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Getting to the root of the Tree of Life

6 Jun, 2011


The tree of life has many branches

All organisms on Earth can be mapped onto the phylogenetic ‘Tree of Life’ – with its dividing branches showing how species have evolved through time. At the very base of the tree are three branches, representing the three major domains of life: Bacteria, eukaryotes and Archaea. You’ve almost certainly heard of the first two – eukaryotes are, after all, organisms made up of cells containing a nucleus, including animals, trees and fungi. But I wouldn’t be surprised if you hadn’t heard of the third.

Archaea are single-celled organisms that look a lot like Bacteria, and they were initially thought to be one and the same. However, these microorganisms possess unique metabolic pathways not found in either Bacteria or eukaryotes and are a completely distinct domain. Not to put too fine a point on it, many Archaea are a bit weird. You might find some species growing quite happily in the boiling acid of a hot spring for example. When I was working as a scientist some of my colleagues were growing them in solutions of concentrated arsenic. At the other end of the scale you’ll also find some Archaea in your gut, helping you to digest your food. Similarly, in helping cows to digest their food they are the largest source of methane production in the world, a big problem in climate change.

Unlike most bacteria, the Archaea show little promiscuity for sharing DNA (think how quickly antibiotic resistance genes move between bacterial species for instance). They seem to keep themselves to themselves and thus far no human, animal or plant disease-causing species have been identified.

One of the longest standing questions in modern biology regards the order in which the three branches of the tree of life developed. It is widely accepted that the Bacteria came first, but until now no one really knew whether Archaea and eukaryotes shared a common ancestor, growing as ‘sister’ branches, or if eukaryotic cells evolved later from a particular group of Archaea.

New research, lead by Dr Steve Kelly from Oxford University, appears to have answered this very question. This work has compared a huge number of genomes to develop a very accurate phylogenetic tree. The problem with previous attempts is that they only compared a small number of genes from a particular pathway, limiting themselves to a fraction of the data available.

Kelly and his colleagues took a different approach, developing their own self-learning computer programme to search all available genome databases repeatedly, looking for groups of genes that were related.

This method meant that many more data were available to the group than previous scientists (the number of fully sequenced organisms is huge), and with it they were able to build a highly detailed phylogenetic tree of the Archaea.

The results were surprising. Although unable to show whether Archaea or Bacteria evolved first, they suggest that the organism at the very base of this phylogenetic tree – from which all other life on earth evolved – was a methanogenic cell, one that produced methane as a metabolic byproduct. This adds weight to the theory that life on Earth began around deep-sea hydrothermal vents – but this is not a theory subscribed to by all scientists.

As Kelly told me, “Of course the geochemists loved [this result] as it backed up what they’d been saying for years. [But] a lot of geneticists simply refused to believe it and told us we were wrong”.

One key line from the paper that stands out though is this: “…we demonstrate that our analyses are both method and model independent”. Regardless of how the data are analysed, the phylogenetic tree always looks the same – the gold standard for research.

The work also showed that eukaryotic cells developed later than Bacteria or Archaea, evolving from a newly discovered group of marine dwelling Archaea known as the Thaumarchaea (‘Wonderarchaea’). These are mesophilic organisms that like to live at moderate temperatures rather than the extreme environments preferred by other species. Thaumarchaea are found everywhere, and are one of the most abundant organisms found in the oceans.

Curiously, we don’t really know how many species of Archaea there are on the planet as we simply don’t know the conditions necessary to grow the vast majority of them in a laboratory (the same is true for most Bacteria). However, we may be able to learn more about these mysterious organisms by approaching the problem in a different way. The rapid progress of DNA sequencing technology means it is now possible to sequence a microorganism’s genome without ever having to grow it or even see it – this burgeoning field is known as metagenomics.

As metagenomics brings new data to the table this may mean that this new phylogenetic tree has to be altered, but Kelly thinks not significantly.

“As we get more information the tree will be refined. However, given that we’ve mapped out all the possible combinations, the branches might move slightly, but not very far.”

Benjamin Thompson

  • Kelly S, Wickstead B, & Gull K (2011). Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proceedings. Biological sciences / The Royal Society, 278 (1708), 1009-18 PMID: 20880885
Image Credit: strollerdos on Flickr
7 Comments leave one →
  1. 6 Jun, 2011 12:42 pm

    Very interesting read, and nice to see that the article it’s based on is open access. Thanks for the great write-up.

  2. Michael Young permalink
    13 Jun, 2011 3:16 pm

    Why do Archaea, and Bacteria, have first letter capitals, when “the third major domain of life” the eukaryotes do not?

    • Benjamin Thompson permalink
      13 Jun, 2011 3:38 pm

      Michael that is an excellent question. Technically the third major domain would be the Eukaryota, which has a capital E. For the sake of simplicity I used the term eukaryote to describe all cells with a nucleus, as I think it is more familiar to people.

      The same is true of the other two domains. If you are talking about the domain Bacteria it has a capital B, but if you are talking about bacteria generally then the lower case is correct.

      Hope this helps! You can learn more about the three-domain system here:


  3. Michael Young permalink
    13 Jun, 2011 3:42 pm

    Thank you, Benjamin. Your full and clear answer is much appreciated.

    Michael Young.


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