Sunday, November 30, 2008

Shameless self promotion.

A few years ago Donat invited me to contribute to this blog, as I was also helping with itself. We haven't been the best at it and our posts have become thin and sparse. Apologies.

My own excuse is that I was finishing my PhD. But it is also true that, since this blog is primary associated with, there were many topics or ideas that I felt were either to off-topic or too personal for me to write here. On the other hand, my dissertation work on ant morphology started to shift my interest from pure taxonomy to morphological evolution, cast differentiation and the role of the developmental process in the first two (i.e., Evo-Devo), all from the perspective of classical comparative anatomy.

I have therefore started my on blog called Archetype to explore some of my ideas on the subject, while at the same time to write about other silly and inconsequential topics that come to my mind.

Wednesday, June 04, 2008

100 Years of the Ant Collection at the MCZ

The ant collection at the Museum of Comparative Zoology (MCZ) turns 100 years this year.

The beginning of what has become a great legacy for ants studies is marked by the arrival at Harvard of William Morton Wheeler in the Fall of 1908 as the newly appointed professor of economic entomology[1]. Two crucial things have turned this collection into the most important ant collection in the World. On the one hand a century of steady activity by a succession of prominent myrmecologists at the MCZ. On the other, myrmecologists world-wide voting with their types: the MCZ has become one of the classical repository for type material when describing new ant taxa. In addition, credit should be given to Stefan Cover, the "guardian angel" of the ant collection over the last few decades.

A centennial celebration dinner was held on May 28, as part of a meeting organized by the EOL and CBOL that brought together ant specialist from around the globe (and your lucky blogger that happens to be in town). Guests were treated to a nice meal while listening to a brief history of the MCZ given by the current Museum director James Hanken and an entertaining account of the early days in American myrmecology through W. M. Wheeler's illustrious career given by Edward O. Wilson. All topped off with a special cake covered with tasty crawling chocolate ants.

Phil Ward and Jack Longino

E. O Wilson and Corrie Moreau

Steve Shattuck and Lloyd Davis

Fernando Fernandez and John Lattke

Mike Kaspari and Stefan Cover

Roberto Keller and Corrie Moreau

Happy centennial to the ant collection at the MCZ and we wish 100 years more!

1. Evans, M.A., H.E. Evans. 1970. William Morton Wheeler, biologist. Harvard University Press, Cambridge, Mass. 363 pp.

Monday, April 14, 2008

How to Identify the Argentine Ant, Linepithema humile

Linepithema expert Alex Wild posted a succinct but thorough guide on how to identify the important Argentine ant:

The Argentine Ant (Linepithema humile), a small brown ant about 2-3mm long, is one of the world’s most damaging insects. This pernicious ant is spreading to warmer regions around the world from its natal habitat along South America’s ParanĂ¡ River. Linepithema humile can drive native arthropods to extinction, instigating changes that ripple through ecosystems. In California, horned lizard populations plummet. In South Africa, plant reproduction is disrupted. Worldwide, the Argentine ant is a persistent house and crop pest. This is not a good ant.

More here.

Thursday, April 03, 2008

Access to descriptions on Google

Whilst sitting at a very stimulating meeting at the Academia Sinica's National Digitization Program in Taipei and listening to talks about Web2.0, it occured to me that we are not actively making our valuable data accessible, since we don't make it easy for Google to find it. One trick, we were told, is to build RSS feeds.

And here is the result: The entire list of all the >5,600 descriptions served on plazi are now accessible through this RSS feed. For example, if you want the description of Probolomyrmex tani, you get it, including all the links to the original publications, the citation or even a Google map of its distribution. Try out on Google yourself!

Wednesday, April 02, 2008

44,614 ant names in the Hymenoptera Name Server

The ant community is in a very comfortable situation that there are two, if not three independent efforts to create a catalogue of the worlds ants. This helped us at antbase at least to cross-examine our online global ant name server with the recently published Bolton catalogue. We now have 44,614 names associated with ants, 12,359 are currently considered by the experts covering accepted species (i.e.g published record) . This includes all of them in Bolton's catalogue, and those which were different have been resolved through consulting our digital library. At least all the original descriptions are linked to the original publication.

Since January 2008, all new names are entered through Plazi's GoldenGate mark-up editor, that means that all the new names are linked to at least the original description exposed at plazi's SRS, as well as the original publication, if it is not copyrighted.

An example is the recently synonomized Pyramica aschnae.

What is clear from these exercises is that nobody is able to produce a DB that is complete and without errors, and in fact our different approaches allow each other to profit from each other, and right now update their own databases. Hopefully soon, this could go automatically through Webservices via Zoobank. This way we can continue not to talk to each other.

What is also clear is that the community should be a little bit more proactive and send error, missing or new taxon names and publications to any of the initiatives.

Tuesday, April 01, 2008

What is a bad taxonomic publication?

In a recent publication by Bolton et al., the authors make a bold statement that this is "one of the most inadequate papers that has ever been produced in ant taxonomy". Is it really?

Makhan's descriptions are so clear that they can simply synonymize them even with the bad images in the publication allow nevertheless identifying even misidentified species without having to resort to check the holotype.

I would think, despite the fact that these are probably synonyms, the descriptions are not so bad at all.

I would also argue, that such a paper is preferable to all the papers by the authors refer to, none of which is open access, and thus neither expert or any other person can make their own mind up without a substantial effort to get the publications, but has just believe them blindly.

It would be much better if the authors would have present images of all the types of the species the refer to, plus their descriptions. They could then make a proper argument and not build upon "authority".

Since we are running a project with Zootaxa, you can read the comments and the original descriptions here, and hopefully in the near future all the Pyramica descriptions mentioned will be online as well through

Friday, March 07, 2008

Now something different: shopping of course...

Surfing is dangerous. But this little online shop called "The Gigantiops Destructor Shop"* I just stumbled upon is my place for gifts, and I guess supports a PhD student as well.

* actually it should read "The Gigantiops Destructor Store" as Kari pointed out: I am impressed that about the lyrics involved in running such a cool business. Now I can't resist longer and need to get one of the apparels!

Friday, February 29, 2008's promotion of

In his recent contribution in SysTax, a German newsletter on German GBIF related activities (aka biodiversity databases that are hardly any longer funded), Martin Pfeiffer writes about

No, it is not about - but when you click on the link, or in fact anywhere on the first page, the home page of opens.

It is confusing, and to be honest, it was confusing from the begining, when Martin Pfeiffer publicized that he started, later renamed When I pointed out that there is already an he just replied he wasn't aware of it, but I guess, from my own experience, got hipped by such things as fishbase, flybase.... So much about Internet literacy.

But anyway, I just wanted to say thanks for this sort of unplanned PR.

Wednesday, February 27, 2008

Launch of

(For a formal release note see the biodivcontext blog) has on February 20, 2008 officially been released. It is the logic next step towards making published taxonomic information in a semantic Web environment accessible.

The goal is to contribute towards the ambitious goal to make all the original and subsequent descriptions of our species (and indeed higher taxa as well) part of a global (taxonomic) knowledge commons: Everybody from anywhere shall have access to this invaluable data. Access will be provide both for human and machine, and everything will be done, to make use of LSIDs and to consult with the respective communities and specialists to not only provide content, but a vehicle that can be used to explore and promote new technologies.

The project has been partially funded through a binational US National Science Foundation/ German Deutsche Forschungsgemeinschaft digital library grant, and more recently by the Global Biodiversity Information Facility (GBIF).

The power of the system lays in its ability to provide a dedicated XML editor allowing not only to mark-up the publications using the taxonomic literature specific TaxonX XML schema, but to enhance them with LSIDs for taxonomic names and bibliographic citations, and if available for specimens, CBOL sequences and more. As soon as ZooBank will be populated with the ant nomenclatorial data, links will be set up with the registry of zoological names. GoldenGate, the editor is modular and allows other communities to join the project and write applications allowing to retrieve LSID for their own taxa, such as fungi or plants.

This offers the unique chance to build up new catalogues using the mark-up process, where at the end all the names are registered with the respective databases, and all the descriptions are online accessible.

For ants, as of 2008, all the new ant systmatics publications will be marked up in Taxonx, the names added to the Hymenoptera Name Server where all the known names reside, and each of the descriptions will be accessible (e.g Probolomyrmex tani ) as full text, pdf or TaxonX documents. For copyrighted material, only the descriptions will be made accessible.

Depending on the resources, the publications can be marked up to very fine granularity, such that all the collecting events can be extracted (e.g. Linepithema humile). Older publications will be added as fast as our resources permit - or collaborators contribute.

All the descriptions are always linked to the original publications and a proper citation is provided to secure the origin of the data.

Anybody can contribute to the growth of this digital archive. The first training courses have been held in Brazil for spider and ant taxonomists. All the programs are open source, and the more people begin to use and help to develop, the more efficient we can populate the archive on

Currently, 3884 treatments are online avaialble, representing a large part of the Malagasy fauna, and more recent publications. Descriptions can be displayed in their original language.

Friday, January 04, 2008

TNT now freely available

TNT stands for "Tree analysis using New Technology". It is a program for phylogenetic analysis under parsimony (with very fast tree-searching algorithms), as well as extensive tree handling and diagnosis capabilities. It is a joint project by Pablo Goloboff, James Farris, and Kevin Nixon.

As of November 2007, the project was subsidized by the Willi Hennig Society, and thus the program is now made freely available, upon agreement on the terms of the License.

More here.