Reconstructing Nemo: An Elegant Paper on Clownfish Evolution
Why would a mycologist be blogging about a paper about clownfish? I'd be the first to admit that my knowledge of marine biology is practically nil. I'm not even particularly interested in fish phylogeny, truth be told. Nonetheless, this particular paper details such elegant research and is written so lucidly that I couldn't resist writing about it. This is great stuff and I think anyone with an interest in molecular biology, biogeography and phylogenetic reconstruction in general will appreciate it, even if you're like me and prefer your fish blackened with a nice herbal crust as a rule.
Authors Simona Santini and Giovanni Polacco conducted the most thorough investigation of the subfamily Amphiprioninae to date. This subfamily has been divided morphologically into two genera comprised of 28 species; the present study includes 23 of these species.
The investigators sequenced or obtained previous sequences from three regions of the mitochondrial genomes in their subject species. Two of these (cytochrome b and 16S rRNA) are relatively conserved coding regions and the third (the first half of the D-loop control region) is non-coding. As one would expect, coding regions are under significant selective pressure while non-coding regions are not, so including all three of these provides a high degree of signal resolution in terms of molecular phylogeny. The molecular phylogeny was then overlaid onto morphological and behavioral reconstructions as well as biogeographical data. The consensus tree resulting from these thorough data sets produce some surprises, not the least of which is that the overall reconstruction defies Mayr's rule-of-thumb that evolution is polarized in the direction of increased specialization beginning with generalist ancestors.
In fact, it appears more likely that clownfish (or more properly, anemonefish) evolved from a specialized ancestral species that dwelt in rock crevices in the Pacific Ocean, more specifically in an area between the Phillipines, Sumatra, the Great Barrier Reef and Melanesia. The evidence supports a morphology quite different than what we see today; the ancestral anemonefish seems to have been a shy, slender-bodied fish with a rounded tail. It is likely that this ancestor formed a symbiotic relationship with one or two anemones. Eventually, the fish dispersed and developed bold, territorial behavior that allowed the descendants to become generalists. In fact, the most generalist clownfish species also have the most derived character states overall. This is an exception to the general rule; we usually see things the other way around. The paper demonstrates that the subfamily forms a true clade and calls for a new taxonomy of Amphiprioninae. In light of the thoroughness of this work, that seems well-justified.
Santini and Polacco's paper is relatively easy to read. They give enough background information on nearly everything they do in their study to make it readily accessible to laymen. It's nice to see such thorough work so carefully explained; even a guy like me who spends most of his time looking at fungi quickly learned a few new things. Those who are trying to get a handle on how evolutionary reconstruction works and how molecular biology enters into the picture could certainly do a lot worse than using this paper as a jumping-off point.
The only critique I have of this excellent publication has to do with the graphics. The trees shown in figure 2, in particular, would be much easier to comprehend if they had been in color rather than various shades of gray. Since biogeography also plays a substantial role in the research, a map showing the current ranges of the anemonefish as they exist today and routes of dispersion from their origins — a historical biogeography — would have been quite helpful in more fully visualizing the conclusions arising from the work. Still, these are minor points in comparison to the outstanding work that's been done here.
Finally, because I don't know much about fish, I'm left wondering about the use of certain morphological traits in constructing some of the phylogenetic trees. For example, things like body depth and caudal fin shape are clearly not discrete character states; they'd be analogous to height and limb length in humans, for example. I would also think that they'd be strongly influenced by environmental effects. I can't really tell from the paper how the authors compensated for these potential shortcomings in reconstructing the phylogenies based upon them.
Two other characters — number of hosts and dependence upon hosts for sheltering — seem to me to rely heavily upon a thorough knowledge of the behavior of the species under examination. The authors mention, however, that several of the species examined have not been well-studied previously. Whether these traits are among those which have been well-documented or whether some other means by which to base a reconstruction upon them was hit upon I can't say. Perhaps someone more knowledgeable about these fish can fill me in on what's known about the behavior of species like Amphiprion latezonatus and A. mccullochi.
Reference: SANTINI, S., POLACCO, G. (2006). Finding Nemo: Molecular phylogeny and evolution of the unusual life style of anemonefish. Gene, 385, 19-27. DOI: 10.1016/j.gene.2006.03.028
