Is a 'tree of life' also a 'tree of death'?

Imagine that you could build an evolutionary tree that included every single organism that has ever existed since the origin of life: including every single bacterium, every single archaeum: every individual organism.

The divisions between groups of organisms would then become blurred. For example, it would be impossible to tell where Homo neanderthalensis ends and where Homo sapiens begins. It would be impossible to detect the exact moment when non-avian dinosaurs turned into birds. This also applies at the unicellular level.

The reason we can distinguish groups in the trees of life that represent evolutionary events, is because we do not see most of the branches: the branches that have gone extinct. It is the absence of these individuals, which did not successfully passed on their genomes to the next generation, that allows for the classification and distinction of different types of organisms.

Therefore, a phylogenetic tree of organisms not only gives insight into the groups of organisms in question, but it also shed lights into the organisms that must have existed but did not make it. You could say that a tree of life is also a tree of death.

It also implies that using a phylogenetic tree we could calculate the amount of diversity that has been lost between the two most closely related branches. Assuming that we know the rate of divergence, and that we could somehow put a number to “amount of diversity”.

Darwin's Tree of Life, 1837

Phototrophy in ancient Actinobacteria

The evolution of photosynthesis is complex, but not intractable. Views on the origin of photosynthesis can be summarized like this:

Photosynthesis evolved in a well-defined clade of bacteria and then it was scattered through the bacterial tree of life via horizontal gene transfer.

I have come to the conclusion based on the phylogenies of reaction centers, chlorophyll synthesis, and bacteria, that photosynthesis originated close to the origin of bacteria or even before the last common ancestor to bacteria (Cardona, 2014).

A recent paper has shown that two strains of non-phototrophic bacteria of the genus Rubrobacter (phylum: Actinobacteria) contain proteins closely related to those in the chlorophyll-synthesis pathway (Gupta and Khadka, 2015). In addition, the authors show that the origin of these genes is very ancient and provide some evidence to argue that they were not obtained via horizontal gene transfer. They suggest that the Actinobacteria might have been originally phototrophic.

If we reexamine the tree of life and highlight the phototrophic clades (see Figure 1), we see that Cyanobacteria, Chloroflexi, and Actinobacteria likely shared a common ancestor. This relationship is well supported by phylogenomics from the past decade. I believe this ancestor was phototrophic.

Figure 1. Tree of life highlighting phototrophic clades. The tree is taken from Segata et al., 2013, it's open access and freely available.

In these phylogenetic trees the phylum Firmicutes always branches before the divergence of the Cyanobacteria-Chloroflexi-Actinobacteria supergroup, see Cardona (2014) and references within. This implies that the origin of phototrophy must have predated the divergence of the Firmicutes and the Cyno-Chloro-Actino supergroup, immediately placing the origin of phototrophy very close to the root of bacteria.