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).

Monday, 31 March 2008

Didn't we discuss this before?

I once walked into my colleague's room and pointed out that his sink was leaking and getting some boxes full of reprints wet. I suggested he should get it fixed or move the boxes. We discussed it a little and after a short while it was forgotten. A year later I noticed that the problem had not been fixed. The reprints were all moldy and the leak had spread staining his carpet. I pointed it out to him again. He simply dismissed it with the line "Didn't we discuss this before?"

That same line is used throughout systematics and biogeography to dismiss lengthy heated debates that never were resolved. Who, for instance, were the victors in the following debates?

  • Cladistics versus Phenetics

  • Pattern Cladistics versus Numerical cladistics

  • Modern Synthesis versus Cladistic Revolution

  • Dispersal versus vicariance

  • It is said that history is written by the victors. Looking at the above examples we assume that cladistics triumphed over phenetics (overall similarity); Pattern cladistics simply lost a pointless debate; The Modern Synthesis was expelled from numerical revolution and that the dispersalist have finally won in their campaign against the dusty old vicariance biogeographers. In every case above, a heated debate occurred, the problems were addressed and everyone went home feeling like something was resolved. If this is the case why is vicariance still the most prominent theory in systematic biogeography? Why does everyone use phenetic methods? Where have all the cladists gone?

    None of the above debates were resolved. Phenetists kept doing phenetics. The idea of overall similarity (a non-cladistic idea) swept over all of numerical phylogenetics. The pattern cladistics never left, the Modern Synthesis never died and vicariance was never abandoned. If we are to complain that this was all discussed before, then isn't it because the debate never really ended?

    In a recent paper all opposition to DNA Barcoding was dismissed has “... having been controversial” (Lahaye et al. 2008). The paper suggests that by doing DNA Barcoding regardless of its flaws, immunizes it from any criticism. I am sure if another paper is published criticizing barcoding it would be dismissed with that one line "Didn't we discuss this before?" This is the same tactic used by phenetists (overall similarity), Modern Synthesists and Dispersal Biogeographers. It seems that history is not written by the victors, but by those with leaky sinks, a stained carpet and no ambition to do anything about it. But surely "we have discussed this before?"


    Lahaye, R., van der Bank, M. Bogarin, D., Warner, J, Pupulin, F., Gigot, G., Maurin, O.,Duthoit, S., Barraclough, T.G., Savolainen, V. 2008. DNA barcoding the floras of
    biodiversity hotspots. PNAS.10.1073/pnas.070993610395.

    Thursday, 27 March 2008

    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.

    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.

    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. [;;].

    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.

    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.

    Sunday, 16 March 2008

    Defining Phenetics, Intentions and Mimics

    Many reading this blog are probably wondering why we seem to call everything phenetics. Phenetics is a term used, incorrectly, to only describe a certain type of methodology, namely clustering based on similarity (i.e., neighbor-joining etc.). In fact phenetics is nothing more than Numerical Taxonomy (Sneath & Sokal, 1973), a topic that we have discussed in a previous blog (Phenetic "Natural" Classifications).

    Phenetics attempts to classify organisms based on over-all similarity. An excellent definition of phenetics, which can be found at Wikipedia, goes one step further:
    "In biology, phenetics, also known as numerical taxonomy, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation".
    Where phenetics becomes problematic is when these classifications are considered to be natural, that is monophyletic. A monophyletic taxon is based on relationship, namely homology. Homology is not a measurement of similarity but an expression of relationship. Phenetically grouped organisms may not necessarily be more closely related to each other than they are to another group. In other words, phenetics cannot distinguish paraphyly from monophyly. An analogous problem exists in biogeography.

    Parsimony Anaylsis of Endemicity (PAE) is a method developed in order find similarities between areas (see Rosen 1988). The method simply requires a data matrix of presence and absences of taxic distributions. In contrast, cladistic biogeography demands that taxa used in analysis are monophyletic, however many fossil groups have no relations that coexisted in the same period. This means that some paleontologists are forced to deal with higher taxon biogeography (i.e. at family or ordinal level) or abandon cladistic biogeography altogether. The idea behind PAE is to use any group within a phenetic context. Monophyly is not a requirement of PAE therefore absences can be used to cluster organisms into areas since no notion of homology or relationship is assumed. As with phenetic findings in systematics, some users have made the mistake of assuming that PAE can find phylogenetic signals based on non-evolutionary data, that is, non-homologous information, in the data matrix.

    On closer examination we find that many systematists and biogeographers intent on discovering homology, monophyly and endemism are nevertheless using phenetic methods. Perhaps this is due to a lack of readily available methods in the literature. After all, cladistics and cladistic biogeography started off as "pen and paper" methods whereas phenetics was always a numerical method (hence numerical taxonomy). The issue at stake is whether using phenetic methods jeopardizes our intent, namely to search for homologies, monophyly and endemic areas. We argue that it does.

    The problems lie in transposing data into a data matrix using neighbor-joining, clustering, parsimony or compatibility as are all phenetic - that is, methods that use overall similarity in order to find classifications. These methods can not distinguish natural (monophyletic) from artificial (non-monophyletic) classifications.

    Our favorite programs are rightly pointed out as black-boxes yet we shrug this off and cite Farris (1983) or recite some algorithm. In some extreme cases we justify our intentions by making sure that our data is compatible to our methods (sensu Patterson 1982). But we cannot continue skirting this issue. Similarity is an anathema that our forebears, Goethe, Vic D'Azyr, Saint Hilaire, Owen, the founders of homology had quickly disposed. Similarity is the foundation of phenetics, not cladistics. Our intent to find homology, monophlyly and endemicity (rather than the superficial cousin, similarity) must be held when selecting methods and programs that we use, ne c'est pas?

    Assumptions held so dearly by some cladists, such as Patterson's test for homology and similarity as a requisite for monophyly, are all phony. Cladists should not use phenetic methods in order to make sense of classification, instead they should use homology and relationships. The only way (if any) which we are able to use phenetics meaningfully is to treat it as a mimic of the real thing (cladistic pen and paper methods). After all that is what phenetics is about, mimicking reality.

    A mimic in cladistics is any phenetic method that attempts to implement a genuine theory or intention. Any phenetic implementation needs to be considered carefully since they were originally not intended for cladistic for biogeographical analysis. Many of the methods and implementations we use today have existed in statistical and mathematical classifications (i.e., data matrix, parsimony, compatibility, clustering, subtrees etc.). Rather than accepting these methods wholeheartedly as being "cladistic", cladists should fool the mimics. This has been successfully done by a program called TAX (Nelson & Ladiges, 1991). TAX fools the program into treating areas of no relationships as questions marks, without treating absences as evidence.

    If cladistics is to survive as an evolutionary field intent on finding homologies and monophyly, it needs to re-examine the phenetic methods that it uses. A field that is becoming dependent on phenetic methdology can easily become phenetic.

    The image above was made by David Maddison in 1981 when "... Cladistics versus Phenetics debates were still fresh in people's minds". We hope that the same image may re-spark some of that debate. The image may be found on his website.


    Farris, J. S. 1983. The logical basis of phylogenetic analysis. pp. 1-47 in Advances in Cladistics, Volume 2, Proceedings of the Second Meeting of the Willi Hennig Society. ed. Norman I. Platnick and V. A. Funk. Columbia University Press, New York.
    Nelson, G., & Ladgies, P.Y. 1992. TAS and TAX: MSDOS programs for cladistics, version 3.0. Pub- lished by the authors, New York and Melbourne.
    Patterson, C. 1982. Morphology characters and homology. In: K. A. Joysey and A. E. Friday (eds.), Problems of Phylogenetic Reconstruction. Systematics Association Special Volume, 21: 21-74.
    Rosen, B.R. (1988) From fossils to Earth history: applied historical biogeography. Analytical biogeography: an integrated approach to the study of animal and plant distributions (ed. by A.A. Myers and P.S. Giller), pp. 437–481. Chapman & Hall,
    Sneath, P.H.A. & Sokal, R.R. 1973. Numerical taxonomy — The principles and practice of numerical classification. W. H. Freeman, San Francisco.