Origins of major archaeal clades correspond to gene acquisitions from bacteria

We have written in the past about the issue of “Strong Tree Thinking” and how it might be problematic in terms of what it allows us to see when we look at genomes and non-eukaryotic genomes, in particular (prokaryotes, viruses, phages, plasmids, etc.).

The most recent manuscript I have become involved with is once again showing that our decades-old perceptions of Archaebacteria and Eubacteria being two distinct “Domains” of life has been constructed by thinking that “There is a Tree”.  When you accept that there is no Great Tree Of Life and instead we have an ensemble of genetic goods, perhaps with a bunch of rules for how these genes are spread around (Hint: it is not a tree-like process), then you get to see so much more.

What is so wrong with the protocol that you first reach for the tools of networks and examine the data in a network framework, then, perhaps (if appropriate), you might move on to a tree-based analysis (Hint: You might do this if the data were genuinely tree-like)?  The worst that could happen is that you are not limiting or blinkering yourself.

This is a simple message and this latest paper is demonstrating a simple thing – Archaebacteria is not a monophyletic taxon in the same way that Vertebrata is a monophyletic taxon.  Why? Because Horizontal Gene Transfer, that’s why.