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. 2007 Dec 21;3(12):e231. doi: 10.1371/journal.pgen.0030231

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© 2007 Kettler et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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The ancestor node in which a gain or loss event took place was estimated by maximum parsimony. Four marine Synechococcus genomes (not shown) were included in the calculation, and the phylogenetic tree from Figure 2C was rooted between the Synechococcus and Prochlorococcus lineages.

(A) The total number of genes gained and lost at each node.

(B) The loss and gain of genes in that could be assigned functional roles through homology. Note that (B) focuses on the small minority of genes that do have an assigned function. Genes were assigned to one of five categories on the basis of keyword matches against the gene name or COG description. “Other Putative Function” refers to genes with assigned function but not belonging to the four major categories. Note the difference in scale for (A and B).