Celebrating the molecular revolution

I forgot to say happy Darwin Day yesterday, but to make up for that, I present to you Max Telford’s extremely cool way of celebrating.

In 1988, on Darwin Day, no less, a 5-page little paper was published in Science that would absolutely revolutionalise the study of animal evolution. Field et al. (1988) was one of the earliest studies to apply this newfangled thing called molecular biology to the phylogeny of animals. Methods for molecular phylogenetics (or indeed any kind of phylogenetics) were extremely limited by the performance of the computers of the time, but that didn’t stop scientists from trying them. And once someone kicked this snowball, the avalanche couldn’t be stopped.

This early attempt yielded some huge surprises. Arthropods, which were thought to have arisen from segmented worms, were not closely related to any kind of worm. Brachiopods, long thought to belong to their own major group, showed up deep among worms, molluscs and other uncontroversial protostomes instead. Cnidarians such as hydras and sea anemones, and bilaterians such as ourselves, arose independently from single-celled ancestors.

Some of their conclusions – among them the last one about several origins for animals – were contradicted by more sophisticated analyses. Nevertheless, what they stirred up was the beginning of our current understanding of animal phylogeny. For the 25th anniversary of this pivotal publication, Max Telford, animal phylogeneticist extraordinaire of University College London, went back to the roots of his field and reanalysed Field et al.’s data (Telford, 2013).

Could the data and methods of the time have yielded a more accurate tree? How does a “modernised” dataset fare under the latest methods? What advances in methodology and understanding led the molecular phylogenetics of animals from the first tentative steps in the 1980s to where we are today?

Analysing the original data with methods similar to the original, of course, repeats most of the original mistakes.  It’s when Telford starts tweaking things that the interesting stuff starts to happen. For example, just switching from the original method to a more complex one that was available but would have taken years to run at the time pulls all animals back together. “Updating” the analysis by using more complete sequences of the same gene, slower-evolving relatives of some original species, and modern methods impossible to run on 80s computers comes very close to today’s consensus. In other words, Field et al. basically did the best they could. Since then, data availability, careful sampling and far more computer muscle have changed some of their conclusion – but confirmed others.

Telford highlights one way in which the classics got lucky, too. Back in the eighties, sequencing nucleic acids was a difficult affair. Field et al. (1988) picked 18S ribosomal RNA mostly because it was less difficult than most others. But, as Telford points out, they also hit on a really good gene for phylogenetics. The 18S is quite long, providing an abundance of data. It has both very conserved and variable regions, so it has something to say on all levels of divergence. And, as Telford’s updated analysis shows, it can actually give reasonably accurate results on its own, which cannot always be said of single genes. For long years after Field et al. (1988), 18S rRNA continued to be used to probe into animal relationships, and had a few more revolutions up its sleeve (Aguinaldo et al., 1997; Ruiz-Trillo et al., 1999) before yielding to huge multi-gene datasets.

Contemplating Telford’s little historical excursion, I’m reminded of Isaac Asimov’s fantastic essay The Relativity of Wrong. We’ve come a long way from our first bumbling attempts at molecular phylogenetics. We were wrong many times, and I can guarantee you we’re still wrong about a lot of things. But I like to think that, as with the shape of the earth, we are not quite as wrong as our predecessors. Over the years, some great branches of the animal tree have crystallised from a sea of studies. With dogged determination, science approaches the truth.

I think that’s a good note to end on when we commemorate the birthday of a scientist who spent decades perfecting his theory of evolution before publishing perhaps the most important book in the history of biology. Happy belated Darwin Day! 🙂

***

References:

Aguinaldo AMA et al. (1997) Evidence for a clade of arthropods and other molting animals. Nature 387:489-493

Asimov I (1989) The Relativity of Wrong. The Skeptical Inquirer 14(1):35-44.

Field KG et al. (1988) Molecular phylogeny of the animal kingdom. Science 239:748-753

Ruiz-Trillo I et al. (1999) Acoel flatworms: earliest extant bilaterian metazoans, not members of platyhelminthes. Science 283:1919-1923

Telford MJ (2013) Field et al. redux. EvoDevo 4:5

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