylogenetic classification" made of taxa.

I haven't read through this paper yet, but somehow I doubt that it will convince the worldwide community of taxonomists, phylogeneticists, and systematists to suddenly drop the monophyly requirement after, and that cannot be stressed enough, this discussion has already been had thoroughly in the early 1970s.

Also, note that the term "phylogenetic classification" is here used for one that contains non-monophyletic taxa, in other words for a non-phylogenetic classification. Can we perhaps go easy on redefining words that already have a clear and widely accepted meaning? That would be nice.

"We often discussed his notions on objective reality. I recall that during one walk Einstein suddenly stopped, turned to me and asked whether I really believed that the moon exists only when I look at it." (Pais 1979)

Yes, that is really between abstract and table of contents. Here, have a random quote that mentions Einstein. The background is presumably the aforementioned bizarre idea that cladists are "anti-realists".

Finally, from the table of contents:

10.2. Paraphyletic Species .... 34

ARGH.

Well, I know one item I will be reading on and off over the Christmas and New Year break.