Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Monday, 7 December 2009

Paraphyly Watch 4: Monoclady and Paraclady

ResearchBlogging.orgJust when you thought all possible abuses and misuses of paraphyly have been thoroughly exhausted, one totally mind-boggling and confused piece of writing appears in the Journal of Paraphyly Taxon. We refer to Taxonomy versus evolution by János Podani, a dainty ditty that transcends all boundaries of comprehension and ventures into the field of evolutionary science fiction.

The story so far...
    On the planet Zog, the Mayrian Monks enforce rigid elections that decide the fate of the foundations of science. One day new heretical “discoveries” of what are called ‘natural groups’ questions the validity of Reptiles - rulers of the land. The heretics have called them a group of ‘unrelated animals’ - nothing more than systematic bastards! The Mayr-Monks are never wrong and, science never gets in their way. A snap election is called, the ballot counted and science-democracy enforced. The vote was unanimous: 130 in favour - zero against. “Good to see science done” says one Monk to another. That night they all sleep peacefully with a clear conscious, awaiting morning when their sun will rotate around their flat earth once again.
The Mayrian Monks will do anything to protect paraphyletic groups. Rather than revise a taxonomic group, evolutionary taxonomists will dabble in systematics in order to change the foundations of classification. This is akin to the alcohol fueled idea of trying the change the laws of gravity in order to balance this year’s Christmas tree in the front sitting room. It doesn’t work. Neither does monoclady and paraclady. Oh dear, where does one start?
Let’s kick off with Podani’s arguement, namely:
    “... that there are four major aspects of taxonomic systems in which achievements of evolutionary biology are not recognized fully and properly, if evolution is considered at all” (Podani, 2009: 1049).
Podani does this by distinguishing diachronous and synchronous classifications (not to be confused with similar terms used in Ebach & Williams [2004] as Podani does). In Podani’s view a diachronous classification includes fossil organisms, which he equates with ‘ancestors’ and synchronous taxa that he describes as extant. Apparently, classifying fossils with extant taxa poses problems hence the need for both classifications. He goes on...
    “If we use a synchronous classification for extant organisms, we are concerned with the result of evolution, history is only relevant as long as common ancestry is to be detected, and an inclusive hierarchy is suitable to summarize diversity of life” (Podani, 2009: 1050).
and...
    “On the other hand, a diachronous classification cannot be Linnaean for two reasons: (1) units of classification and the groups change in time and, more importantly, (2) wide gaps necessary for separating supraspecific taxa are evolutionary absurdities in the spatio-temporal continuum of populations” (Podani, 2009: 1050).
Got it? Now, onto the next bit...
    “The only tool for representing the diachronous pattern of life adequately is the Darwinian phylogenetic tree, showing ancestor–descendant relationships between extinct and extant populations” (Podani, 2009: 1050-1051; original emphasis).
...so [drum roll]...
    “I suggest restricting the original definition of monophyly to phylogenetic trees, so that it is a diachronous phenomenon and can only be examined in a diachronous classification. For cladograms, I introduced the new term monoclady: a group is monocladistic if it includes all terminals of a given clade. This condition has to do with extant taxa and is particularly meaningful for a synchronous classification” (Podani, 2009: 1051; original emphasis).
...therefore...
    “Reptiles are most certainly para- phyletic because extinct ones include the ancestors of birds and mammals as well. Extant reptiles are paracladistic, since crocodiles are sister to birds rather than to other reptiles” (Podani, 2009: 1051).
...and to sum it all up...
    “If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic. Paraclady means that the group cannot be embedded into a monophyletic taxon, and it is therefore indication of paraphyly or even polyphyly in the corresponding diachronous classification. A Linnaean taxon, which is preferably synchronous as the above logic dictates, can only be monocladistic, paracladistic or polycladistic and the monophyly/paraphyly problem vanishes. Paraphyly, as understood earlier, may often be reflection of the disagreement of a diachronous classification with a synchronous analysis. Therefore, the central tenet of contemporary taxonomy is perhaps not about paraphyly and monophyly, but around the contrast between synchronous and diachronous classifications” (Podani, 2009: 1052).
In order to keep this argument short we will not discuss Podani’s bogus adventure into nomenclature, but start with his first and last points, namely, “... the central tenet of contemporary taxonomy is perhaps not about paraphyly and monophyly, but around the contrast between synchronous and diachronous classifications”. Is it? Taxonomy has always remained considerably neutral about how one groups extant and extinct taxa together, why then should there be two classifications? Because extinct taxa are more likely to be ‘ancestors’ and, genealogical relationships (as Podani correctly points out) make poor classification systems. So where does this leave taxonomy? Well, where it has always been - as a neutral way to classify taxa without needing to know who is ancestor to whom. The same is true for cladograms - extinct and extant taxa are placed at the terminals because there are related in some way. It appears that Podani has missed something here, such as the whole cladistic revolution from the 1960s to the 1980s. Cladograms remove the need for phylogenetic trees as all relationship can be shown equally. So both the diachronous and synchronous classification systems are utterly pointless as taxonomy remains neutral about ancestors and fossil taxa (they classify along with extant groups) and equally useless in systematics, as all taxa are treated equally. Podani’s rasion d'être for two classification systems is a vain attempt to preserve paraphyletic groups (number 2 for this year after Stuessy and Koenig [2009]).

Here is how it works. First debunk monophyly as irrelevant to classification by assigning them as problems found in phylogenetic trees. Since phylogenetic trees are diachronous and diachronous classifications “cannot be Linnaean” and, are therefore invalid. Clever. Now he introduces a new term monoclady and monocladistic, which means, “If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic” (Podani, 2009: 1052). There we have it. Monocladistic groups can be paraphyletic seen from a phylogenetic perspective. Get it?

Let’s put it another way. Take an existing term like monophyly and replace it with a similar term like monoclady (“includes all terminals of a given clade”), which of course does not change its overall meaning. Now dismiss monophyly as irrelevant to classification, but relevant to 19th century Haeckelian phylogenetics, hence radically changing not only its meaning but also its usage. Here comes the best bit - do the same to paraphyly. Replace its overall meaning with another term, like paraclady, and then dismiss paraphyly as irrelevant to classification. No problems here (as it is not relevant to classification). The coupe de grace is defining some forms of monoclady (formerly monophyly) as paraphyly! Wow, the sheer audacity!

Yes folks, I think we have a clear forerunner in the 2009 Pewter Leprechaun for the misuse and abuse of paraphyly.

As you read, judges are conferring in what is to be some pretty stiff competition. The results for the Winner of the 2009 Pewter Leprechaun will be announced very soon. Stay tuned!

References
Ebach, M.C. & Williams, D.M. (2004). Classification. Taxon 53: 791–794.
Podani, J. (2009). Taxonomy versus evolution Taxon (58), 1049-1053.
Stuessy, T.F. & König, C. (2009). Classification should not be constrained solely by branching topology in a cladistic context Taxon, 58, 347-348.

4 comments:

Christopher Taylor said...

Sorry, I'm afraid I'm not really getting what the proposed system is here (sounds like double-talk to me, but that may just be because I'm not of a philosophical bent). Is this a re-working of the "paraphyletic taxon X would not have been paraphyletic in the Permian" argument?

jp said...

To be fair… the above blog was fairly unfair and biased. The paper cited does NOT advocate the use of paraphyletic taxa at all, as suggested in the blog, and is not a Mayrian monk either. The paper starts from the MOST GENERAL definitions of monophyly and paraphyly, and then shows that these two relate to spaning trees, and not to Steiner trees, i.e. to phylogenetic trees rather than to cladograms. And then what follows is purely mathematics when one demarcates groups in these trees…And the blog is absolutely confused about monclady versus paraphyly, but again: “If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic” - for which recent gymnosperms and all those ever lived are well-known examples.
Of course, alternative definitions have been suggested for monophyly (started by Haeckel), which may end up with different outcomes, and everyone would be happy to see straight scientific argumentatitions or fair discussions… but no comments in such violent style, even in blogs. Nevertheless, if one wishes to use the style of this blog, a correct response reads like this:
„Taxonomy has always remained considerably neutral about how one groups extant and extinct taxa together…”
Oh well, Linnaeus, for example, classified fossils among rocks…But this is just the begining…
„The same is true for cladograms - extinct and extant taxa are placed at the terminals because there are related in some way.”
Got it? „Related”, well… Now, get onto the next bit...
„Cladograms remove the need for phylogenetic trees as all relationship (sic) can be shown equally.”
Now, this is very very nice masterpiece… I would say, clever. A cladogram with all living and extinct organisms as terminal nodes shows all „relationships”, and does better than phylogenetic trees? Oh, if Darwin could read this…
and so on…
bye for now

Milka said...

I recently came accross your blog and have been reading along. I thought I would leave my first comment. I dont know what to say except that I have enjoyed reading. Nice blog. I will keep visiting this blog very often.

Alena

http://smallpet.info

Efraín De Luna said...

You should see the exchanges at the IAB blog about this post and Podani´s paper! Some bryologists, not all, like that paper http://internationalassociationofbryologists.blogspot.com/2009/12/re-iab-blog-new-comment-on-bryonet-from_19.html
Other posts are under label "monophyly".