Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to Phytophthora genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes.Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by a posteriori interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different a priori assumptions inherent in competing evolutionary hypotheses.Completely sequenced eukaryotic genomes represent large and complex data sets, and phylogenomic investigations generally uncover numerous conflicts among individual gene phylogenies [1,2]. When a given gene produces a phylogeny with strong support for an alternative relationship to what generally is accepted, it is viewed as a likely candidate for horizontal (or lateral) gene transfer (HGT) [3]. Multiple genes from a given genome supporting the same discrepant relationship are interpreted as evidence of correlated HGT, stemming from an historical endosymbiosis in the organism's ancestors [4-6].Genomes of all photosynthetic eukaryotes contain numerous sequences acquired via HGT from cyanbacterial ancestors