The official pin. The H stands for Croatia, of course.

I just returned from the meeting of the International Union for the Study of Social Insects, an every-forth year affair that brings together scientists from around the globe under the common umbrella of social evolution. This year the venue was Copenhagen, Denmark, with over 700 participants.

Among the many colleagues I encounter, I had the pleasure of finally meeting ant ecologist Jelena Bujan, vice president of the Croatian Myrmecological Society (HMD). To my surprise, I was made a honorary member of the society and presented with the elegant pin pictured above in recognition of my outstanding efforts in education about ant morphology through this blog… Ok, ok, I’m exaggerating. I know the pin is really for people who are fans of the HMD. But Jelena did mention she likes my blog and I always wanted to visit the Balkans. The pin now decorates my camera bag (the pin is not huge– my camera bag is really tiny).

And this brings me to another point. Many of my professional colleagues told me how much they enjoy my Homology series. Which does encourage me to put more effort, once in a while at least, into this otherwise neglected blog.

Main Entry: cla·dis·tics
Pronunciation: \kl?-?dis-tiks, kla-\
Function: noun plural but singular in construction
Date: 1965

: a system of biological taxonomy that defines taxa uniquely by shared characteristics not found in ancestral groups and uses inferred evolutionary relationships to arrange taxa in a branching hierarchy such that all members of a given taxon have the same ancestors

— cla·dist \?kla-dist, ?kl?-\ noun
— cla·dis·tic \kl?-?dis-tik, kla-\ adjective
— cla·dis·ti·cal·ly \-ti-k(?-)l?\ adverb

I don’t know when was this entry actually added to the dictionary, but it is nicely defined.

I want to call your attention to a new blog written by Kurt Pickett, a colleague and close friend of mine. Kurt and I meet at the American Museum of Natural History a few years back. He was a postdoc and I a grad student, both working with James M. Carpenter.

The blog, Apoica, is named after the genus of rare nocturnal paper-wasps (Vespidae) he studied during his Ph.D. at Ohio State University. Kurt is currently an assistant professor at the University of Vermont where he continues his research on phylogenetics and the evolution of social behavior in the paper-wasp family. We are actively collaborating on a project involving ants (of course), combining molecular and morphological data for phylogenetic analysis.

In his blog Kurt writes not about his discoveries on wasp behavior, but about another major discovery he came upon by the end of his postdoc years: he has lymphoma. He recently underwent a bone marrow transplant, the ultimate treatment for his kind of cancer. He blogs about the up and downs of his recovery with the eye of the excellent scientist he is. Kurt has a great sense of humor, but don’t expect his posts to be anything but rather dark in tone.

Cretaceous African ant in amber (Courtesy of Vincent Perrichot via http://myrmecos.wordpress.com)

1. A peer-review paper gets published;
2. The media gets hold on the story;
3. The blogs react: scientists and general public fill the comments section (in the genuine tone of the internets);
4. The authors of the original paper join in the discussion.

Discussion may get heated, comments may get bitter, but the results are always rewarding for all.

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Do not forget to tune in to tomorrow’s phyloseminar where Noah Rosenberg will be speaking about consistency properties of species tree inference algorithms under the multispecies coalescent. February 24th at 1pm PST.

You can watch him live from the comfort of your computer, but you may want to take some minutes before the seminar to set up your computer and microwave some popcorn.

"Oecophylla smaragdina can carry more than 100 times its own body weight while upside down on a smooth surface, thanks to its sticky feet." Image: Thomas Endlein, University of Cambridge via NewScientist

NewScientist posted photographs from the competition held by the UK’s Biotechnology and Biological Sciences Research Council to showcase images of their latest research. In a single iconic image, the first one shows the weight that an ant is capable of carrying and how strong the suction devices in her feet are.

I have blogged about these adhesive devices in the ant’s feets before (called arolia in leet speak, singular arolium), and the very first image I used back then happens to be from the same ant species in the image above.

Foot of a Oecophylla smaragdina worker. Pretarsal claws and manubrium in red; arolium in yellow; tarsi in green (Scanning Electron Micrograph, Roberto Keller/AMNH)

(h/t to P. Beldade)

Ready to rock.

My colleague Corrie S. Moreau, Assistant Curator at the Field Museum of Natural History in Chicago, got interviewed by ScienceWatch.com in occasion of her highly cited paper in Science published back in 2006.

It’s a nice interview, but I have a couple of reservations though. She states that:

This well-resolved phylogeny reinforced some previous hypotheses about the morphological evolution of the ants, but we also were able to demonstrate that the modification or reduction of the stinger happened twice independently within the ants.

By twice she refers to subfamilies Dolichoderinae and Formicinae which, true they are characterized by extensive reduction and disarticulation of the sting apparatus or complete disappearance of it respectively, so that the finding that they are not sister groups entails that loss of sting ocurred independently in the common ancestor of each clade. But there are various other parts of the ant tree where the sting is reduced and useless as a weapon, so this was known to happen more than twice even before molecular phylogenies were out. Think the army ant Dorylus and the myrmicine genus Cephalotes (turtle ants) just to name a couple of examples.

The other is Cories’ reply to the question:

Do you foresee any social or political implications for your research?

Because here I was really, really hoping that instead of her actual answer she would had said something like “Biological weapons of course! Just think of the Alien series of movies.”

Finger puppet!

I agree with her, preparing animals that have the skeleton on the outside is way easier and much more cleaner.

Now, the fact that the registration fee includes ethanol and ethyl acetate (for preserving the locally collected fauna) should tell you something about the level of geekiness of the crown that normally attends these meetings. But, it’s professional geekiness mind you.

You can find more information here (pdf).

The idea behind phyloseminar.org is to hold regular live online seminars in phylogenetic methodology open to anyone around the globe. This is a challenge given the time zone differences of the possible participants, but it does makes the whole event fun: I watched it after dinner at 9:00pm; the presenter gave it at his 4:00pm; while the moderator was there after lunch at his 1:00pm. I saw at least one person among the audience that watched it from the future after breakfast in New Zealand the next day at 10:00am.

We used the software EVO, a free tool specifically designed for scientific communication (unlike the Internets that was designed for… nevermind). Prior to a seminar, you need to install and create an user account so you can then join the phyloseminar channel. It works really well. You see a window with the slideshow and a window with video stream for each participant (to keep things simpler, only the presenter and the moderator had video enabled last night).

For Wheeler’s talk we were twelve people, and looking at their user accounts (where you can set your location), there were people listening in California, Kansas, New York, Lisbon and New Zealand at least. The talk was 45 minutes long and went on for another 15 minutes of discussion. We could type questions using the chat tool of the software, which were then read by the moderator (again, rather than each person talking to keep things simpler).

Looking right into Wheeler's desktop.

Wheeler’s talk, Dynamic homology and phylogenetic systematics, was about alignment, or rather methods to avoid having to perform an alignment for phylogenetic inference altogether, something he has been championing for many years now. The idea behind these methods, called direct optimization methods, is easy to understand: when you are comparing DNA sequences in order to reconstruct how species (or genes) are related to each other, you need to match them together to determine which positions along a sequence correspond to which positions in another one, a process called sequence alignment. Only then can you asses whether different species have the same or a different base composition in each position– the raw evidence for evolutionary relatedness. But it happens that, because those sequences are the result of a process of mostly branching evolution (where one species splits to gives rise to two descendant ones), the proper format for comparison between multiple sequences is not a matrix of rows and columns but a phylogenetic tree. The problem is that we don’t know the shape of this tree because that is what we seek to reconstruct in the first place.

The most common way to address this problem is to perform alignments using tree shapes that we know are a good approximations. Once we find a satisfactory match between our sequences, we proceed with the phylogenetic reconstruction proper, searching for the tree(s) that maximizes our optimality criterion (e.g., parsimony, likelihood). But one caveat of the procedure I just caricatured is that by running the analysis in two steps (alignment and tree search), you impose a restriction on the number of possible combinations you will evaluate. Direct optimization lifts this restriction by performing the sequence matching and tree evaluation in just one step, with the potential result that you may find more optimal solutions. In other words, direct optimization methods are able to perform more thorough exploration of the space of possible solutions.

Now, while the method is easy enough to describe in a post, its mathematical and computational implementation is not simple at all. The amount of operations needed to evaluate just a single tree shape increases exponentially in comparison with vanilla tree searches, and you will be better off performing these calculations in a computer cluster.

The aspect that caused more unease during the talk was Wheeler’s explanation of the difference between truth and optimality inherent in all these methods (direct optimization or not). Apparently, when you simulate sequence data in order to run it through different programs and evaluate how well each alignment methods does, they all invariably find solutions that are more optimal (more parsimonious, more likely or more probable) than the simulated one. That is, most of the time the optimal solution is different from the true one. The consequence of this is that, since in phylogenetic reconstruction we will never know for certain the true evolutionary history, we are forced to abandon the search for the true solution and will have to content with finding the optimal one.

If this talk was representative of the series, I said the seminars are not for the general audience: you needed a very good grasp of phylogenetic theory; alas, if you know Ward Wheeler you know that his brain runs as fast as his supercomputers. A good thing is that the seminars are being recorded and can be revisited anytime. You can watch the first one by Marc A. Suchard here and the one by Ward Wheeler there soon. The next seminar will address the problem of reconciling gene tress with species trees, and the next three seminars are decided by popular vote.

The whole experience was a first for me, and it was real fun.