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Monday, February 28, 2011

Problems with the Eukaryotic Tree of Life

Here's the ninth question my students have to answer. This is the end of the series since the test is tomorrow.
The positions of animals, fungi, and plants in the eukaryotic tree of life have been clear for decades. So why is there so much controversy today about how to construct a valid tree of eukaryotes? What are the main problems, according to Keeling et al. (2005), and how will those problems be overcome?

Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J., Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol. 20:670-676. [doi:10.1016/j.tree.2005.09.005]


  1. Every super group is based on different lines of evidence. (Some based on morphological features (e.g. exoskeleton) combined with overlapping molecular, data, while others just based on pure molecular data). It's hard to come to a unanimous consensuses in such a situation.
    Furthermore, I believe Keeling et al say that every monophylogentic lineage has at least one piece of conflicting evidence. It's easy to imagine why there would be a controversy if you have conflicting evidence....

  2. Problems? What problems? Don't y'all worry, everything's fine if you squint at it the right way... ;-)

    Actually, given the total mess a mere 10-20 years ago, it's amazing how relatively stable the larger groups are, generally-speaking. There are problems with the finer branchings in many areas, as well as issues with deep branching and rooting of the tree overall (eg. relationships between supergroups) and some weird incertae sedis lineages, but overall groups like Alveolates (and dinos-ciliates-apis within), Stramenopiles, Opisthokonts+Amoebozoa, even Rhizaria and Excavates have pretty decent support (with the latter being perhaps the sketchiest in terms of possible paraphyly, but still decent). Internally, groups like Amoebozoa and Rhizaria are a pretty nasty mess though...
    (also, Rhizaria is now firmly among [former] Chromalveolates, between Alveolates and Stramenopiles. Probably nobody cares, but they're easily my favourite supergroup ;-))

    Given the overwhelming breadth and magnitude of diversity we're dealing with there, it's pretty amazing we can have something tree-like at all. And *massive* progress from the past protozoa-algae-sporozoa systems and Margulis' awkward, disconnected phyla. Hence why it irks me how many undergrad courses completely ignore the last 20 years of progress when introducing the protists. Even if there's only 1h max of protists in a class, a nice recent-ish eukaryotic tree is not too much to ask for, is it?

  3. One would imagine that a significant problem for the broader tree would be gene transfer and loss. These organisms typically have branches at a much greater depth than the multicellular forms that dominate our thinking, and their germ line is generally not buried deep within a protective soma. So there is much more time, and much more mechanistic opportunity, for signal-scrambling to occur than in our rather more well-trimmed segment of the bush (an assumption of neat genealogy is something of a local prejudice).

    Then we factor in the influence of the statistical method chosen, and the evolutioanry model assumed upon the tree yielded.

    Nonetheless, as psi says, there is pretty good resolution, and the current tree a lot more satisfactory than those based upon eyeball, light microscopy and prejudice of a few years back.

    What's the stem group, though?

  4. long-branch attraction.

    Big problem.
    so I'm told.