Phylogeology – A New Revolution in Phylogenetics

From the Wollongong Herald

Evolutionary biologists were stunned this week by the news of Geological Phylogenetics. "Genetics is dead" says geologist Prof. Trevor Bruce of the University of Ulladulla, Australia. For 20 years molecular DNA has changed the way biologists do phylogenetics. Geological Phylogenetics, or Phylogeology, proposes to dispense with biological data all together. Prof. Bruce explains, "Molecular systematics has removed any notion of morphology, anatomy and taxonomy. We intend to get rid of molecules, making phylogenetics essentially free of any biological data". The benefits of phylogeology are that only atoms will be analyzed. "All you need is a very large industrial-strength food processor and a mass spectrometer". Prof Bruce's team has successfully pureed an array of organisms including two pot plants, a goldfish and Dr. Hall's cat. "She wasn't too happy about it, so we made her first author" says Prof. Bruce. "So far we have analyzed percentages of 30 common elements including carbon, calcium iron and copper". And success! Already Prof. Bruce's team has the data for most common household pets and their relationships. "It's simple" explains Dr. Hall, "a dog and a cat will have a similar atomic make-up, just like two similar rocks. As genetics has brought its methods and theory into phylogenetics, we bring geological techniques. Pureeing and 'mass-specing' critters are one of them".

But phylogeology has its critics. Molecular systematists have dismissed Dr Hall's contribution. "DNA and molecular data is the basic unit of heredity. Nothing can replace it" say Drs Goodray and Frat. "Rubbish!" retorts Prof. Bruce, "molecular data is fraught with paralogy, xenology and dodgy alignment. They may be dealing with a 'basic unit of heredity', but we are dealing with the basic unit of all matter". Already new applications have been proposed. "Forget DNA Barcoding, now we have 'Tricording' – a way to measure all matter within an organism" says Dr. Hall. The proposal has lead large funding bodies to drop proposals for DNA research. The NSF, NERC and other national grants are excited by phylogeology. "Finally we can get rid of that expensive out-of-date DNA mumbo-jumbo. Now we can categorize phylogenetics as organic chemistry" says Dr. Komby of the Research Funding Board. "Imagine how much money we'll save, not sequencing data, getting rid of the Tree of Life (AToL) and all other biological systematic projects. This heralds a new age in evolution".

'Darwin Year', marked by the 200th anniversary of the father of evolution, represents a new era of development - from the biological toward the physical sciences. "Biology is simply stamp-collecting" remarks Prof. Bruce, "we're better off working out how the origin of the cosmos has shaped life on Earth". Even creationists have responded to Prof. Bruce's call. "This is the end of evolution" states Mark McCall, Director of the DIY Creationist Center, Kansas, "This new development disproves life altogether". Phylogeology has already made an impact on financiers who understand its cost-effective nature. Investors, like Arnold Grady, are beaming, "Considering that the technology behind food processors is rapidly evolving, we could puree, say a dog, in five seconds and have it mass-speced in ten. I'd buy into that".

Biology may be on its last legs, but what of the bird-watcher or fish-fancier? We ask amateur fish breeder Allan Cement, "They are fish, not atoms! Can't scientists just study them?"

Malte C. Ebach

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 Culture of Molecular Systematics

The longer one reads papers on molecular systematics, and speaks to molecular systematists, the more one is convinced that there is a prevalent molecular systematic culture. What makes it so convincing is the consistency of language, attitude and ignorance that is standard worldwide. What then is this molecular systematic culture?

Consider this response to a recently rejected manuscript:

"This manuscript seems inappropriate for [journal name removed]. Its purpose is to question the foundation of molecular phylogenetics, a well-established field. Moreover, the definitions of phylogeny, genealogy, cladogram are non-standard, and poorly articulated. I doubt that the readership of [journal name removed] would find the arguments presented particularly compelling. It is well known that DNA is the material of inheritance, and that morphological homoplasy is common. Nucleotide sequence similarity due to homoplasy is detectable using standard cladistic methods. No new data are presented, and most of the arguments rehash discussions from 20 to 30 years ago".

The response is an exemplary in its language, attitude and ignorance of comparative biology, that is taxonomy, systematics and biogeography.

Let us start with the first point, namely, attitude:

"Its purpose is to question the foundation of molecular phylogenetics, a well-established field".

Molecular Systematics, like any other field in science, is open to questioning. It is not immune like faith or religion as some, I suspect, believe. Moreover, it is not "well established", that is based on a sound foundation. There is little discussion about the foundations of molecular systematics, which the next comment reveals, namely:

"the definitions of phylogeny, genealogy, cladogram are non-standard, and poorly articulated".

These "non-standard" definitions are presented below:

Homologies are the only evidence for relationship; A molecular tree based on the relationships of taxa at the terminal branches is not a genealogy, but a cladogram. A cladogram however can be tested and represents all possible relationships in a taxon

One might ask, "Where is homology in molecular systematics?" The question of homology has been raging in morphological systematics for almost 300 years. In molecular systematics it is simply ignored. I ask what are the foundations of molecular systematics? What makes it so well established? Why is it one of the few fields in science where its foundations are rarely discussed? These questions make sense in the light of molecular systematic culture.

Molecular systematics also uses a convincing language. Stating that "DNA is the material of inheritance" creates an air of reverence that defies questioning. In fact it is a diversion. We are the material of inheritance. DNA is just part of it. The above statement is reductive, that is to say, it says that only our smallest 'bits' are relevant. We may take that statement further and say that 'Morphology is simply an expression of DNA', or take it one step further and state 'DNA tells us everything about genealogy and phylogentics, morphology is irrelevant, after all morphological homoplasy is common'. Language can be used in a deceptive way as the above example demonstrates.

Ignorance is another part of the molecular systematic culture. Consider for instance this statement:

"Nucleotide sequence similarity due to homoplasy is detectable using standard cladistic methods".

This conflates a few important points. Firstly homoplasy, that is, the "correspondence between parts or organs acquired as the result of parallel evolution or convergence" (Merriam-Webster's Dictionary Online), is not exactly 'detectable' in cladistic analysis. It causes characters to conflict resulting in polytomies, that is the absence of pattern, and therefore, of information. Cladistic analysis is there to find patterns, not uncover homoplasy.

Ignorance of history is another vital part of the molecular systematic culture, for instance:

"No new data are presented, and most of the arguments rehash discussions from 20 to 30 years ago".

We have addressed this point in an earlier post. No matter how old an argument or discussion is, the points made may still be relevant today. In the case of the above comment, the discussions of yesteryear still have not concluded. The discussions were replaced by a thirst for technology. Molecular systematics is enslaved in a technological culture. The algorithms or black boxes determine which phylogeny is best. The question of whether it is really homologous is never discussed. The foundations of molecular systematics lies in its applications, literally the programs made to run molecular sequences. We ask, is this a science that is based on solid foundations - a "well established field"?

The Problem of Similarity

Systematics and Biogeography has a problem: similarity. Ever since Goethe, naturalists and biologists have been rejecting similarity. It is the foundation of artificial classifications, non-evolutionary groupings and the basis for many arguments against evolution (i.e., homology).

Similarity implies that organisms are similar and not the same, that is it remains silent about sameness. The difference between being similar and the same is astronomical. Any two things in the universe can be similar. It is not a discovery. It demands no explanation. It is a means unto itself. However, when two things are discovered to be the same, they require explanation. This is when the study of evolution begins. By denying sameness -- or ignoring it -- we remain in the realm of artificial classification.

So why, then, is similarity so popular? All methods in molecular systematics use "similarity methods", herein phenetics, in order to measure nothing more than similarity. No evolution is (or can be) discovered, nor even touched upon. Molecular trees are simply meaningless in the context of evolution. They tell us nothing about sameness and therefore demand no explanation whatsoever. Regardless of this fact, all molecular systematists seem to explain similarity as if it means sameness. A molecular tree is generated and not discovered. They are means unto themselves. The gargantuan task of sequencing, aligning and building trees to find similarity ends with nothing at all. We are by no means poo-pooing similarity methods (phenetics).

Similarity methods are vital for understanding in non-evolutionary fields, such as geology. The chemical composition of rock is important for classification and identification. The same is true for biological keys and other artificial classifications. They helps us identify organisms based on their characteristics. The key will still work if the characters are homologous, not homologous or a mixture of both. Similarity will never be able to show which is which. Phenetics is useful outside of systematics and biogeography and evolutionary biology as its popularity shows. But popularity alone will not validate phenetics, or any similarity, in evolutionary biology.

What do we do with all the data, the matrices and the trees, produced by phenetics? We hope that their owners have fluked it - actually found a meaningful evolutionary, that is a monophyletic group. The sad news is that they'll never know.

Of course, molecular data have meaning and we should not be understood as attempting to trash molecular systematics. We simply feel they have been sold short. Maximum likelihood, parsimony optimization, and so on, are all kinds of phenetics: they are similarity methods. They are useless in the pursuit of evolutionary patterns, namely homology and monophyly. Molecular systematists need to stand up and shake loose the shackles of similarity, realize that their data and their methods are two separate issues and question those that wrongly promote similarity methods as "evolutionary".