antbase

Conflicting Ant Meeting Schedules

2011-03-05T01:06:00.005-05:00

Though the resources in ant taxonomy are globally used (eg antbase.org, see clustermap, antweb.org) the organizers or ant conferences are not. In fact, this year the two major conferences on ants, the ANeT conference
and the Simpósio de Mirmecologica that attracts over 400 participants mananges to have their meetings almost exactly at the same dates 17-21 October and 16-20 October respectively. The meeting of the Oesterreichische Myrmekologentreffen, that has a very local target audience is another one this year.
It would make sense to alternate the conferences so that one could attend both, not least so that the global efforts could be coordinated.
Global efforts, collaboration? This is still a "Fremdwort" in the myrmecological world, where too many try compete to build the ultimate global ant information system, and most of them miss the resources to deliver nor do they have a plan for long time maintenance of their databases. Though this reflects to some extend the amateurish aspect of scholarly online communication, it is at the same time a tremendous waste of resources, and a lot is done by copy-paste of already existing material, such as pdfs, taxonomic lists, images.

Fungi making zombie ants

2011-03-04T06:22:00.003-05:00

I was always puzzled by the fungis growing out of ants in the tropics, as well as Microcoelia parasitize ant and before they kill their pray alter their behavior so that it is to the benefit of the parasite. In the case of fungi the spores have to be disseminated, in the case of the Microcoelia the entire and has to be placed so that the next sheep will eat the ant whilst it is browsing.

The story in PLoS One reported in Wired magazine is not just cool and explains mechanisms, but it is in a geeks journal.

Ant Meeting: Österreichisches Myrmekologentreffen

2011-02-24T06:49:00.002-05:00

During this year, there will be several ant meetings which I will list once they are posted.
The first this year is the Österreichisches Myrmekologentreffen
Montag, 7. März 2011, 900 – 1700 Uhr
Fakultätszentrum für Biodiversität
Rennweg 14, 1030 Wien

It has the following program:
Programm
ab 9:00 Ankunft und Kaffee
10:00 Begrüßung Konrad Fiedler
10: 20 – 12:00 Myrmekologische Forschung in Österreich
und angrenzenden Regionen
10:20 ‐ 10:40 J. Chlumský, Veronika Jílková, P. Koutecký, M. Štech
Dispersal possibilities and adaptations for myrmecochory
in genus Melampyrum
10:40 ‐ 11:00 Melanie Tista
Preliminary results on macroecological patterns in European
ant communities
11:00 ‐ 11:20 Herbert Zettel, Daniela Magdalena Sorger
Schnappkiefer, Widerhaken, blaue Piraten und andere Merkwürdigkeiten –
die Philippinen, die Galápagos‐Inseln Asiens
11:20 ‐ 11:40 Line V. Ugelvig
Pathogen response in ant societies is influenced by geneticdiversity
11:40 ‐ 12:00 Veronika Jílkov, L. Matějíček, J. Frouz
Changes in the pH and other soil chemical parameters in soil
surrounding wood ant (Formica polyctena) nests
12:00 – 13:30 Mittagspause
13:30 – 13:50 Florian M. Steiner, Birgit C. Schlick‐Steiner, Herbert Zettel
Die Entwicklung der Myrmecological News (vormals
Myrmecologische Nachrichten) zu einem international
beachteten Fachjournal
13: 50 – 15:10 Heimische Ameisenfauna
13:50 ‐ 14:10 Florian Glaser
Gefährdung und Schutz ostalpiner Ameisen und die
Verantwortlichkeit Österreichs – ein Aus‐ und Überblick
14:10 ‐ 14:30 Herbert C. Wagner
Zum faunistischen Stand der Ameisen Südösterreichs
14:30 ‐ 14:50 Erich Zormann
Artenvielfalt von Ameisen im Wienerwald
14:50 ‐ 15:10 Johann Ambach
Schwindende Vielfalt? – Eine Myrmekolologische
Bestandsaufnahme Oberösterreichs
15:10 ‐ 16:00 Kaffeepause
16:00 – 17:00 Heimische Ameisenfauna (Fortsetzung)
16:00 ‐ 16:20 Florian Glaser, Herbert C. Wagner
Die große Kerbameise (Formica exsecta) – Insekt des Jahres 2011
16:20 ‐ 16:40 Herbert C. Wagner
Ein neuer arboricoler Temnothorax für Österreich
16:40 ‐ 17:00 Melanie Tista
Sammelmethoden bei Ameisen – Ist eine Aufwandsreduktion möglich?

Please register before the end of Februrary 2011.
Mag. Melanie Tista
melanie.tista@univie.ac.at, 01/4277‐57411
www.univie.ac.at/animal_biodiversity

The meeting is organized by
Univ.‐Prof. Mag. Dr. Konrad Fiedler
Mag. Melanie Tista
Department für Biodiversität der Tiere
Universität Wien

Overwintering of Ants

2011-02-08T01:11:00.002-05:00

When I visited Genady Dlussky in Moscow in 1985, he told me about all the ecological research going on Magadan in the Fareast of the former Sowjet-Union. He explained the mechanisms ant use to survive up to -30degree C. Finally, 2010, a comprehensive publication Overwintering and Cold-hardiness of Ants in the Northeast of Asia is a comprehensive book

summing up 30 years of studies on the ecology and physiology of ants under extreme northern conditions, virtually at the northern boundaris of their geographical distribution.

.
It has lavish illustrations and an account for each species studied.

It is a very helpful summary and ought be a read well beyond ant ecologists: It covers another edge of the ants that is really amazing, and in fact a lot of the results, especially the physiology, might apply too other invertebrates living under these harsh conditions.

The book is available from Pensoft Publishers, Sofia.

Myrmica monograph

2011-02-06T12:55:00.003-05:00

In the coming days a huge monograph "Myrmica ants (Hymenoptera: Formicidae) of the Old World" will be published.

It is the first taxonomic review of the entire Old World fauna of the widespread temperate ant genus Myrmica that is famed for its interactions with many social parasites of high nature conservation interest, e.g. Large Blue butterflies (Phengaris spp.)
This about 800 pages monograph is more than a traditional taxonomic review, it gives the history of the taxonomic treatment of Myrmica, summarizes the current knowledge of the social biology and ecology of the genus, analyses the zoogeography of the various species and outlines the author’s views on the evolution and speciation within the genus.
The authors currently recognize 142 extant and 5 extinct species from the Old World and they provide Identification Keys to the species for each of seven geographic regions. This should make the Keys more user-friendly for non-specialists.
The locations of the type specimens are noted in the taxonomic catalogue, which is arranged alphabetically by species, as are the accurate line-drawings of every species. These illustrate features such as the shape and sculpture of the head and body, used in the identification keys. This arrangement makes it easy to find the data for any particular species.
There is a full list of all names ascribed to genus Myrmica and a table of synonyms from among the valid names is provided. The etymology of many of the names is interesting and provides insights to thoughts of the original authors as does the short biographies are made for all authors of more than one valid species of Myrmica.
The authors believe that there are many species of Myrmica yet to be discovered, particularly in the Indo-Oriental regions and in the southern mountains of Eurasia. This book provides the essential starting point for future studies.
Radchenko is one of Europe’s leading ant taxonomists and an expert on the ant fauna of the Palaearctic, while Elmes is an ecologist and eco-physiologist who has made a particular study of Myrmica ants over a 45 year career.

Both authors, Elmes and Radchenko have already extensively published on the subject, and it is very helpful to get all their widely scattered publications in one large monograph. In the old tradition of ant myrmecologists, the monograph is pretty costly and not open access and thus it will as such not be widely accessible. The challenge will be how to process 800 pages and make the descriptions online accessible at Plazi to share already available Myrmica treatments, and thus complete all the treatments for the Old World species in places like EOL or antweb.

The details of the publication are as follows:

Myrmica ants (Hymenoptera: Formicidae) of the Old World
Alexander G. Radchenko and Graham W. Elmes
ca 800 pages, 332 figs, 162 maps; hardcover, 165 x 235 mm.

Editor: Natura optima dux Foundation, Warsaw, Poland
Issue data: December 2010

Price: 150 EUR + postage (after 31 January 2011)

Orders:
Natura optima dux Foundation
Wilcza 64
00-679 Warszawa, Poland

orders@miiz.waw.pl
fax 48 22 629 63 02

Leaf cutter ants: the frenzy of publishing

2011-01-27T02:45:00.007-05:00

If you like lavishly illustrated books on ants, you might want to consider Hölldobler and Wilson's latest oeuvre: The Leafcutter Ants: Civilization by Instinct. If you prefer those images moving - images that are even more impressive then you might want to get Thaler's movie Ameisen, die heimliche Weltmacht. One of the most impressive scene is the concrete mould of an entire attine nest in Southern Brazil. This book is an excerpt of a chapter on the authors book "The Superorganism: The Beauty, Elegance, and Strangeness of Insect Societies" that has been extended. Attines are at the very moment one of hte most fascinating area in research well beyond ants that has generated a huge amount of insights, enabled mainly through DNA technologies that allows to study their fungi, their bacterias and other commensals living in this often huge system.
That it is hip is more than confirmed by the authors of the present book: Both of them are very eloquent writers but for my taste a bit too opportunisitc by summing up ideas in a form, that are neither scientific nor popular in a general sense. The ideas presented get referenced in scientific writing later on, and not so much the original authors. This is a long history going back at least to the begin of the sociobiology debate and Bill Hamilton's genetic theory on social behavior.

A differnt kind of critique is in Mikheyev's review in Myrmecological News.

(...) a part of me wants the comprehensive fungus-gardener reference that will serve as the cornerstone of attine research, one that focuses on the cuttingedge discoveries and debates. But is it possible to write such a book today? Probably not, given the accelerating pace of research in this field, and the admittedly limited market niche. But perhaps books are no longer the best format for
this sort of material. Rather, knowledge can be better summarized in wiki-based repositories built by the community, which can remain up to date and relevant continuously.
Although the current academic system does not reward individual scientists for investing into such endeavors, perhaps, as well-acknowledged masters, HÖLLDOBLER and
WILSON could lead the way. What if the next version of The leafcutter ants would exist as a beautifully written community maintained online reference?

At the current time, there is no fame and money involved in Wiki's and too much of altruism required to run such a tool, that, without doubt will be the future; certainly not in Wilson's and Hölldobler's generation, may be not even in our, but the next generation of scientists.

[Photocredit: Thaler]

A new Asphinctopone and way of publishing

2010-06-10T01:14:00.002-04:00

Peter Hawkes just published the description of a new species of Asphinctopone, A. pilosa. This is an interesting read and shows some ways on how to present taxonomic data.

The extensive description of only one specimen, the holotype, is followed by lavish, standard digital photography, and most importantly, distribution maps. It shows not just where the ant has been found, but where its congers have been found, pointing out that this find is important because it dramatically expands the distribution to the East of Africa. What I like though is that he added an additional map, the potential distribution map derived from a bioclimatic model (BIOCLIM). One might discuss, whether this approach can be applied to an entire genus (as done here) rather than a single species, but it shows clearly a way that would help to understand the distribution of species much better than how we ordinarily present our data.
The missing point is, that the data of this analyis is not available nor in the present publication nor GBIF.

How many specimens are good enough for a description?

2010-04-20T08:04:00.004-04:00

Paknia and Radchencko describe in their recent paper two new Cataglyphis species from Iran: Cataglyphis pubescens and Cataglyphis stigmatus based samples from one and two locations respectively.

The descriptions are not accompanied by either DNA (Bar-)-Codes nor adequate images. The gray scale images do not live up to standards in the ant world (antweb.org), nor are they good enough to see the characters, nor are they available on existing antsites, not are the males described whose genitalia are the ultimate species level identification tool.

This study contributes to a fauna that is only known from literature references, including a compilation of names that one ought to believe the authors. That this could be done differently demonstrate to recent publications by McArthur and Heterick covering both Australia: The former with a lavishly illustrated compendium and key of the Camponotus of South Australia, the latter with a detailed account and key to the ants of Western Australia.

For anybody working in such an area, it would be of tremendous help, if those species would properly be documented.
I also would recommend to refrain from describing new species from one or two samples outside the context of a generic revision that provides the background why this species deserves to be described based on such poor data.

Of wood ants and bioindicators

2010-03-15T04:12:00.002-04:00

Bernasconi et al concluded in their study of European wood ants that their result "represents a clear breakthrough for discriminating between F. lugubris and F. paralugubris and is likely to be helpful in large-scale biomonitoring".

The red wood ants are the dream candidate of the last fifty years for bio-control and monitoring, but they made it never to be actually used. Why do they remain a candidate? May be there is something behind, that they are nevertheless not as good and too complicated and little understand as all the many authors would like to have it. Citing Gösswald 1990 (G¨osswald, K. (1990) Die Waldameise. Band 2: Die Waldameise
in ¨Okosystem Wald, ihr Nutzen und ihre Hege. AULA-Verlag,
Wiesbaden.) seems to be rather ironic and making the point.

This study is also a part of the tradition of European taxonomists and related specialists to claim by solving a local problem to have found the solution to the complex taxonomy, better complex demography of wood ants. First, wood ants are not just lugubris and paralugubris, but include more species. Second, they both have an extensive range with quiet some variation, especially the widely distributed lugubris. Third, there is hybridization observed in several populations.

Why not do what Dlussky already 1967 in this revision of the genus suggested, that the entire populations ought be included? If this genus is so important, a large scale study should be conducted to clean up the mess and produce genetic markers that are based on the entire population of wood ants.

All 2009 ant taxonomy publications online

2010-02-07T00:22:00.002-05:00

We are almost there where we want to be: To have an instant feed of new ant taxonomy publications into the Web, through linking the taxpub-converted treatmetents from EOL, Zoobank, HNS. We are not there, because we still get new publications, such as Hetericks "Ants of Western Australia". But this shows the sluggishness of our publication system. First, few people are aware of what is happening. Then it is published locally, and wouldn't there be connections, nobody besides few people in Western Australia and some ant colleagues would know about this.

[Sorry, I can't add link, because my system at the AMNH is down due to a snowstorm on the East coast of the US - we'll take care of this later]

Taxononomist's sloppiness - a solution

2009-11-29T03:10:00.002-05:00

I have been quiet for a long time - it was a very creative phase during which we achieved a lot regarding making taxonomic descriptions online accessible on Plazi. See following blogs.
One new tool we created at Plazi in GoldenGATE, our mark-up tool, is to find all the citations in a publications, parse its element out which then allows to link all the references within the publications to those citations the author provides.

This helps to provide, if all will goes well, to have immediate access to the original literature from within the descriptions we post on plazi.

But it also is a fantastic editorial too, since it finds all the references that are not cited at the end.

For example, Seifert's revision in Myrmecological News of the Formica rufibarbis group has three omissions: Linnaeus 1758, Latreille 1798, and Seifert 1992.

Shameless self promotion.

2008-11-30T11:45:00.005-05:00

A few years ago Donat invited me to contribute to this blog, as I was also helping with antbase.org 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 antbase.org, 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.

100 Years of the Ant Collection at the MCZ

2008-06-04T14:19:00.019-04:00

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!

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

How to Identify the Argentine Ant, Linepithema humile

2008-04-14T11:07:00.003-04:00

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 Paraná 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.

Access to descriptions on Google

2008-04-03T04:37:00.003-04:00

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!

44,614 ant names in the Hymenoptera Name Server

2008-04-02T10:29:00.007-04:00

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.

What is a bad taxonomic publication?

2008-04-01T09:56:00.002-04:00

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 plazi.org.

Now something different: shopping of course...

2008-03-07T04:32:00.003-05:00

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!

antbase.net's promotion of antbase.org...

2008-02-29T07:53:00.005-05:00

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 www.antbase.net.

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

It is confusing, and to be honest, it was confusing from the begining, when Martin Pfeiffer publicized that he started antbase.de, later renamed antbase.net. When I pointed out that there is already an antbase.org 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.

Launch of Plazi.org

2008-02-27T07:53:00.003-05:00

(For a formal release note see the biodivcontext blog)

Plazi.org 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 Plazi.org

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.

TNT now freely available

2008-01-04T11:25:00.000-05:00

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.

Graduate studies in Comparative Biology

2007-11-04T22:20:00.000-05:00

Some months ago, the American Museum of Natural History (AMNH) in New York City was granted official authority to award its own Ph.D. degrees. What this means is that, starting in the Fall of 2008, a first generation of graduate students will be able to pursue a full state-of-the-art program in Comparative Biology at the best setting possible: an institution devoted to collection-based science.

The AMNH has already a long history in graduate level education through its join programs with Columbia University, NYU, CUNY and Cornell University. Many courses are already taught right in situ by the Museum's curators, and the students enjoy use of the various resources for their research (besides the collections, there are molecular laboratories, digital imaging with a SEM facility, and the fastest computer clusters for phylogenetic analysis ever assemble, just to name a few). However, further governing autonomy will surely create a more cohesive atmosphere and save a few headaches to its students. Nevertheless, as far as I know, the AMNH will keep its join programs with the universities.

This post was prompted by the launching of the new Ph.D. program website. The application deadline is December 28, 2007. I highly recommend anyone interested to contact some of the curators and apply for this or subsequent academic years.

IISE Planet Bob: bringing Taxonomy to the public

2007-10-25T11:33:00.000-04:00

This week the International Institute for Species Exploration (IISE), a new research institute based at Arizona State University, released Planet Bob. This short, humorous film is the first effort within the IISE's commitment in educating and bringing the science of Taxonomy closer to the public. It does a good job in shaking off Taxonomy's reputation as a dead science and in describing the field's central role in biodiversity studies.

Watching the clip reminded me how unbelievable it seems that ants entered the realm of cybertaxonomy more than 10 years ago with the creation of antbase by Donat Agosti.

Publication of species names on the Web

2007-10-09T21:04:00.000-04:00

I recently found a letter Donat Agosti, Jim Carpenter and I sent to the journal Science some years ago. The letter was prompted by the journal's publication of a new species of a pre-Cambrian bilaterian fossil. The issue was that no introduction of a new scientific name was to be found in the printed version of the article, since this had been relegated to the electronic, on-line only, supplemented materials. The fossil, thus, remain unnamed in accordance to the Zoological Code of Nomenclature.

Our letter never got published, but we did receive a reply from the journal some months later. I for one was pleasantly surprised that the editors consider the matter and cared to write us back. It is very interesting. You can read both our original letter and Science's reply below.

The issue of electronic publishing of scientific names for organism continues unsolved, but great progress has been made by the International Commission on Zoological Nomenclature itself with initiatives like ZooBank.

(Submitted to Science magazine on July 13, 2004)

The report on the oldest bilaterian fossils by Chen and co-workers (“Small Bilaterian Fossils from 40 to 50 Million Years Before the Cambrian,” 9 July, p. 218) invites reexamination not only of current theories of metazoan evolution but of the rules of zoological nomenclature as well. Although the interpretation of the fossils and discussion of the relevance of the discovery appeared in both the printed and online versions of this journal, the systematic paleontology section introducing the new generic and specific names appeared as an online supplement only. The International Code of Zoological Nomenclature (ICZN), regulating the application of scientific names of animals, is yet to regard as valid publication of “text or illustrations distributed by electronic signals (e.g., by means of the World Wide Web)” (Art. 9.8.) exclusively. No scientific name for the new bilaterian fossils is thus yet available.

It is worth quoting Art. 8.6. of the ICZN as it also pertains online publication: “For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself.” The explicit rejection by the International Commission on Zoological Nomenclature of the WWW as a mean of publication responds to valid concerns regarding the permanence of such electronic media. The growing popularity of exclusively electronic, peer-reviewed, scientific journals is a welcome trend, and there is no reason why publication of scientific names for organism shouldn’t follow in that direction. However, permanence of electronic-only published scientific research should be a universal concern and not just an issue of zoological nomenclature. Greater discussion and involvement in this area by the scientific community and the publishers can result in a successful model that will prompt the ICZN to modify its rules to allow the use of electronic media as a valid form of publication for the purpose of scientific nomenclature.

Roberto A. Keller, Donat Agosti and James M. Carpenter
Division of Invertebrate Zoology, American Museum of Natural History, Central Park west at 79th Street, New York, NY 10024, USA

(reply by Science on April 27, 2005)

Dear Dr. Keller,

Thank you for your letter regarding the policies of the International Code of Zoological Nomenclature (ICZN) regarding publication of new generic and specific names on the WWW. We were unaware of that policy. We feel that the publication of electronic only information has reached a level of sophistication such that we are confident in the ability of libraries, of HighWire Press (our online publisher), and other non profit institutions to maintain copies of our electronic only publications in perpetuity. Sciences online version is the journal of record and multiple redundant copies are held at HighWire Press and at numerous libraries. Science has been published since 1880 and is fully confident that its archives from the first issue indefinitely onward will be available for future scholars. Thus we disagree with the premise of the ICZNs policy and would urge them to revisit it.

Nevertheless, we will keep the ICZNs view in mind in the future when reporting new species in the pages of Science.

Best wishes,

Katrina L. Kelner, PhD
Deputy Editor, Life Sciences

Since the bilaterian fossil publication, I have not seen new species published in Science magazine where the nomenclature does not appear in the printed version. I will always wonder how much our letter played a role in that.

Iberian Ants

2007-09-12T12:12:00.000-04:00

It seems that hormigas.org updated its interface last March (2007). The site is devoted to the ants of the Iberian Peninsula (Spain and Portugal) and its curated by Kiko Gómez and Xavier Espadaler. It is now a site easier to navigate and its data is now handled with a proper built-in database. It is also a pleasant-looking site with a simply design.

Looking at their ClustrMaps site counter it is interesting to note that the bulk of the site's hits come from Latin America. This is not surprising given that the site is one of the few such sources in Spanish. The general information on ants provided by hormigas.org is of universal use of course (classification, glossary on ant anatomy, etc). However it does shows the need for such sites and web-resources for Spanish-speakers interested in the native ants of the vast and species rich Latin American region.

Incoming Book: Ants of North America

2007-09-04T12:37:00.000-04:00

Schedule to be released in November 2007:

Brian L. Fisher and Stefan P. Cover
Ants of North America
A Guide to the Genera
$34.95, £19.95 paperback
978-0-520-25422-0

* New keys to the 73 North American ant genera illustrated with 250 line drawings ensure accurate identification
* 180 color images show the head and profile of each genus and important species groups
* Includes a glossary of important terms

You can read more at The University of California Press' website.

antbase useage

2007-08-30T16:34:00.001-04:00

ClustrMaps - our tool to visualize the geographic origin of our users - is now running for exactly one year showing almost 110.000 visits on antbase, in most cases to use the digital library and as starting point for the Ant Name Server (Hymenoptera Name Server).
I am glad we can offer a service to a truly global user community.

Nomenclatorial sloppiness (5) and a solution

2007-08-24T04:53:00.000-04:00

Christiana Klingenberg suggested being more constructive in this blog about typos and others misspelled names, and to offer my own little personal tool to the community.

Here it is. I once made two files for my MS-Word spell checker, one including all the species terms we have an the Hymenoptera Name Server for ants (of about 2002: ) and a second one for all the morphological and anatomical terminology of social insects in Torre Bueno.

And here how you use it: Save the files best directly in the location where MS World hast the spell check custom.dic file. This is in my case c:\Documents and Settings\donat\Application Data\Microsoft\Proof. Then open MS Word, Tools, Options, Spelling and Options, Custom Dictionary and add it.

The species file is not up to date, so I will figure out a way to get a new one – but for the moment, here it is.

iPod + Taxonomy = Taxon-podcast

2007-04-12T11:02:00.000-04:00

During a recent visit by Brian Fisher I showed him some Scanning Electron Micrographs from my work on ant morphology that I had stored on my iPod as a curiosity. While these gray-scale SEMs look already very good on the iPod screen, we decided to upload some full-color images from AntWeb. The results were fantastic.

Then the idea came of some sort of taxon-podcast. One can, for example, load into the iPod the ants of Arizona before going into the field or all the species of Pogonomyrmex
before sitting at the microscope in the Museum. However, for the regular AntWeb user the only way to currently upload sets of ant images into an iPod is to painstakingly save into one’s hard-drive each image individually from the desired biogeographic or taxonomic set to have iTunes read the resulting folder. Ideally taxon-podcasts could be automatically produced the way now AntWeb capably produces field guides in pdf format.

One drawback is that the iPod doesn’t have the same capabilities for dealing with images the way it can deal with a collection of audio and video files by way of hierarchical categories (artist, album, genres, composers, etc) and playlists. One can turn to Pocket PCs that are “proper” computers with touch screen interfaces. In fact, Kevin Nixon from Cornell University has had a fully functional version of WinClada for such devices for some years now, including a powerful algorithm to manage identification keys in matrix format with the ability to include images. However the idea here is to utilize the most popular electronic device to date for research and education.

Such taxon-podcasts are not going to be needed when wireless networks become global and iPhone type devices with full web capabilities become common, so we can tap directly into antbase and AntWeb. For now, with 100m units sold, iPod seems the logical choice.

The Importance of Ants...

2007-03-22T06:06:00.000-04:00

I have always suspected that ants are not just very important in any ecosystem in the world, but in our scientific world as well. Nature's bibliography project "Connotea" confirms this suspicion with hard facts: Formicidae are more important than HIV and cancer.

Thanks to Jochen Bihn's work, almost all of the digital versions of the ant taxonomic publications are now also accessible through Connotea, a bibliographic tool aimed at the general science audience.

Check it out, add you own tags, and let us known for innacuracies, wishes and more

rss feeds and new names alerts

2007-03-15T04:46:00.000-04:00

I just discovered the new UBio RSS-Nomina Nova feed for new names. This is much more professional then what we have at antbase.org, but it also has a different function, that is to discover new names in the literature. And of course, that's what we are out for to secure we have a catalogue as complete as possible.

If you compare the results from NominaNova and with our still simple "New Taxa Notifyer" for the year 2006, the results are very different: 5 publications when searching for "Formicidae" of which one is counted twice, and 105 species described (including those in the NominaNova publictions) on our system, plus two more publications or10 species for 2007 .

As a collector of new names, I would like to be NominaNova to be complete, and in return, I would like to have the possibilty to send a feedback, if I discover a publication, that is not in their feed. This is my personal interest.

But there is also a wide service to the community, since other Website providers are using the UbioRSS-feed on their website to inform their audiences about new publications (eg antweb, the ant of the cachoeira nature reserve.

There is an additional suggestion. Since all the new ant systematics publications are read, the names checked for whether they are already in the Hymenoptera Name Server, and if not, the the name is linked to an existing name and a decision is made, of what kind the relation is and then entered into the HNS, it would be ideal, if this could flow directly into the Ubio system as well - which I hope Norm Johnson at the Hymenoptera Name Server, where the ant data reside as well, and UBio can sort it out?

Nomenclatorial sloppiness (4) and a stinking dead cow

2007-03-05T16:49:00.000-05:00

Sloppiness and a dead cow

Another paper I entered recently which make me think of the value of entering names into our databases so we could in future read all our publications by machines. But it needs somebody going through often confusing prose....

here the problems I encountered in Collingwood and Van Harten's "Additions to the ant fauna of Yemen":

Pachycondyla senaarensis; ought to be sennaarensis
Cardiocondyla yemene: ought to be Cardiocondyla yemeni
Cardiocondyla schuckardi: ought to be shuckardi
Crematogaster flaviventris Santchi, clandestinely raised to species in this paper
Monomorium phoenicium: ought be phoenicum (see quadrinomen below). But originally described as Monomorium salomonis subopacum var. phoenicia by Emery 1908: 677, then cited as Monomorium (Xeromyrmex) subopacum v. phoenica Emery in Santschi 1927 in his listing of Monomorium (Xeromyrmex) subopacum v. phoenicum
Monomorium wahibiense: ought to be wahibense
Technomyrmex bruneipes Forel: clandestinely raised to species
Camponotus spissinodis Forel: clandestinely raised to species
Lepisiota opaciventris (Finzi): clandestinely raised to species

Quadrinomen, a (stinking) dead cow
I am not sure, but it was Bolton who decided to get rid of quadrinomen by just dimissing them. The Code allows to disregard quadrinomen, and so, tacitly, the first author using the name at least as trinomen becomes the author. But many of them, like Santschi in the case of Monomorium phoenicum (and more recent authors as well), didn’t care, and implicitly accept the type of the new species as the one belonging to the quadrinomen and so fixed unintentionally, thus the new species is not valid, since no type species has been fixed properly. So, following suit of Bolton's iron broom, we ought to dismiss all the subsequently raised taxa.

But this is only part of the story: If we want to collect all the names though the Biodiversity Heritage Library and Ubio, then we need somebody sitting here, like I right now, curating all these names. I have the priviledge to have a system, where I can look up all the original literature, but spend nevertheless on the above document so much time, that I think twice about the value I am getting out of this. Clearly, getting the name is only one part - and in fact none with which I can get any scientific cridentials. It only begins to add up, once I can access all the localities mentioned in this paper - but this is yet another nut to crack, and a huge time investment.

So, when I think about building up an Encyclopedia of Life project which has hardly any money for this kind of work - work that can not be done by machine nor by untrained people - I just wonder where we end up. And this Yemen paper is just a simple paper....

Nomenclatorial slopiness (3) - a positive note

2007-02-20T10:51:00.000-05:00

Entering all of Seifert's Cardiocondyla revision is like day and night to the publication I critized earlier. Reading through the former is very easy, and most of the spelling of the original combinations is actually following the original citation. Also, it is very clear, what nomenclatorial action is being taken.

Both Seifert's and Alex Wild's revision of Linepithema (including the notorious Argentine ant) include also a list of citation of the species by various authors which is opening yet another cattle of fish: taxonomic concepts.

Ubio is currently the leader in collecting all species names ever published, from the original scientific - they get from specific namer servers - to identifications used in non-taxonomic works to vernacular names, which are especially important in feathery and fury taxa. If we really do want to build up a global digital library of our legacy data (such as the Biodiversity Heritage Library might provide), then we need also to make sure, that we list these taxonomic concepts once we know the proper name of the voucher specimens used in earlier work. Only this way (through the experts opinion) crosswalks using species names can be produced. So, please make sure you add them in your systematics work!

Nomenclatorial slopiness (2) - a positive note

2007-02-19T09:33:00.000-05:00

Csösz et al.s paper recently published paper "Taxonomic revision of the Palaearctic Tetramorium chefketi species complex (Hymenoptera: Formicidae)" in Zootaxa 1405 is a nice example, where all the names can easily be found and if not present, added to a Name Server, in this case the Hymenoptera Name Server.

Norm Johnson has created a set of online data entry tools which allows entering new citations and data from any remote place to anybody who has an interest to collaborate.

In the case of Csösz' paper, I am opening up the paper, just copy and paste the respective elements and it shows up in most cases immediately up and I can view the changes through antbase.org. The HNS has even the feature allowing to subsribe to an alert to become aware of such changes. This way, the system is kept up to date as much as possible, of course depending also, whether we are aware of the papers published around the world and in places one would not expect to find new descriptions.

The advantage of Zootaxa paper over Myremcological News is, that once a pdf is available (Myrmecological News provides open access, Zootaxa only on a pay per artcile base), one can easily copy and paste any text, which is not possible generally from Myrmecological News, with the exceptions, when they provide publications with taxonomic content to be included in antbase.org.

Nomenclatorial slopiness

2007-02-19T04:53:00.000-05:00

Cataloging and entering nomenclatorial relevant data is best done by machine (if not even better generated by machine and coded accordingly). However, this needs some discipline by the authors to allow at least semiautomatic processing.

Right now, I am looking at Seiferts paper on west Palaearctic Myrmica species where he raises two subspecies to species and makes some synonymies. At least that what he mentions in the abstract.

When you actually read the paper you are overwhelmed by extensive measurements, but very incomplete information on the specimens he used to derive his conclusions. In other words, nobody could reproduce this paper- a standard scientific expectation.

Within the paper he has for some of the taxa a section header, so it is clear he talks about a particular taxon for which he at least provides a list of the taxa he is including (and only from the abstract does one knows that he is actually synonymizing them). It would be much easier for any one abstracting this paper, not to speak of the computer, if there would be a simple acronomy ".n.syn.". But then, for Myrmica spinosior, it is completely implicit that he is rasising this taxon to species level.

There is also the issue about the original citation. For example, he lists "Myrmica lobicornis var. lobulicornis Nylander" as "Myrmica lobicornis lobulicornis" which is a simple detail not necessary for the computer, but an inconsistency because in other places he is using the original citations. When I asked him about another case he just replied that I would surely know what he meant, and that he might have confused this name with what was written on the label. This has no nomenclatorial consequences, as he points out, but it means a lot more work and a lot of hassle for Zoorecord or us who actually try to keep a record of what is being published. And it makes it very difficult to write programs like GoldenGATE, which actually ought to help to transfer our systematics knowledge into a digital world, where all our colleagues could take advantage of. For a taxonomist, who now has allmost all the publications available as pdf, this might be just one step to actually check the original publication and extract the proper original combinations.

In the next case though, it might have consequences. He lists "Myrmica lobicornis lobicornis var. lissahorensis" Stärcke as synonym of Myrmica lobicornis. But this is a quadrinomen, and thus not an available name. The name has been made available by Stitz in 1939:100. Furthermore, in this case, Seifert hasn't looked at the type, but the description only.

Automatic updates on publications, sequences, taxa ...

2006-10-25T03:45:00.000-04:00

In the ideal world, I would like to focus on research rather than searching for existing information and keeping this database up-to-date.

Bibliographies:

Antweb.org 's "In the News" section based on an RSS feed from UBIO

Semant library at Connotea created by Rod Page is also initiatlly based on UBio's RSS feed, but then allows more refined searches. Detailed explanations are at Rod's semant blog. It would be intersting, if more colleagues would try it out, add more tags and eventually papers the use in their research, and we could get an integration of FORMIS and antbase.org's reference bibliography of the online catalogue, and through it have acccess to the original online literature. It would also be helpful, if those colleagues self-archiving their papers, which are otherwise not online accessible, could add their link to the semant library. Would ease the process of finding a publication much easier, and warrant a higher chance, that your papers would be read and cited.

New Taxa

Norm Johnson recently installed a very simple new taxon notification alert at the Hymenoptera Name Server / antbase.org. You can sign up at the bottom of the taxa pages you get when searching for a particular taxon, for example at antbase.org.

Thoughts on the future of antbase

2006-10-11T09:03:00.000-04:00

Whilst doing some research for an "open access" newspaper article, I found this interesting piece on Web2.0 by Tim O'Reilly.

One interesting aspect is clearly how to harvest the wisdom of all the users of antbase so we can let antbase grow and improve: what is needed that users contribute?

Digital Library Issues

2006-09-05T07:45:00.000-04:00

Improved Access to Systematics Publications: Releasing the Power of Legacy Data

Systematics publications are unique among scientific publications. Besides their quasi legal status as a conditional part of the description of a new taxon recommended by the International Code for Zoological Nomenclature (ICZN for animals, with similar codes for plants, bacteria, virus and fungi), they are highly structured and standardized. All the descriptive content is linked to a particular taxon, and they are very rich in descriptive data, the original (and subsequent) description of the taxon. These descriptions are not just taxon hypotheses but include various amounts of morphological and more recently molecular characters, materials examined, notes on behavior and distribution (an interpretation of materials examined), nomenclatorial sections, phylogenies, bibliographic references and visual art. Finally most of the content is factual knowledge, or a description of a piece of nature. Recent publications share additionally some of the structural elements of standard scientific publications (e.g. abstract, introduction, acknowledgments, etc.).

Over the centuries (since 1758 or the 10th edition of Linnaeus’ Systema Naturae), the basic structure of descriptions have not changed substantially. In its most basic lay out, they include a title (title and author) and a list of treatments. They include a nomenclatorial section containing minimally a name of the taxon, a brief description and mentioning of its distribution.

Each element in the descriptive part of a systematic publication can thus be related to a particular taxon, in particular position in a particular publication.

“Red head” of taxon X on page Y in publication Z is enough to locate it in the entire body of our legacy data. To make this machine readable, this entire relationship can be standardized, using ontologies (or controlled vocabulary), DOIs and LSIDs identifying each elements. Rod Page shows how to retrieve it. The page number is given by original designation of the position within the hard copy, which is no longer available from electronic publications. The taxon LSID can be automaticall retrieved from the Hymenoptera Name Server. A controled vocabulary or ontology is being developed by a group within the International Society of Hymenopterists, including antbase and HNS participation.

This nested structure makes systematics publication a prime candidate for automated data extraction, which we currently try to develop using, among other taxa, ant literature as pilot group (see TWiki on ants). TaxonX is the XML schema we developed and are now applying to an increasing body of publications to see its strength and value.

In fact the enormous amount of data collated over the last 250 years is the prime reason to make an effort to find ways to extract this information. For ants alone, systematics publications include over 90,000 pages, and most likely several 10 million pages for all the world’s currently described species. If we are lucky, some of it will be made accessible through the Biodiversity Heritage Library, the Biologia Centrali Americana, Animal Base and other digitization efforts.

At antbase we are currently looking into marking up all the ca 120 publications covering the Malagasy ant fauna, the ant publications from within the American Museum of Natural History Novitates, and incoming new publications.

Since descriptions are factual knowledge, they can not be copyrighted and thus be made accessible over the Web. Scientific practice demands a acknowledgement of the authorship, which at the same time is the proof of quality (i.e. it has been published).

Some comments on the ant phylogenetics symposium held at Washington D.C. Part II.

2006-08-29T19:46:00.000-04:00

Ant phylogenetics: New molecular trees to address old problems in ant biology. XV Congress IUSSI. August 1, 2006. Washington D.C.

Part I dealt only with the first four talks of the symposium; those happened to be the talks addressing phylogenetic problems at the highest hierarchical levels within Formicidae. The rest concentrated mostly on single genera or less inclusive clades with an improvement on detail. As such, they also highlighted the reasons behind phylogenetic reconstruction: improve taxonomy (Schöning et al.; LaPolla and Schultz; Wild); test predictions about the evolution of behavior (Savolainen and Vepsäläinen; Peeters); and introduce a historical component to ecological questions (Crozier et al.; Schultz and Brady; Solomon and Mueller). Rather than reviewing each of the remaining talks here I want to comment on two of them.

Alex Wild (Tucson, Arizona) presented part of his work on Linepithema. The revision of this genus is important not only because the taxonomy of the included species was outdated, but also because the Argentine ant, Linepithema humile (Mayr), is a predominant invasive ant worldwide. What is worth noting is Wild’s integrative approach to species delimitation. He draws data from morphology, mitochondrial and nuclear molecular markers and combines the information looking for agreement. The project is a painful reminder of the current state in ant species-level taxonomy; while female workers are the most commonly collected and therefore used cast in classification studies, adult males seem to display the greatest morphological diversity useful at the species level. Incidentally, Wild also showed that pure molecular approaches may be insufficient for the task, as with the use of a short COI barcode where calibrating an adequate threshold to reflect species circumscribed by an integrative approach proved daunting. Wild states in print that he explicitly follows E. Mayr’s biological species concept (Phil Ward’s fault I suppose), however it seems to me that by searching for congruence of the different lines of evidence he is really reconstructing species as historical units of the sort advocated by the phylogenetic species concept, a result that is conveniently more in line with phylogenetic reconstruction in general.

Riitta Savolainen (Helsinki) talk presented some preliminary results on a phylogenetic study of the host-parasite association between Formica and Polyergus. Previous phylogenetic work using both morphology and molecular data support a close or sister relationship between these two genera. My understanding is that the possibility exists that Polyergus may be a derived subgroup within the large Formica genus. It was puzzling to see, therefore, that a phylogeny for each genus was reconstructed independently, even though the molecular markers used were the same. Even if both genera are monophyletic, the best reconstruction within each genus will be achieved by pooling together all the species into a single matrix and rooting the result at the branch between them or using the more distant outgroups originally included.

In comparison with the similar symposium held at the previous IUSSI meeting in Sapporo (2002), the number, scope and quality of the talks presented at Washington D.C. was far superior and reflects the long overdue incorporation of cladistic methods at all levels of ant taxonomy. We have to congratulate Sean Brady and Riitta Savolainen for organizing such a stimulating symposium.

Some comments on the ant phylogenetics symposium held at Washington D.C. Part I.

2006-08-21T20:00:00.000-04:00

Ant phylogenetics: New molecular trees to address old problems in ant biology. XV Congress IUSSI. August 1, 2006. Washington D.C.

The general mood of the symposium was good. In part this had to do with the fact that the venue was adequate for the event; a large and well-lit conference room at its full capacity. Phil Ward (Davis, California) opened the symposium talking about their Ant-AToL project clearly feeling grand about the full attendance and with the advantage of presenting before Moreau et al.’s talk, yet with characteristic lusterless. Their result so far is the same as the one recently published by Moreau et al.’s in Science (and it better be, since they have practically the same taxon sampling and genes, except using EF1-alpha instead of CO-I), but, unlike the Science report, they voiced the concern that the ant tree may be rooting in the wrong place; an analysis including just the ant sequences results in a topology that cannot be rooted to achieve the same results as with outgroups included. Basically there cannot be a Poneroid clade independent of Leptanillinae (see Moreau et al. 2006). They proceeded to constrain the root at different places within the ingroup comparing the parsimony/likelihood/probability scores (Lumberg-rooting style) to argue that in any case placing the root inside the large Formicoid cluster produces highly suboptimal results. I fail to see the point of this exercise since the global optimal solution for these data (including the ingroup and outgroup sequences simultaneously) already showed that the root doesn’t end up inside that clade. At the end recovering a highly supported Formicoid clade seems to be what most excites the AtoL group.

Corrie Moreau (Harvard) followed Ward's talk. She gave a good and fluid talk and stood pleased even though it was a repetition of results from the previous talk (yet already published by her group), but including the part of dating and correlation with the diversification of Angiosperms. She also cast doubts on the root position, mentioning the fact that both Myrmecia and Amblyopone have been hypothesized as the most primitive ants even though you cannot have both, since they occur well nested inside unrelated groups. Both her and Ward said that it will probably be necessary to sequence the other nominal Leptanillinae taxa to break the assumed long-branch attraction artifact. However the question remains if the problem if confined to Leptanillinae alone or if the whole so-called Poneroid clade is acting as an “attractor” of the divergent outgroup sequences and thus the ant tree is getting rooted upside-down. After all this “clade” contains several long branches (e.g., what is the lone Paraponera clavata doing in the middle of it?). A more promising solution would be to balance the outgroup portion of the analysis, but we will have to wait for the HymATol team for this.

Chris Schmidt (Tucson, Arizona) talked next. He is working on a phylogeny of the Ponerinae sensu Bolton and not wasting any time since he downloaded many sequences from Moreau's et al. to include as many outgroups as ingroup terminals. This talk was much more sophisticated than the rest in the symposium in terms of phylogenetic methods (probably under the influence of D. Maddison), and talked about the use of mixed models instead of the traditional way of applying the same model across a given gene or a priori codon partition. The results on the tree topology are very different, with the exception of Platythyrea that always comes as a long branch sister to Ponerini. The use of mixed models seems to be a good trend among researches fond of model-base approaches, and I wonder how far will they go before realizing they came back full circle to the realm of parsimony. I only regret that C. Schmidt omitted a discussion of the taxonomic and nomenclatural problems of this group as advertised in his abstract, since sorting out taxa like Pachycondyla is going to be the real challenge for this subfamily.

After this came the second turn for the Ant-AtoL team with a talk by Sean Brady (Smithsonian), co-organizer of the symposium. In this talk the AtoL team addressed the issue of dating the molecular ant phylogeny. The results are, again, basically the same as the ones published and presented by Moreau et al. However Brady also showed that his team is exploring the sensibility of their estimations to different parameters like models, taxon sampling and tree topology. This is important given the apparent problems with the ant tree reconstruction itself discussed earlier.

I will end this already long first part noting that all of the above speakers in some way or another acknowledged the need to incorporate morphology into the picture. In part to ameliorate the issues of poor resolution and indecisiveness that the current molecular data is showing about the relationships among the ant subfamilies, but also to be able to incorporate the fossil information more precisely and achieve a more complete picture of the ant’s phylogenetic history. In all, this positive attitude towards morphology is the best thing coming out of a molecular phylogenetics symposium.

To Part II

2006-06-21T02:44:00.000-04:00

Rod Page reminded me on his SemAnt blog, that my antbase blog is still unpopulated. There is no excuse for this, but that I am not sure, how to structure this blog. Shall it be the history and thus a documentation of the development of antbase, which begun as the Social Insects World Wide Web? Shall it be about the social interactions in which we were involved building up this Web site? Shall it be about the ideas and the technical implementation? Shall it be about visions and strategic planning?

I don't know - I can't make up my mind - there are a lot of thoughts, experiences and dreams in dire need to be sorted out.

So, I will use this blog to help me sort out the various issues and write down ideas, bits of history as they come along. Hopefully, at some point, it will morph into a nice structured representation of a rathe complex world.

For those interested in the goals of antbase, there is a brief description at antbase. Write up and outreach are at this site. One of the most important development, the building of a semantic type digital library is here.

More general issues are placed either in biosyscontext for systematics specific issues, or biodivcontext for issues relating to biodiversity science, conservation and sociology.