Template talk:Paraphyletic group

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What is the classification for?Edit

What are we supposed to do with the parameters like regnum, classis, etc? Are they for the largest group which includes all the included groups? If so, then seaweed would be Life (if the cyanobacteria are included) or Eukaryote if not. The whole thing is potentially confusing - taxoboxes start at the top (typically kingdom) and proceed to the taxon for the article (the same as the one in the "name" parameters) in a parameter is species, group, etc. What is the list of taxa in this template supposed to end with?

A related question: what about polyphyletic groups like seaweed? Is this template supposed to be for them or just for paraphyletic groups? Kingdon (talk) 14:51, 28 June 2008 (UTC)

Perhaps "Artificial group" would be a more appropriate name for the template? I had intended the classification, if specified, to be for the largest common group; it won't mean much in instances such as "seaweed" if we include cyanobacteria, so should be left blank, but in cases such as the non-avian dinosaurs, or reptiles, it would be helpful to put animalia -> chordata. Martin (Smith609 – Talk) 15:11, 28 June 2008 (UTC)
I'd probably leave the name as Paraphyletic group but clarify in the doc that it is for both paraphyletic and polyphyletic (the distinction between the two is not always known, as it relies on direct or indirect information about the common (extinct) ancestor). Maybe there is a better name but "artificial" feels too POV to me (see any number of essays by Stephen Jay Gould on traditional versus cladistic classification for example - the gist of which is that one might considered how far the pheonotype of a derived group has diverged from the ancestral group). I've updated the documentation but feel free to change it further. Kingdon (talk) 15:56, 28 June 2008 (UTC)
Template:Polyphyletic group now redirects here. Thanks for your comments, and feel free to advertise the template if you wish! Martin (Smith609 – Talk) 16:05, 28 June 2008 (UTC)

Included taxa versus Included groups versus ?Edit

So I was trying to add this to Dicotyledon, a paraphyletic (or polyphyletic, one of those cases where I don't think it is fully clear which) group which has had a taxobox for a while. I gather some are dubious about taxoboxes on paraphyletic groups, but the problem here is adding the included and excluded groups. 6 of the 8 are (or could be) taxa, but not eudicot or magnoliid (eventually there will perhaps be well-accepted taxa for these, but right now most researchers in the field seem to use unranked names for these, not taxa in the sense of the ICBN). Would a good fix be to rename "included taxa" to "included groups" or "included clades" or some such?

I was going to put in included as:

and excluded as:

Kingdon (talk) 17:31, 28 June 2008 (UTC)

I guess that taxon implies a rank; clade would be the correct term to use; perhaps it should be wikilinked for the non-specialist. I've implemented this edit Martin (Smith609 – Talk) 17:50, 28 June 2008 (UTC)
Yes, taxon implies a rank. Clade implies monophyly, and in some cases there hasn't been enough research to really know (or perhaps there is enough research to know it isn't monophyletic but not enough to know what clades do exist, or the systematists have reclassified something but the rest of the world hasn't picked it up yet). So I'd probably prefer "group". Or maybe even just "Included" without a second word? Kingdon (talk) 18:00, 28 June 2008 (UTC)
Just "includes" is a little ambiguous; I guess group works but it implies that the list contains "non-clades". Surely it is acceptable to list things that are currently assumed to be clades, and to amend boxes if necessary, if and when future research invalidates them. Martin (Smith609 – Talk) 19:06, 28 June 2008 (UTC)
OK. I'm not thinking of an example where we'd want to use this template, and we'd be unable to list clades (or groups suspected to be clades, anyway). So sticking with clades, at least for now, sounds fine. Kingdon (talk) 16:39, 29 June 2008 (UTC)
Three "groups" that would be very challenging to list clades for would be Fish, Algae, and Protist. There have been phylogenetic studies, but there is little agreement concerning the highest-level groupings. --EncycloPetey (talk) 21:21, 14 July 2008 (UTC)
Good points, and I found another one: Green algae, in which we are calling Charophyta a clade when it surely is not. I think the above discussion has a consensus for "included groups" and "excluded groups", and I'd be willing to make that change although there is a small amount of template "programming" involved in terms of getting rid of the wikilinking to clade (specifically, the code to link to it only once, regardless of whether includes, excludes, or both are specified). Kingdon (talk) 14:46, 21 July 2008 (UTC)
I've changed "clade" to "group" although someone who is more of a template programmer than I could simplify things a bit. Kingdon (talk) 04:38, 3 August 2008 (UTC)

Quotation marks in headerEdit

The quotation marks surrounding the group name were recently removed from the template. I have restored them, because scientific convention denotes paraphyletic groups by placing quotation marks around the group name. It is important to make this distinction, as the paraphyletic group box looks at a glance like a standard taxobox, and readers should not be misled into thinking that a paraphyletic group forms a natural clade. Martin (Smith609 – Talk) 12:56, 3 October 2013 (UTC)

Wasn't it a bit hasty to revert? WP:BRD, after all. Regardless, are you certain this convention is 1) understood by the readers and 2) consistently applied in all disciplines? I've read quite a bit of literature on paraphyletic groups but haven't seen the use of quotes applied. It just looks odd to me. I also think this is the wrong way to implement such a style. The term in |name= is set by editors on each page and may either be a common name or the paraphyletic group name. It may not be appropriate in every use of this template. I do think it's important to somehow flag this template as different from the regular taxobox format, however, I think it should be clearer than just quotes in the name field, which to a reader isn't a clear indicator of paraphyly. This may not be a high-profile template like the taxobox, but let's leave it as it was until it's clear this is the right change to make. Rkitko (talk) 01:21, 4 October 2013 (UTC)
This is the scientific consensus, whether the group name is "formal" or "informal". Here are some examples, pulled at random.
  • . JSTOR 2400955. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  • . JSTOR 1306778. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  • http://www.app.pan.pl/archive/published/app49/app49-161.pdf
  • http://archosaurmusings.wordpress.com/2008/12/19/monophyletic-paraphyletic-and-polyphyletic/
Can you give an example of when a common name will not be a paraphyletic group name?
Martin (Smith609 – Talk) 16:21, 7 October 2013 (UTC)
For every example you give, I can find others that do not use quotes. How widely used, then, is this style? Where was it suggested and agreed upon as the style to denote paraphyletic groups? Is this also the style convention for polyphyletic groups -- don't forget that {{Polyphyletic group}} redirects here and is in use on a couple of articles. As the style does not appear to be consistently applied in the literature (e.g. with respect to the searches I did on progymnosperms or bryophytes), it's probably not wise to adopt it automatically at the template level for every article it is used on. I note that our articles don't use this style in the lead when introducing the term, so why use it only in the name parameter of the infobox? Rkitko (talk) 20:18, 7 October 2013 (UTC)

virus_groupEdit

How can I get the virus_group parameter to show up? See Torque teno sus virus. --Nessie (talk) 02:19, 23 August 2018 (UTC)

@NessieVL:, this template has had very little development, and I suspect that there are a bunch of parameters supported by taxoboxes that aren't supported here. I don't really know what I'm doing with template coding, but I added rudimentary support for |virus_group= by copy-pasting the code for one of the other rank parameters and changing it for virus_group. By rudimentary support, I mean that it only shows the parameter value exactly as entered (e.g. "ii"); I guess another template needs to be called to show the description of the nucleic acid composition for each virus group, and I'm not sure how to do that. Maybe @Peter coxhead: can help bring this template up to date. Plantdrew (talk)
@Plantdrew and NessieVL: yes, there do seem to be quite a few updates to other manual taxoboxes that haven't migrated here. Support for viruses generally can be limited in all kinds of taxoboxes, because, so far as I can see, virus taxoboxes haven't been seriously maintained since editors like Bob the Wikipedian worked on them. (There also seems to be confusion over how we format virus taxon names here.)
I'm working on Module:TaxonItalics at the moment, trying to automate italicization and abbreviation of taxon names, but I'll add this template to my to-do list (which is ever-growing!). I think that Bob may be around again, so perhaps he could help. Peter coxhead (talk) 09:43, 24 August 2018 (UTC)
Created a sandbox version of the template ({{Paraphyletic group/sandbox}}), calling the group links from {{taxobox/core}} copied into a new template ({{Virus group}}). There are some oddities (e.g. the centering) that need to be dealt with, but is this more or less what is wanted? It's used in Torque teno sus virus.   Jts1882 | talk  19:19, 24 August 2018 (UTC)
Yea, looks good. Thanks @Jts1882:. --Nessie (talk) 01:42, 25 August 2018 (UTC)

@Peter coxhead, Plantdrew, and NessieVL: I've grasped the opportunity to delve into the inner workings of the taxobox systems and have knocked up a prototype Module:Paraphyletic group for template {{Paraphyletic group}}. The formating still needs some more work and not all the features have been added, but it's a start. Some examples including algae, lizards and Torque teno sus virus can be found at my test page User:Jts1882/sandbox/test/taxobox.   Jts1882 | talk  14:32, 25 August 2018 (UTC)

With the 10th ICTV revision and all the discoveries made with {{virusbox}} now i think we don't need the Virus Group, as it's paraphyletic on it's own. Still would be good to have it more automated, kinda like {{hybridbox}} --Nessie (talk) 04:03, 19 January 2019 (UTC)
You can use the automatic taxonomy system in the taxobox with {{paraphyletic group}} by adding |auto=yes. A better version is in {{Paraphyletic group/sandbox}} and I should update this. Some examples are in User:Jts1882/sandbox/test/taxobox/para, including an example using Torque teno sus virus with the automatic taxonomy (set using |auto=virus).   Jts1882 | talk  10:23, 19 January 2019 (UTC)
What‽ There's an auto mode? So you just need |auto=yes and |parent=? --Nessie (talk) 13:38, 19 January 2019 (UTC)
Yes, now I've updated the main version, |auto=yes and |parent= should work. Using |parent= means the last taxon is wikilinked. Use |taxon= if you don't want it linked. For viruses use |auto=virus. There are a number of virus taxoboxes using {{paraphyletic group}} which should be able to now use the automatic taxobox system. I think I have it so the behaviour is the same as {{virusbox}}, but let me know if there are any differences.   Jts1882 | talk  14:37, 19 January 2019 (UTC)
@Jts1882: is it possible to add aticles using the template but lacking |auto=yes to a maintenance category such as Category:Paraphyletic group infoboxes with manual taxonomy ( 4 )? --Nessie (talk) 19:03, 22 January 2019 (UTC)
Oh, and I converted Human T-lymphotropic virus to auto and it's not italicizing the names of the higher taxa (order, family, and subfamily). --Nessie (talk) 19:22, 22 January 2019 (UTC)
It needs |auto=virus so |virus=yes gets passed to the automatic taxobomy module.
On the category, I'll look into that.   Done   Jts1882 | talk  08:06, 23 January 2019 (UTC)

AuthoritiesEdit

I'm running across a few articles using this template that use an obsolete taxon for the grade along with the authority. Examples include Rhamphorhynchoidea, Agnatha, and lizard (the last two have the authority commented out). Is there a way to display these in automated mode, or must it be in manual? --Nessie (talk) 19:37, 22 January 2019 (UTC)

The authorities can be displayed in the normal manner. I've set the taxon and authority in Rhamphorhynchoidea and Agnatha. Note I've used |taxon= rather than |parent= in the usual automatic taxobox manner. The parent parameter is used with the automatic taxonomy handling of viruses, but can also be used to force a wikilink (e.g. in whale). I don't think that suborder Lacertilia should be displayed for lizard as it is no longer used.
Incidentally, there is a |excluded_text= which can change the heading for the excluded groups. It defaults to "Cladistically included but traditionally excluded taxa" because that was past practice, but it is a very clumsy phrase and I think the simpler "Groups excluded" is more suitable in most cases.   Jts1882 | talk  07:59, 23 January 2019 (UTC)

Cladistically included but traditionally excluded taxaEdit

This seems very odd in context. It lists a number of entities that aren't included, but that -- in the examples I've encountered, which are all viruses -- do not fall within the purview of the title of the article, eg HIV. In some cases a long list is unattractive and throws out the formatting of the article. Can this be made optional, or hidden in some way? I can't see how it is helpful to readers. Espresso Addict (talk) 20:48, 25 January 2020 (UTC)

@Espresso Addict: It is optional. Just remove the |excludes= parameter. Obviously this needs consensus on the relevant pages. The lists can also be hidden using collapsible content. If you can give an example of content to hide I can show you how to do it.   Jts1882 | talk  21:13, 25 January 2020 (UTC)
@Jts1882: I haven't seen a page where it's useful, so I'd suggest defaulting to hide, but I mainly edit virus pages, which might not be representative. Can it be collapsed on HIV, for example? Espresso Addict (talk) 21:16, 25 January 2020 (UTC)
@Espresso Addict: I think it's useful, as it distinguishes the group from a clade. Without it I think many readers would be easily misled. I admit the visuals may not please all, but like with some lengthy lists of subtaxa in {{Automatic taxobox}} a simple link to a section in the body can be provided. --Nessie (📥) 02:36, 26 January 2020 (UTC)
Human immunodeficiency viruses
 
Scanning electron micrograph of HIV-1 (in green) budding from cultured lymphocyte. Multiple round bumps on cell surface represent sites of assembly and budding of virions.
Scientific classification 
(unranked): Virus
Realm: Riboviria
Kingdom: Pararnavirae
Phylum: Artverviricota
Class: Revtraviricetes
Order: Ortervirales
Family: Retroviridae
Subfamily: Orthoretrovirinae
Genus: Lentivirus
HIV viruses
Non-HIV viruses in same clade
@Espresso Addict: The main point of this template is to show the other taxa for paraphyletic groups, so hiding it by default would defeat the purpose. But if you don't want to display the excluded groups just don't set the |excludes= parameter. The example to the right shows you one way how to collapse the list (using {{Collapsible list}}) and also how to change the text header from the rather awkwardly phrased default.   Jts1882 | talk  09:54, 26 January 2020 (UTC)
Thanks for the detailed response, Jts1882. It would be good if these instructions were collated on the main template page.
I think perhaps one problem is that this taxobox is being placed on some articles where this information is not relevant -- including all the virus examples I've seen. I was having nightmares last night about its use on a page such as common cold! For future reference, could you give me an example of proper use, where this material is actually cogent? Espresso Addict (talk) 22:05, 26 January 2020 (UTC)
Answering my own question, I see from the deletion discussion, fish and jellyfish are suggested as a good usages. These seem to me to be intrinsically very different from say human immunodeficiency virus, where the scope is clear and the other lentiviruses are clearly not in scope. Espresso Addict (talk) 22:31, 26 January 2020 (UTC)
@Espresso Addict: To be extra clear, in cases where consensus deems that the box should be removed, no other taxobox should be used. An example of a page that should not have a taxobox is mosaic virus. --Nessie (📥) 12:07, 27 January 2020 (UTC)

|subdivision_ref=?Edit

I feel this box could use |subdivision_ref=, like with {{Automatic taxobox}} and {{virusbox}}. Is that possible? --Nessie (📥) 16:41, 3 February 2020 (UTC)

All the list sections have a ref option. So parameters |subdivision=, |includes=, |excludes= and |synonyms= have corresponding parameters |subdivision_ref=, |includes_ref=, |excludes_ref= and |synonyms_ref=. There are also _text suffix parameters that can change the heading title.   Jts1882 | talk  17:00, 3 February 2020 (UTC)
@Jts1882: Ah, I see now why it didn't show up on Ekpoma virus: I used |subdivision_ref= without using |subdivision=. I switched to |includes_ref= and |excludes_ref= and it displays now. Thanks! --Nessie (📥) 17:43, 3 February 2020 (UTC)

Category:Paraphyletic groupsEdit

@DexDor:, why not add pages to Category:Paraphyletic groups ( 131 ) using this template? --awkwafaba (📥) 01:37, 25 March 2020 (UTC)

Because (1) that's very non-standard, (2) it makes it much harder for anyone else working on categories (e.g. to split the category into subcategories should that become necessary) and (3) it can cause all sorts of pages (drafts in userspace, portal subpages ...) to be incorrectly in the category. Reason 3 could partly be alleviated by adding code to the template to look at what namespace the page is in and/or to have a "nocat" parameter, but that adds complexity (to the template and for editors working on articles). I've also seen things like this causing confusion when an editor copies a template to create a new template. Fundamentally, it's best not to assume that just because a page contains a particular infobox template that the page meets the criteria for being in any category. DexDor (talk) 07:37, 25 March 2020 (UTC)
(edit conflict)
Despite the name the template isn't used exclusively for paraphyletic groups. It is also used for polyphyletic groups and for some common names which are debatably paraphyletic or polyphyletic or neither. It's essentially for any group that doesn't fit a clearly defined classification and needs exclusions. Also many paraphyletic groups just use {{taxobox}} so it would add confusion of adding categories in multiple ways. —  Jts1882 | talk  07:56, 25 March 2020 (UTC)
Yes, we can't assume that an article using this template to generate the taxobox is actually a paraphyletic group, nor do all articles which are actually about paraphyletic groups use this template (rather than a manual taxobox or no taxobox). It's better to add the paraphyletic group category to appropriate articles manually. Plantdrew (talk) 16:44, 25 March 2020 (UTC)
list
Would someone like to check whether any of these should be added to one of the categories? (I'm not sure that my knowledge of taxonomy is sufficient to do this correctly) DexDor (talk) 08:23, 26 March 2020 (UTC)
I've added my opinions to a few of list. —  Jts1882 | talk  09:29, 26 March 2020 (UTC)
Are all these categories needed (e.g. is the last one redundant to the others)? Are there some simple rules about what articles belong in which of these categories? DexDor (talk) 21:14, 27 March 2020 (UTC)
Para/polyphyletic group categories were created by an editor with minimal contributions to organism articles. I've been heavily involved in building the "common names" category tree (and "historically recognized" plant categories). In my view, a "common name" article shouldn't have any relevant scientific name in existence, but there should be some shared characteristic that makes them a group (eagles=very large birds of prey). Para/polyphyletic and obsolete taxa should have a relevant scientific name in existence (and perhaps a redirecting scientific name should get the category when a common name is the title? E.g. Pisces, not "fish"). Plantdrew (talk) 22:13, 27 March 2020 (UTC)