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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.

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.

Starting next year I will be working as a postdoc in the laboratory of Patrícia Beldade at the Instituto Gulbenkian de Ciência in Portugal. This is an evolutionary developmental biology lab, an area of research fondly know as EvoDevo.

EvoDevo ask questions that are of a different nature than the classical Neo-Darwinian ones. For example, in the latter you always presuppose that variation exists in populations and that there is a link between what you see at the level of an organism’s morphology (its phenotype) and the underlying genetics (its genotype), and you study how natural selection then goes to mess things around. In EvoDevo you don’t give these things for granted. Rather, you ask how do new features (novelties and innovations) arise in the first place and exactly how does the link between genotype and phenotype comes about through the developmental process. From there, what you seek is to understand evolution as a process of modification of development.

Now, one cool thing about the Variation: Development and Selection lab of Patrícia Beldade is that her research focuses right at the area of confluence between the two views just described. She seeks to understand the mechanism by which development generates phenotypic variation of the sort that is important for natural selection to act upon.

We will be working with ants, of course, looking at the evolution of the caste system in the group. Most studies into caste evolution take the Neo-Darwinian approach to the problem. The classical work on the subject is Oster and Wilson 1978 book Caste and Ecology in the Social Insects¹, where the authors specifically set to focus “attention on the ecological and evolutionary aspects of caste, as distinct from developmental and physiological processes”². For example, there is a lot of work in this area on optimal caste ratios, looking at the proportion of the different castes within a colony in terms of how costly they are to produce. In contrast, we will look at the problem in terms of the potential that the developmental system has to produce a variety of alternative caste morphologies as dramatic as fully winged queens versus completely wingless workers.

Worker ants are, ecologically, the most conspicuous adult forms, so we often take this caste for granted. But from a comparative perspective workers are the odd ones: the flightless form arose in the common ancestor of the group as a modified version of a winged female. Once this ability originated, once this extreme plasticity in development was gained, it evolved as ants speciated giving rise to the extraordinary diversity of castes and forms we see today. But, for the most part, queens remain fully winged individuals, so in understanding ant evolution it is important to keep in mind that we are dealing with a caste-producing developmental system– just concentrating on workers wont do.

The project was written in collaboration with Christian Peeters from the Université Pierre et Marie Curie in Paris. As I have mentioned before, he specializes in all those ant species where the queen is not a winged individual, but rather a wingless form intermediate between the typical queen and the worker. This component is also important for our project, not only because such peculiar type of queens gives us more insight in this plastic developmental system, but also because queen morphology has a direct impact in the reproductive strategy of colonies. So this is a way to tie morphology and development with behavioral ecology and thus ask questions on selection and adaptation.

Does this means I am turning away from systematics? Not at all (again, for the joy of some and fear of others). My research centers on understanding the evolution of form, and while comparative anatomy and systematics serve to establish evolutionary patterns, it is development that provides the process side of the explanation. In fact, the first part of the project is pattern oriented, our goal been to identify and characterize relevant anatomical modifications. Besides, I still have a backlog of systematic manuscripts from my PhD research that I am preparing for publication.

Expect to see more on this topic in the coming months.

Notes and references

We ought not to think that a conception or definition or hypothesis that works in one part of biology must work in all others, and yet biologists themselves often behave as if this were true. That is another challenge: why is this? The answer, I believe, is that biology is both highly diverse, and also massive.

Read the rest in his post: Counterintuition: Bdelloid Rotifers « Evolving Thoughts.

Published online before print August 28, 2009, doi: 10.1073/pnas.0908357106

Caterpillars evolved from onychophorans by hybridogenesis

Donald I. Williamson
Marine Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom

Abstract:
I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals. “Caterpillars,” the name for eruciforms with thoracic and abdominal legs, are larvae of lepidopterans, hymenopterans, and mecopterans (scorpionflies). Grubs and maggots, including the larvae of beetles, bees, and flies, evolved from caterpillars by loss of legs. Caterpillar larval organs are dismantled and reconstructed in the pupal phase. Such indirect developmental patterns (metamorphoses) did not originate solely by accumulation of random mutations followed by natural selection; rather they are fully consistent with my concept of evolution by hybridogenesis. Members of the phylum Onychophora (velvet worms) are proposed as the evolutionary source of caterpillars and their grub or maggot descendants. I present a molecular biological research proposal to test my thesis. By my hypothesis 2 recognizable sets of genes are detectable in the genomes of all insects with caterpillar grub- or maggot-like larvae: (i) onychophoran genes that code for proteins determining larval morphology/physiology and (ii) sequentially expressed insect genes that code for adult proteins. The genomes of insects and other animals that, by contrast, entirely lack larvae comprise recognizable sets of genes from single animal common ancestors.

I think Lynn Margulis went too far this time…

In the absence of specific arguments to the contrary, shared patterns of gene expression should not lead us, per se, to homologise organs that a comparative morphologist would never try to compare.[p.23]

Alessandro Minelli 2003. The Development of Animal Form: Ontogeny, Morphology, and Evolution. Cambridge University Press. Cambridge.

Each session was more or less arranged around controversial topics and the organizers made an effort to include people across disciplines- there were biologists, philosophers, anthropologists, linguists and even the odd economist. The latter is working on applying a Darwinian framework to study the evolution of political institutions, but appears to have a hard time convincing his peers that Darwinian evolutionary theory does not implies teleology nor does it provides a scientific justification for racism. Good luck with that.

The highlight for me was to meet philosopher of biology John Wilkins, who keeps one of my favorite blogs at ScienceBlogs. During his talk he covered the murky and much discussed topic of species. One of the basic premises of his work is that if you take the Essentialist story seriously and set out to study all those pre-Darwinian taxonomists who believed that species had essences and were therefore unable to accommodate evolution into their worldview, you won’t find any. Not even all the way to Aristotle. It is yet more research arriving at the conclusion that Ernts Mayr constructed a straw-man of unenlightened typologists just for marketing purposes while promoting his version of the Biological Species Concept. The fruits of Wilkins decade-long research on species is about to be published in the form of two books.

I was able to harass him during coffee breaks and dinner with annoying questions about philosophy of taxonomy. He is a very clear thinker and I’m happy to report that he answered all my questions graciously. And in case you were wondering, irl he looks just like the great white gorilla in his blog’s avatar. I know, it’s freakish.

Their main argument is an historical one, namely that the concept of homology predates the general acceptance of evolution, and hence its definition should remain non-evolutionary. Not doing so will be “whiggish history”. They seems not to realize, however, that the language of science, its concepts and definitions, behave like scientific hypothesis themselves, changing and adjusting as more knowledge about the world accumulates. Yes, surely Belon did not think in evolutionary terms and Owen was a closeted transmutationist, but they did realize that there was something behind those patterns that called for an explanation, they just didn’t know what it was (or were not ready to accept). Their pre-darwinian concepts and definition of homology reflected the  standards of their times, something that prepared Natural History for the big change in the way of viewing things that was about to come.

But today, objecting to the notion that the human five-fingered hand and the five-toed foot of a lizard, as homologous features, were both inherited from our common ancestor is equivalent to objecting at the definition of water as H2O. Water, and most of its properties, were know before the atomic theory of elements, but it is through this theory that we are now able to explain and predict the behavior of this compound. Today, we gain nothing by insisting on a non-atomic definition of water.

Like Ebach and Williams, I am fond of pre-darwinian concepts (as the title of this blog should reveal), and thus welcome that historians and philosophers of science are shifting focus away from Darwin an into the interesting nineteen century science that has been eclipsed by The Origin of Species. I also share the view that the discussion on just how much we need to assume about the evolutionary process in order to reconstruct evolutionary patterns is an interesting one. On a general level, I do think that questioning our epistemological limits is a healthy exercise. Nevertheless, I also share John S. Wilkins recent remark that one shouldn’t make of the pattern everything that there is.

Ebach and Williams close their post stating that “[t]here is a misconception in science that everything needs to be explained.” Well, in science everything does need to be explained. That the explanation into why we have a given paraphyletic group has to do with a taxonomist’s misjudgment or preference for non-natural groups rather than due to the existence of some evolutionary processes is another matter.

References
Anastasia Thanukos (2008). Bringing Homologies Into Focus. Evolution: Education and Outreach, 1 (4), 498-504 DOI: 10.1007/s12052-008-0080-5