Rooting the Tree of Life

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What is the point?

  1. To be able to identify the root of a "universal tree" and describe how it was identified.

Where in the 'Big Universal Tree of Life' is the last common ancestor? To answer this question, you need to root the tree, but as we saw earlier, in order to root a tree you need an outgroup, and how do you have an outgroup in a universal tree?

The solution to this quandary lies in the fact that the trees generated in a molecular phylogenetic analysis are trees of gene sequences, not organisms. This distinction can be used to create a rooted phylogenetic tree of all organisms by using gene sequences that span a broader evolutionary breadth than do all known organisms. In other words, you can use gene sequences that are outgroups of a tree of other gene sequences that span the entire phylogenetic diversity of organisms.

This is done by using gene sequences from gene family pairs that split before the last common ancestor. Good examples of these are ATPase subunits alpha vs beta, initiator vs elongator tRNA(Met), EF-Tu vs EF-G, or any pair of related aminoacyl-tRNA-synthetases (e.g. Leu vs Ile).

When you do this, you end up with a dendrogram with two main clusters, one cluster for each type of sequence. The sub-tree from one member of the gene family serves as root for the other!

EF-Tu/G tree


Phylogenetic tree of an alignment containing both EF-Tu and EF-G sequence

The root turns out to be very close to the base of all three Domains, on the branch dividing the Bacteria from the Archaea & Eukarya. In other words, the Archaea and Eukarya are related, not the Bacteria & Archaea (i.e. prokaryotes), as most people thought. This conclusion is being substantiated more & more by analysis of genome sequences.

Universal Tree

The Archaea are, therefore, an early, primitive branch of the eukaryotic lineage. This is the reason for a lot of the interest in Archaea these days; these organisms probably resemble, more than anything else we know of, the ancestor of eukaryotes, and certainly have much to tell us about where eukaryotes (i.e. us) came from.