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 Enduring Legacy of Misinterpreting Darwin

Kevin Padian's (2008) claim that Charles Darwin founded the main principles of biogeography and ecology is clearly incorrect. Biogeography was alive and well long before Darwin's birth, in fact Augustin Pyramus de Candolle and Alexander von Humboldt produced the founding works of biogeography four years before Darwin was born, while the younger Alphonse Candolle and Ernst Haeckel erected the foundations for chorology and ecology in 1855 and 1861 respectively.

Prior to the publication of Origin of Species in 1859, Darwin would have had access to an extensive array of literature, including biogeographical concepts espoused by Charles Lyell, Louis Agassiz, Joseph Dalton Hooker and Phillip Lutely Sclater. Furthermore, Padain's claim that in "Darwin's day, dispersal through migration was the only mechanism thought possible for species to move among continents" (p. 633) is also erroneous as concepts such as vicariance were already in existence. Darwin's contribution to biogeography and ecology was to provide a synthesis or unifying mechanism that explains why organisms are distributed the way they are today, namely natural selection.

References
Padian, K. 2008. Darwin's enduring legacy. Nature 451: 632-634.
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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.

Divisions: Who watches the philosophers of science?

There are a few things for the poor old philosophers of science to get over.

If Peter Lipton is right, namely that,

"Astronomers study the stars; philosophers of science study the astronomers. That is, philosophers of science—along with historians and sociologists of science—are in the business of trying to account for how science works and what it achieves" (Lipton, 2005: 1259).

then philosophers of science have to able to see beyond current trends and political avarice. After all who watches the philosophers of science?

The trend of embracing apparent dichotomies within systematics and biogeography rather than question them, is one of things that philosophers of science need to get over. Philosophers of science need to question, examine and assess such divisions and not blindly accept them as many seem to do.

Below we list the top 10 dichotomies in systematics and biogeography that philosophers of science need to get over:

1. Morphology and Molecules
2. Homology and analogy
3. Homology and homoplasy
4. Transformational and Taxic Homology
5. Synapomorphy and symplesiomorphy
6. Congruence and consensus
7. Cladistics and Phenetics
8. Simultaneous analysis and separate analysis
9. Ecological and Historical Biogeography
10. Dispersal and Vicariance

Just because scientists use these divisions does not mean they actually exist. Dichotomies often groups "us" from "them". Science is not immune from subjectivity or distortion of "the facts" through clever manipulation. Scientific decisions too are sometimes decided upon politics, personality and fashion.

Philosophers of science are there to make sure that fish caught last Sunday afternoon was indeed "that big". In believing, rather than questioning, the divisions between certain ideas that are made by scientists, philosophers of science are unable to for "account for how science works". For some philosophers of science, the one that got away was "ooh .. so big, bigger than anything you have ever seen".

Lipton concludes

"Indeed, one might go so far as to worry that if philosophy did have any impact on scientists, it would be pernicious, depriving them of the kinds of commitment and confidence upon which their practice depends" (Lipton, 2005: 1269).

Philosophers of science have already influenced science, based on some of the highly questionable divisions listed above, to the extent that that it has been fashionable to attribute the cladistics/phenetics "war" in systematics to real events rather than to a poor account of how science functions (i.e., Hull, 1988).

References
Hull, D.L. 1988. Science as Process: An Evolutionary Account of the Social and Conceptual Development of Science. Chicago: University of Chicago Press.
Lipton, P. 2005. The Medawar Lecture 2004: The truth about science. Philosophical Transactions of the Royal Society of London B, 360, 1259–1269.

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.