Saturday, April 11, 2009

Phylogenomics and Metazoan Evolution

During the course of constructing a “Tree of Life” based on more than 120 gene sequences and fifty-five different species, a group of scientists led by Gert Wörheide of Munich have reached two conclusions; one, all Porifera (sponges) share a common sponge-like ancestor, and two, that ancestor did not give rise to the Bilateria.

According to Wörheide, “If the ancestral animal would have had a sponge-like organization or body, as some earlier molecular studies repeatedly claimed, then we would all be descendents of such sponge-like organisms. This proposition generated a lot of attention in the past. But our results clearly disagree with it."

The origin of many of the defining features of animal body plans, such as symmetry, nervous system, and the mesoderm, remains shrouded in mystery because of major uncertainty regarding the emergence order of the early branching taxa: the sponge groups, ctenophores, placozoans, cnidarians, and bilaterians. The ‘‘phylogenomic’’ approach has recently provided a robust picture for intrabilaterian relationships but not yet for more early branching metazoan clades. We have assembled a comprehensive 128 gene data set including newly generated sequence data from ctenophores, cnidarians, and all four main sponge groups. The resulting phylogeny yields two significant conclusions reviving old views that have been challenged in the molecular era: (1) that the sponges (Porifera) are monophyletic and not paraphyletic as repeatedly proposed, thus undermining the idea that ancestral metazoans had a sponge-like body plan; (2) that the most likely position for the ctenophores is together with the cnidarians in a ‘‘coelenterate’’ clade. The Porifera and the Placozoa branch basally with respect to a moderately supported ‘‘eumetazoan’’ clade containing the three taxa with nervous system and muscle cells (Cnidaria, Ctenophora, and Bilateria). This new phylogeny provides a stimulating framework for exploring the important changes that shaped the body plans of the early diverging phyla.

Phylogenomics is the science of comparing genetic compliments, such as genes, nucleotides or entire genomes from different species, and through the application of statistics determining the “best fit” in terms of any evolutionary history (phylogeny) that the organisms share. Frequently these studies result in multiple “possible fits” and determining the most parsimonious model isn’t always a simple task, but in the case of this current study, it appears that the bar has been raised.

(A) Schematic section of an adult sponge (bottom) and SEM picture showing a choanocyte, the sponge collar cell (top, choanocyte from Chelonaplysilla noevus, Demospongiae). The arrows indicate the direction of circulation of water in the aquiferous system of the sponge. Abbreviations: atr, atrial cavity; cb, cell body; cc, choanocyte chamber; col, collar of microvilli; ex, exhalant canal; fl, flagellum; in, inhalant canal; mes, mesohyl; osc, osculum (or exhalant orifice); ost, ostium (or inhalant orifice); pin, pinacoderm (thin epithelial layer, limiting the sponge body on its external surface and within the canals); sp, spicule.

(B) Most parsimonious scenario for the evolution of sponge body plan characters, imposed on a scheme of sponge paraphyly.

(C) Most parsimonious scenario assuming sponge monophyly.

In (B) and (C), the gray branches indicate the presence of sponge body plan characters (aquiferous system, internalized choanocyte chambers, pinacoderm) and the black branches indicate the absence of these characters. The gray horizontal line indicates character acquisition; the hollow horizontal line indicates character loss. ‘‘Sponges 1, 2, and 3’’ correspond to the major lineages (silicisponges, homoscleromorphs, and calcisponges), of which exact branching order varies among published studies recovering sponge paraphyly.

Incidentally, if your interested in the search for the urbilaterian (common ancestor of Bilateria), I’d recommend a look at a recent paper by Neil Shubin, Cliff Tabin and Sean Carroll titled Deep homology and the origins of evolutionary novelty. This article was published this past February in Nature.

Philippe, H., Derelle, R., Lopez, P., Pick, K., Borchiellini, C., Boury-Esnault, N., Vacelet, J., Renard, E., Houliston, E., & Quéinnec, E. (2009). Phylogenomics Revives Traditional Views on Deep Animal Relationships Current Biology DOI: 10.1016/j.cub.2009.02.052

Shubin, N., Tabin, C., & Carroll, S. (2009). Deep homology and the origins of evolutionary novelty Nature, 457 (7231), 818-823 DOI: 10.1038/nature07891

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