Talk:Felidae

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Labels in Clade box?Edit

I'm a little worried about those labels in the {{Clade}} box at § Phylogeny and whether they meet WCAG contrast standards. (I'm referring to the contrast between labels like "Lynx lineage", "Caracal lineage", etc. and their associated background colors.) But my main question is, why is "Domestic cat lineage" placed as a |footer= in its box, instead of a |caption= like all of the others? I'm tempted to be WP:BOLD and just change it, but it's so obviously a deliberate choice that I wanted to check whether there's some reason I don't know about for doing it this way. -- FeRDNYC (talk) 22:25, 5 January 2019 (UTC)

You may have a point about the colours. Is there a way of checking if they cause a problem and should be removed. I created this diagram when testing the options in the module behind the {{clade}} template. There are a few other coloured ones (iirc, in Canidae, Hyaenidae, Mustidae) but I stopped making more because of this concern.
Each {{clade}} template in the schematic can only have one caption. The last pair of lineages are sisters in the same clade template so can only have one caption. All the others have further clade templates nested as the second child. If you want to use a caption for consistency, you could put the Felis lineage in a nested clade template with a single chiild, i.e. instead of |label2=Felis|2={{clade ... use |2={{clade|label1=Felis|1={{clade ... }}. This would lengthen the branch to the Felis bracket, but allow a caption.   Jts1882 | talk  08:02, 6 January 2019 (UTC)

Classification tableEdit

Recently, BhagyaMani added a table to the Classification subsection, seemingly to show that the new List of felids was an unneeded fork. At this point, however, not only has List of felids been expanded to be more distinct from this article's list of species, but no effort has been made to correct what I see as flaws in the table in this article: that 1) it takes up a full half of the length of the article, overwhelming it, and 2) that it's a rather awkward table to begin with, with massive images and little detail. I think it should be reverted back to how it was on March 15- a straightforward bulleted list of species/lineages/genera, with a {{seealso}} link to List of felids for the full table with images. I don't want to edit war, so I'm starting a discussion instead. As both Jts1882 and Reywas92 have expressed opinions about the list/this table, I invite them to discuss as well assuming they're not watching this talk page. --PresN 02:49, 23 March 2019 (UTC)

The table on this article does not look good, as it combines six fields into just three columns. The List of felids is much higher quality with more information. This article should be restored to the bulleted list of species as a summary style, with a {main} link to the list.
And what the heck are the colors? This version should be restored with a link to List of felids. Reywas92Talk 18:23, 26 March 2019 (UTC)
I agree that the simpler list and throw to List of felids is the better option. The tabel list as is is overwhelming and while the colour matching between the table and phylogeny is clever it would only really work if you could see all of the data in a single page. Sabine's Sunbird talk 21:15, 30 March 2019 (UTC)

Likely error in phylogeny cladogramEdit

The cladogram in the "Phylogeny" section likely has an error in the (bottom) "Domestic cat lineage" part. It seems to indicate that "Domestic cat (F. catus)" is NOT directly descended from "African wildcat (F. lybica)". It therefore disagrees with the WP cat, African wildcat, and Wildcat articles. Unless another editor shows me that I misunderstand, I will modify this cladogram to conform with those other articles.

While I understand what you're saying, the problem is that this is exactly what the source used says. If we're going to use that particular citation as a source for the cladogram, we have to make sure that they match, otherwise WP:SYNTH applies. If we can find another, equally good (or better) source that gives a different pattern for the whole thing, then we can use that, but until then we're stuck. We could, of course, add some commentary to make it clearer, using the sources elsewhere in the article to back up that specifically. Anaxial (talk) 06:54, 17 May 2020 (UTC)
Yes, that is the problem, one that has bothered me for some time. The cladogram follows the source and a number of reviews since continue to use that arrangement, even though we know it is doesn't accurately represent the domestic cat relationship within the wildcat complex. We could use a different reference for Felis (there are arguments why this wouldn't be synthesis), but the main study on this has two different arrangements in difference analyses (position of bieti) and the position of the domestic cat in nested within lybica. Adding text for clarification is always a good thing, but we have to be careful not to overdo one issue in this broad scoped article.
That said, the cladogram doesn't strictly follow the Johnson et al (2006) study. The position of the jaguar and leopard is swapped, following later studies (Davis et al, 2010; Li et al, 2016)) and the second clouded leopard species, which was recognised after the study, is included. However, the Li et al (2016) study includes these changes in their nuclear genome analysis. I've added this reference. I also think we should change the position of the bay cat lineage to that of the biparental nuclear genome analysis in Fig 1 of Li et al (2016). —  Jts1882 | talk  09:15, 17 May 2020 (UTC)
Li et al. (2016) was already used in the previous subsection, so I replaced the full ref by the already named one. -- BhagyaMani (talk) 09:35, 17 May 2020 (UTC)
Since apart from position of bay cat lineage, there are a few more differences between the 2 models : perhaps we should use the later one in the cladogram and merely present differences to the former one in text ? -- BhagyaMani (talk) 09:46, 17 May 2020 (UTC)
Here are the changes relative to Johnson et al (2006) if we go for the biparental nuclear genome analysis in Fig 1 of Li et al. (2016)
  1. Position of leopard and jaguar (as in current cladogram; also matches Davis et al, 2010).
  2. Includes Sunda clouded leopard (as in current cladogram).
  3. Includes Sunda leopard leopard (missing in current cladogram).
  4. Position of Andean mountain cat in ocelot lineage.
  5. Includes two tigrina specimens. Do these match the new species divisions?
  6. But it still has the domestic cat as sister to the European wildcat.
Any I've missed? —  Jts1882 | talk  09:59, 17 May 2020 (UTC)
Perhaps, it is also relevant to mention the difference in sample size. Li et al. (2016) analysed 100 cat samples. How many did Johnson et al. (2006) use? -- BhagyaMani (talk) 10:27, 17 May 2020 (UTC)
I've updated the cladogram on one of my user pages (see User:Jts1882/phylogeny/Felidae#Modular_version) —  Jts1882 | talk 
  Felidae  
Panthera lineage
  Pantherinae  
  Panthera  

Leopard (P. pardus)

Lion (P. leo)

Jaguar (P. onca)

Snow leopard (P. uncia)

Tiger (P. tigris)

  Neofelis  

Clouded leopard (N. nebulosa)

Sunda clouded leopard (N. diardi)

  Felinae  
Caracal lineage
  Caracal  

Caracal (C. caracal)

African golden cat (C. aurata)

  Leptailurus  

Serval (L. serval)

Ocelot lineage
  Leopardus  

Geoffroy's cat (L. geoffroyi)

Kodkod (L. guigna)

Southern tiger cat (L. guttulus)

Oncilla or Northern tiger cat (L. tigrina)

Pampas cat (L. colocola)

Andean mountain cat (L. jacobita)

Ocelot (L. pardalis)

Margay (L. wiedii)

Bay cat lineage
  Catopuma  

Bay cat (C. badia)

Asian golden cat (C. temminckii)

  Pardofelis  

Marbled cat (P. marmorata)

  Lynx  

Eurasian lynx (L. lynx)

Iberian lynx (L. pardinus)

Canada lynx (L. canadensis)

Bobcat (L. rufus)

Lynx lineage    

Puma lineage
  Puma  

Cougar (P. concolor)

  Herpailurus  

Jaguarundi (H. yagouaroundi)

  Acinonyx  

Cheetah (A. jubatus)

Leopard cat lineage
  Otocolobus  

Pallas's cat (O. manul)

  Prionailurus  

Rusty-spotted cat (P. rubiginosus)

Flat-headed cat (P. planiceps)

Fishing cat (P. viverrinus)

Sunda leopard cat (P. javanensis)

Leopard cat (P. bengalensis)

  Felis  

Jungle cat (F. chaus)

Black-footed cat (F. nigripes)

Sand cat (F. margarita)

  wildcats  

Chinese mountain cat (F. bieti)

African wildcat (F. lybica)

European wildcat (F. silvestris)

Domestic cat (F. catus)

Domestic cat lineage    

Sorry for late reply! I already saw your cladogram on your user page. And you know what I would like a lot: to show the cladogram the other way round : namely the early divergers at the bottom and the later ones on top. So that the clouded leopards and Panthera are shown at the bottom and Dom cat on top. Is that difficult to implement ? -- BhagyaMani (talk) 18:42, 18 May 2020 (UTC)
It's not difficult to implement, but I understand there is a weird way the cladograms are displayed when using Safari on Apple devices (different HTML table rendering) that makes the cladograms look worse when done that way. I can't verify that myself as I have no suitable devices. —  Jts1882 | talk  19:57, 18 May 2020 (UTC)
Do I understand you correctly that the rendering of above in Safari on Apple is correct, and only the rendering of upside-down cladogram weird? -- BhagyaMani (talk) 20:37, 18 May 2020 (UTC)
No. My understanding is that all the Safari rendering of HTML tables is weird, different from all other browsers, but I can't verify this. I've been told they look better when the more nested groups are at the bottom. I think this arrangement makes sense for web presentations where you are scrolling down, whereas the other way is better suited to the printed page. —  Jts1882 | talk  09:48, 20 May 2020 (UTC)
A possible solution is perhaps to take a screenshot of the cladogram and embed it as a jpg file ? The hyperlinks are not really needed, as they are already provided in the text. -- BhagyaMani (talk) 20:37, 18 May 2020 (UTC)
I'm not so keen on this as it becomes difficult for editors to make changes (albeit sometimes this is useful). One thing I want to do in future is use the {{clade}} template to output SVG code, which could then be used to generate the images. —  Jts1882 | talk  09:48, 20 May 2020 (UTC)

Returning to the (inconsistent) wildcat and domestic cat lineage: Tx to all for all of the commentary, which shows me that I should defer to you others to resolve this. I only note that at least one of the wildcat-related WP articles cites this 2017 paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5612713/ , which posits a different phyl. sub-tree for wildcats, et al. (That paper's discussion of genome analysis is over my head, for now.) Acwilson9 (talk) 07:43, 20 May 2020 (UTC)

The authors of this *2007* article had a) a much different sample size and b) from a much smaller spectrum of species for analysis than above mentioned author teams. And they grouped several as subspecies under F. silvestris that are recognized as distinct species today. But because of their focus, their proposed cladogram is not so relevant for the cladogram of the whole family, imo. -- BhagyaMani (talk) 09:07, 20 May 2020 (UTC)
I think it would be valid to change the wildcat complex arrangement based on a different source, as long as stated clearly. I don't think this qualifies as synthesis because no new conclusions are introduced. Alternatively we could add a footnote explaining the discrepancy. —  Jts1882 | talk  09:48, 20 May 2020 (UTC)
Seems entirely reasonable to me, as long as we make it clear. Anaxial (talk) 17:34, 20 May 2020 (UTC)
As a placeholder until an expert in both kitty phylogeny and Apple-device display can implement this, and to inform readers that the editors are aware of this imperfection, I added "{{Corrections to Felis/Domestic cat lineage await a better source|date=July 2020}}". (As I noted above on 20 May, I myself am not competent to implement this.) Acwilson9 (talk) 22:53, 30 July 2020 (UTC)
The source is the best available for now. It's apparently your device and browser used that cannot render the info correctly. Just read the source. -- BhagyaMani (talk) 08:08, 31 July 2020 (UTC)
That source also has three slightly different trees, the mitochondrial DNA tree, which places bieti basal to the rest of the complex, consistent with its currently recognised species status, and the two SNP trees (with and without hybrids), which places bieti in the lybica/domestic cat clade. The latter is probably the best result as it is nuclear DNA, but would be confusing in the Felidae article because the Chinese desert cat is recognised as a species. The Driscoll paper clearly treats bieti as a subspecies, but I can't think of any taxonomic paper or resource doing the same. It's a shame they haven't revisited the genetics of this complex, although doing so woould probably cause problems for conservation of the Chinese desert cat. —  Jts1882 | talk  08:42, 31 July 2020 (UTC)

cladograms for discussionEdit

For reference. —  Jts1882 | talk  09:22, 31 July 2020 (UTC)
Return to "Felidae" page.