Paraphyly Watch 4: Monoclady and Paraclady

Just 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.

Paraphyly Watch 2: Paraphyly & the Catalogue of Life

A recent draft discussion document, Towards a management hierarchy (classification) for the Catalogue of Life (Gordon, 2009), contains a discussion on paraphyly:

"It is not the purpose here to summarise the various viewpoints but a need to consider what we want from a classification is inescapable. Cavalier-Smith (1998) has given a useful discussion. One bone of contention in recent decades has been whether or not to allow the use of paraphyletic taxa in classification. A paraphyletic taxon is a monophyletic group that does not contain all the descendents (derivatives) of that group. One of the best-known examples is that of Reptilia, nominally a class of Chordata. Since it is agreed that birds (nominally class Aves) have a reptilian ancestor, and Reptilia by convention does not include Aves, then Reptilia is a paraphyletic group. But paraphyletic groups potentially abound at all levels of the taxonomic hierarchy. Indeed, there are many thousands of taxa where it is not yet known if they are paraphyletic (including some of the descendants) or holophyletic (including all of the descendants). Cavalier-Smith's classical understanding of monophyly is pragmatic, including both paraphyletic and holophyletic groups. On this understanding, Reptilia + Aves [+ Mammalia] is holophyletic whereas Reptilia alone is merely paraphyletic; either way, both are monophyletic" (Gordon, 2009, Online).

Note the definition of paraphyly: "A paraphyletic taxon is a monophyletic group that does not contain all the descendents (derivatives) of that group". This is of course an incorrect definition of paraphyly. Moreover, it uses monophyly to validate paraphyly as a 'natural' group. Paraphyly is an artificial assemblage of unrelated taxa. Dubious definitions of paraphyly fall under the category of misuse, thus making Gordon (2009) a contender for the coveted Pewter Leprechaun. But Gordon (2009) goes further: "Since it is agreed that birds (nominally class Aves) have a reptilian ancestor …" Is it? If reptiles are a group of unrelated taxa, that is some 'reptiles' are more closely related to mammals than they are to other reptiles, then it would mean birds would have multiple ancestors and therefore multiple origins. Gordon (2009) does not stop there: "Cavalier-Smith’s classical understanding of monophyly is pragmatic, including both paraphyletic and holophyletic groups. On this understanding, Reptilia + Aves [+ Mammalia] is holophyletic whereas Reptilia alone is merely paraphyletic; either way, both are monophyletic." This is a case of abuse. Reptila cannot be automatically assumed to be monophyletic just because grouping them with mammals and birds results in a monophyletic group.

The draft manuscript is a typical protest for paraphyletic groups commonly made by evolutionary taxonomists in places like Taxon or Taxacom. The usual comments are made such as plea for 'traditional Darwinian classification' and confusing cladistics with phylogenetic classification. I do hope that the problem of paraphyly is not over-looked in the final manuscript. Who am I kidding? Of course it will!

Malte C. Ebach

References
Gordon DP (2009). Towards a management hierarchy (classification) for the Catalogue of Life: Draft Discussion Document. In Species 2000 & ITIS Catalogue of Life: 2009 Annual Checklist (Bisby FA, Roskov YR, Orrell TM, Nicolson D, Paglinawan LE, Bailly N, Kirk PM, Bourgoin T, Baillargeon G., eds). CD-ROM; Species 2000: Reading, UK.

Myths that Evolutionary Taxonomists live by

Confused evolutionary taxonomists have once again made a stand in the pages of Taxon. The editorial by Brickell et al. (2008) represents a vote of no confidence in favour of paraphyletic groups - as if democracy in science has (or ever had) any valid scientific or empirical merit. This time the confusion stems from

"Recent developments in taxonomic theory have resulted in the production of classifications of the Flowering Plants that are causing concern to all involved in horticulture — gardeners (both amateur and professional), nurserymen, landscape architects, foresters, designers, conservationists, and journalists, as well as to botanists engaged in many different, non-taxonomic disciplines and to other users of plant names generally" (Brickell et al., 2008:1047).

One wonders what those nasty molecular phylocodists and monophyly-peddling robbers of horticultural dignity are up to? Perhaps plotting horrid phenetic-cladogram-trees?

They certainly are a confused mob as the above mockery demonstrates. One way out of this wet paper bag is to see the world from a evolutionary point-of-view. Artificial classifications, which are useful in identifying plants, for example, are not necessarily evolutionary (in the sense of monophyletic). Some may turn out to be, but only empiricism will provide us with the necessary evidence. That is we need cladistic methods to test taxonomic claims of relatedness (i.e., monophyly). Evidence and empiricism, however, appear to be of no use to Brickell et al.(2008).

"Cases such as these (and there are more that could be quoted) have arisen from a fundamentalist approach to cladistic methodology, which requires that a classification should not include paraphyletic taxa"(Brickell et al., 2008:1047).

I tire of saying this: Paraphyletic taxa are not of any use. They do not represent natural classifications. They are not a result of a common shared history. Paraphyletic groups are not anything other than names, just as 'leprechauns', 'unicorns' and 'griffins' are only names. Why then do horticulturalists and evolutionary taxonomists want them in their classifications?

This is because paraphyly is not a phylogenetic problem (phylogenies are essentially monophyletic - don't get confused with genealogies, which have nothing to do with classification). Paraphyly is taxonomic problem that evolutionary taxonomists refuse to face. If a group is paraphyletic, it means it has failed an empirical test for natural grouping. It needs to be revised. Revising groups is what taxonomists do best. Instead of embracing cladistics as a valuable tool, evolutionary taxonomists like Brickell et al. (2008) dismiss it because their favorite taxonomic groups under threat from revision. Acknowledging that one's group is paraphyletic and therefore requiring revision does not make you a bad taxonomist. Keeping non-existent groups however is. I don't want to say that Brickell et al. (2008) are 'bad taxonomists'. They a bunch of misguided evolutionary taxonomists who are confusing different things, namely artificial and natural classifications - an on-going problem since the 18th century. This confusion has led to several 'myths that evolutionary taxonomists live by'. I use Brickell et al. (2008) as an example.

Myth 1: If it ain't broke, don't fix it

One common misconception is that of historical 'significance' or 'pragmatism' in science. For example, 'Reptiles' is a wonderful term and describes all manner of organisms such as fire-breathing dragons, sea serpents and the Sea Devils from Dr. Who. (Remember them?) This does not mean that the Reptilia are immune to scrutiny or empiricism - in fact they're not. The same is true for taxa within the angiosperms

"We, as horticulturists and horticultural taxonomists, wish to express our strong support for these pragmatic views, which will encourage the retention of familiar and widely used taxa [e.g., Dionysia, Dodecatheon, Soldanella, Omphalogramma, and Cortusa] which are distinctive and historically important" (Brickell et al., 2008:1047).

I empathize. Good names that are linked to poorly defined groups (which, incidentally is what makes them paraphyletic) sucks. But that's life ... sorry, that's systematics.

Myth 2: Taxonomy needs to be 'stable'

There is no such thing as a completely stable classification of living things. This is not because everything is fluid and 'moving' and 'unclassifiable'. As new evidence comes to light (e.g., molecular data), so do new discoveries. But Brickell et al. (2008) beg to differ

"We are not against taxonomic change, which will continue to be a standard outcome of taxonomic research, but insist that horticulture needs a stable (though not static) classification and nomenclature that can be understood and applied effectively by horticulturists (and others) who exhibit a very wide range of levels of taxonomic sophistication.

Clearly they are against taxonomic change as that is what paraphyletic groups inevitably lead to - taxonomic change.

Myth 3: The needs of end-users are important

Let's face it, the end users of taxonomy are mostly other taxonomists. Regardless of the descriptions and keys out there, trilobite collectors and purveyors of fossils for instance, still insist on calling any large brimmed harpetid from the Devonian rocks of Morocco Scotoharpes. (The aforementioned genus does not occur in Morocco or in the Devonian). The concerns of end users is quite topical at the moment and will not be discussed in depth here (see Wheeler et al. 2004). The fact of the matter is that end users have to share the burden of changing taxonomies. This may make horticulture and conservation for example harder to do, but many are attempting to reduce this burden through employing new electronic media, which has created new emerging fields such as biodiversity informatics and cybertaxonomy.

Myth 4: Molecular systematists and cladists are all phylocodists

This is a myth that has been exacerbated by Brummitt (2006, 2008). Not all molecular systematists and cladists agree with the phylocode. In fact some of the most ardent critics of the Phylocode are cladists who use molecular data (e.g., see Nixon et al. 2003). Moreover, supporting monophyletic taxa does not automatically make you a Phylocodist or anti-Linnean. Here is an example from (Brickell et al., 2008:1047)

"(cf. Brummitt in a note to a colleague: ‘By any logical consideration either one has a monophyletic system with an infinite number of nodes but no ranks, for which the PhyloCode is designed, or you have the Linnaean system with ranks at very few levels, and paraphyletic taxa’".

Classifications are not divided into 'the Phylocode' versus 'Linnaean taxonomy'. This dichotomy is false. The Linnaean system of taxonomy remains silent about paraphyly or monophyly. Biological classification consist of artificial and natural systems, the modern Linnaean System belonging to the later. As taxonomists, we aim to find natural groups (a.k.a 'monophyletic groups') in our Linnaean System. But paraphyletic groups, like Linnaeus sexual system, are artificial. They may be useful in identifying organisms, but they do not reflect natural evolutionary groups and should be exempt from our classifications. Brickell et al. (2008) are misguided and confused if they are to believe that paraphyletic groups are 'natural' or even evolutionary in anyway.

Myth 5: What does the Molecular data mean?

There are many ways to tell someone to p*ss off and this is a beaut:

"In saying this we do not wish to imply that phylogenetic studies are unimportant or uninteresting; only that the purpose for which they are produced is not applicable to horticultural needs and practices. (Brickell et al., 2008:1047-1048)"

I agree. Molecular trees (which is what Brickell et al., 2008 are referring to above) do not have any characters listed at their nodes. If horticulturalists are to follow our lead and adopt new groups based on molecular data, then show us the characters that support it as a monophyletic group. If the group is paraphyletic then do the revisionary taxonomy. There is however a catch. Molecular systematists do not necessarily do all the work. Saying that something is paraphyletic and in need of revision without any morphological evidence is hard for any taxonomist or horticulturalist to swallow. I think that Brickell et al.(2008) are on to something here and it is well worth pursuing. Consider this myth busted.

Unfortunately Brickell et al. (2008) do not qualify for this year's Pewter Leprechaun although their attempts at misusing paraphyly have reached a particular zenith.

References
Brickell, C.D., Crawley, M., Cullen, J., Frodin, D.G., Gardner, M., Grey-Wilson, C., Hillier, J., Knees, S., Lancaster, R., Mathew, B.F., Matthews, V.A., Miller, T., Noltie, H.F., Norton, S., Oakeley, H.J., Richards, J., Woodhead, J. (2008). Do the views of users of taxonomic output count for anything? Taxon 57:1047–1048. Nixon, K. C., J. M. Carpenter, and D. W. Stevenson. 2003. The PhyloCode is fatally flawed, and the "Linnaean" system can easily be fixed. Bot. Rev. 69: 111–120. Wheeler, Q. D., Raven, P. H., Wilson, E. O. 2004. Taxonomy: Impediment or expedient? Science 305: 285.

The Evolution Slogan

The term "evolution" can be used recklessly in a variety of ways: "If evolution was outlawed, only outlaws will evolve", "Paraphyly is evolution all the way" (Brummitt, 2002:40) and most recently, "Because we understand how evolution happens, we can also guess where it will go next" (Jones, 2008; see also John Wilkins's post). The two main points of contention, highlighted in the latter statement by Steve Jones, are our "understanding" of evolution and our ability to "guess".

The late Colin Patterson, ichthyologist at the then British Museum, Natural History in London, gave a presentation that questioned the term. The talk, titled "Systematics and Creationism", was given at American Museum of Natural History (Patterson, 2002) in November 1981. There Patterson noted:

"...the theory is evolutionary theory, descent with modification" (Patterson, 2002:23; see also Martin Brazeau's post)

Combined with the above slogans we may suggest that 'evolution' is: a process of descent with modification that results in paraphyly problem arises. How do we see this process?

In order to know we need to be able to observe or measure. Paraphyly, for instance, cannot be observed. It exists only when an artificially delineated taxonomic group is discovered to be monophyletic (homologous) - like 'invertebrates' or 'aliens'. Descent with modification is also difficult to see in action. Although we can see genealogy and ontogeny, they do not constitute 'descent with modification', at least not in the way Jones uses the term.

What systematists and biogeographers know is that evidence for evolution is based on retrodictions - that is past 'predictions' or patterns. These patterns are homologies or relationships - evidence for evolution. Our task as systematists is to discover whether our groups are a result of evolution, rather than poor taxonomy. Evolution should not be taken for granted - just because we know it exists doesn't mean we should stop looking. Reptiles, for example, are not an evolutionary group. They are a poorly defined taxonomic group like 'insectivores' and 'creepy, crawling things'. Discovering that taxa within the reptilia share closer relationships with taxa in mammalian than with any other taxon does not validate reptiles as an evolutionary group. The task of herpetologists is find those evolutionary groups and, not to defend existing names that have no evolutionary significance. Patterns, homologies, relationship and monophyletic groups are all the same thing: evidence for evolution.

Now we return to Jones. He, like many other evolutionary biologists, has committed a classic error - assuming that life progresses from an incomplete to complete phase: also known as 'primitive to derived'. A typical example is the 'primitiveness' or 'plesiomomorphy' of Archaeopteryx lithographica. The half bird-half reptile is always considered to be transition - fossilized in the middle of evolving. Like all living things dead or alive, Archaeopteryx is perfect in its own right. It has no hidden agenda, no purpose other than to be Archaeopteryx. If we were to assume, unwittingly and in hindsight, that it was primitive, then we are advocating some purpose or teleology, namely that Archaeopteryx was aiming to become a bird. This sort of thinking gives evolution a bad reputation and opens it up to attack from protagonists of anti-science. The logic behind it does not work. Let us assume for the moment that we could go back in time, back when Archaeopteryx was alive. We would assume, that this is a highly evolved 'reptile', a derived form. See the problem? Archaeopteryx is both derived and primitive at the same time in form and space but not in geological time. The whole 'primitive – derived' argument is based stratigraphic sequence and not evolution (homology).

To counter Jones's argument - we are complete, so is Archaeopteryx and all other life that has ever existed and will ever exist on this planet. What does this completeness say about evolution? Absolutely nothing at all. Instead it tells us of a desire for explanation.

We may think 'nothing in biology makes sense except in the light of evolution' (Dobzhansky, 1973), but without a doubt, evolution only makes sense in the light of homology. Biological classification provides us with the tools to discover relationships and a way to understand the evolution of life. Without it we are just telling never-ending stories. I am sure that in 200 millions years time, an octopod biologist, will wonder how something as incomplete and primitive as Homo sapiens lived for as long as it did.

References

Brummitt, R. K. 2002. How to chop up a tree. Taxon 51: 1-41.
Dobzhansky, T. 1973. Nothing in Biology Makes Sense. Except in the Light of Evolution. The American Biology. Teacher, 35:125-129.
Jones, S. 2008. Evolution is complete: so where do we go from here? Daily Telegraph Online, http://www.telegraph.co.uk/earth/main.jhtml?xml=/earth/2008/10/07/scievolution107.xml
Patterson, C. 2002. Evolutionism and creationism. The Linnean 18: 15-33.