Carl Zimmer at Loom discusses (see also here) mounting evidence from genetics for a new "domain" in the family three of life to rival the current three: Eucarya (animals, plants, fungi, and some of their invertebrate ancestors), Bacteria, and Archaea (mostly extremophiles in thermal vents and the like).
The new kid on the block? Giant viruses.
[O]fficially called Nucleocytoplasmic Large DNA Viruses (NCLDV). I’m just going to call them giant viruses, because they are quite huge. Grotesquely so. As I write in my upcoming book, A Planet of Viruses, they were mistaken for years as bacteria. They were a hundred times bigger than any virus known at the time.. Giant viruses are indeed viruses, however. They hijack host cells the way all viruses do, for example.
But giant viruses also explode a lot of conventional ideas of what viruses are supposed to be. Not only are giant viruses monstrously big, but they are overloaded with genes. A flu virus has just ten genes, for example, but a number of giant viruses have well over a thousand. Giant viruses even get infected by viruses of their own.
Studies of DNA chunks disaggregated from particularly organisms in sea water even suggest that there might be a fifth domain:
[T]hey compare versions of the RpoB gene in giant viruses, bacteria, eukaryotes, and archaea. Two branches that turned up in the global ocean survey are . . .Unknown 2 [which] seems to be like the giant viruses, but Unknown 1 is just off the map.
Looking at the chart above showing the genes, one could imagine Unknown 1 being a divergent branch of bacteria.
Another chart, above, from the recently published paper, similarly makes "Unknown 1" look like a basal branch of bacteria, while Unknown 2 is a harder fit.
A final chart from the study (which I can't seem to manage to upload), suggesting a more distant relationship between Bacteria and "Unknown 1",but a closer relationship between giant bacteria and Unknown 2, is found here
UPDATE (March 23, 2011):
An author of the study has provided the following comment to the original post:
Jonathan Eisen said...
It is hard to tell what these Unknown groups are -- and there is one problem we did not discuss in our paper which is where we placed the root in the trees we drew. Technically, these trees should have been drawn unrooted, as one of the trees is in the linked paper on Google Knol. We drew them in the papers as rooted in part because some people I sent the paper to said that most people have trouble interpreting unrooted trees.
So it is possible with some of the rootings that some of our unknown groups could represent VERY divergence members of the bacteria, for example. I think this is unlikely b/c the unknown groups seem to be quite distant from bacteria. We are working on new analyses to try and pin down the positions of these groups more accurately ...
3/22/2011 8:58 PM
2 comments:
It is hard to tell what these Unknown groups are -- and there is one problem we did not discuss in our paper which is where we placed the root in the trees we drew. Technically, these trees should have been drawn unrooted, as one of the trees is in the linked paper on Google Knol. We drew them in the papers as rooted in part because some people I sent the paper to said that most people have trouble interpreting unrooted trees.
So it is possible with some of the rootings that some of our unknown groups could represent VERY divergence members of the bacteria, for example. I think this is unlikely b/c the unknown groups seem to be quite distant from bacteria. We are working on new analyses to try and pin down the positions of these groups more accurately ...
Thanks for the clarification. I really appreciate it.
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