Planctomycetes and Eukaryotes are both interesting, but not specifically related

We have finally published our analysis of the relationships between Planctomycetes, Verrucomicrobia and Chlamydia (the so-called PVC group) and Eukaryotes.  In other words, we have shown that these two groups of organisms share superficial similarities, but have no close relationship.  The manuscript has been published in BioEssays and you can access it here [1].

If you take a look at two papers in particular [2,3] - though there are many more on the subject - you can see that thousands of eukaryotic genes can trace their origins to prokaryotic taxa, but there has been no systematic large-scale study to date that has been able to show that any appreciable number of genes group eukaryotes and PVC bacteria together to the exclusion of all other taxa.

This is the gold-standard test.  Can we use careful reconstruction of the evolutionary histories of large numbers of genes to infer the prokaryotic ancestry of eukaryotes?  To a certain extent, we can.  However, it is fraught with difficulties, both in modeling evolutionary history and also incorporating horizontal gene transfer, which tends to obscure the histories somewhat.

Nonetheless, when we actually carried out these analyses, we can see clear patterns emerge.  We can see that there is a large component of the eukaryotic cell that is specifically linked to organisms that are in the alpha-proteobacterial group.  We can see a large component that is specifically associated with the archaebacteria and we can see a large component associated with the cyanobacteria.

The fine-grained placement of these eukaryotic genes is very difficult and I feel that more work needs to be done in this area, but nonetheless, one other thing emerges: There is no strong association between PVC bacteria and eukaryotes.

Right now, as far as the data is concerned (and remember, the data wins, not our pre-conceived notions or our preferences - we have to do science, after all) there is no specific link between PVC bacteria and eukaryotes.

Which is why it is annoying when people ignore the evidence and put forward claims that only look at part of the data [4].

A number of papers have tried to claim that PVC bacteria are in some way intermediate between bacteria and eukaryotes.  This is nonsense. Emboldened with this kind of success, the authors have gone off on a tangent claiming that this in some way validates ideas about autogenous evolution of the eukaryote cell (that the eukaryote cell arose first without any fusion event) and so on.

The problem for these other scientists and their claims is that the real evidence is out there, it has been published and it is very difficult to get around.  Several labs from several countries have looked at these data and there is no real problem with interpreting the data - the phylogenetic signals linking eukaryotes to prokaryotes are easy to find and they link eukaryotes to three main lineages - cyanobacteria, alpha-proteobacteria and archaebacteria.  All other linkages can be explained by small amounts of horizontal gene transfer of some kind.

Finding endocytosis-like processes in Planctomycetes is great [5].  This is indeed an interesting feature of a bacterium.  Does it automatically follow that by studying this bacterium, we will know more about eukaryotes?  Not necessarily.  It might, but it is not a logical conclusion that it will.  Consider, for instance, a birds wing and the wing of a jumbo jet.  Nothing about a birds wing will tell you how a jumbo jet's wing works.  Engineers gave up at a very early stage when they tried to make aeroplanes with flapping wings.  The two entities both are used for flight, but it is not logical to say that studying one might provide an insight into the other.  The only insights we might get will be dull and uninformative for the most part.

So, if you want to study eukaryote endocytosis, then study it in eukaryotes - there are plenty eukaryotes.

I say it again: PVC bacteria are not specifically related to eukaryotes.  You can find more detail in the paper.

References

1. McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, et al. Planctomycetes and eukaryotes: A case of analogy not homology. Bioessays 2011; 33:810-7.

2. Pisani D, Cotton JA, McInerney JO. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol 2007; 24:1752-60.

3. Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, et al. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 2004; 21:1643-60.

4. Devos DP, Reynaud EG. Evolution. Intermediate steps. Science 2010; 330:1187-8.

5. Fuerst JA, Sagulenko E. Protein uptake by bacteria: An endocytosis-like process in the planctomycete Gemmata obscuriglobus. Commun Integr Biol 2010; 3:572-5.

 

 

James McInerney
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