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Eubacteria: Phylogeny


See the page for relationships of Eubacteria to Archaea and Eukarya, and the working basal phylogeny of Eubacteria.

Relationships within eubacteria are extremely uncertain at almost all levels of divergence, and many of those that have been suggested make little obvious sense. A number of factors have resulted in this situation – one is the general reliance on trees to the exclusion of other data sources. rRNA trees have been shown in recent years to be sensitive to variations in evolutionary rates in eukaryotes, leading to such errors as the placing of low down in the eukaryote tree, instead of in or near the . rRNA trees also show low resolution between most branches at high levels.

The other major issue with tree construction which has received a lot of attention is lateral or horizontal gene transfer (LGT), the direct transfer of genes from one species to another. The occurrence of LGT in prokaryotes between unrelated species is undoubted – however, opinions differ as to just how prominent it is. Some regard its occurrence as minimal (e.g. Cavalier-Smith, 2002), others feel that LGT may be so common as to render the construction of an organismal phylogeny for prokaryotes effectively impossible. This page tends away from the latter view, of course – if for no other reason than that otherwise we might as well give up and go home. Cases of LGT might even be potentially used as characters to support clades.

I have rather arbitrarily selected the rRNA tree in Miroshnichenko et al. (2003) to represent the general trend of current eubacterial phylogeny:

  |--
  `--+--
     `--+--
        `--+--Dictyoglomus
           `--+--+--
              |  `--
              `--+--
                 `--+--+--Caldithrix
                    |  `--+--Deferribacteres
                    |     `--+--Nitrospina
                    |        `--Thermodesulfobacterium
                    `--+--+--
                       |  `--+--
                       |     `--+--
                       |        `--
                       `--+--+--
                          |  `--
                          `--+--
                             `--

Compare this to the tree in Cavalier-Smith (2002), constructed using mostly ‘morphological’ or physiological characters:

  |--
  `--+--+--
     |  `--+--+--
     |     |  `--
     |     `--+== (paraphyletic)
     |        `--
     `--+--
        `--+--
           `--+--
              `--

As different as these two trees are, there are some similarities. Most notably, if both trees are unrooted, the Gram-positive bacteria (, and ) are close to Neomura (corresponding to the ); the are mostly further away. The relationships within Didermata are more contradictory, but seem poorly supported in both papers (though neither paper actually gives any real measure of support). The exception is , which are closest to Monodermata in both trees.

The differences in positions of the and are the most significant differences between the trees. Aquifex has been widely accepted as the basalmost eubacterium due to its position in rRNA trees. However, Aquifex has a double membrane, suggesting a position within Didermata. Some protein trees place it within the ε-proteobacteria, and this was the position accepted by Cavalier-Smith. Placing Aquifex in its position on the rRNA tree implies multiple gains or losses of the outer membrane.

is the second-most basal major branch in rRNA trees, but is grouped with on many protein trees, by comparison of indels, and by the gene-content tree. As such, I accept the latter position on this page. The differences in position of the Thermotogae and Aquificae are probably due to long-branch attraction in the rRNA tree, and a high proportion of G+C in the genomes of these two taxa and .

The reposition of these two taxa has significant implications for one of the conclusions drawn from the rRNA tree of life – the supposed hyperthermophilic nature of Luca. This theory was supported by two of three domains having hyperthermophiles as basalmost members. With the eubacterial tree shown here, Archaea is the only domain that is still potentially basally hyperthermophilic, and a mesophilic Luca seems more likely. A hyperthermophilic origin of life, while thought to be consistent with widespread conditions on the young, newly-formed earth, is not consistent with the reduced stability of RNA at high temperatures.

In the tree used here, the order of branches between the base and Cyanobacteria is based on the Cavalier-Smith tree, while relationships within the Didermata exclusive of Cyanobacteria are, for now, based on the more familiar rRNA tree in light of their greater uncertainty. Most of the taxa are based on clusters in gene trees, and may be lacking in morphological apomorphies.

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These are mostly Gram-negative Eubacteria have a double membrane – the inner cytoplasmic membrane, and the more porous outer membrane.

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Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52: 7-76.

Miroshnichenko, M. L., N. A. Kostrikina, N. A. Chernyh, N. V. Pimenov, T. P. Tourova, A. N. Antipov, S. Spring, E. Stackebrandt & E. A. Bonch-Osmolovskaya. 2003. Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage. International Journal of Systematic and Evolutionary Microbiology 53: 323-329.


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