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).

Thursday, 11 June 2009

Paraphyly Watch 3: Transitional Fossils, Microbes & Patrocladistics

ResearchBlogging.orgIt looks like there is some pretty stiff competition for the 2009 Pewter Leprechaun. This month alone we have: an article showing us the virtues of transitional fossils (Prothero, 2009); a plea that protists are microbes too (Caron et al. 2009) and a defense of patrocladistics (Stuessy & König, 2009).

The Wonders of Transitional Fossils

Evolutionary Transitions in the Fossil Record of Terrestrial Hoofed Mammals by Donald R. Prothero is a somewhat perplexing article. It attempts to identify "transitional fossils" as evidence for evolution and ancestors. Not exactly 'new' or 'exciting' by any standard, but it is why and for whom the article is written - Evolution: Education & Outreach. Not exactly the best way to promote evolution to an audience of science school teachers, especially when you have this to say:
    "Creationists often scoff at the notion that there are fossils that show how the giraffes evolved, but they could not be more mistaken […] However, Nikos Solounias (2007, personal communication) is currently publishing a description of a new fossil of the giraffid Bohlinia that preserves a neck that is intermediate in length between Giraffa and the okapi. Thus, we do know how the giraffe got its long neck, and we have the transitional fossils to show how and when it occurred! Once again, the fossil record has provided a specimen whose very existence the creationists have long denied" (Prothero, 2009:297-298).
And this:
    "Creationists attempt to discredit these examples by saying that our switch from an orthogenetic linear model of the 1920s to the modern bushy branching pattern somehow denies that this fossil evidence does show change through time, but this only reveals the creationists’ lack of training in anatomy and paleontology" (Prothero, 2009:301).
Oh, and this:
    "Arguments such as this reveal the dogmatism and complete intellectual and scientific bankruptcy of creationists" (Prothero, 2009:301).
We would like to start with this disclaimer - We are not, never have been and never intend to be creationists. We do not defend creationist dogma or any other idea disguised as creationism (i.e., Intelligent Design). We do, however, point out where evolutionary biologists make unwitting mistakes, which may fuel further creationist attacks. Creationists are getting cleverer and are starting to see through arguments supporting paraphyly (i.e., ancestors, transitional fossils, transformations etc.). We warn our fellow evolutionist colleagues not to fall into this trap. We also urge them never to intellectualize the arguments of creationists by entertaining them at any level (i.e., defending paraphyly). Doing so makes matters worse, as we shall show using the case of Prothero (2009).

Discovering "that preserves a neck that is intermediate in length between Giraffa and the okapi" is not evidence for a transition between a short and a long neck. Firstly, we have no evidence to suggest that either taxon is ancestral to the other, thus leaving the "short neck – medium sized neck – long neck" a hypothetical transformation that is as equally valid as "long neck – medium sized neck – short neck". Prothero (2009) is using a very old paleontological argument that was rejected in systematics many years ago during the cladistic revolution. No matter how well we understand our group, its taxonomy, paleontology and anatomy, we can never know if one taxon is ancestral to another. Identifying an ancestor is purely speculative and subjective and not empirical in any sense. So, sadly for Prothero (2009), the fossil is merely, well, a … fossil. Not "transitional fossils to show how and when [evolution] occurred!"

Another example is the discovery of a four legged sirenian:
    "Known as Pezosiren portelli ('Portell’s walking sirenian'), it has the characteristic skull and teeth of a sirenian and even the dense bones of the ribs so typical of the group. Yet this creature had four perfectly good legs complete with terrestrial hands and feet, not flippers as seen in the living sirenians [...]One could not ask for a better example of a transitional fossil! It closely parallels the intermediate pattern of locomotion seen in walking whales such as Ambulocetus (Thewissen, this volume). When creationists have addressed this discovery at all (on their websites; none of their books mention it yet), they show their complete ignorance of the basics of anatomy and paleontology. Their argument boils down to 'if it has four legs and feet, it can’t be a sirenian,' even though the details of the teeth, skull, and even the ribs share the specializations unique to the entire order Sirenia" (Prothero, 2009:301).
The creationists are of course wrong. The four-legged Pezosiren portelli is a sirenian. But the presence of legs instead of flippers doesn’t mean it's a transitional fossil. For instance, the number of possible evolutionary scenarios is endless - sirenians may have come back to land and then returned to water. The discovery of Pezosiren portelli does not constitute the discovery of a transitional fossil and ancestor.

The danger of inventing transitional fossils in this way degrades systematics and makes it far easier for creationists to prey on evolutionary biologists. We have all the evidence we would ever need to state that sirenians are an evolutionary group. Namely monophyly:
    "In the past decade, the monophyly of the Tethytheria was also confirmed by later molecular analysis" Prothero (2009:300).
The article by Prothero (2009) would benefit the readers of Evolution: Education & Outreach (e.g., science teachers) if it actually listed the evidence for evolution, not evolutionary scenarios that are immune to testing.

We nominate Prothero (2009) for the 2009 Pewter Leprechaun for the abuse of paraphyly by unnecessarily using transitional fossils to support arguments for evolution when other sufficient evidence exists (i.e., homology and monophyly).

A Plea: Protists are microbes too!

Not so much a Paraphyly Watch but more of a 'non-group quest', Caron et al. (2009) make the request that "Protists are microbes too". Now, one might wonder what a microbe is. Caron et al. (2009) provide some insight:
    "Strictly speaking, microorganisms [microbes] are defined by their size; that is, organisms that are smaller than can be resolved by the naked eye ..." (Caron et al., 2009:6).
    "If we define microbes by cell size, then most protists qualify as microbes" (Caron et al., 2009:6).
They provide a figure that plots approximate size range of certain organisms against their membership of a particular supergroup, with a mark at about the size visible to the human eye. What they mean by this is that each organism plotted on the table is a representative of a supergroup that is suspected to be monophyletic. There is no correlation between size and supergroup. So clearly they recognize that (1) size does not mark out any natural group at all; (2) that supergroups (putatively monophyletic) groups are independent of any possible group called or assembled under the name of microbe. It’s a non-group, para- or more likely, polyphyletic.

Of course, they never get around to defining a protist – because they are undefinable as well – and paraphyletic (or even polyphyletic). Given this logic, we ask "Why stop there?" Let's add mites, fleas and tardigrades too!

In defense of Patrocladistics

Oh dear:
    "Rigid cladistic viewpoints in classification face a serious difficulty in that they disregard evolutionary data (Stuessy & König, 2009:347).
Welcome to evolutionary taxonomy – a field where genealogies are classifications and classifications are genealogies. In the evolutionary taxonomic cosmos cladograms are best guess estimates for phylogenies and nodes ancestors. A branching bifurcating tree represents cladogenesis and anagenesis is totally ignored. Here monophyly is paraphyly and parapyhyly is monophyly:
    "For us, paraphyly is a type of monophyly (groups with a single common ancestor […]), and this is acceptable in classification depending upon the degree of divergence of the derivative group from its progenitor" (Stuessy & König, 2009:347).
    "Cladistics has provided us with significant quantitative avenues to reconstructing branching patterns of phylogeny, but quantitative evolutionary approaches offer classification with the highest information content and predictive value for society. Self-limiting only to branching patterns, however easy it may be, is not the solution for evolutionarily based biological classification" (Stuessy & König, 2009:348).
There is not much to say about patrocladistics other than mass delusion on part of evolutionary taxonomists. They don't seem to understand that evolution and classification are separate entities and that only the latter is the key to the former. To them cladistics rejects evolution entirely and taxonomy should use all available evolutionary evidence. Thus, the creation of a super-duper form of cladistics:
    "We propose here a method of incorporating patristic distances, or evolutionary divergence within lineages, into an explicit method of producing a branching diagram (called a patrocladistic tree or patrocladogram) […]morphological divergence). This should eliminate, or at least significantly reduce, the controversy over how to deal with paraphyletic groups. Discussion will rather shift to the characters and states involved with patristic distance and their relative weighting against synapomorphic character states. Such discussions on which" (Stuessy & König, 2008:595).
We don’t know whether to cry to bang our heads against the wall. We blame Ashlock (1971) (to whom most evolutionary taxonomists refer) as the Root of all Evil Blunders in systematics - but we'll leave that for another post.

Our money is on Stuessy & König (2009) as winners of the 2009 Pewter Leprechaun (at least by 2 lengths). We hereby nominate Stuessy & König (2009) for the coveted prize for the misuse of paraphyly by confusing it as monophyly or meaningful.


Ashlock, P.D. (1971). Monophyly and associated terms. Systematic Zoology 20:63-69.
Caron, D., Worden, A., Countway, P., Demir, E., & Heidelberg, K. (2008). Protists are microbes too: a perspective The ISME Journal, 3 (1), 4-12 DOI: 10.1038/ismej.2008.101
Prothero, D. (2009). Evolutionary Transitions in the Fossil Record of Terrestrial Hoofed Mammals Evolution: Education and Outreach, 2 (2), 289-302 DOI: 10.1007/s12052-009-0136-1
Stuessy, T.F. & König, C. (2009). Classification should not be constrained solely by branching topology in a cladistic context Taxon, 58, 347-348


AK said...

IMO you're being a little too rigid here. I just discovered your campaign when I saw your post on Research Blogging, but I've read all the previous posts, before creating my response.

I've posted my response on my own blog, where you're welcome to comment, or answer here.

Just to summarize, however, IMO the study of the evolutionary process can sometimes make very good use of paraphyletic groups.

David Marjanović said...

"We propose here a method of incorporating patristic distances, or evolutionary divergence within lineages, into an explicit method of producing a branching diagram (called a patrocladistic tree or patrocladogram) […]morphological divergence). […]"

So... they take a cladogram, get the branch lengths from it, somehow add the branch lengths to the data matrix, run this logically circular construct through a cladistic analysis again, and call the result a "patrocladogram"? Have I understood that right?

(BTW, sorry for still not having replied to your responses to my comment a few threads and weeks ago. I'll get to that on the weekend.)

theshortearedowl said...

I've never been comfortable with the idea of 'transitional' fossils anyway - surely everything is transitional between something and something else? (unless it's the last one!)