In defense of ‘prokaryotes’

Fine, I get it. “Prokaryotes” is a wrong taxonomic term. It’s wrong to lump bacteria and archaea together. That would be like saying “eutoichic” to lump all bacteria, archaea, plants and fungi together because they have cell walls. (“τοίχος” =wall in Greek. My Google Translate-foo is STRONG!)  Still, there are so many things in common among bacteria and archaea: small, unicellular, cell wall (most), no well-defined organelles (but see this), fission (most), compact genomes, few introns, prophages, genomic islands… and the list goes on.

Not a cell wall

So, for example, when I am developing computational metagenomics analysis tools, they invariably tend to target both bacteria and archaea. However, these tools are usually not good for microbial eukaryotes, due to different rRNA size, the larger genomes with more non-coding regions, lack of operons, organelles genomes, introns, etc. So for this utilitarian purpose, “prokaryotes” would be a good verbal shortcut to the cumbersome “bacteria and archaea” when describing or documenting the software. So can we all agree on “prokaryotes” as a verbal shortcut of necessity but not as a taxonomic definition? Or am I missing something substantial here?

An illustrative example of the rational, cool-headed debate that may ensue:

Herpetology Credit:


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10 Responses to “In defense of ‘prokaryotes’”

  1. Dan Gaston says:

    I personally think it is fine, and use it myself all of the time. I prefer taxonomically meaningful labels whenever possible but non-taxonomically meaningful labels can still be useful. Take protists for example, also not a good name, since now “Kingdom Protista” actually exists. But as a shortcut for “non-fungal, non-secondary unicellular eukaryotes” it works rather well, and is far less cumbersome. Same goes for prokaryotes.

    Descriptive labels are good, we only run into problems when using them carelessly and in company that may think it implies discussing a monophyletic assemblage.

  2. I have no problem with “prokaryote”, but stay away from “Monera”.

    Incidentally, operons are not a universal feature of bacteria. Helicobacter pylori, which has enormous rearrangement of the genome between strains has almost no operons—the genes each have their own promoter.
    Vibrio cholera, on the other hand, has almost virus-like packing of its genes, with overlapping reading frames in operons.

  3. You are just in presence of a clear case of a “paraphyletic” group. The prokaryotes group is paraphyletic because it is defined by the exclusion of another group, the eukaryotes group. It is the same problem with reptiles and birds.

    I think you can stay with the word “prokaryotes”, as everybody knows that prokaryotes means bacteria+archaea.

  4. I think it makes perfect sense to give a name to all species that descend from an ancestor A but do not descend from B, B having acquired some notable feature (e.g. nucleus).

    I would make it clear that the name I give to A-minus-B is not a clade. As others said, prokaryotes with lowercase ‘p’ seems fine. Monera or Prokaryota would be bad.

  5. While not meaningful in a evolutionary view, ‘prokaryotes’, as well as ‘invertebrates’, are useful terms.

  6. I don’t believe [eu]bacteria are holophyletic (ie, I think that unless some pretty fucking strong data show otherwise, it’s by far most sensible that eukaryotes and archaeans arose from *within* eubacteria), so if [eu]bacteria is valid, so is prokaryote. Being a protistologist, I don’t mind paraphyletic terms all that much 😉 and protists are way more paraphyletic than bacteria (three independent non-protist groups arise from within protists, only one non-bacterial clade arises from within bacteria/prokaryotes). The example with the cell walls is quite different because those are *poly*phyletic, and do not share a common ancestry, unlike bacteria, protists and prokaryotes. Polyphyletic groups are a no-no (technical term) in my opinion…

    As for formal taxa, I’ll let the taxonomists fight those out amongst themselves…

  7. Iddo says:

    @Psi I don’t think evolutionary relationship matters if we have a functional definition that serves some purpose. What I was trying to get across in my post is that a useful classification can be considered without deferring to a phylogenetic benchmark.

  8. Ian Holmes says:

    “a useful classification can be considered without deferring to a phylogenetic benchmark” — exactly. Like “sea creatures”. Or “trailer trash”

  9. Iddo says:

    Interesting illustrative examples you give there, Ian….

  10. I’m with Ian. Classification of organisms should be by phylogeny. Period. Are there cases where it is useful to use terms that refer to groups that are not monophyletic. Sure. But those come at a cost. And I think the cost is most of the time much higher than the cost of just using different terminology and not being lazy.