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closeearly-diverging bacteria?
Posted by sbkroken on 20 Mar 2011 at 19:09 GMT
Fascinating stuff. One thought, based on the topology of the rpoB tree, as an alternative hypothesis to toss out there. If the unknown 1 clade is from cellular organisms, might they be found be be Bacteria, and more interestingly, the deepest branch yet found? That would be similar to the the discovery of the novel phyla of Archaea that are also early-diverging lineages. Of course this question of ranking depends on finding the organisms and determining if their cellular and genetic organization is bacterial or something very different.
RE: early-diverging bacteria?
jeisen replied to sbkroken on 20 Mar 2011 at 19:24 GMT
Excellent point and one we did not really discuss in the paper but should have.
A key issue is where to root these trees. We kind of arbitrarily rooted them in the figures. If the rooting we used is correct then indeed the Unknown 1 group in the RpoB trees and the RecA-like SAR1 group in the RecA tree could indeed in essence be deep branching novel bacteria. However, the definition of bacteria in a sense would have to be expanded phylogenetically to include these new clades.
Obviously it would be critical to know from what things these sequences come. But even if we found the source and found that they were from cellular organisms that looked like bacteria and showed that our rooting in the figures was correct, I am not sure that would give us an answer to whether to call them a new group or deep branching bacteria. I guess it would depend on whether one was a splitter or a lumper in terms of major branches in the tree of life.