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For sexually reproducing organisms, the scope of a species is somewhat fixed by reproductive compatibility. However, this all collapses for organisms that exclusively reproduce asexually. Here, my impression is that historical momentum is the primary driving factor of species scopes, i.e.: Clades continue to stay on the species level to maintain continuity, while they would be categorised with a higher or lower rank if clades had to be taxonomically ranked from scratch without respect to history.

For example, the species of Escherichia coli and Pseudomonas aeruginosa have been discovered (and thus have been made species) very early and now comprise a diversity of subspecies. In particular, the genus of Shigella appears to considerably overlap with E. coli or is even thought to be a subspecies of it.

I am here looking for references supporting (or refuting) my impression, for example:

  • Has this ever been prominently noted?
  • Are there any instances of species being split on account of being “too large” (as opposed to other miscategorisations)?

Background: Why I care

As long as the taxonomy is phyletic, what does it matter at what level clades are ranked? Right now, this affects me in several ways (assuming that my impression is correct):

  • The common way to present the composition of an ecological community is showing the abundances on a fixed taxonomic level. For example: “Our community contained 80 % Pseudomonas, 15 % Escherichia, and 5 % Bacillus.” and analogous graphical representations. Of course, I can deviate from this (e.g., by listing lower ranks for diverse clades), but then I have to justify it – and here the desired reference might help.

  • If differing subspecies of a “big” species are present in an ecological community, this may lead to a superficial underestimation of the community’s diversity. Mind superficial: I am aware that this does not affect any good quantification of diversity. However, it does affect superficial diversity as estimated from representations such as that mentioned in the previous point, and the resulting discrepancies between objective and subjective diversity often demand an explanation.

  • Biosafety classifications are often determined on the species level, in particular, if the subspecies is unknown. For example, even though P. aeruginosa lives on our skins, it automatically gets classified as risky on account of some black-sheep subspecies.

Wrzlprmft
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  • One issue is that I don't know what you mean by "historical momentum". Do you mean, when humans found the organisms in question? – Maximilian Press Jun 22 '21 at 13:48
  • @MaximilianPress: I mean, e.g., that E. coli continues to be a species only because of its history as opposed to what would be a more balanced taxonomy given our current knowledge. – Wrzlprmft Jun 22 '21 at 15:33
  • Right- I talk about that specifically a little, below. I would then ask a different question: are species definitions themselves only still around because of historical momentum? Somewhat related: it might be helpful to read / learn more about classification, here is a video from Joe Felsenstein, old warhorse of computational phylogenetics, discussing this question (starts ~8 minutes): https://www.youtube.com/watch?v=PcD15i7yzJ8 – Maximilian Press Jun 22 '21 at 16:12
  • are species definitions themselves only still around because of historical momentum? – To some extent sure, but then there is some merit to having a rough idea of how diverse a clade is by its level. Anyway, this is something I cannot change. – Wrzlprmft Jun 23 '21 at 15:12
  • Our exchange has served to confuse me further regarding your question. Is your argument, basically, that E. coli is more diverse than a species first described yesterday because the type strain for E. coli was described first and it has therefore undergone more evolution since then? (That doesn't make any sense to me, but I'm having trouble understanding any other meaning.) – Maximilian Press Jun 23 '21 at 23:44
  • @MaximilianPress: E. coli is more diverse than a species first described yesterday because the type strain for E. coli was described first – Yes, though the reason is not evolution, but rather things like: 1) The definition of E. coli had to be expanded to maintain monophyly in light of new insights. 2) New insights on the properties of E. coli or strains thereof. 3) The definition of E. coli is overly broad by modern standards either due to new insights on what aspects matter for bacteria or general changes of standard as to how narrow a species should be. – Wrzlprmft Jun 24 '21 at 09:34
  • I'm going to delete my answer because it doesn't seem to be helpful here. Based on our exchange, I remain puzzled about how the presentation of results at a fixed taxonomic level is methodologically enforced compared to the (to me) clearly superior phylogenetic method, there is a bunch of literature on this as we've discussed. Potentially editing the question would clarify this. – Maximilian Press Jun 25 '21 at 05:39
  • @MaximilianPress: The presentation of community composition is not methodologically enforced, because it is not about methods or quantification, but about presentation. Just to be very clear, I am talking about things like “Our community contained 80 % Pseduomonas, 15 % Escherichia, and 5 % _Bacillus._” and graphical representations of similar information. I have no idea how I can make things much clearer, but am open to suggestions. – Wrzlprmft Jun 25 '21 at 10:27
  • "Our community contained 80 % Pseduomonas, 15 % Escherichia, and 5 % Bacillus.” and graphical representations of similar information." I think that this is a much clearer statement of what you anticipate needing (or expect people to want from you) than I am getting from the question. I think that in your question you could take such a statement and then talk about what you think is wrong with it, and what kind of statement you would prefer to make instead. And also, to be very explicit about how it interacts with history (where I think I get confused). Also, asexuality seems irrelevant to me? – Maximilian Press Jun 25 '21 at 15:11
  • @MaximilianPress: Edited. Asexuality is relevant, because for sexual organisms species levels get readjusted based on insights on reproductive compatibility AFAIK. While this is not perfect either, it regulates the scope of species to at least some extent. – Wrzlprmft Jun 25 '21 at 15:35
  • FWIW I think the question is clear, it's just hard to find the sorts of sources requested, especially reliable ones. It's more the thing that people talk about at a conference rather than writing papers on. I suspect you might find some discussion in an article arguing for a change but I've gone through several of these now and not found anything to quite back this up. – Bryan Krause Jun 25 '21 at 15:56
  • I have tried to ask a similar question from a rather different prospective: basically, whether taxonomic categories can eb defined by differentiating between quantitative and qualitative evolutionary changes. – Roger V. Jun 25 '21 at 17:09

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