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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)

Finger puppet!

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

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.

Here is a hidden treasure in the web.

Robert E. Snodgrass was an American entomologist who published extensively on arthropod anatomy and evolution during the first half of the twentieth century. He was as knowledgeable about arthropod morphology as he was a superb artist– you can see some of his illustrations decorating the banner of this blog. His name is synonymous with insect morphology: his 1935 textbook on the subject (reedited by Cornell University Press in 1993) is still the main reference for any modern course in entomology.

Snodgrass was a lecturer in the University of Maryland for most of his academic life. In 1960, two years before his death, he gave a series of three lectures that were recorded in audio tape. Fortunately for us Jeffrey W. Shultz, professor of entomology at Maryland, has digitized and made these lectures available through a nicely designed page called The Snodgrass Tapes.

Adding to the audio files, Shultz provides well annotated transcripts and, even more impressively, has taken the time to got through Snodgrass’ extensive body of anatomical illustrations to incorporate those suitable for each passage. You have the option of following the lectures in your web-browser with sound, text and illustrations, download the transcripts as pdf files, or just the audio as mp3 files and put them into your iPod¹.

The audio itself is a real treat. Adding sweet to the lectures is the constant sound of chalk against the blackboard as Snodgrass masterly drew his illustrations for the audience. But these are not dry lectures. As he deals with the particularities of arthropod anatomy he constantly pauses to introduce the listener to general terms and concepts of evolutionary theory, all done with parsimonious grace and elegance. For example, when laying out the difference between the often confused pair of terms rudiment and vestige (the former referring to ontogeny while the later to phylogeny), he states:

[...]the rudiment is something that has a future, and a vestige is something that has a past.

The page also provides links to pdf versions of Snodgrass biography and list of publications compiled and published by Ernestine B. Thurman in 1959.

Note

We are please to announce that the 5th Portuguese Evolutionary Biology Meeting will take place at Instituto Superior de Psicologia Aplicada (ISPA) in Lisbon on December 21st 2009. It is being organized by Unidade de Investigação em Eco-etologia and Centro de Biociências do ISPA (Rua Jardim do Tabaco, 34, Lisbon).

The Portuguese Evolutionary Biology Meetings aim to bring together Portuguese researchers and to promote Evolutionary Biology in Portugal. They are held in late December to allow researchers in foreign institutions to attend, given that many spend their Winter break in Portugal.

To celebrate this special year, we will have Prof. Douglas Futuyma (Stony Brook University, NY, USA) as an invited speaker. The remainder presenters will be either Portuguese or working in Portugal.

Presenters should register by sending a message to biologia.evolutiva at gmail.com with the following information:

- Presentation title,
- Name and affiliation,
- Topic
- Short abstract

The deadline for registration is November 30th. Portuguese and English will be the official languages of the meeting.

Also, we are happy to announce that we will discuss the creation of the Portuguese Evolutionary Biology Association. This idea has been on table for some time now and we will decide if this is the time to formalize it.

We would appreciate ample distribution of this announcement.

Best regards,

The Organizing Committee

The International Institute for Species Exploration (IISE), Arizona State University (ASU), invites applications and nominations for a postdoc available January 1, 2010. Duties include dissections, descriptions, and digital illustrations of beetles for print and Web publications, participating in the Institute team working on various cybertaxonomy initiatives, and supporting the research of the director, currently including taxonomic studies of Eleodes (Coleoptera, Tenebrionidae).

ASU is an equal opportunity/affirmative action employer. Women and minorities are encouraged to apply. Submit statement of interest, CV, and names/email addresses of three references to: Quentin Wheeler, Vice President and Dean, College of Liberal Arts and Sciences, Arizona State University. Please submit electronically to tyna.chu@asu.edu with subject line Morphology Postdoc. Review of candidates will begin immediately and continue until the position is filled.

There are very few positions advertised these days within organismic biology that do not include the word Genomics, or another molecular flavor, prominently in the title. While the extensive molecularization of the field has been a welcome trend, it has pushed aside fundamental studies into morphology.

This position is the dream job for anyone interested in beetle morphology and taxonomy. The IISE is a state-of-the-art place for the study of biological diversity. Quentin Wheeler has been my friend and colleague for many years now–I cannot think of anyone more passionate for taxonomy, and he is an engaging person to work with for sure.

(Besides, I know from good sources that the position’s salary is among the bests you will find as a postdoc.)

George Campbell Eickwort (1949–1994)

The Department of Entomology at Cornell University saw a time of great research and teaching in insect morphology at the end of the Twentieth Century, most of which came from the efforts by two extraordinary systematists: William L. Brown Jr. and George Campbell Eickwort.

Brown was the premier ant systematist of his time. His publications on ant taxonomy exude his masterly grasp on morphology, and he supervised a multitude of students doing dissertations on basic comparative anatomy for the group. Two excellent examples are Thomas Eisner’s 1957 work on the proventriculus¹ and Gotwald’s 1967 detailed work on mouthparts². Eickwort main research focused on sweat bees, but as a teacher he was responsible for the course on insect morphology that covered all insects groups plus relevant outgroups. Sadly, by the end of the 1990’s both men had died.

Eickwort course was legendary. I know of students pursuing PhDs on other prominent universities, like Harvard, that spend one semester at Cornell just to take this course. The main part of it consisted on laboratory practices that gave students direct experience with morphology while at the same time it introduced basic techniques on dissection, microscopy and drawing. The last of these is essential for understanding morphology: drawing forces you to truly look at the details of the structure under analysis.

Eickwort’s laboratory manual was compiled and it is available on the web as a series on pdf’s. This is the version of the course I took during my graduate student years at Cornell. It is a great teaching resource. Oh, and the drawing in the cover is by yours truly.

Notes

Raghavendra Gadagkar

I believe that most working scientists should spend part of their time explaining and discussing their work with a larger audience. There are at least three important reasons for this. One is that science needs to become an integral and essential part of society and not be perceived as an outside force that is at loggerheads with society. Second, scientists need to recruit the best young minds to make up the next generation and that can only happen if we devote time to communicate with the general public. Third, I have no doubt it will help us appreciate our own work better.

From the book review of  Keller, L. & Gordon, É. 2009: The lives of ants. – Oxford University Press, Oxford, UK, XI + 252 pp.¹