Evidence that choanoflagellates are an outgroup of Metazoa, not derived from sponges

From ChoanoWiki

NOTE FROM NICOLE: I'm planning to write this up as a brief perspective for publication, so I would appreciate any input or advice.

There is a persistent misconception that choanoflagellates are derived from sponges. Three lines of evidence demonstrate that choanoflagellates are the sister group of animals and, importantly, not derived from sponges. Using three different types of molecular data, animals (including sponges) are found to be monophyletic to the exclusion of choanoflagellates.

1) molecular phylogenetic analysis using individual genes from choanoflagellates, diverse sponges, and diverse eumetazoa

• Carr M, Leadbeater BS, Hassan R, Nelson M, Baldauf SL. (2008). Molecular phylogeny of choanoflagellates, the sister group to Metazoa. Proc Natl Acad Sci U S A. 105(43):16641-6.

• Steenkamp, ET, Wright, J & SL Baldauf. 2006. The protistan origins of animals and fungi. Mol Biol Evol 23(1):93-106.

2) molecular phylogenetic analysis using genome-scale data from nuclear genes of a choanoflagellate, representative sponges, and diverse eumetazoa

• King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 2008 Feb 14;451(7180):783-8.

• Rokas, A., Kruger, D. & Carroll, S. B. Animal evolution and the molecular signature of radiations compressed in time. Science 310, 1933–1938 (2005).

• Jimenez-Guri, E, Philippe, H, Okamura, B & PWH Holland. 2007. Buddenbrockia is a cnidarian worm. Science 317:116-118.

3) comparative genomics (gene presence/absence) and molecular phylogenetic analysis of mitochondrial genomes from a choanoflagellate, diverse sponges, and diverse eumetazoa. The mitochondrial genome of Monosiga brevicollis contains many genes never seen in any eumetazoan or sponge mitochondrial genome.

• Ruiz-Trillo I, Roger AJ, Burger G, Gray MW, Lang BF. A phylogenomic investigation into the origin of metazoa. Mol Biol Evol. 2008 Apr;25(4):664-72.

• Lavrov, D. V., Forget, L., Kelly, M. & Lang, B. F. Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution. Mol. Biol. Evol. 22, 1231–1239 (2005).

• Burger, G., Forget, L., Zhu, Y., Gray, M.W., and Lang, B.F. (2003). Unique mitochondrial genome architecture in unicellular relatives of animals. Proc. Natl. Acad. Sci. USA 100, 892–897.

• Lang, B.F., O’Kelly, C., Nerad, T., Gray, M.W., and Burger, G. (2002). The closest unicellular relatives of animals. Curr. Biol. 12, 1773–1778.

NOTE: This is not an exhaustive list of relevant papers. Here I have emphasized those in which the analysis includes diverse sponges, as well as choanoflagellates and eumetazoans.