The 1998 paper leaves much to be desired. Its deficiencies reflect the excitement of the first hour. The state of the art at that time may be gleaned from an authoritative paper that came to the opposite conclusion: A.R. Mushegian and E.V. Koonin “Gene order is not conserved in bacterial evolution”. TIG 1996, 12, 289–290. The gene cluster table of 1998 was mainly retrieved from the annotations in published genomes and constructed manually with paper and pencil. The state of information technology at that time is reflcted by the fact that the table was folded an individually pasted by hand into each issue by the publisher.
Given my interest in the bioinformatics of gene content and order, I took the liberty of studying the brief Systematic & Applied Microbiology paper to check the validity of the “reconstruction” methods of Figure 1. The algorithmic implementation that is described is quite raw and does not extract important information that is embedded in the clusters of conserved gene segments. Important algorithms have been devised since the initial work of Sankoff in the sixties and seventies to do exactly that. I refer to the work of Pevzner, Tesler and Bourque as good examples, but also of Warnow. I also recommend visiting GRIMM (http://grimm.ucsd.edu/GRIMM/) and perhaps using the server to confirm or extract additional information from the alignments that are summarized in Figure 1. The Wächtershäuser algorithm makes use of conserved elements of gene content and order but discards information provided by the actual rearrangement operations that erase gene order history. The algorithm does not describe how gene homology was detected, how the limited set of genes was selected, and how the alignments were constructed (I imagine by hand). It is not clear if a guiding tree was used in the alignment (though this is mentioned in Line 65), since this is not made explicit in the 1998 publication. An alignment implies a tree but usually alignment algorithms are greedy and problematic and represent the most important limiting step of a phylogeny (the field is thus moving to the joint alignment and tree reconstruction). Therefore, I do not think the ancestors were properly reconstructed (the tracing of features in ancestor nodes of trees are not described, nor the actual trees). Regardless of all of these limitations, the tight conservation of certain segments is enough to show the existence of a core of ribosomal proteins that is universally present in cellular organisms. This in itself is valuable. Of course, a sample of 19 microbes may not be enough to encompass molecular diversity and the absence of Eukarya may also be problematic for any global evolutionary statement. In other words, the risks of sampling bias are clearly present and should be mentioned in the manuscript.