Ancient bacteria with modern DNA, problem for evolution?

Two groups have since used phylogenetic analyses of 16S rDNA sequences to argue that isolate 2-9-3 is unlikely to be 250 Myr old. Graur and Pupko (2001) used a relative rate test to compare evolutionary rates of 16S rDNA on the branches leading to isolate 2-9-3 and S. marismortui and found no differences between the evolutionary rates. Considering the possibility that S. marismortui may also be ancient (Arahal et al. 1999 ; Vreeland, Rosenzweig, and Powers 2000 ), they also compared the evolutionary rates of isolate 2-9-3, S. marismortui and Virgibacillus proomi, a close relative of S. marismortui, and again found similar rates of evolution (Graur and Pupko 2001 ). More recently, Nickle et al. (2002) also performed relative rate tests using 16S rDNA with the same result; the branch leading to isolate 2-9-3 is not extraordinarily short, as would be expected of an organism that has not been evolving for millions of years. Nickle et al. (2002) used evolutionary rates derived from enteric bacteria to argue that if isolate 2-9-3 has not been evolving for 250 Myr, then S. marismortui must itself have been evolving 5-10 times more slowly than did aphid endosymbionts on which the rate calculations were based. We note that although the evolutionary rates calculated from enterics and endosymbionts are the best estimates we currently possess, it is entirely likely that rates of sporeformer evolution may indeed be slower by several orders of magnitude. Sporeformers have been shown to remain in the metabolically dormant spore state, thus not replicating their DNA, for conservative estimates of anywhere from 102 to 104 years between times of growth (Kennedy, Reader, and Swierczynski 1994 ; Nicholson et al. 2000 ).As the analyses discussed above used 16S rDNA genes, the evolution of which may not be representative of the organism as a whole, we wanted to know if the similarities between isolate 2-9-3 and S. marismortui are seen with protein-coding genes as well as with 16S rDNA genes. We therefore analyzed phylogenetic relationships between strain 2-9-3 and S. marismortui, using the spore-forming bacteria as our comparison group. The rationale for this design was that the evolutionary rate among the sporeformers would more closely approximate that of 2-9-3. We used amino acid data from two genes, recA and splB. The recA gene is found throughout all bacteria, and its product is required for homologous recombination and DNA repair. Because of the functional constraints on recA evolution, it can be used to resolve the older evolutionary relationships. The splB gene, on the other hand, has to date only been reported in gram-positive spore-forming bacteria and is important in the repair of spore-specific DNA damage resulting from UV radiation during spore dormancy (Nicholson et al. 2000 ). Because splB is only found in gram-positive spore-forming bacteria, it can be assumed to have a more recent origin than recA has and might be useful in resolving closer evolutionary relationships.The results of our analyses are consistent with the phylogenetic relationships shown by Graur and Pupko (2001) and Nickle et al. (2002) .

Either the molecular dating is wrong, or the dating based on the geology is wrong.

Now, you and other raise the issue of contamination, but this is not the first ancient bacteria showing similarities to modern bacteria. Are we to continually assume contamination every time, even with stringent sterilzation measures?

So there appears to be a double-standard in the standards evos use to accept or reject data, stricter standards for data that is problematic for evos, ...