Literature

Darwin provided the underlying concept and Haeckel popularised the metaphor of a tree to represent the organic unity of all living things. Prokaryotes collectively have featured as the lowest form of life, but the relationships between the many different prokaryotic organisms have been very difficult to resolve. There are no embryological or morphological characters to give substance to an evolutionary phylogeny. Consequently, up until the 1960s, "bacteriology had to proceed without an evolutionary framework".

Prokaryotes are described as the most 'simple' life forms on Earth.

The change came with the advent of molecular phylogenetics.

"In the 1960s, Zuckerkandl and Pauling defined the new research area of molecular evolution. Within a decade, Woese and colleagues, using indirect methods of oligonucleotide cataloguing from small-subunit rRNA (SSU rRNA), identified one particularly important split within the prokaryotes: that separating the Archaebacteria from the Eubacteria. The identification of this split meant that there might be a third major category of living things on the planet, as divergent from Eubacteria and Eukaryota as each is from the other. Confirmation of the monophyly of these three potential groups seemed to be found in 1989, when the SSU rRNA tree was rooted using anciently duplicated genes."

This work provided a boost to evolutionary perspectives of prokaryotes. Since the breakthrough came with SSU rRNA, this was perceived as "the ultimate molecular chronometer".

"Optimism concerning the existence of a single unifying tree of life was at its peak; the SSU rRNA tree was crowned as the "universal tree of life," and was used to devise a new (three-domain-based) phylogenetic classification of life. The legacy of this work is that today there are more than 400 000 SSU rRNA sequences in the public sequence repositories, the vast majority of which have been sequenced for phylogenetic purposes."

With the advent of more data, this evolutionary picture has become blurred and confused. "Phylogenies inferred from alternative markers were often found to be incongruent with the topology of the SSU rRNA tree." "It became less clear why the SSU rRNA should have been preferred over other markers to derive the universal tree of life." Optimism was replaced by pessimism: "a gene that could be considered a universal chronometer that has kept track of the clonal history of cellular life since its origin is thus unlikely to exist."

ID advocates have repeatedly argued that design inferences are not based on ignorance, but on knowledge. Compare that argument with this:

"The new uncertainty at the end of the last century was different from that of half a century before. Prior to the molecular era, the absence of data caused uncertainty. With the arrival of complete genomes, uncertainty was not anymore caused by lack of data. Instead, now the very existence of the universal tree of life was on trial."
[. . .]
"Evidence accumulating during the 1990s and the earliest years of the new millennium seemed to suggest that there was no tree of life, [. . .]."

The key mechanism that was proposed as an explanation of the data was horizontal gene transfer (HGT). But this mechanism undermined the method for recovering a phylogeny from genetic signals. "Even if a prokaryotic tree exists, its most basal nodes might not be recoverable because of phylogenetic signal erosion, HGT, ortholog misidentification or a combination of all three."

"The minimal assumption for the existence of a prokaryotic tree is the existence of a core set of non-transferable (i.e. vertically inherited) genes, but evidence suggests that such a core set of genes cannot exist."
[. . .]
"In the next 10 years, as an ever-increasing number of genomes will become available, we might see either the rebirth of the tree of life hypothesis or its ultimate downfall. It is still too early to say in which direction the evidence will swing."

Unfortunately, there are only two options being considered by most of the researchers. The first is that further work will eventually find a way around these problems and a robust Tree of Life for prokaryotes will emerge. The second is the genetic annealing model proposed by Carl Woese, with HGT as initially dominant in single-celled communities - replacing the tree metaphor with a network. But there is a third option: that we are discovering evidences for the polyphyletic origin of prokaryotes. What we would like is to have this option on the table for academic discussion. The presumption that everything has evolved from an original self-replicating cell needs to be tested, not accepted as the unchallenged default.

The prokaryotic tree of life: past, present . . . and future?
James O. McInerney, James A. Cotton and Davide Pisani
Trends in Ecology & Evolution, 23(5), May 2008, Pages 276-281.

Abstract: No accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data were available for its construction. For 20 years, through the 1980s and 1990s, rRNA phylogenies were the gold standard. However, beginning in the last decade, findings from genomic data have challenged this new consensus. Gene trees can conflict greatly, and strains of the same species can differ enormously in genome content. Horizontal gene transfer is now known to be a significant influence on genome evolution. The next decade is likely to resolve whether or not we retain the centuries-old metaphor of the tree for all of life.