Figure 1.

Specific tests of the chromalveolate versus ochrophyte-specific models. A. The chromalveolate model assumes the plastid present in modern ochrophytes was adopted as a red algal endosymbiont in the distant ancestor of all chromalveolate taxa, meaning this plastid was lost from oomycetes after they diverged from ochrophytes. Thus, the model (H1: yellow box and arrows) makes explicit and testable predictions. In contrast, an ochrophyte-specific origin of the diatom plastid (H2: orange box and arrow) makes alternative predictions. B. Fisher exact tests for excess gene signal in heterokont genomes from red algae versus the amoebozoan control. When adjusted for genome size, there are proportionally more first hits to red algae than to amoebozoans in P. ramorum but not in P. sojae. Both diatom genomes display highly significant excess signal from red algal genes. C. The same tests on only those genes present in all eukaryotic groups, showing the strong red signal in diatoms is not simply from plastid-related genes. D. Same tests (on genes present in all eukaryotic groups) on second hits when the first hit is to the sister heterokont. There is no indication of an excess red algal signal in either oomycete genome. More significantly, the extraordinary signal for a red contribution to the diatom genomes disappears in gene specifically conserved between oomycetes and diatoms. Significant results after adjustments for multiple tests in B-D are shown in blue bold text.

Stiller et al. BMC Genomics 2009 10:484   doi:10.1186/1471-2164-10-484
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