Summary of that special issue

(The following is the tenth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Okay, time to wrap this overly long series up. This is what the special issue contributes to the discussion around paraphyletic taxa:

Stuessy & Hörandl, Evolutionary Systematics and Paraphyly: An Introduction, pp. 2-5.

Introduces the special issue and provides some background.

Lockhart et al., We are Still Learning About the Nature of Species and Their Evolutionary Relationships, pp. 6-13.

Does not actually try to make the argument that paraphyletic supraspecific taxa should be recognised but merely points out that there is sometimes ongoing hybridisation between very closely related species. The entire contribution appears to be based on the misunderstanding that phylogenetic systematics (AKA cladism) does not accept paraphyletic species, which is further based on the misconception that the term "paraphyletic species" has an actual meaning for sexually reproducing organisms, which, however, it hasn't. Where phylogenetic structure is absent things cannot be "-phyletic", be it mono or para.

Hörandl, Nothing in Taxonomy Makes Sense Except in the Light of Evolution: Examples from the Classification of Ranunculus, pp. 14-31. 

Argues that classifications accepting paraphyletic taxa are more informative than any other classification, and that the approach restricts the options for classification more than any other. I consider both claims to be false: Because the end user cannot know if a taxon in an 'evolutionary' classification is monophyletic or defined by some symplesiomorphy, the information content of such a classification is zero.

Or in other words, the misconception underlying the paper is that "using a lot of information when making the classification" translates into "the end-user can get a lot of information out of it", but that is not a given. In the present case, they cannot deduce the meaning of any individual taxon without backtracking to the original rationale of the taxonomist. The thing is, making that laborious backtracking process unnecessary is precisely the point of having a classification in the first place.

As for the second claim, because there are myriads of ways how a taxon can be circumscribed as paraphyletic and myriads of characters that one could consider 'important' enough to be used as a defining symplesiomorphy, this approach actually has the largest possible number of options for classification.

George, The Case Against the Transfer of Dryandra to Banksia (Proteaceae), pp. 32-49.

The main argument appears to be that Dryandra should not have been sunk into Banksia because the relevant studies had not sampled 100% of the species, some small mistakes were made by the authors, gene trees were incongruent in some irrelevant details, and so on. In other words, nitpicking to distract from the real issue, which is that Dryandra is conclusively known to be nested in Banksia. The author also suspects that Dryandra is polyphyletic, which if true would make the taxon unacceptable to most of his allies.

Stuessy, Paraphyly and Endemic Genera of Oceanic Islands: Implications for Conservation, pp. 50-78.

Argues that the enforcement of monophyly will make currently endemic genera disappear into more widespread genera, and that this would make it harder to conserve the relevant species. It is hard to interpret this contribution as anything but a 29 pages long appeal to base taxonomic decisions and the classification of biological diversity on political convenience. If it isn't I must have missed its point.

Ehrendorfer & Barfuss, Paraphyly and Polyphyly in the Worldwide Tribe Rubieae (Rubiaceae): Challenges for Generic Delimitation, pp. 79-88.

An extremely interesting review of the state of knowledge about phylogenetic relationships in a group that includes such well-known genera as Galium and Asperula. But although the authors want to mentally assign unknown and unavailable ancestors to one of their descendant clades, the classification they propose is nonetheless for all practical purposes an entirely phylogenetic one because those ancestors will not appear in it anyway.

Brummitt, Taxonomy Versus Cladonomy in the Dicot Families, pp. 89-99.

Reiterates an argument that Brummitt made in earlier papers: Linnean ranks and phylogenetic systematics are incompatible because classifying an ancestral species into a genus will make that genus paraphyletic to all the genera its descendants are assigned to except itself. This is true as far as it goes, but of course Brummitt took it for granted that one could ever know that one is faced with an ancestor as opposed to a side lineage, that fossils should be treated as ancestral as opposed to terminals, and that when faced with the incompatibility he argues for one should prefer the pre-Theory-of-Evolution concept of Linnean ranks over phylogenetic systematics. One can certainly challenge all three assumptions, to say the least.

Zander, Support Measures for Caulistic Macroevolutionary Transformations in Evolutionary Trees, pp. 100-107.

Although it also proposes the titular support measures, most of the paper is a mixture of criticism of phylogenetics and explanations of the author's own approach to systematics. The fundamental problem here is that Zander's methodology depends on considering some present-day organisms to be the ancestors of other present-day organisms, but well, they simply aren't. It is like claiming that my brother is my ancestor because he looks more similar to our father than I do. If, however, we sensibly conclude that two contemporary groups have a common ancestor in the past instead of one being the ancestor, the whole argumentation of the paper collapses immediately.

Liu & Viña, Pandas, Plants, and People, pp. 108-125.

I cannot see any connection to the topic of paraphyly. In fact it seems unclear why this paper has been published in that specific journal, and I half suspect that the inclusion of this paper in the special issue is down to some kind of database mix-up.

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In summary, not counting the introduction and the Panda article there are seven serious contributions in this special issue advocating the recognition of paraphyletic supraspecific taxa. Of these, two do not actually appear to argue for paraphyletic supraspecific taxa at all and feel as if they are merely based on potentially easily resolved misconceptions. Of the remaining five, one uses a very distinctly non-scientific and political argument, and one argues that you shouldn't make any taxonomic changes the author doesn't like unless you have achieved an unreasonably high level of sampling and of confidence in the results.

Even apart from me disagreeing with the arguments of the final three, this special issue brings to mind an English saying I have heard. Something about barrels and their bottoms. Of course, one good argument would be enough in a case like this, but once more I cannot see it.

As before, the only one who got close is Richard Brummitt, but the problem is that his best argument also contains the seed of destruction for paraphyletic taxa: As our attention is drawn to the problem of classifying ancestors, we start to realise that they break the 'long branches' and significant 'evolutionary divergence' that paraphylists use as cleavage points when circumscribing paraphyletic taxa; evolution is gradual. And then we are soon drawn to the conclusion that a rank-free phylogenetic system is the only solution for a classification across the history of life on this planet. This is not what Brummitt wants, but it is the logical consequence of trying to accommodate ancestors in the classification.

Stemmy large-evolutionary changes (that special issue)

(The following is the ninth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

The final contribution to the special issue advocating paraphyletic taxa is Richard Zander's Support measures for caulistic macroevolutionary transformations in evolutionary trees. There are two ways of addressing it, and with previous papers in this issue I have sometimes taken one and sometimes the other: Either one can go through the paper bit by, carefully analyse the argumentation, rebut one claim here but concede another there, and so on; or one can take a step back, point at the fundamental assumption underlying the whole line of argumentation, and explain in a few words why one considers it to be wrong.

Because I am tired and have much else to do, I will mostly use the second approach and then spend just a bit more time addressing other random aspects of the paper that stick out to me.

Really it is very simple: Richard Zander sees groups of organisms that exist today as the ancestors of other groups of organisms that exist today. I, and with me presumably most systematists and evolutionary biologists, believe that a group of organisms that exists today cannot possibly be the ancestor of another group of organisms that exists today.

Unless one were to push them forcibly into a working time machine, today's chimpanzees are not going to become our ancestors, today's fish are not going to become the ancestors of the land animals, and today's ferns are not going to become the ancestors of the flowering plants. Instead, these groups have common ancestors in the past, and thus, no matter how much Zander ridicules the concept, “unknown hypothetical ancestor → (one extant group, another extant group)” remains the most appropriate way of describing evolutionary history. As a group of individuals in a time slice, the ancestral taxon is separate from all of its descendants, and as an evolutionary lineage through time it is identical to all of them, but it does not make sense to equate it with only some.

So again, I do not accept the premise that would enable us to even start thinking in terms of what Zander calls “caulistic macroevolutionary* transformations”, and thus for me the entire argumentation of this paper never even gets onto its feet. Conversely, Richard Zander does not accept the premise that ancestors should actually be ancestral to their descendants, and so nothing I can write would ever convince him. Agree to disagree and all that, I guess.

Are Linnean ranks and cladism incompatible? (That special issue)

(The following is the eighth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

The next contribution is that of the late Richard Brummitt who died between the Melbourne symposium promoting paraphyletic taxa and the publication of the resulting special issue. The manuscript was apparently adopted from a talk he gave at the symposium.

Brummitt's death was a great loss to the botanical community; he was influential, knowledgeable and had friends across the entire planet. In the present context, I respect him as the only proponent of paraphyletic taxa whose argumentation ever made sense to me – if, that is, certain controversial assumptions are accepted. This may sound like faint praise, but it is more than can be said about many other arguments that are used in the discussion.

Brummitt was also certainly a good writer, as will be evident in what follows, but nonetheless I find myself unable to agree with his conclusions. I will go through the paper from the beginning until we hit the crux of his case.

Much ado about absent ancestors

(The following is the seventh part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Pages 79 to 88 of this special issue meant to promote the acceptance of supraspecific paraphyletic taxa in biological classifications are taken up by a contribution entitled Paraphyly and polyphyly in the worldwide tribe Rubieae (Rubiaceae): Challenges for generic delimitation. Written by Friedrich Ehrendorfer, Michael Barfuss and Vladimir Vladimirov, it is perhaps best described as a concise review article summarising the current state of knowledge about phylogenetic relationships in their group of interest, and as such I found it extremely interesting and rewarding to read.

Even if they are not familiar with the scientific name, most people in the northern hemisphere will know Rubieae. They are characteristic herbs with seemingly whorled leaves; only seemingly because in reality there are only two true leaves, and the additional members of each whorl are derived from stipules, as demonstrated by the fact that only up to two side branches arise from each node. The flowers of these plants are usually small, radiate and white or yellow. The group has an extremely wide distribution; there are even native representatives here in Australia.

The phylogenetic studies discussed in the paper show that the two largest genera that are traditionally accepted in the Rubieae, Galium and Asperula, are horribly non-monophyletic in their current circumscriptions. Faced with this situation and considering the context in which the paper has been published, one would now expect, or at least I would expect, that the authors argue for the continued acceptance of these genera as non-monophyletic. That was, after all, the whole point of the symposium in Vienna that inspired the special issue.

Island endemic genera and phenetics (that special issue)

(The following is the sixth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Following an introduction and the contributions of Lockhart et al., Hörandl, and George, the fifth full paper in the special issue is Stuessy et al.'s “Paraphyly and endemic genera of oceanic islands: Implications for conservation”.

The main argument is quickly summarised, and it has actually already been made before by the same author, only then in a considerably more concise manner (Hörandl & Stuessy, 2010). When new species arrive on oceanic islands via long distance dispersal, in the most extreme cases as a single seed or a single pregnant female, they may find themselves presented with many new possibilities. Some selection pressures from their original habitat may not exist on the island, and there may be unused niches ready for the taking. The new arrivals also undergo a severe genetic bottleneck, carrying only a small fraction of the genetic diversity of the mainland population in themselves.

This means that island colonisers often have the chance of undergoing spectacular adaptive radiations in a short time. Echium and Sonchus in the Canary Islands, fruit flies or the Silver Swords in Hawaii are just some examples. In the words of Stuessy et al.,

Because of the speed of the divergence, it might be that the island genera are genetically not so divergent from the continental relatives, but they are usually very divergent morphologically, hence their recognition at the generic level.

So because they looked superficially very distinctive after their adaptive radiation into new niches, island lineages were traditionally often treated as genera distinct from the mainland genera they evolved out of. With the advent of phylogenetic systematics, however, they are sunk into these mainland genera, so that these island lineages are not island-endemic genera any more; they are just the island's representatives of the widespread mainland genus.

So what? So, according to Stuessy et al., this:

these actions could have a substantial effect on world island conservation.

This is, as far as I can see, as explicit as the paper makes the argument for paraphyletic taxa, but it is still clear what this is about. The idea is undeniably that one should keep island endemic genera because they make a better sell for conservation politics than mere endemic species.

An eighteen pages long perfect solution fallacy (that special issue on paraphyly)

(The following is the fifth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

As I am looking at the next contribution to Annals of the Missouri Botanical Garden's special issue on how awesome it would be if only we would accept paraphyletic groups as they did in the 1950ies, it seems as if I should start with the following disclaimer.

I want it to be understood that I have the highest respect for the life works of everybody involved, and for their publications other than the one we are currently dealing with. I do not wish to offend, but merely to critically discuss the scientific merits of 'evolutionary' systematics versus phylogenetic systematics, and specifically whether the arguments presented by the former school of thought make any sense. It also needs to be understood that my opinions expressed here are my own and are not necessarily those of my employer, nor those of my line manager, of my colleagues, of my friends, of my relations or, for that matter, of my pot plants. The same applies to all my posts, of course.

With that out of the way: the contribution I will discuss today, The case against the transfer of Dryandra to Banksia (Proteaceae) is … not a terribly well written paper.

For background, several years ago it was found that both molecular and morphological data showed Western Australian Dryandra to be phylogenetically nested within more widespread Banksia. It is no exaggeration to say that a Dryandra is just a Banksia with a shorter inflorescence, and consequently most taxonomists and systematists decided to unite the two genera. However, the “loss” of Dryandra as a distinct genus has left many people profoundly unhappy. One of these people appears to be the author of the present contribution.

'Evolutionary' classifications still do not have any information content (that special issue on paraphyly)

(The following is the fourth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

(Updated 29 December 2014 to increase clarity and to make the style a bit less strident.)

Next we come to the contribution written by Elvira Hörandl (2014). I could say that the paper is a strange thing, but then again most of them are seeing as how they generally do not fall into the usual categories of publications in my area, either original research or review articles. In the present case, the paper could perhaps most accurately be described as a review article, but one looking back not, as usual, across a rich and productive field that the author now attempts to summarise, but looking back instead onto a single previous publication: a classification of the buttercup genus Ranunculus also published by herself (Hörandl & Emadzade, 2012).

This means that except for lacking the methods section and extensive supplementary material this paper has pretty much the same content as that earlier publication: it describes the same classification and extols it as superior to one that would accept only monophyletic taxa. It contains much rapid-fire criticism of phylogenetic systematics but mostly revolves around two central claims, and it is those two which I will focus on in this post.

The word paraphyletic still doesn't apply to groups of sexually reproducing individuals (that special issue on paraphyly)

(The following is the third part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

(Updated 29 December 2014 to increase clarity and to make the style a bit less strident.)

Although I have yet to read through all of them, I can already say that the first proper paper in the special issue, Lockhart et al.'s “We are still learning about the nature of species and their evolutionary relationships”, seems a bit out of place. It focuses mostly on one idea: there might be ongoing gene flow between the entities we currently recognise as species, and therefore the currently used coalescent species tree methods might be inappropriate to reconstruct phylogenies in those situations.

If that were it, one could happily agree, all cladists could happily agree, and we could call it a day. However, this paper was submitted as a contribution to a campaign for the recognition of paraphyletic supraspecific taxa, and so the clear implication is that the observation of occasional introgression between closely related species somehow means we should not classify organisms by their relatedness. The other authors of the special issue will surely cite this paper as supportive of that position over the next few years, and Lockhart et al. must be aware of that.

Circular reasoning works because circular reasoning works (that special issue on paraphyly)

(The following is the second part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

The first paper is titled EvolutionarySystematics and Paraphyly: Introduction, and was written by Tod Stuessy and Elvira Hörandl, the organisers of the original IBC symposium. It can be read not only as an introduction to the topic but also a kind of summary of the whole special issue, and thus it might potentially make more sense to discuss it after the others. Also, it is densely packed with a great variety of claims, generally without developing or supporting them, because that job is quite reasonably left to the individual contributions to the special issue. Still, I will follow the sequence of papers as presumably intended by the editors.

Unfortunately, where one can discuss the central argument of more focused papers, in this case due to its nature there is hardly any alternative to going through the piece claim by claim and rebutting them individually, which makes for a less pleasant reading experience.

Yay! A special issue all about paraphyly!

(The following is the first part of a series of posts on an Annals of the Missouri Botanical Garden special issue on "Evolutionary Systematics and Paraphyly". All posts in this series are tagged with "that special issue".)

In 2011, the International Botanic Congress, the largest meeting of plant scientists on the planet, and indeed so large a meeting that it is only held every six years or so, took place in Melbourne. Among the symposia organised at the IBC in that year there was one with the title “Evolutionary Systematics and Paraphyly”, chaired by some of the few botanists who still insist that paraphyletic supraspecific taxa should be accepted.

Sadly, I missed that symposium because I went to a more important parallel session. Recently, however, a special issue based on the symposium appeared in the Annals of the Missouri Botanical Garden. Time to blog about phylogenetic systematics again, it seems. My plan is to go through the articles one by one (with the exception of the last one, which for some unfathomable reason appears to be about Pandas and has nothing to do with classification; indeed one wonders whether they mixed up the journal in which that paper was supposed to appear). But before I start, I want to clear my throat, so to say.