Fig 3. Cartoon overlayed phylogenies to demonstrate hypothesized history of HGT and ghost lineage.

Underlying topology derived from backbone (bacterio)chlorophyll synthesis genes (BchH/D/I/M) (black). BchLNB and BchXYZ are derived from a common ancestor in stem group phototrophs. BchLNB (green) was inherited together with BchHDIM into extant phototrophs; BchXYZ (red) diverged in the ghost lineage before being introduced into extant anoxygenic phototrophs via HGT (a first HGT event introduced it into the stem of the proteobacterial lineage; a second HGT event introduced it into the stem of the WPS2/Chlorobi/Chloroflexi lineage; subsequent HGT introduced it into the Chloracidobacteria and Heliobacteria lineages). Type 1 reaction centers (RC1 and PSI) and Type 2 reaction centers (RC2 and PSII) diverged in stem lineage phototrophs. Type 1 reaction centers (peach) were vertically inherited into extant phototrophic lineages. Type 2 reaction centers (blue) diverged in the same ghost lineage as BchXYZ, and were introduced into extant clades via HGT (first into stem group Cyanobacteria, leading to PSII, then into stem group Proteobacteria and the stem lineage of WPS2, Chloroflexi, and Chlorobi). The most parsimonious history consistent with the data involves a secondary replacement of RC2 with RC1 in Chlorobi. Alternative evolutionary histories are similarly parsimonious, but all involve many events of HGT of individual phototrophy components and most involve secondary loss and replacement in some lineages. The inclusion of one or more ghost lineages improves parsimony and provides a good explanation for long branches between RC1/RC2 and BchLNB/BchXYZ homolog pairs. A summary of hypothesized HGT events is presented in Table 2.