evolgen reports on debates in Nature about whether the term "prokaryote" is meaningful. Norman Pace argued that the term is a negative one ("privative" in Aristotle's sense), defined by what they do not have (which is to say, a nuclear membrane surrounding the genetic material). Now Bill Martin and Eugene Koonin have weighed in with a letter in which they say
Prokaryotes are cells with co-transcriptional translation on their main chromosomes; they translate nascent messenger RNAs into protein. The presence of this character distinguishes them from cells that possess a nucleus and do not translate nascent transcripts on their main chromosomes. Although historically founded on a negative trait (lacking a nucleus), the term prokaryote does indeed specifically designate organisms that are defined by a positive character.
The issue here is whether this is a plesiomorphy, or ancestral character to all life or not.
The figure above, published in Scientific American in 1969 indicates how the tree of life was understood in the early days of investigation into bacterial evolution. It is based on Haeckel's idea of the universal tree of life. Before the "three kingdoms", there were two groups - "protists" and "monerans" - which had the "ancestral" properties of being single celled, lacking nuclear membranes, and which were thought to underlie later evolution. In short, "protists" were defined as those organisms which weren't multicellular organisms in the three kingdoms.
In 1962, two bacteriologists, Stanier and van Neil, revived and redefined the term introduced en passant by Edouard Chattam in 1937 of "prokaryote", which was the "primitive" form of having no defined chromosomes and lacking the nucleus (the history can be found in Jan Sapp's paper listed below). Over the next 30 years the term became a standard one.
Recent work, associated with Carl Woese and W. Ford Doolittle, has begun what is now called the "deep phylogeny" movement. It is also called the "five kingdoms" hypothesis. On this approach, nucleated single cells are called "protists" while un-nucleated cells are called "monerans". But the Universal Tree of Life (image below) turns out to be much more complex - apart from a number of lateral transfers of genes and organelles, all of the major groups (of which "Eukarya" is only one, and which animals, plants and fungi are small branches of) have their own defining characters. The argument against "prokaryote" as a natural group is that it is a privative group, or in cladistic terms, paraphyletic. This means it is the complement of the tree of life (or "shrub", or "tangle", whatever) once you take out the Eukarya.
If "prokaryotes" have a shared character as Martin and Koonin say, this is insufficient to group these remaining branches as one. It might be that each group has its own unique traits, each as different from the each other as they are from Eukarya. Paraphyly is something to be avoided, because it is dependent on what the investigators think are significant, not on the overall properties of the organisms themselves. The "shared property" that Martin and Koonin pick on is probably a plesiomorphy, or ancestral character, but each group has continued to evolve in its own way since Eukarya split off from them, and in objective terms, each group should be defined as those that have their own particular traits, which is what Sapp argues for. The terms "Bacteria" and "Archaea" denote monophyletic groups. "Prokaryote" doesn't.
Sapp, Jan (2005), "The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology", Microbiology and Molecular Biology Reviews 69 (2):292-305.
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I wonder if prokaryote is a more useful distinction ecologically. Alas, I don't know enough prokaryotic ecology to know if archaea and eubacteria share similar types of niche.
Bob
Bob, Archae and Bacteria are each more ecologically diverse than eukaryotes. There is no common niche at that level of taxonomic classification.
John, beware, I got in trouble for claiming that prokaryote is a paraphyletic taxon. There is some literature that suggests that prokaryotes may be monophyletic and the root of that tree is in some weird places. Hardly the discussion I expected in my comments.
I've heard that claim. It is possible that prokaryotes are monophyletic, I guess. But the trees I've seen don't indicate this. More work will tell, I hope. I've even heard someone claim that eukaryotes came before eubacteria, and that they are the derived group, not the eukaryotes. It's a crazy time...
The tree is not well enough rooted to say that prokaryotes are monophyletic, and probably they are not. IMO
John Wilkins says,
I agree that we don't know the answer. Thus it's too early to get all upset about the fact that "prokaryotes" may be paraphyletic and too early to discuss possible pleisiomorphies, right?
The only reason to engage in this kind of criticism of prokaryotes is if you are already convinced that you know the answer to the question of rooting the tree. Norm Pace falls into that category but that's no reason for the rest of us to follow suit.
Let's wait until we know where the root is before we revise our nomenclature. Doesn't that sound reasonable?
My own bias is that the two main branches are bacteria and eukaryotes and archaebacteria are the result of a fusion between a primitive gram positive bacterium and a primitive eukaryote. The evidence for this is just as good as the evidence for any other fusion. :-)
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No, it does not sound reasonable, because we'll never agree on how well supported something has to be before we "know" it.
More importantly, what is this talk about "revising nomenclature"? There is no authority on this. In Linnaean nomenclature everybody has the right to make their very own classification; and indeed, you won't find two textbooks that use exactly the same, let alone two papers in the primary literature.
As for the genome fusion idea, the most parsimonious hypothesis is that the α-proteobacterial genes of eukaryotes are all imported from the mitochondria.
I must correct the original post here: the "five kingdom" hypothesis was formalised in the late 1960s (although first proposed much earlier), while the "three domain" hypothesis first emerged in the late 1970s and only became prominent in the 1990s. "Deep phylogeny" is an outgrowth of the latter. Really, "deep phylogeny" is a replacement for the "five kingdom" hypothesis. Those of us in the field of deep phylogeny (including Woese, Doolittle, and Koonin) tend at least to ignore and at most actively to oppose the "five kingdom" hypothesis as hopelessly paraphyletic, to the point of offering no scientific value whatsoever. Some (Ernst Mayr, for instance) argue against the emphasis placed on microbes (the "two empires" hypothesis, placing the basic split between prokaryotes and eukaryotes) or (Jim Lake, for example) propose alternate phylogenies (the eocyte/"Ring of Life" hypothesis), but as far as I know only Lynn Margulis still argues that the "five kingdom" system represents a scientifically valid approach to the diversity of life on Earth.