Talk:Phylogenetic classification of bony fishes

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Title case

Why is the title of the article currently in title case, contrary to WP policies? The article at doi:10.1186/s12862-017-0958-3, from which the latest version is derived, doesn't use title case. It's not the title of a book or other specific publication. The article should be moved to "Phylogenetic classification of bony fishes". Peter coxhead (talk) 08:54, 2 December 2019 (UTC)[reply]

 Done The article has now been moved by another editor. Peter coxhead (talk) 17:12, 2 December 2019 (UTC)[reply]

Proposed split to Osteichthyes and Acanthomorpha

The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section. A summary of the conclusions reached follows.
No Consensus - Interesting discussion. Please feel free to start a new discussion about this before again proposing to split the page. - jc37 17:20, 3 August 2021 (UTC)[reply]

I can't quite see why there would need to be a separate article for these cladograms. Both are already present in the respective top-level taxa articles: Osteichthyes#Phylogeny and Acanthomorpha#Phylogeny. So this is something of a duplication, and normally we should just be looking at a redirect here. The cladograms displayed here are possibly more up to date than the ones already in use, and in the case of Acanthomorpha, more detailed. So I guess it might be useful to port them over (and adorn the terminal points with the lil' icons), then redirect this title to Osteichthyes#Phylogeny. Otherwise I don't think that the added level of detail and the fact that common names are added to the terminal points justify a standalone article. --Elmidae (talk · contribs) 20:20, 5 January 2020 (UTC)[reply]

  • Support - as stated, we usually just put the cladograms into the articles concerned, and we should do that here, there's no reason why not. Chiswick Chap (talk) 20:28, 5 January 2020 (UTC)[reply]
  • Oppose for a number of reasons.
    1. The Deepfin project is one of the major projects attempting to make a comperehensive phylogeny of the fishes. The Angiosperm Phylogeny Group have series of pages on their phylogeny of angiosperms and its development, so I think this can be considered similar, although not as well established yet.
    2. This page has the complete phylogeny produced from one source. The cladograms in the higher taxa articles tend to get edited to respond to recent primary works so they become composites (and arguably original research or synthesis), often without proper exlanations or references. Many of the large trees in higher taxa articles no longer match the references.
    3. I would suggest using this page as the source for the phylogeny in the other articles using partial transclusion. Alternatively, if it is considered that the article contains insufficient additional information, then it could be moved to template space and similarly used for transclusion to the cladograms on the other pages.
  • Another posibility would be to expand the scope of this article and compare the Deepfin phylogeny with the Fish Tree of Life phylogeny.   Jts1882 | talk  07:11, 6 January 2020 (UTC)[reply]
Both of these suggestions sound useful.
  • For the comparative article approach, are there several clearly "competing" cladogram structures that have current support and could be contrasted?
  • For the transcluded template, is that already being done somewhere? I didn't know these kinds of large structure could be served in templated form. One issue - wouldn't that restrict editing access, or at least visibility, of the source document? --Elmidae (talk · contribs) 18:50, 6 January 2020 (UTC)[reply]
@Elmidae: There are two main systems for the phylogenetic trees for fishes, the Deepfin trees and Fish Tree of Life trees. They are quite similar and don't diverge too much above Percomorpha. It's within percomorphs that the bigger differences occur. There are even bigger differences between these and Fishes of the World, the recommended project reference. I have some analysis of the differences at User:Jts1882/phylogeny/Fish#Comparison_of_Osteichthyes_divisions_above_Percomorpha
There are a few examples of phylogenies that are transcluded, e.g. {{Laurasiatheria Cladogram}}, {{Clade polysporangiophyte}} (and related templates), {{Cladogram of Proechimys species}} (and others of form {{Cladogram of ...}}), and presumably many others that I'm not acquainted with. You raise a good point about restricted editing, which is why I think its best suited to high level systems (e.g. Deepfin, APG IV) that shouldn't be edited often. The phylogenies in many higher level taxa articles have been extensively edited and too many are now unsourced or not following the listed sources and effectively original research. I think it would be better if there were stable phylogenies agreed by the projects and that they shouldn't be changed without consensus.
Another issue was flexibility of use. There are limitations on partial transclusion from templates that limit their use. I have been developing a system for doing this. The template {{clade transclude}} allows partial transclusion from any {{clade}} cladogram using the |label= parameters (as well as the <section> markup), with options to include or exclude images and authorities. The trees can also be pruned to remove unwanted clades or even replace them with another subtree. There are a few examples of how it could be used at {{Phylogeny/APG IV}}, {{Phylogeny/Squamata}} (using Zheng & Weins, 2016), and {{Phylogeny/Passerines}}. I haven't used any of these in the main article space yet, partly as I haven't finished testing and also because I realise there are some issues to address first.   Jts1882 | talk  09:32, 7 January 2020 (UTC)[reply]
Looks like you have most of the makings of such a comparative article ready to go at User:Jts1882/phylogeny/Fish#Comparison_of_Osteichthyes_divisions_above_Percomorpha, if you think this material could go here. Transclusion could then follow if/once the tech works? (nice 45 degree splash there, BTW :D) --Elmidae (talk · contribs) 00:32, 8 January 2020 (UTC)[reply]
The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Wikimedia software Template depth exceeded

Regardless of the outcome of the discusison above, this page is hitting the limits of Wikipedia's software. This can cause proplems with the page. It also puts the page in Category:Pages where expansion depth is exceeded. For technical details, see the text at the top of that category's page.

The most straightforward fix is to "split" the first cladogram at Clupeocephala and split the second one at Percomorpha or perhaps at the unnamed branch one level above Eupercaria. davidwr/(talk)/(contribs) 06:49, 14 February 2020 (UTC)[reply]

@Davidwr: The expansion depth error is strange as nothing is broken and the rendering is correct. A number of pages in the category have this error even though the transclusion is successful. A few months back I checked the category for pages using the {{clade}} template and fixed the ones that were broken (i.e. error messages on the page). This started when they changed how the transclusion depth was calculated in a Wikimedia update last summer and created a lot of expansion depth errors. Simple templates used to able to nested 40 deep, while now the limit is 20. This created errors on the Wikimedia help pages explaining transclusion. My questions about the change never got answered.   Jts1882 | talk  08:49, 14 February 2020 (UTC)[reply]
So you are saying that when they "improved" the Wiki, the literally broke the wiki? davidwr/(talk)/(contribs) 15:18, 14 February 2020 (UTC)[reply]
They certainly left broken template code and red error messages in a number of mainspace articles. The transclusion depth was always confusing and the new behaviour follows the explanations better, i.e. the 40 depth limit is met by 20 nested transclusions because it is one expansion of the template and one expansion of the template parameters for each use of the template. However before the change, some simple nested templates could go 40 deep and the cladograms could go about 23 deep (why 23, indeed?). The help page on Wikimedia (Help:Expansion_depth) still shows supposed demos of the deeper behaviour that now gives errors. Anyway, the change motivated me to find another solution and I added the |subclade= parameter to allow subtrees in cladograms so now there is no theoretical limit.   Jts1882 | talk  17:06, 14 February 2020 (UTC)[reply]
For the record, Wikimedia have increase the allowed expansion depth from 40 to 100. I think this is sufficient for any cladogram on Wikipedia. If the limits are being challenged, the cladogram is probably too large to be useful to the reader. —  Jts1882 | talk  08:08, 22 April 2024 (UTC)[reply]

Scope of the article

This article is unusual in that it is dedicated to a particular classification, from the Deepfin group and specifically their 2017 paper.

Thomas Near have been working on a new phylogenetic classification, more lumped and more phylocody. This is based on the phylogenetic analysis by Ghezelayagh et al (2022)[1] and presented in full in Near and Thacker (2024),[2] which has just being published.

Should this article be expanded to cover both classifications? They both are in agreement over much of the phylogenetic tree, with the main differences being the number of orders, especially in Percomorpha. —  Jts1882 | talk  08:06, 22 April 2024 (UTC) —  Jts1882 | talk  08:06, 22 April 2024 (UTC)[reply]

  1. ^ Ghezelayagh, A., R. C. Harrington, E. D. Burress, M. Campbell, J. Buckner, P. Chakrabarty, J. R. Glass, W. T. McCraney, P. Unmack, C. E. Thacker, et al. 2022. Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous. Nature Ecology and Evolution 6:1211–1220. https://doi.org/10.1038/s41559-022-01801-3
  2. ^ Near, Thomas J.; Thacker, Christine E. (2024). "Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)". Bulletin of the Peabody Museum of Natural History. 65 (1): 3–302. doi:10.3374/014.065.0101.
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