Wikipedia talk:WikiProject Tree of Life/Archive 58

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Is there an index WIP?

I noticed that in our header template there is a hidden code showing pages such as "Wikipedia:WikiProject Tree of Life/New article listing" and "Wikipedia:WikiProject Tree of Life/Index". Is there any plan to make the index a reality? As in, an index of all WP:TOL pages? How would it be made? —Snoteleks (Talk) 08:04, 20 October 2023 (UTC)

Probably too simple, but: gather them via an 'insource'-search on (to begin with) 'taxobox'? (74,282 hits, at the moment)

Or is there a better way/word to recognize, to search the pages-to-be-indexed? Kweetal nl (talk) 08:38, 20 October 2023 (UTC)

(speciesbox => 290,000 hits) Kweetal nl (talk) 09:11, 20 October 2023 (UTC)

I wouldn't take the hidden code as evidence for a plan. Someone mentioned a header banner so I copied the one from WP:PLANTS and added some existing subpages and commented out the rest. As for getting page numbers, you can add the number of articles with taxoboxes using hastemplate:taxobox (85,478), hastemplate:"automatic taxobox" (74,890), hastemplate:speciesbox (292,517) and other taxoboxes. hastemplate:"WikiProject Tree of Life" picks up 121,034 talk pages, but subprojects would need to be counted separately There are also category searches with incategory: and deepcat: Alternatively, Petscan might be the best way. Plantdrew is our resident expert there. — Jts1882 | talk 14:54, 20 October 2023 (UTC)

The article alerts report for TOL uses Category:Articles with 'species' microformats as well as the talk page WikiProject banner to identify relevant articles. The category has 461,741 articles. The category is populated by most of the taxobox templates, as well as the plant cultivar infobox, some of the infoboxes for animal breeds, and an infobox for individual animals. Template:Population taxobox, Template:Infraspeciesbox special and Template:Paraphyletic group do not populate the category and there are 185 articles that use on of those templates. There are relevant articles in Category:Obsolete taxa that don't have taxoboxes, and possibly relevant articles in Category:Common names of organisms (some of which have {{Taxobox}} or {{Paraphyletic group}}). The TOL WikiProject banner is mostly used on articles about taxonomy and systematics in general, although it is also on a few articles about taxa (which all should have taxoboxes). The taxon articles with the TOL banner are the top level articles for subprojects (plant, fungus, insect, etc.), articles about taxa above the level of any subproject (eukaryote, opisthokont), and some enigmatic fossil taxa that can't be placed to a kingdom.

I don't think Petscan would be helpful for constricting an index. If Petscan is used to search categories, it's possible to drill too far down and pick up irrelevant articles (e.g., those in Category:Citrus drinks), and how far down is too far varies across the category tree. A Petscan search for templates is going to have some of the same issues as the "Articles with 'species' microformats" category (although we could exclude the templates for individual animals and breeds/cultivars that populate the category if that is desired).

It would be nice to have a TOL-wide new article report but somebody needs to write the rules for it. There is User:AlexNewArtBot/SpeciesSearchResult which uses these rules: User:AlexNewArtBot/Species. It doesn't pick up new articles for higher taxa though. Plantdrew (talk) 16:16, 20 October 2023 (UTC)

Arguably the easiest way to track all taxa articles would be to add the WikiProject ToL banner to all taxa articles. Which I suppose could be done by bot? But might cause other objections. I'm not arguing for or against it, just stating it as a possibility. Happy editing, SilverTiger12 (talk) 16:23, 20 October 2023 (UTC)

Opisthoteuthidae or Grimpoteuthidae

There is a comment on Template talk:Taxonomy/Grimpoteuthidae asking this question. Jo-Jo Eumerus (talk) 16:09, 20 October 2023 (UTC)

Grimpoteuthidae is a recently created article (20 September 2023). WoRMS recognizes the family (apparently also only recently; the family record had a change on 18 September). WoRMS is followed for other molluscs (bivalves, gastropods), but I don't think there has ever been any discussion about a source to follow for cephalopods. Plantdrew (talk) 16:23, 20 October 2023 (UTC)

The Bison conundrum

Earlier in September, an IP user made the decision to unilaterally change the infobox of several bison articles to Bos. Chumzwumz68 (who I'm pretty sure is a sock of Ddum5347, see Wikipedia:Sockpuppet investigations/Ddum5347) has recently gone on a spree of mass changing all Bison article to Bos, including titles. I've just reverted most of this (except two titles which I am currently pending a technical request to change back). This issue has caused problems before. In my opinion, while all authors agree that the exclusion of Bison makes Bos paraphyletic, the usage of the genus Bison should be retained for nomenclatural stability, because the vast majority of the scientific literature discussing bison continues to use it. The changing of the titles is especially problematic, because in some cases it is essentially WP:OR, like the recent change to Bos occidentalis, which as far as I can tell has never been used in the scientific literature at all [1]. Hemiauchenia (talk) 04:54, 6 October 2023 (UTC)

I will check a few things on this one, need to consult some colleagues who a mammologists, I am a herpetologist this is out of my area of expertise but I know people who work with this. Give me a couple of days. Cheers Scott Thomson (Faendalimas) ^talk 11:29, 6 October 2023 (UTC)

Before Scott reports back, I think it's very clear that any changes unsupported by bibliographic references are completely unfounded and would be considered original research (like you said). I suppose it's an attempt to get ahead of the curve but it's irresponsible, since those are changes not yet made to the systematics. Also, what if they end up dividing it into several new genera? In summary, those changes should be reverted I think. —Snoteleks (Talk) 12:34, 6 October 2023 (UTC)

agreed, basically I am going to see if there are any very recent refs supporting any changes, and get them for you all. If not absolutely, revert this is my view. I just like to give benefit of doubt and check things first. Cheers Scott Thomson (Faendalimas) ^talk 13:16, 6 October 2023 (UTC)

Thanks for doing it, Scott. It's a good strategy. —Snoteleks (Talk) 13:44, 6 October 2023 (UTC)

When removing sourced statements you don't agree with (B. bison, B. bison bison, B. bonasus, B. bonasus hungarorum), please also remove the references rather than appropriating them for claims they in fact contradict.

The ASM-MDD have adopted an expanded Bos to include Bison (see here). This is potentially problematic. They don't treat many extinct species so cannot be used as a source for Bos occidentalis if we decided to follow them for the extant species. However, the general practice of the mammal project is to make the changes when both the IUCN and MDD have moved on from MSW3. The IUCN still recognise genus Bison so the problem is for the future. Addition: Groves and Grubb (2011) also recognise an expanded Bos in their Ungulate Taxonomy. — Jts1882 | talk 12:42, 6 October 2023 (UTC)

Several molecular phylogenetic studies of the extant Bovini have been published. Although the exact phylogeny obtained using mtDNA differs from that from autosomal DNA, the studies agree that Bison is embedded within Bos. For example see Wu et al 2018, and Supplementary Fig 12, Zhang et al 2020. - Aa77zz (talk) 13:25, 6 October 2023 (UTC)

MT DNA represents only a single locus, and therefore can be entrained by incomplete lineage sorting or minor introgression. The position of bison as the sister group to yaks based on nuclear DNA is undoubtedly the correct one. It gets even more confusing when one considers fossils, as it is suggested that bison evolved from the extinct genus Leptobos. Does that mean that Leptobos is nested with Bos too? Hemiauchenia (talk) 13:41, 6 October 2023 (UTC)

There are numerous reliable sources from recent publications that found bison to be nested within Bos, namely:

Verkaar et al, 2004^[1]
Groves & Grubb, 2011^[2]
Wu et al., 2018^[3]
Grange et al, 2018^[4]
Wang et al., 2018^[5]
Zhang et al., 2020^[6]
Zver et al, 2021^[7]
ASM, 2021^[8]

"Retainig nomenclatural stability" in the face of new scientific evidence is no value in of itself. Until Reeder et al. get their act together, an encyclopedia should adapt to newly established knowledge. Science has progressed since 2005 and there is no reason for WP not to. 89.206.112.12 (talk) 10:01, 17 October 2023 (UTC)

References

^ Verkaar, Edward L. C.; Nijman, Isaäc J.; Beeke, Maurice; Hanekamp, Eline; Lenstra, Johannes A. (July 2004). "Maternal and Paternal Lineages in Cross-Breeding Bovine Species. Has Wisent a Hybrid Origin?". Molecular Biology and Evolution. 21 (7): 1165–1170. doi:10.1093/molbev/msh064. PMID 14739241.
^ Groves, Colin P.; Grubb, Peter (2011). Ungulate taxonomy. Baltimore (Md.): J. Hopkins university press. ISBN 978-1-4214-0093-8.
^ Wu, Dong-Dong; Ding, Xiang-Dong; Wang, Sheng; Wójcik, Jan M.; Zhang, Yi; Tokarska, Małgorzata; Li, Yan; Wang, Ming-Shan; Faruque, Omar; Nielsen, Rasmus; Zhang, Qin; Zhang, Ya-Ping (July 2018). "Pervasive introgression facilitated domestication and adaptation in the Bos species complex". Nature Ecology & Evolution. 2 (7): 1139–1145. Bibcode:2018NatEE...2.1139W. doi:10.1038/s41559-018-0562-y. ISSN 2397-334X. PMID 29784979. S2CID 29154258.
^ Grange, Thierry; Brugal, Jean-Philip; Flori, Laurence; Gautier, Mathieu; Uzunidis, Antigone; Geigl, Eva-Maria (18 July 2018). "The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters". Diversity. 10 (3): 65. doi:10.3390/d10030065. ISSN 1424-2818.
^ Wang, Kun; Lenstra, Johannes A.; Liu, Liang; Hu, Quanjun; Ma, Tao; Qiu, Qiang; Liu, Jianquan (19 October 2018). "Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent". Communications Biology. 1 (1): 169. doi:10.1038/s42003-018-0176-6. ISSN 2399-3642. PMC 6195592. PMID 30374461.
^ Zhang, K.; Lenstra, J. A.; Zhang, S.; Liu, W.; Liu, J. (October 2020). "Evolution and domestication of the Bovini species". Animal Genetics. 51 (5): 637–657. doi:10.1111/age.12974. ISSN 0268-9146. PMID 32716565. S2CID 220798740.
^ Zver, Lars; Toškan, Borut; Bužan, Elena (September 2021). "Phylogeny of Late Pleistocene and Holocene Bison species in Europe and North America". Quaternary International. 595: 30–38. Bibcode:2021QuInt.595...30Z. doi:10.1016/j.quaint.2021.04.022. ISSN 1040-6182.
^ American Society of Mammalogists (2021). "Bos bison". ASM Mammal Diversity Database. moved from Bison to Bos to retain monophyly within Bos since both species of Bison are phylogenetically embedded within Bos

Setting policy for lists of synonyms?

Hi, all. I started a thread earlier over here, and the feeling was that the thread should be posted here instead to get broader feedback. In a nutshell: there does not appear to be an "official" policy regarding whether to display lists of synonyms in taxoboxes in alphabetical order versus chronological order. The example given in the guidelines for taxoboxes is neither. It's been pointed out that since most botanical taxoboxes don't give years of publication for synonyms, that formalizing alphabetical as the policy there makes sense. However, as I noted, pretty invariably in print catalogues of zoological names, synonyms are given chronologically. One reason this is helpful is to highlight cases where one or more of the synonyms is older than the valid name (e.g., homonyms or nomina nuda), which would otherwise be pretty much invisible in an alpha-list. I am suggesting that the existing example in the "automated taxobox" guidelines be changed, and that instead it should say the following: Where the years of publication are given in the list of synonyms, the list should be organized chronologically, but if years are not given, then (and only then) the list should be alphabetical. This would allow existing botanical taxoboxes without years to remain as they are, but more importantly (1) give guidelines for editors who are creating new articles (especially if in bulk), to provide for consistency (2) give a policy that allows for dispute resolution where multiple editors are in disagreement. Given that there is no present policy, I would hope that this proposal would not face much resistance, but I'm opening the discussion to see how people feel. I'm frankly surprised if this really hasn't come up before. Dyanega (talk) 23:47, 16 October 2023 (UTC)

Sounds reasonable to me! MeegsC (talk) 09:02, 17 October 2023 (UTC)

I agree that, when a taxon's year is given, the list should be in ascending chronological order. Also, such a policy could explicitliy encourage editors to provide year and authority when creating or expanding a synonyms list. In lists containing both dated and undated synonyms, the dated ones in ascending chronolgical order should precede the undated synonyms that may be sorted alphabetically at the bottom if not removed. 89.206.112.12 (talk) 10:27, 17 October 2023 (UTC)

Policy is that dates are not (normally) used with names under the ICNafp. Peter coxhead (talk) 11:06, 17 October 2023 (UTC)

Sorry, I had zoological names in mind. Maybe the policy should distinguish. 89.206.112.12 (talk) 12:04, 17 October 2023 (UTC)

It would be useful for plants to clarify that where sources, such as Plants of the World Online, list homotypic and heterotypic synonyms separately (and alphabetically), we will use a single alphabetical list.

Another issue is what synonyms should be included. This is a general encyclopedia, not a specialist taxonomic work, so I do not think we should attempt to include all synonyms. For example, I personally don't include infraspecific plant synonyms where the species is a synonym unless the infraspecific name is well known. Peter coxhead (talk) 11:06, 17 October 2023 (UTC)

And skip any nomen dubium. At Cat (meaning the domestic kind) we have listed a handful of legitimate synonyms, but there was a late-19th-to-mid-20th-century "taxonomic fad" of defining various cat breeds as subspecies, which was later completely abandoned, and at one point that article actually listed a whole bunch of them (Felis catus siamensis, etc.), which was an unencyclopedic mess of nomina dubia. — SMcCandlish ☏ ¢ 😼 11:18, 17 October 2023 (UTC)

Agreed. Peter coxhead (talk) 11:24, 17 October 2023 (UTC)

At Potato there is a section that lists hundreds and hundreds of apparent synonyms, seemingly cultivars (without a source). Sub31k (talk) 06:19, 20 October 2023 (UTC)

I don't agree as far as zoological names are concerned. WoRMS uses an alphabetical list of synonyms and so should we. This comes very handy when comparing an article in wikipedia with the data of a database. There should be consistency in this matter. I have been using an alphabetical list of synonyms for the past 19 years. In the WikiProject Gastropods this means close to 43,000 articles. I have no idea how many articles in other wikiProjects are concerned. But the number must be huge. Changing our policy (and practice) would be catastrophical. JoJan (talk) 14:02, 17 October 2023 (UTC)

Rules creep. I use chronological when I know the dates, but that isn't always. While I'm sympathetic to the desire to standardize a detail, there's also no practical way to enforce or implement this one. Happy editing, SilverTiger12 (talk) 15:05, 17 October 2023 (UTC)

I'd be OK with indicating a preference for a chronological sorting, but not having it as a requirement. Most of the synonym lists on Wikipedia are copy-pasted from taxonomic databases which vary in the way they present synonyms. I wouldn't want to discourage anybody from adding synonyms from a database with an alphabetically sourced list by requiring them to re-sort the list before adding it (and, there shouldn't be any perceived preference for alphabetical sorting that leads editors to re-sort chronologically sorted lists to alphabetical; this apparently happened at Hemibagrus menoda, where FishBase has synonyms sorted chronologically)

Some of the database Wikipedia follows present lists of "synonyms" that should not be used on Wikipedia without further research. The Reptile Database lists chresonyms under the heading "Synonym". Amphibian Species of the World also list chresonyms in a section with no explicit heading. Mammal Species of the World lists bare species epithets with no indication of whether they have ever been treated as subspecies, full species or both (there were a whole bunch of binomial redirects created for horse subspecies that had never been treated as full species). The IOC checklists for birds don't list synonyms at all, and there's typically a mess with subspecies redirects left pointing to the wrong target whenever the IOC checklist is updated and elevates some subspecies to full species.

Species Fungorum has synonym lists sorted both alphabetically and chronologically, although the link to the synonyms from a given species page only goes to one of the sortings. FishBase lists synonyms chronologically. The chronological sorting in Species Fungorum and FishBase groups homotypic synonyms together; this is much easier to do under the zoological code where homotypic synonyms (mostly) have the same date. Under the botanical code, dates vary for each combination; an epithet that has been treated as a subspecies, variety or full species will have different dates for each rank (and more dates for every genus in which it has been placed).

Plants of the World Online groups homotypic synonyms of an accepted taxon in a separate alphabetical section before the alphabetical section of heterotypic synonyms. However, any homotypic synonyms of a heterotypic synonym aren't grouped. I don't really understand why the present synonyms that way. It does make a basionym more prominent than it would be in a single alphabetical list, but if they have the capability to group homotypic synonyms for an accepted name, I'd assume they have the capability to group all homotypic synonyms together. Plantdrew (talk) 16:01, 17 October 2023 (UTC)

Maybe each project should decide a preference, which would largely be determined by the preferred sources. The ToL guidance could state a general preference for chronological (if that is the preference) and have list of projects which prefer alphabetical (e.g. Gastropods and others using WoRMS), plants using POWO (although their synonym list have dates). I also agree that the synonym lists should be practical and shouldn't be long lists of obscure names. — Jts1882 | talk 17:17, 17 October 2023 (UTC)

In principle, having each project set a policy seems fine, but looking at the "hierarchy" of Wikiprojects, there really are a lot of them, and I'm not clear on how exactly we could methodically canvass opinions and feedback from each and every one, to see about building a consensus. I hadn't expected to find that there were groups within zoology that had established their own policy (as Gastropods seems to have done), and that certainly complicates things. But I'll be clear: if I knew that a given Wikiproject did in fact HAVE a posted policy, then I would personally abide by whatever policy is in place for a given taxon, while also expecting other editors to respect policies the same way; my feeling is that it is better to have something posted and agreed upon, because it's otherwise too easy to have disputes and edit wars. I did in fact recently have reason to edit the synonym list for the Oxymeris article, and I put the revised list in chrono-order when it had been alphabetical before. Now that I know that gastropods follow a different policy, I'll go back and fix that. Dyanega (talk) 20:32, 17 October 2023 (UTC)

Maybe I should have presented my comment the other way around. I'm in favour of setting guidelines and think chronological order is better (I like how it presents the history). So set a general policy, but have provision for certain projects to use a different guideline where they have an established way of doing things. I suspect most projects have no policy and the general ToL guideline would by default apply to them. — Jts1882 | talk 09:43, 18 October 2023 (UTC)

Again, I would be willing to comply under those circumstances, but I don't see how an editor working across "taxonomic boundaries" would know when they're running afoul of a policy, as I did accidentally when I edited a gastropod article. I don't see any easy way for an editor to know what the rules are for one Wikiproject versus another, other than a prohibitively time-consuming "deep dive" into the project pages. Yes, most articles do have a talk page template that shows which Wikiproject is relevant, but that template doesn't give such minute details. How can this be made practical and painless? Or can it not? Dyanega (talk) 00:17, 19 October 2023 (UTC)

How about a special template, designed to list taxonomic synonyms, that allows the reader to view the list in either chronological or alphabetical order, with the click of a button? Esculenta (talk) 20:37, 17 October 2023 (UTC)

This would be difficult. As far as I'm aware, Wikimedia software currently only allows sorting in tables. For it to work the synonym list would need a separate date column or to use sort keys. A custom solution parsing the authority would have to use javascript and wouldn't be available to everyone; it would need a user script or gadget. A module could present a sorted list from an unsorted one, but the sort style would be set in code rather than an interactive option for readers. — Jts1882 | talk 09:53, 18 October 2023 (UTC)

I think I would rather have all the information inside the taxobox. —Snoteleks (Talk) 07:53, 20 October 2023 (UTC)

I guess as a zoologist I have a preference for chronological order as it follows what a synonymy is meant to be (a way to assess nomenclatural priority), at least from a zoological perspective. The Global Species List whose parameters are still being tested will have this in chronological order when its available. But I guess what Dyanega is getting at is a way to make it clear on each project page what method is the prefered method for their subset of pages. I would hazard we could probably get it to a given way for most groups which would likely be chronological requiring only changes to be defined on those pages where this is relevant. So unless otherwise stated it should be chronological. Cheers Scott Thomson (Faendalimas) ^talk 10:39, 20 October 2023 (UTC)