Monday, May 07, 2007

Theme: The Three Domain Hypothesis

 
This is a series of postings that describe the Three Domain Hypothesis. The Three Domain Hypothesis is the idea that life is divided into three domains—bacteria, archaebacteria, and eukaryotes—and that the archaebacteria and eukaryotes share a common ancestor. An example of this tree of life is shown on the Dept. of Energy (USA) Joint Genome Initiative website [JGI Microbial Genomes] (left).

The hypothesis was promoted by Carl Woese in the 1980's but the pure form has now been abandoned and replaced with a “net of life” concept of early evolution as shown in the figure below. This figure is taken from Ford Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American




The Three Domain Hypothesis (part 1) (Nov. 17, 2006 )

The Three Domain Hypothesis (part 2) (Nov. 22, 2006)

The Three Domain Hypothesis (part 3) (Nov. 26, 2006)

The Three Domain Hypothesis (part 4) (Nov. 29, 2006)

The Three Domain Hypothesis (part 5) (Dec. 8, 2006)

The Three Domain Hypothesis (part 6) Carl Woese (Dec. 31, 2006)

Now the IDiots Don't Get Evolution (Feb. 14, 2007)

The Web of Life (March 15, 2007)

Is "Prokaryote" a Useful Term? (October 4, 2007)

Celebrating the Three Domain Hypothesis (October 18, 2007)

The Tree of Life (May 22, 2008)

Sequence Alignment (June 22, 2008)

On the Origin of Eukaryotes (December 27, 2008)

The Tree of Life (July 29, 2009)

Perspectives on the Tree of Life: Ford Doolittle (July 30, 2009)

Perspectives on the Tree of Life: Day One (July 31, 2009)

Perspectives on the Tree of Life: Day Two (August 1, 2009)

Perspectrives of the Tree of Life: Day Three (August 7, 2009)

11 comments :

  1. You've mentioned before that the Three Domain Hypothesis has been abandoned; is this a premature statement? It is still widely used in the literature, even in the top tier journals (Nature, Science, PNAS). I don't necessarily disagree with you, but the rest of the universe hasn't seemed to catch on.

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  2. I'm used to being ahead of the rest of the universe. :-)

    Seriously, Woese did such a good job of selling the Three Domain Hypothesis that most people have just accepted it as fact without checking to see if it's holding up in the molecular evolution literature.

    Once a new fad gets promulgated it's very hard to convince people to stop believing.

    I hate to be the one to break it to you but there are lots and lots of things in Nature, Science, and PNAS that aren't true. Sorry. :-)

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  3. This is all fascinating reading, and I thank you again for (re)posting it. I'd like to repost my comment-question from last time:

    If the deep phylogeny of cells/organisms/genomes is, then, unknowable, what CAN we say?
    Eukarya seems unquestionably monophyletic (leaving mitochondria and plastids aside, of course) and so we are left with a huge, diverse, possibly paraphyletic (but we'll never know) and possibly even polyphyletic??? (but we'll never know) Domain Monera?
    This is rather unsatisfying, but if that is the situation, so be it.

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  4. CCP says,

    If the deep phylogeny of cells/organisms/genomes is, then, unknowable, what CAN we say?
    Eukarya seems unquestionably monophyletic (leaving mitochondria and plastids aside, of course) and so we are left with a huge, diverse, possibly paraphyletic (but we'll never know) and possibly even polyphyletic??? (but we'll never know) Domain Monera?
    This is rather unsatisfying, but if that is the situation, so be it.


    It's worse than you imagine.

    At the deepest level, you can't say that eukaryotes are any more monophyletic than bacteria. That's the whole point. The first identifiable eukaryotic species emeged from the mix several billion years ago but before that the lineages are so intertwined that there's no point in distinguishing eukaryotes and prokaryotes.

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  5. Surely you are not suggesting that extant eukaryotes are not monophyletic. You mean that the prokaryotic ancestors of extant eukaryotes were part of the whole horizontally-gene-transferring mess. Right?

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  6. viruses are...special. I was first taught at school that they were bits of 'lost' DNA that had escaped from things and managed to somehow surround themselves with proteins. Recently though, I'e come across the idea that virus's are 'escaped' DNA that have got out and found they can live a life of their own.

    I'm currently working on bacteriophages, which in some cases can carry bit of DNA from bacteria, making them...related? Viruses are, thinking about it, another reason this hypothesis is starting to crumble.

    to Cameron: The reason this is still used is probably because it's a very useful model, despite probably not being wonderfully correct.

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  7. It is very difficult to overturn the pioneering significance of Woese's discovery of the Archaea. Admittedly he's a great self-promotor and who can condemn this given how the establishment resisted his Tree-Thinking as applied to what came to be called the microbosphere? [see for overview - Morell, V. (1997) Microbiology's scarred revolutionary. Science 276:699-702]

    There is much more at stake in his manifesto and in how Woese turned microbiology back to face the reality of microbial diversity. I rate these essays as amongst those great's one should read at least once/year :-)


    Woese, C. R. and N. Goldenfield (2009) How the microbial world saved evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis. Microbiology and Molecular Biology Reviews 73:14-21.

    Woese, C. R. (2004) A new biology for a new century. Microbiology and Molecular Biology Reviews 68:173-186.

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    Replies
    1. Most of Woese's writings are confusing and internally self-contradictory. Usually you can't tell what he believes. Those papers are no exceptions.

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    2. On the subject of diversity and viruses' role therein...

      would recent hubris regarding the complexity of Pandora Virus be yet another example of self-promotion

      or

      is there merit to the suggestion that Pandoravirus presents cogent support for the suggestion of a fourth domain???

      http://www.sciencedaily.com/releases/2013/10/131014102357.htm

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