Phylogeny of PAL/TAL/HAL. Unrooted bayesian tree of a representative sampling of PAL/TAL/HAL homologues. Characterized bacterial PALs are shown in red font, while characterized bacterial TALs are shown in blue font. Although it is difficult to decide where the root lies, it is clear that eukaryotic HAL (blue square) and fungi/land plants PAL (orange and green squares, respectively) have distinct origins. Moreover, taxonomic distribution of HAL and PAL orthologues indicates that the ancestor of eukaryotes harbored a HAL (blue arrow) while a PAL was introduced by HGT in the ancestor of Dikarya fungi (orange arrow) and the ancestor of land plants (green arrow). The source of this HGT is likely in a group of sediment/soil bacteria including characterized cyanobacterial PAL and uncharacterized sequences from Methylobacterium sp. and Herpetosiphon aurantiacus (red square). Probable HAL orthologues of Methylobacterium sp. and Herpetosiphon aurantiacus are indicated by red asterisks. The amoebozoan Dictyostelium discoideum appear to have acquired a PAL in the course of a recent HGT from soil bacteria (pink arrow). Numbers at nodes represent posterior probabilities (for clarity only PP relevant for discussion are indicated). The scale bar represents the average number of substitutions per site. The same tree with full accession numbers and PP is provided as Additional file 1. A maximum likelihood analysis gave very similar results and is provided as additional file 2.