Molecular phylogenetics has revolutionized our understanding of biodiversity and evolution like no tool before it. The advent of using the divergence among the gene and protein sequences of different organisms as both a proxy for the biological species concept (at the species level) and a way to compare organisms with no obvious shared morphological or cellular features has resulted in the most sweeping change of how we classify the diversity of life since Linnaeus. Like any paradigm shift, however, the new data available opened up a Pandora's Box of new issues that needed to be grappled with.
One of the major discoveries that came to light was that prokaryotic organisms (often called "bacteria", but actually made up of two very distinct lineages, the Eubacteria and Archaea) are not quite what we thought they were. You see, Darwinism laid the foundation for how evolutionary biologists interpret the world, and while Darwin got a lot of things right, there were many things he had no idea even existed, that have shaped how we understand evolution today (as there will be many things we don't know about today that will shape how scientists in 150 years understand evolution). While Darwin's concepts for descent with modification fit the multicellular world pretty damn well, things get a little muddled in the unicellular world, especially when we leave the eukaryotic cells many of us know, and move to the bacteria.
Bacteria don't play by the rules that work so well for the multicellular among us, and the differences are at the heart of a scientific debate that has been playing out for two decades. In the early stages of molecular phylogenetics, it was thought that the history of life's evolution could be revealed if we compared the sequence of a ubiquitous gene across all taxa. The small subunit (SSU) of the ribosomal RNA was chosen as the appropriate gene because no life form lacks ribosomes, and because of it's important role, the DNA sequence that codes for the functional RNA is highly conserved. As a result, the SSU is the most diversely sequenced gene around and is used today as the gold standard for comparison of bacterial and some eukaryotic species.
But there was a surprise in store when people started to sequence other genes from diverse bacterial lineages. The phylogenetic trees resulting from these new data did not match those of the SSU. In some cases, the differences were dramatic. It had been clear for some time that bacteria could exchange DNA, but the extent and potential evolutionary distance of the exchange took the community by surprise. Indeed, there are some bacterial genomes that appear to be a mixed bag of genes from diverse sources, such that their closest sister taxon can not be identified with certainty (e.g. Zhaxybayeva et al 2009). The evolutionary picture within and among bacterial groups is so confounded by lateral gene transfer (LGT), that the term "Tree of Life" has been abandoned by many, in preference of some variation on "Web of Life".
On top of the issues with LGT, there is the problem that bacteria just don't speciate the way eukaryotes do. The most recent issue of Biology & Philosophy (2010, 25(4)) is dedicated to the discussion of bacterial evolution and how it differs from that of eukaryotes, but the paper by Lawrence and Retchless (2010) really drives to the heart of the problem: we can not use models fashioned after evolutionary patterns in eukaryotes to understand prokaryotic evolution because the speciate in fundamentally different ways.
This message has been repeated far and wide and several researchers are actively proposing novel models for use in prokaryotic systems (e.g. Bapteste et al. 2009). Despite this, paper after paper are churned out using traditional phylogenetic methods to try and classify bacteria using the same assumptions applied to eukaryotic systems. What the hell is going on?
To tell you the truth, I don't know. I think part of the issue is availability and acceptability. Tried and true phylogenetic methods are well known and reasonably well understood by a large community of people. If one is writing a paper or grant proposal, introducing controversial or novel methodology is one way to make the process exceedingly more difficult on yourself (a whole new thing for reviewer 3 to reject outright without understanding it!). Playing it safe means that you can cite the large body of literature that is also applying the same methods, in some sort of schooling fish mentality. Another factor might be the radicalization of the LGT movement by researchers not willing to abandon the Tree of Life idea, for personal or political reasons. Rarely have I seen such vitriol unleashed at conferences as when the topic of rampant prokaryotic LGT comes up.
But the data are the data. It is abundantly clear that bacteria violate the assumptions inherent in the methodology currently used to model evolutionary history (even worse than eukaryotes do, but that's a different story). Until the bacterial evolution community comes up with and embraces new methods to model prokaryotic evolution, leaps in our understanding of that process will be limited.
Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, & Noll KM (2009). On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proceedings of the National Academy of Sciences of the United States of America, 106 (14), 5865-70 PMID: 19307556
Lawrence, J., & Retchless, A. (2010). The myth of bacterial species and speciation Biology & Philosophy, 25 (4), 569-588 DOI: 10.1007/s10539-010-9215-5
Bapteste, E., O'Malley, M., Beiko, R., Ereshefsky, M., Gogarten, J., Franklin-Hall, L., Lapointe, F., Dupré, J., Dagan, T., Boucher, Y., & Martin, W. (2009). Prokaryotic evolution and the tree of life are two different things Biology Direct, 4 (1) DOI: 10.1186/1745-6150-4-34