Willi Hennig (1913 - 1976)

The great entomologist Willi Hennig (1913—1976), founder of ‘Phylogenetic Systematics’, was born on this day. Had he lived, he’d be 98.

Australian Postgraduate Award in Biogeography Available at UNSW

An Australian Postgraduate Award (APA) is available for a PhD in the Biogeography Lab of Dr Malte Ebach at the School of Biological, Earth and Environmental Sciences, University of New South Wales. The Biogeography Lab investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification over time. We seek a highly motivated student with a good honours or Masters degree in biology/ evolutionary biology or geology/palaeontology to choose from two projects:

1. Evolution and biogeography of water-bugs of Eastern Australasia

This project, in collaboration with Professor Gerry Cassis (UNSW), examines the morphological and molecular systematic relationships of selected endemic taxa of water-bugs (Gerromorpha and Nepomorpha) in Australasia and the relationships between the biotic areas they inhabit. The broader project investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification. Requirements: Interest in evolutionary biology, taxonomy, biogeography, field work and natural history. Experience in either systematics, biogeography and molecular techniques would be an advantage.

2. Palaeozoic biogeography and trilobite evolution

This project, in collaboration with Dr John Paterson (UNE), investigates the systematic biology of Carboniferous trilobites (Proetida) and their evolutionary relationships in order to infer palaeogeographic and tectonic reconstructions. The broader project investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification.

Requirements: Interest in palaeobiology, palaeobiogeography, field work and natural history. Experience in either sedimentology, biostratigraphy and taxonomy would be desirable.

Please note that applicants must be a citizen or permanent resident of Australia.

Please direct all enquiries and applications to Dr Malte Ebach (mcebach@gmail.com).

Systematics and Biogeography: Cladistics and Vicariance Online!

Every now and then a scientific discipline undergoes a revolution, an episode that changes the way a subject is perceived, the way it is understood and undertaken – a new vision emerges that prevents a return to the subject matter as it was before, a paradigm change, some genuine progress. In the last century, there was a revolution in phylogenetics and systematics that began with the work of entomologist Willi Hennig (1950, 1966) and its interpretation by Lars Brundin (1966), a chironomid specialist. The need for revolution was succinctly put by palaeontologist Colin Patterson, some years later

“By about 1960 palaeontology had achieved such a hold on phylogeny reconstruction that there was a commonplace belief that if a group had no fossil record its phylogeny was totally unknown and unknowable” (Patterson 1987:8).

That ‘commonplace belief’ was eventually rejected in favour of determining relationship from evidence (characters, homologies) provided by organisms (living or extinct), a shift from the preoccupation of discovering ancestry directly from the fossil record to determining common ancestry. As Brundin later noted, “little by little some palaeontologists have perceived that Hennig’s principles of phylogenetic systematics meant a revolution to their science.” Hennig called his approach Phylogenetic Systematics, the title of his 1966 book (Hennig 1966), an approach that eventually became known as cladistics, hence the cladistic revolution: the cladistic revolution overturned the central position of palaeontology in determining phylogenetic relationships: turning Ernst Haeckel’s Systematische Phylogenie into Hennig’s Phylogenetic Systematics.

By the early 1980s three books were published, all dealing with cladistics. Each approached its topic from a different perspective: Phylogenetic Analysis and Paleontology by Joel Cracraft & Niles Eldredge (Columbia University Press, New York, 1981), Phylogenetics: The Theory and Practice of Phylogenetic Systematics by Ed Wiley (New York: Wiley Interscience, 1981) and Systematics and Biogeography: Cladistics and Vicariance by Gary Nelson and Norman Platnick (Columbia University Press, New York, 1981).

While all three books have their merits, it is the last, Systematics and Biogeography: Cladistics and Vicariance that broke into new ground; and it is the last that, some 28 years after its first appearance and almost impossible to get a copy, is being made available by the University of California Press at http://www.ucpress.edu/books/series/spsy.php

Cladistics, as outlined in Systematics and Biogeography: Cladistics and Vicariance, might be understood as a reaction to phylogeny reconstruction, or more specifically, Haeckel’s paleontological version of it, developed by Matthews and Simpson. Systematics and Biogeography is a detailed critique of Haeckel’s legacy and an outline of what can be understood as natural classification, as first sketched by Candolle in his Théorie élémentaire de la Botanique – the question addressed being: How do ancestor—descendant relationships relate to natural classification?

Since Systematics and Biogeography there have been discourses on ‘tree-thinking’, ‘group-thinking’ and ‘population-thinking’, none seemingly appropriate for classification: Classification (and phylogeny, and systematics) are all best referred to as relationship-thinking, of which Systematics and Biogeography is a meditation on.

Download this book now from the University of California Press website – and see if you can start another revolution.

The Science of Systematics

In a recent post, by John Wilkins (Evolving Thoughts), there is a quote by Borgmeier (1957):

"As the science of order ("taxonomy"), Systematics is a pure science of relations, unconcerned with time, space, or cause. Unconcerned with time: systematics is non-historic and essentially static; it knows only a simple juxtaposition of different conditions of form. Unconcerned with space: geographical factors are not primary criteria in the definition of taxonomic units. Unconcerned with cause: systematics has no explanatory function as far as the origin of the system is concerned; it is merely comparing, determining, and classifying" (Borgmeier, 1957: 53).

On further reading we find this:

"Systematics is independent of the theory of descent. This is admitted today [1957] even by convinced evolutionists. The reasons are as follows. (1) Systematic methods provide definite results without reference to the idea of evolution; phylogenetics has no special methods, it is essentially the interpretation of systematic facts. (2) Systematics is a science; phylogeny is a hypothesis of a historical process containing a fundamentally unverifiable element (Thompson) and can therefore never be the foundation of a science. (3) Systematics is [an] investigation of facts; phylogenetics is often 'a dangerous play with mere possibilities' (Hennig); Kant called it 'a daring adventure of the mind'

Of course, any systematist is free to speculate on the probable phylogeny of certain species or genera, on the basis of systematic facts" (Borgmeier, 1957: 54-55; see also Williams & Ebach, 2009).

Notice the date – 1957. Cladism was gestating at the height of the Modern Synthesis. Mayr had already named his enemy – 'typology' – and created the essentialist myth. What was Borgmeier playing at? Was he an early cladist (Wilkins pers comm., 2009), or, was he someone, like Candolle (1813), who understood the importance of classification over inference?

The insistence that systematics and phylogeny should be treated separately would ally Borgmeier with Naef (1919) and Systematic morphology, rather than with the emerging numerical methods that would later predominate Hennigian cladistics. Borgmeier was not a cladist, but someone who understood the difference between phylogenetic inference and systematic classification, two fields that were as confused then as they are now. Borgmeier's message was aimed at readers of Systematic Zoology, namely evolutionary biologists and phylogenetists who insisted that their phylogenies (trees) were classification schemes (cladograms).

Borgmeier's points above may appear slightly heretical to modern day evolutionary biologists. After all 2009 is Darwin Year and a time to celebrate the achievements of evolutionary biology, rather than to dissect them. But if we do wield our scalpel at the underbelly of evolutionary biology, what do Borgmeier's three points mean for present day phylogenetics?

Decoding Borgmeier's Points for the 21 Century Phylogenetist

Point 1 "Systematic methods provide definite results without reference to the idea of evolution; phylogenetics has no special methods, it is essentially the interpretation of systematic facts." This quote consists of three parts. Take the relationship A(BC) for example. The result is definite in the sense that it states a relationship (i.e., homology, monophyly). This relationship is part of a classification, not a genealogical or phylogenetic lineage. That is, A does not necessarily have to be an ancestor of of either B or C. In fact A could be an extant mammal where as B and C could be trilobites (now extinct). This means there is no notion of time or transformation in cladograms (e.g., trilobites did not evolve from mammals). Cladograms are classifications, which depict systematic relationships that may include numerous hypothesized genealogical or phylogenetic lineages. If we skip to the third part of Borgmeier's point, namely '... it is essentially the interpretation of systematic facts', we see that phylogenetic inference comes from systematic relationships, not the other way around. In a modern context, we can hypothesize genealogical or phylogentic lineages once we discover cladograms and not the other way around (i.e., evolutionary taxonomists hypothesize lineages prior to finding classifications, hence the creation and acceptance of paraphyletic groups).

The second part to Borgmeier's point, '... phylogenetics has no special methods' is more relevant today than it was in 1957. Phylogenetic 'methods' are based only on inference. This means phylogenetic 'methods' are confused with phylogenetic models. Since models are immune to testing hypotheses, from a historical context, they fail. That is, models themselves are hypothetical and not based on actual observations. Phylogenies therefore remain hypothetical whether they fit the model or not. We will never know if A is actually ancestral to B or C through scientific methodology (i.e., testing). We can however only hypothesize which model is most 'likely', 'parsimonious' or 'similar'.

Point 2 "Systematics is a science; phylogeny is a hypothesis of a historical process containing a fundamentally unverifiable element (Thompson) and can therefore never be the foundation of a science." Point 2 proposes an interesting problem - Systematics as a science and phylogenetics as a hypothesis. Given this, the term Phylogenetic systematics appears to be an oxymoron. At one level taxa are treated in a systematic way (i.e., no concept of time or transformation), whereas on the other, characters and their states are treated as phylogenies (i.e., transformation, reversals, dating nodes etc.). Borgmeister may have seen the flaw in Hennig's system, however he didn't refer to it directly. Separating systematics as 'a science' from phylogenetics as 'a historical process' muddies the waters of cladistics. Hennigian cladistics happily confuses the two, whereas pattern cladists (sensu Brady, 1982) treats them separately (see Ebach et al. 2008). Moreover, Borgmeier's statement today would read differently; phylogenetics is now considered as a science and systematics its method. The confusion still continues.

Point 3 "Systematics is [an] investigation of facts; phylogenetics is often 'a dangerous play with mere possibilities' (Hennig)" I will not go into what 'facts' are, but for the purpose of this argument we may refer to systematics as an investigation of relationships. Point 3 is a more concise rephrasing of Point 1. Any systematic relationship may contain multiple hypothetical phylogenetic or genealogical lineages. The 'play with possibilities' becomes 'dangerous' once we use systematics to choose between them. Considering that systematics is silent about time, transformation and descent, it is impossible to use cladograms to choose one possible phylogeny over another. Other evidence is needed. After all, it is not the goal of systematics to find or propose lineages or find ancestors.

Borgmeier's three points are still relevant today. Whether phylogenetists will understand the dangers of confusing systematics with phylogenetics is another matter. The literature on this topic is readily available, but many do not realize that there is a problem. Understanding the nature of systematics and phylogenetics, their role in our research and their limitations, has more to offer than just another computer algorithm.

Malte C. Ebach & David M. Williams

References

Candolle de, A. P. (1813). Théorie élémentaire de la botanique ou exposition des principes de classification naturelle et de l'art de décrire les végétaux. Paris.
Borgmeier, T. (1957). Basic Questions of Systematics Systematic Zoology, 6, 53-69
Brady, R.H. (1982) Theoretical issues and 'pattern cladistics'. Systematic Zoology 31: 286–291.
Ebach, M.C., Morrone, J.J. & Williams, D.M (2008). A new cladistics of cladists. Biology & Philosophy 23: 153-156.
Naef, A. (1919). Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen). Verlag von Gustav Fischer, Jena.
Williams, D.M & Ebach, M.C. (2009). What, Exactly, is Cladistics? Re-writing the History of Systematics and Biogeography. Acta Biotheoretica DOI:10.1007/s10441-008-9058-5.

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

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".

Biogeography & Systematics: Call for Papers

Biogeography is a complex discipline, in the sense that it deals with complex processes — of evolution of life in space through time — not directly observable, occurred in the geological past. Biogeographical reconstructions demand precise and complex data — systematic and distributional information — and intricate methods. It should be no surprise to learn that evolutionary biogeography is a relatively recent area of research within the history of comparative biology.

The late 1970s and early 1980s faced an especially rich period of development of biogeographical theory and methodology, with the inclusion of the concept of vicariance in the mainstream of biological literature. The journal Systematic Zoology played a major role in the publication of papers in this area during that period. The intricacies of the subject, however, along with decisions concerning the policies of the primary main journals of the subject — Systematic Biology, Cladistics and Journal of Biogeography — resulted in problems publishing large papers with analytical studies of historical biogeography. Typically large papers with biogeographical studies also contain analyzes of the relationships of a group of organisms, often requiring new taxa to be named, to properly identify the nodes on a cladogram.

To fill this publishing void, the Systematic and Evolutionary Biogeography Association (SEBA) has decided to launch a new, open-access online journal, Biogeography and Systematics, to occupy such niche in the primary literature.

Biogeography & Systematics will publish original papers on historical biogeography and phylogenetic systematics. The journal will have the following sections:

Invited Papers — for topics of major interest in biogeography and systematics under invitation from the editor-in-chief;
Original articles – on analytical, historical, epistemological, and methodological aspects of biogeography and systematics, without page limit;
Forum – opinion pieces on any topic of biogeography or systematics (maximum, 3000 words).
Book Reviews – usually under invitation, but submitted reviews (including classical works) may be considered (max. limit 1000 words).

The editorial policy of Biogeography & Systematics is to ensure that articles published are of the highest quality and relevant to the interests of our readers. The journal is peer-reviewed. The journal is not biased towards any biogeographic region, in terms of taxa studied or author affiliation, nor any method of analysis. All papers shall be written in English (US spelling).

The first number of the journal is scheduled for August, 2008.

Please click here to see the Guide for Authors.

Editorial Policy
Biogeography & Systematics has an editorial policy in order to ensure that the articles we receive are of high quality and relevant to the interests of our readers.

• Biogeography & Systematics publishes in English (US spelling) only.


• Biogeography & Systematics publishes original research papers in biogeography and systematics.


• Biogeography & Systematics is a peer-reviewed journal.


• Biogeography & Systematics publishes monographic taxonomic, systematic and biogeographical treatments.


• Articles may cover any aspect of biogeography, systematics or taxonomy.

Types of Articles
Biogeography & Systematics publishes the following types of articles:

• Biogeographical anaylses, revision of methods or epistomological reviews.


• Systematic revisions that may include biogeographical analyzes.


• Taxonomic treatments that include systematic analyzes.


• Historical revisions in biogeography, systematics and taxonomy, including biographies.

If you have been invited to contribute an article please submit your manuscript as an .odt, .rtf or .doc. We ask authors to only use Primary (bold) headings.

Citations
All citations are to be made without using commas between author and year (Wallace 1855) and commas between multiple authors (e.g. Nelson and Platnick 1981, Brandon-Jones 1998). Quotes should be cited as (Willis 1922, p. 100). Please refer to this issue for further usage of figures (see figure 1 or Fig. 1), tables and numerals.

References
Please include the full titles of journals and books. Do not use abbreviations! Please keep your references in the styles listed below.

Brandon-Jones D. 1998. Pre-glacial Bornean primate impoverishment and Wallace’s line. In Hall R, Holloway JD eds. Biogeography and geological evolution of SE Asia. Leiden: Backhuys Publishers, pp. 393-404.

Heads M. 2006. Panbiogeography of Nothofagus (Nothofagaceae): Analysis of the main species massings. Journal of Biogeography 33: 1066-1075. Merriam CH. 1898. Life zones and crop zones of the United States. U.S. Department of Agriculture Division Biological Survey Bulletin 10: 1-79.

Nelson G, Platnick NI. 1981. Systematics and biogeography: Cladistics and vicariance. New York: Columbia University Press.

Wallace AR. 1855. On the law which has regulated the introduction of new species. Annals and Magazine of Natural History 16 (2nd series): 184-196. [http://www.victorianweb.org/science/science_texts/wallace_law.html; http://www.wku.edu/~smithch/wallace/S020.htm; http://www.zoo.uib.no/classics/new_species.txt].

Proofs
Authors will be given a chance to proof their paper prior to publication. The final proof will be published on the SEBA website simultaneously as the journal is printed.

Copyright Form
Authors will be asked to complete a copyright form upon acceptance of their manuscript.

Submissions
Please submit your articles in electronic format to the Editor-in-Chief, Dalton de Sousa Amorim

Biogeography & Systematics is printed by the Instituto Venezolano de Investigaciones Científicas, Venezuela.

Wag the Dog: Mimics, False Prophets and Phenetics

Near enough is not good enough should be the motto of cladistics. For many however, near enough is not only better, but something worth pursuing. Phenetics is that "something". It is a mimic and some of its proponents are false prophets who prefer a "near enough" result to a real understanding. Systematics and biogeography can not rest on its numerical laurels too long. Already in molecular systematics the numerical method is defining the field. When the mimic starts to dictate what the science should be, we have a severe case of the dog’s tail wagging the dog.

Mimics

Artificial classifications are a key or classification based on a particular organ. This forms a System, one that can predict or mimic a natural classification.

Taxonomists, systematists and biogeographers often use artificial classifications or Classification Systems in order to identify and classify taxa. People around the world use classification systems everyday. This is one that many learn at school:

1. Fish have scales and no limbs.
2. Amphibians lay eggs on land and live in water.
3. Reptiles lay eggs, have scales and live on land.
4. Birds lay eggs and have feathers.
5. Mammals have skin and hair, mothers feed their young milk.

Classification systems are helpful in identifying taxa but they only mimic real relationships. In the case above only mammals and birds are natural (monophyletic) groups, but the classification system for birds may also apply to taxa that are categorized as reptiles. In other words, the system above only mimics the natural group (i.e., birds), but it does use the homologies that define that group.

Linnaeus was the first person to define a classification system that attempts to mimic natural groups. The system can still be used today in order to identify plants. What Linnaeus’s, or any classification, does not do is purport to be a natural method.

A method is a key or classification based on all of the organs of a taxon; methods are sub-divided into artificial and natural depending on their purpose.

Classification methods not only mimic, they also may predict. In either case they attempt to generate classifications that are near the mark. Phenetics uses a method in order to generate a classification that mimics a natural group. The method for doing so can be useful in order to work out similarities between taxa, but the method is only a mimic. Phenetics becomes problematic when it starts getting closer to the mark. In some cases a phenetic analysis can replicate a true relationship – a homology – without the need for homologies. Although these methods are praiseworthy, they do not actually find homologies. A mimic only replicates something, it does not actually discover. A phenetic analysis may for instance replicate a monophyletic group perfectly, using an assortment of homologues, but since the method uses similarity (i.e., non-relationships) it cannot, by definition, discover homologies, even though it replicates them perfectly.

An analogy would be to state that anything that lives in water and lays eggs on land is an amphibian. Although this behavioural trait is more likely to be common amongst toads, frogs, salamanders and newts, it is not a homology as it is something not unique to that group. Birds may lay eggs and bear feathers, but so do a number of therapod groups. Similarity is not a relationship, only a measurement of likeness based on one or more hypotheses.

False Prophets

Phenetics becomes problematic when it confuses the mimic for the real thing. Certainly phenetics can create a classification system using a method of similarity, but it does not discover natural groups. Therefore the term Natural System is a contradiction. A system cannot be natural as it is based on a single characteristic or assumption and not relationship. Natural groups, as pointed out in the post Phenetic "Natural" Classifications, are not based on a priori assumption:

"... system of classification is the more natural the more propositions there are that can be made regarding its constituent classes" (Sokal & Sneath 1963: 19).

Sokal and Sneath (1963) have turned the mimic into natural group.

Phenetics as purveyor of natural groups is erroneous and prophetic. Stating that natural groups can be reached through a system of quantification and similarity is appealing to those that rely on statistical programs. Most systematists and biogeographers rely on such programs and have swallowed the “phenetic prophesy” hook, line and sinker. Natural groups, it seems, is just a matter of quantity.

Wag the Dog

The phenetic prophesy states that similarity* is relationship, and can discover natural groups. This is wagging the dog.

Taxonomists, systematists and biogeographers can only discover patterns, homologies that give us insight into relationship. Before we do this we may impose a system of beliefs, hypotheses and theories about our own groups and their relationships. Some times we test these assumptions by discovering homologies and find that we were right. That is the nature of a robust scientific discipline. Once we turn that around and impose our own “natural” law, then we can only formulate more hypotheses in differing ways, never discovering only generating. Molecular systematics is now in a unique position to learn from 300 years of systematic theory that has discovered time and time again that homology is not similarity. Unfortunately many in the field ignore the past systematic literature and read that of the phenetic prophesy.

One day someone bent over a PCR machine may come to realise that they are part of a 300 year cycle of wagging.

*There are two forms of similarity. One is that of simile “That kangaroo looks like a rat”. The other is quantifiable and is born from statistics (i.e., divergence and possibility) “The ape is 22% banana”. We refer to the latter form throughout this post.

References

Sokal R.R. & Sneath P.H.A. 1963. Principles of Numerical Taxonomy. W. H. Freeman, San Francisco.

Artificial and Natural Classifications: A Clarification

It was not by accident that we referred to de Candolle (1813): "Naef's concern was with the discovery of natural, as opposed to artificial classification, a problem examined in detail by A. P. de Candolle (1813)".

This is what de Candolle had to say about artificial classifications:

"Others have as their essential goal to give to persons who know nothing of the names of plants an easy way to discover the names in the books by inspection of the plant itself. These classifications have been given the name of Artificial Methods."

And,

"...there are those persons who want to study plants, either in themselves, or in their real relations among themselves, and to class them so that those plants most closely related in the order of nature are also those most closely related in our books. These classifications have received the name of Natural Methods."

De Candolle considers Systems and Methods.

A system is a key or classification based on a particular organ - leaf, flower, etc.

A method is a key or classification based on all of the organs of a plant; methods are sub-divided into artificial and natural depending on their purpose.

De Candolle again:

"classes that are truly natural, established on the basis of one of the major functions, are necessarily the same as those established on the basis of the other."

That is, congruence.

Bar-coding, based on "a particular organ", interpreted as a piece of DNA, is, in this sense, a system. It might be seen as an artificial classification as its purpose is to find the name of any given plant or animal.

Now, is molecular systematics a system or a method? It too is based upon "a particular organ", so it too might be considered a system. Now if considered a method, we see that there is no notion of congruence at all as no other datasets are given consideration. Molecular systematics as a form of measuring similarity constitutes a system, not a method.

Ancestors and other mechanical explanations are not of any concern in the debate between artificial and natural classifications. One does not decide on homology in advance. It is either there or it is not. Homology, as we understand, is a relation. A similarity such as 11, or AA, is not a relation. Thus, all molecular systematic studies are phenetic as they ignore relationship, that is, homology.

Adolf Naef - A Potted Biography

Who was he?
Adolf Naef was a Swiss systematist, malacologist and a proponent of systematic morphology. He was born in Niederhelfenschwil on 1st May 1883 and passed away on May 11th 1949.

What did he do?
Naef studied at the University of Zurich, under the guidance of Arnold Lang (1855—1914), a former Professor of Jena University and close friend of Ernst Haeckel. Naef visited and worked in Anton Dorn’s Zoological Station in Naples, Italy in 1908, studying the squid Loligo vulgaris, the subject of his dissertation (Naef, 1909a, b). Naef returned to the Naples Zoological Station in the mid 1920s to study cephalopods, publishing a two-part monograph in the Station’s Fauna und Flora des Golfes von Neapel und der Angrenzenden Meers-Abschitte (Fauna e Flora del Golfo di Napoli) series (Naef 1921d, 1923c, 1928, later translated into English, Naef, 1972a, 1972b, 2000), which formed the basis for his two short but significant monographs on systematic theory (Naef, 1917, 1919). In 1922 he became Professor at the University of Zagreb, and in 1927 was Professor of Zoology at the University of Cairo.

What’s the big idea?
Naef’s studies were framed within Systematische Morphologie (Systematic morphology) (Naef, 1917, 1919), the details he sketched out as early as 1913:

“Phylogenetic and natural systematics deal with the same factual material, and although each has different basic concepts, both disciplines can be united in a single concept because their objects are so similar. I have therefore proposed the name ‘systematic morphology’ for this concept (Naef, 1913: 344)…It is intended to show that there is an inner relationship between natural systematics and (comparative) morphology” (Naef, 1921-23: 7, from the English translation, Naef, 1972a: 12).

Naef’s concern was with the discovery of natural, as opposed to artificial classification, a problem examined in detail by A. P. de Candolle (1813). Naef expressed it as so:

“For decades, phylogenetics lacked a valid methodological basis and developed on the decayed trunk of a withering tradition rooted in the idealistic morphology and the systematics of pre-Darwinian times. There was talk of systematic ‘tact’ and morphological ‘instinct’, terms which were felt rather than understood and consequently insufficient to form the frame of a science which required sound definitions and clearly formulated principles” (Naef, 1921-23, pp. 6-7, from the English translation, Naef, 1972, p. 12).

And thus was born ‘Systematische Morphologie’, perhaps the beginnings of cladistics, in its most general form (of which more in a further post). Towards the end of his career, Naef published several detailed accounts of ‘Systematische Morphologie’ (Naef, 1931a, b, 1933a), including a succinct summary in the widely read 2nd edition of the Handwörterbuch der Naturwissenschaften (Naef, 1933b).

Naef might be considered a man out of time – as might many morphologists today, relative to the explosion of molecular data. In Naef’s day palaeontology and the post World War II hegemony of the modern synthesis was attracting the young minds. Today it is molecular systematics and DNA barcoding – versions of artificial classifications.

References

Candolle, A.-P. de (1813). Théorie élémentaire de la botanique ou exposition des principes de la classification naturelle et de l'art de décrire et d'étudier les végétaux. Deterville, Paris.
Naef, A. (1909a). Die Organogenese des Cölomsystems und der zentralen Blutgefässe von Loligo. Jenaische Zeitschrift für Naturwissenschaft, 45, N.F. 38:221—266.
Naef, A. (1909b). Die Organogenese des Cölomsystems und der zentralen Blutgefässe von Loligo. Inaugural-Dissertation, Univers. Zurich, 46pp.
Naef, A. (1913). Studien zur generellen Morphologie der Mollusken. 2. Teil. Das Cölomsystem in seinen topographischen Berziehungen. Ergebnisse und Fortschritte der Zoologie 3: 329—462.
Naef, A. (1917). Die individuelle Entwicklung organischer Formen als Urkunde ihrer Stammesgeschichte: (Kritische Betrachtungen über das sogenannte “biogenetische Grundgesetz”). Verlag von Gustav Fischer, Jena.
Naef, A. (1919). Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen). Verlag von Gustav Fischer, Jena.
Naef, A. (1921—23). Die Cephalopoden (Systematik). In: Fauna e Flora del Golfo di Napoli, Monograph 35 (I-1), Pubblicazioni della Stazione Zoologica di Napoli. R. Friedländer and Sohn, Berlin, pp. 1—863.
Naef, A. 1931a. Allgemeine Morphologie. I. Die Gestalt als Begriff und Idee, pp. 77—118 in Bolk, L, Göppert, E., Kallius, E. & Lubosch, W., (editors) Handbuch der vergleichenden Anatomie der Wirbeltiere 1. Berlin: Urban & Schwarzenberg.
Naef, A. 1931b. Phylogenie der Tiere, pp. 1—200 in Baur, E., & Hartmann, M., (editors) Handbuch der Vererbungswissenschaft, Gebrüder Borntraeger, Berlin 13 (3i).
Naef, A. 1933a. Die Vorstufen der Menschwerdung. Eine anschauliche Darstellung der menschlichen Stammesgeschichte und eine kritische Betrachtung ihrer allgemeinen Voraussetzungen. Jena: Verlag von Gustav Fischer.
Naef, A. 1933b. Cephalopoda, pp. 293—310 in Dittler, R., Joos, G., Korschelt, E. Linck, G., Oltmanns, F. and Schaum, K. (editors) Handwörterbuch der Naturwissenschaften, 2nd edition, volume 2. Jena: Verlag von Gustav Fischer.
Naef, A. 1933c. Morphologie der Tierre (Allegmeines und Grundsätzliches), pp. 3—17 in Dittler, R., Joos, G., Korschelt, E. Linck, G., Oltmanns, F. and Schaum, K. (editors) Handwörterbuch der Naturwissenschaften, 2nd edition, volume 7. Jena: Verlag von Gustav Fischer.
Naef, A. 1972a. Cephalopoda. Fauna and Flora of the Bay of Naples (Fauna und Flora des Golfes von Neapel und der Angrenzenden Meers-Abschitte), Monograph 35, Part I, [Vol. I], Fascicle I. Smithsonian Institute Libraries, Washington.
Naef, A. 1972b. Cephalopoda (systematics). Fauna and Flora of the Bay of Naples (Fauna e Flora del Golfo di Napoli), Monograph 35, Part I, [Vol. I], Fascicle II. Washington, Smithsonian Institute Libraries.
Naef, A. 2000. Cephalopoda. Embryology. Fauna and Flora of the Bay of Naples [Fauna und Flora des Golfes von Naepel]. Monograph 35. Part I, Vol. II [Final part of the Monograph No. 35], pp. 3-461. Washington, Smithsonian.