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This talkpage has been used for general discussion of issues with the automated taxobox system as a whole – taxobox templates like {{Speciesbox}} or this one, taxonomy templates like Template:Taxonomy/Aves, or the design and coding of the system. It is suggested that these should now be discussed at WT:Automated taxobox system, and this page reserved for specific problems with this template.

How to deal with existing articles that are of synonyms?

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I was just about to convert Dysgraphhadena to use {{automatic taxobox}} instead of {{taxobox}}, but while investigating I discovered that Dysgraphhadena is apparently a junior synonym of Rhiza. This was unmentioned on both pages. So, I added the synonym to Rhiza's page, but I'm not sure what is supposed to be done with Dysgraphhadena's. Should it be replaced with a redirect to Rhiza? Should it just be deleted entirely? Should it be largely left as is but with text added mentioning that it's a synonym? If it's left in place (and not made into a redirect), should anything special be done to its taxobox? Or something else entirely? - Rwv37 (talk) 21:51, 4 December 2024 (UTC)[reply]

@Rwv37: in this case I would simply make it into a redirect; there's no useful information in the article that needs to be merged into Rhiza. Peter coxhead (talk) 07:39, 5 December 2024 (UTC)[reply]
OK, I did that, and in the process discovered there's actually a specific rcat template intended for this: {{R from alternative scientific name}}. Thank you! - Rwv37 (talk) 08:19, 5 December 2024 (UTC)[reply]
@Rwv37: indeed. Where there is any substantial history of editing the redirected article, you can also add {{R with history}}, but it's not necessary in this case in my view. There is a need for more guidance on dealing with articles found to be at synonyms. Peter coxhead (talk) 09:49, 5 December 2024 (UTC)[reply]

Proper handling of stem taxa

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I was trying to clean up some stem-Ctenophora inconsistencies and discovered that I apparently don't know how to handle stem groups. The current tree is something like:

The way Siphusauctidae is handled is what I was expecting: There is a Ctenophora/stem-group taxon with rank "stem group" that is used as the parent, and Ctenophora/stem-group has the same parent as Ctenophora. This indicates that Siphusauctidae is a group along the Ctenophora stem.

But what is going on with Dinomischidae? I did not think that a group that did not have /stem-group on the end should be given rank "stem group"? The way this appears on the Dinomischus page makes it look to me like Dinomischus is in the stem group of Dinomischidae, the family of which it is the type genus. Surely this is not correct?

I was going to re-parent Dinomischidae to Ctenophora/stem-group and change its rank to familia, but I wanted to check and see if I'm understanding this correctly. Perhaps it should be added to the documentation? Or is there somewhere else I should be looking?

Ixat totep (talk) 18:44, 16 December 2024 (UTC)[reply]

Poking around a bit more, I'm pretty sure that the way of handling I think is correct is correct, so I'm just going to make that change and see if anyone objects. Which makes this question more about whether this should be documented. I'm hesitant to do that myself as this is a much-used template and I am not at all confident of my understanding of its details.
Ixat totep (talk) 20:09, 17 December 2024 (UTC)[reply]
@Ixat totep:, the Dinomischidae template was edited from how it was initially set up on 30 September. It originally had rank as familia and parent as Ctenophora/stem-group. I'd guess the person who edited it just didn't know what they were doing. Plantdrew (talk) 22:08, 17 December 2024 (UTC)[reply]
Thanks @Plantdrew yeah I noticed that when I went to change it- don't know why I didn't think to look earlier. Thanks for confirming!
Ixat totep (talk) 23:23, 17 December 2024 (UTC)[reply]
I find that arangement strange. Surely stem group Ctenophores should be part of Ctenophora or if the latter is a crown group both should belong to a total group. —  Jts1882 | talk  11:06, 18 December 2024 (UTC)[reply]
I agree. Ctenophora seems to be treated as a total group, at least in our article, so the parent at Template:Taxonomy/Ctenophora/stem-group should surely be Ctenophora, not jump to Animalia. Peter coxhead (talk) 11:13, 18 December 2024 (UTC)[reply]
Is the stem group template needed? There aren't a large number of taxa, so why not just put the two families under Ctenophora? The articles on Fasciculus, Maotianoascus, and Scleroctenophora refer to them as stem-group Ctenophora, but they aren't place under the stem group template. There's also a Template:Taxonomy/Ctenophora/?, although that doesn't seem to be used.  —  Jts1882 | talk  11:32, 18 December 2024 (UTC)[reply]
@Jts1882, @Peter coxhead— This isn't specifically about Ctenophora. Take a look at Template:Taxonomy/Entoprocta/stem-group, Template:Taxonomy/Bilateria/stem-group, Template:Taxonomy/Bilateria/stem-group, Template:Taxonomy/Ambulacraria/stem-group, Template:Taxonomy/Arthropoda/stem-group... this is how stem groups work, and Ctenophera should not be changed without considering the broad impact.
The way to think about it is kind-of like this:
  • Animalia
    • Ctenophera (total group) [no Template:Taxobox/Ctenophora/... for this]
      • Ctenophera/stem-group
      • Ctenophera (total group) [just uses the regular Template:Taxobox/Ctenophera]
The difference being that with "/stem-group" (given the "rank" of "stem group"), we know that the groups are along the stem in some order rather than implied to be direct sister-groups.
But I think what you're really objecting to is the lack of an entry for the total group, which is just implied by having both a crown group and a stem group.
I suspect this is beause stem groups were added to the system much later, and no one wanted to go and create a whole bunch of crown and total groups when for many taxa there's no need for a separate stem group. Plus for wholly extinct taxa the concept isn't really relevant — you can't have a stem group when there's no surviving crown group. Linnaean taxonomy and cladistics have an uneasy relationship, unfortunately.
The articles on Fasciculus, Maotianoascus, and Scleroctenophora refer to them as stem-group Ctenophora, but they aren't place under the stem group template.
@Jts1882 sounds like an opportunity to fix something! Either the description or taxonomy is less correct than it could be. Ixat totep (talk) 15:48, 18 December 2024 (UTC)[reply]
@Jts1882 I'm not familiar enough with ctenophores to evaluate those other groups. If there is debate, then they go under the crown group (e.g. Template:Taxonomy/Vetulicolia, which might be a monophyletic sister to Tunicata, and therefore a clade in the crown Chordata, or it might be an evolutionary grade of stem chordates. There's currently too much debate to move it to Template:Taxonomy/Chordata/stem-group (which doesn't exist, presumably because all putative stem-chordates are hotly debated).
Ixat totep (talk) 18:25, 18 December 2024 (UTC)[reply]
OK I decided to WP:BEBOLD and add documentation since the correct action is clearly not obvious. I only go it "right" (I think) because I happened to look at an example that was done that way the first time I needed to use a stem group.
It's a bit unclear to me if stem groups are used pervasively or only with higher taxa where there are large or significant branches of extinct organisms. That's mostly where I've been poking around recently, but I don't know that, for example, you'd talk about "stem hominins", and I don't see any stem-group definitions for Hominini/Homininae/Hominidae/Hominoidea. If there's any sort of policy on that it should get added to the docs. I might add a tentative note. Ixat totep (talk) 18:08, 18 December 2024 (UTC)[reply]

@Ixat totep: sorry, but I don't think there's a consensus for your addition to the documentation. The definitions of the terms are clear; the only correct arrangement according to the definitions is:

Total‑group X

Stem-group X (paraphyletic)

Crown-group X

Stem-group ctenophores are ctenophores. Stem-group arthropods are arthropods. And so on.

  • Yes, in practice, as you note above, the boundary between what is treated as stem-group and what is treated as crown-group is often fuzzy, but this doesn't alter the basic relationships between the groups.
  • My reading of sources on the internal phylogeny of ctenophores is that "stem-group" is used vaguely, effectively to mean "basal".

But this doesn't meant that a stem-group of any taxon X isn't included in taxon X. Peter coxhead (talk) 07:51, 19 December 2024 (UTC)[reply]

Agreed, stem-taxa are part of the parent taxon.
I have a general problem with using the taxonomy templates this way. Taxa using the {{Taxonomy/Ctenophora}} template display as Phylum Ctenophora in the taxobox, indicating that the phylum is called Ctenophora. Taxa using the {{Taxonomy/Ctenophora/stem-group}} template display as Stem group Ctenophora in the taxobox, which implies a taxon called Ctenophora that is a stem group. But Ctenophora is not a stem group. If taxa are to be grouped in to stem groups, it would be better to display it as Phylum Ctenophora (stem-group). It's the same with the other templates.
For the record:
  • A search finds 32 templates using the stem-group suffix.
  • There are 39 instances of taxonomy templates using stem-group templates as |parent=Taxon/stem-group
  • Only three of these groups have more than two child taxa (Onychophora 7, Corallinales 5, Priapulida 3), 12 have one child taxon, and 12 are unused.
If it is to be used, I think the stem-group "rank" would be better applied to paraphyletic groups that have a taxon name.  —  Jts1882 | talk  12:53, 19 December 2024 (UTC)[reply]
@Peter coxhead @Jts1882 I'm not proposing something here, I'm documenting a clear pattern that is already in use. (@Plantdrew any thoughts?)
No one is disputing that the real phylogeny has the total group containing both crown and stem. But how is that implemented in a way that displays meaningfully in a template:Automatic taxobox? Point that out to me, please. I have no interest whatsoever in coming up with something new, only documenting the expectations already present in the system. I am a bit frustrated that you both seem to be acting like I'm making this up as my own thing.
Is there a way to get someone involved who set this up? Because clearly someone did the work to make these taxa show up that way. That's the person you're arguing against. I'm just trying to make it less confusing while you're proposing re-doing this whole system that has clearly been working fine for other people (Since this construct is really only used at the very high level, where there's likely to be a significant stem between named groups, I wouldn't expect to see very many of them).
And "stem-group Ctenophora" is a common way of saying "within the paraphyletic stem between total group Ctenophora and crown group Ctenophora". Cladistic approaches prefer not to name paraphyletic grades. We just have names for a lot of them for historical reasons (and because sometimes it's just not clear).
Ixat totep (talk) 14:06, 19 December 2024 (UTC)[reply]
@Ixat totep: "within the paraphyletic stem between total group Ctenophora and crown group Ctenophora" – no, "within the paraphyletic stem of the total group Ctenophora before the crown group Ctenophora".
There isn't one person that "set this up". There are two parts to the display in the taxobox:
  1. Accepting and displaying the 'rank' of "Stem group" – this goes back to December 2010 in this edit by Smith609 who initially implemented the automated taxobox system. (Almost all the subsequent edits to this template were by me.)
  2. Setting up the "Taxonomy/X/stem-group" templates to have the parent as the taxon above X rather than X – for {{Taxonomy/Ctenophora/stem-group}} this was Monster Iestyn on 18 July 2024.
But how is that implemented in a way that displays meaningfully in an Automatic taxobox – the point that Jts1882 and I are trying to make is that at present it isn't. Stem-group X is part of X, as is crown-group X (total-group X just is X). This isn't at present conveyed properly in taxoboxes. Just changing {{Taxonomy/Ctenophora/stem-group}} to have |parent=Ctenophora, which is taxonomically accurate, produces:
Phylum: Ctenophora
Stem group: Ctenophora
which clearly doesn't look right. My preference is for something like
Phylum: Ctenophora
Grade: Stem-group Ctenophora
where "Grade" could be replaced by other terms, such as "Informal group" or "Paraphyletic group". Peter coxhead (talk) 15:03, 19 December 2024 (UTC)[reply]
I prefer that too.
Incidentally there are six [total group taxonomy templates, which could be used as a parent of a stem group. None of them match the stem group templates.  —  Jts1882 | talk  15:13, 19 December 2024 (UTC)[reply]
@Jts1882@Peter coxhead OK, again, I do not care what the system is, I just care that it is documented because I don't like following clear exaples and having people come after me saying I'm doing it wrong when it is not written down anywhere what the correct thing is. So, please, replace my documentation edit with whatever you want and I'll be happy to follow it, and update anything that doesn't match that I come across. You don't need to sell me on anything, just document it so that when someone else objects to my next edit, I can point them to the docs.
Ixat totep (talk) Ixat totep (talk) 15:23, 19 December 2024 (UTC)[reply]
@Ixat totep: understood. I've removed your added documentation for now, but I do agree that more about stem groups is needed when the discussion reaches a clear conclusion. Peter coxhead (talk) 15:51, 19 December 2024 (UTC)[reply]
Thanks, I look forward to seeing the outcome!
Ixat totep (talk) 16:21, 19 December 2024 (UTC)[reply]
The crown group article cites a source that says "tetrapod and angiosperm systematists have adopted crown-group concepts of established taxa whereas specialists in almost all other areas have adopted a total-group perspective". Is that true for the taxonomic literature (or was that true? source is from 2005)? I don't think that is true for Wikipedia's classification. Aves (Neornithes) is treated as crown group. There was discussion at Wikipedia_talk:WikiProject_Amphibians_and_Reptiles/Archive_8#Caudata_as_the_order_for_salamanders that didn't end up resulting in any changes. Plantdrew (talk) 17:14, 19 December 2024 (UTC)[reply]
@Plantdrew: as I understand it, those cases and discussions involve taxa with their own names, i.e. not names like "stem-group X", "crown-group X" or "total-group X". My suggestion only concerns those cases where there are no separate names. Thus this source says that Xianguangia sinica is "[p]roposed as a sessile stem-group ctenophore", so its taxobox should somehow reflect that proposed placement. Peter coxhead (talk) 17:50, 19 December 2024 (UTC)[reply]
@Jts1882: do you prefer "Grade:" or some other term? A preload template along the lines of Template:Automatic taxobox/editintro/sameas could be set up to pre-fill suggested values for a /stem-group taxonomy template. Peter coxhead (talk) 15:51, 19 December 2024 (UTC)[reply]
I went and looked up some systematic phylogeny involving stem groups in a few papers and found a variety of ways of handling it, so if there's a clear precedent in the literature I cannot discern it.
@Peter coxhead
BTW that usage ("a sessile stem-group ctenophore") in an earlier comment of yours is what I meant when I said that I read "stem group Ctenophora" as meaning "withi the total group, along the stem leading to the crown group."
Regarding "Grade".. I thought a stem group was paraphyletic by definition and therefore shouldn't need further marking? Also, it would be good to be able to distinguish between the general concept of an un-named stem group, and the scenario where the stem group has a Linnaean name that is now seen as a paraphyletic grade. Again, I don't so much care how it's handled, just that it's clear.
Also, should Plesion be a term under consideration? I've seen it used extensively in some sources with stem groups, but not mentioned at all in a lot of others.
BTW if you want a test case, I'd like it to be clear how to handle all of the vetulicolians per the Mussini et al. 2024 cladogram under Vetulicolia#Cladograms as an example. I do not mean that that cladogram is accepted or that I'd try to change things, it's just a good example of a complex stem group where several taxonomy names are paraphyletic in sequence along a stem group. With some monophyletic groups along the stem as well, and some genera that do not have a higher taxon other than the parent total group.
Ixat totep (talk) 18:36, 19 December 2024 (UTC)[reply]
@Ixat totep: I share your experience of being unable to find clear usages in the literature around this area (early cnidarians and ctenophores). Sometimes "stem-group X" is just used to mean something like "basal X", and there's no clear concept of a "group". Only when there's a cladogram is it clear how the terms are being used.
To reproduce the placement of Vetulicola in this cladogram in a taxobox would need something like:
Clade: Total-group Cordata
Paraphyletic group: Vetulicolida
Family: Vetulicolidae
Genus: Vetulicola
In reality, from my limited reading of the literature, the classification of Vetulicola is too uncertain and too varied to present a taxobox in this detail. Peter coxhead (talk) 07:46, 20 December 2024 (UTC)[reply]
I find it hard to see how a stem-group template could be properly sourced, unlike an arrangement with crown-group (strangely not available) and total-group. There will be sources describing stem taxa for a taxon X, and sometimes the stem group might be given a name, but they wouldn't be assigned to a taxon named stem-group X. In traditional taxonomy the paraphyletic taxon would get a taxon name and phylocode only uses monophyletic groups. None of these seem appropriate for the rank column in the taxobox, they are more qualifiers for the taxon, so Vetulicolida (paraphyletic group) or Chordata (total group) might be a better presentation. This would also allow the ranks to be given (class and phylum, respectively, in the example. In contrast "Grade" is used as an informal rank in traditional taxonomy. (e.g. Nelson's Fishes of the World).  —  Jts1882 | talk  11:44, 20 December 2024 (UTC)[reply]
In reality, from my limited reading of the literature, the classification of Vetulicola is too uncertain and too varied to present a taxobox in this detail.
@Peter coxhead Oh, goodness, I did not mean to suggest that! I meant to just use that cladogram as an examples of scenarios that any system needs to support. That's why I said
I do not mean that that cladogram is accepted or that I'd try to change things
But whether that specific cladogram ever turns out to be close to correct or not, it shows a lot of useful scenarios: Nested and sequential named paraphyletic grades, with named monophyletic clades within them.
Ixat totep (talk) 15:10, 20 December 2024 (UTC)[reply]
As a temporary measure I changed the parent of {{Taxonomy/Ctenophora/stem-group}} to {{Taxonomy/Ctenophora/total-group}}. The result can be seen at Dinomischus. While the relationship makes more sense (and would be better for crown-group taxa), I don't like this solution. For one thing, the rank of phylum is not shown.  —  Jts1882 | talk  15:39, 20 December 2024 (UTC)[reply]
Yeah I'm not entirely sure that's an improvement on how @Mlvluu had set up Template:Taxonomy/Dinomischidae (giving it a rank of "stem group" and a parent of Template:Taxonomy/Ctenophora.
I've collected some examples from the literature for consideration:
Shu, D.-G.; Conway Morris, S.; Han, J.; Zhang, Z.-F.; Liu, J.-N. (2004). "Ancestral echinoderms from the Chengjiang deposits of China". Nature. 430 (6998): 422–428. Bibcode:2004Natur.430..422S. doi:10.1038/nature02648. PMID 15269760. S2CID 4421182.
  • Total group Ambulacraria
    • Stem group Vetulocystida
      • Family Vetulocystidae fam. nov.
        • Vetulocystis catenata gen. et sp. nov.
I find this weird because "stem group" isn't a rank, it's a relative position. Also, Vetulocystida is monophyletic (or, rather, Vetulocystidae appears to be, and Vetulocystida only conctains Vetulocystidae). So this uses "stem group" for a monophyletic clade within a paraphyletic stem grade.
Zhang, Z.; Holmer, L. E.; Skovsted, C. B.; Brock, G. A.; Budd, G. E.; Fu, D.; Zhang, X.; Shu, D.; Han, J.; Liu, J.; Wang, H.; Butler, A. N.; Li, G. (2013). "A sclerite-bearing stem group entoproct from the early Cambrian and its implications". Scientific Reports. 3: 1066. Bibcode:2013NatSR...3E1066Z. doi:10.1038/srep01066. PMC 3548229. PMID 23336066.
  • Total group Lophotrochozoa
    • Stem group Entoprocta
I had not previously noticed the combination of total group Lophotrochozoa and stem group Entoprocta, for what is described (in the paper title) as a "stem group Entoproct." If this were read llike the pervious example, it would imply that Entoprocta is a clade within the Lophotrochozoa stem grade. But obviously that is wrong as Entoprocta is extant.
So this seems to read that Cotyledion is a member of the Entoprocta stem grade, and then i have no idea why "total group" is stuck on Lophotrochozoa as it would seem by definition that Entoprocta is a crown-lophotrochozoan clade?
Lorna J. O'Brien & Jean-Bernard Caron (2012). "A new stalked filter-feeder from the Middle Cambrian Burgess Shale, British Columbia, Canada". PLoS ONE. 7 (1): e29233. Bibcode:2012PLoSO...729233O. doi:10.1371/journal.pone.0029233. PMC 3261148. PMID 22279532.
  • Unranked stem-group bilaterian
I'm not actually sure what to do with "unranked stem-group bilaterian" here (just as an example, I believe it was later assigned to stem-Ctenophora but I can't find that paper right now).
Zhao, Yang; Vinther, Jakob; Parry, Luke A.; Wei, Fan; Green, Emily; Pisani, Davide; Hou, Xianguang; Edgecombe, Gregory D.; Cong, Peiyun (April 2019). "Cambrian Sessile, Suspension Feeding Stem-Group Ctenophores and Evolution of the Comb Jelly Body Plan". Current Biology. 29 (7): 1112–1125.e2. doi:10.1016/j.cub.2019.02.036. hdl:1983/40a6bcb8-a740-482c-a23c-7d563faea5c5.
  • Eumetazoa
    • Total-group Ctenophora
This just uses a total-group parent instead of mentioning the stem group explicitly.
Holmer, L. E.; Caron, J. B. (2006). "A spinose stem group brachiopod with pedicle from the Middle Cambrian Burgess Shale". Acta Zoologica. 87 (4): 273. doi:10.1111/j.1463-6395.2006.00241.x.
Here we have single quotes used to signify.. something? Anyway, the stem group is the parent, and no parent for it is shown.
S. Conway Morris & D. H. Collins (1996). "Middle Cambrian ctenophores from the Stephen Formation, British Columbia, Canada". Philosophical Transactions of the Royal Society B: Biological Sciences. 351 (1337): 243–360. doi:10.1098/rstb.1996.0024. JSTOR 56388.
  • Phylum Ctenophora Eschscholtz, 1829
    • Class and order Uncertain
      • Family Fasciculidae fam. nov.
      • Family Xanioascidae fam. nov.
      • Family Ctenorhabdotidae fam. nov.
(yes the italics are like that in the paper, idk why I bothered capturing it).
Another example that basically ignores denoting the stem group even though it's pretty well-established that any Cambrian ctenophores are outside of the crown group.
So... yeah. If I find more interesting variations I'll add them.
Ixat totep (talk) 17:37, 20 December 2024 (UTC)[reply]
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