Wikipedia talk:WikiProject Tree of Life

Imperial conversion for μm

Today I removed a convert template to convert micrometers to inches in the article Paleoserenomyces. The text reads "with the 240–480 μm (0.0094–0.0189 in) around by 180–240 μm (0.0071–0.0094 in)-thick locules". My removal of the template was reverted by @Kevmin:, with the justification "its not our fault imperial doesnt have smaller units". Can anyone explain to me how the presence of the imperial measurement here could be useful to anyone? I've performed similar edits to other ToL-related articles in the past, but this is the first time I've been reverted, so perhaps my understanding needs to be recalibrated. MOS:CONVERSIONS isn't especially helpful for this particular instance, but says "Generally, conversions to and from metric units and US or imperial units should be provided, except: In some topic areas ... it can be excessive to provide a conversion for every quantity." At what point does providing these values become ridiculous? As someone who spends quite a bit of time staring down a microscope, I can't see any use for this conversion ... are there contrary opinions? Esculenta (talk) 16:32, 10 December 2022 (UTC)

Yes, this is pointless. Unit conversions between metric and imperial are intended to provide readers who are more familiar with the one or the other with a relatable value. No one can relate to 1/100 or 1/1000 inch measurements because they are simply not used - all measurements at this scale are reported in metric units, always (unless you are a retired American clockmaker, I suppose...). --Elmidae (talk · contribs) 17:10, 10 December 2022 (UTC)

It's OK to give an article's only substantial contributor some leeway over minor style questions. It's not exactly that anyone's understanding of the article would be hindered by the presences of inches in brackets. Still, it does look bizarre. Do American books ever express dimensions at the micro scale in inches? – Uanfala (talk) 17:17, 10 December 2022 (UTC)

PCBs are often still specified in mil in the UK, and I would wager also in the US. Different field though. Most serious scientific measurements should be in SI units. YorkshireExpat (talk) 17:34, 10 December 2022 (UTC)

(edit conflict) There are non-metric units of length smaller than inches that are in use in specialized fields, but I don't think enough people are familiar with them to really be relatable. I have some sense of how big a 12-point font is, but I don't have a sense of how big a single point is. The article on line (unit) says it was used by biologists, but I've never encountered it (and I do use floras published in the 1950s). Plantdrew (talk) 17:39, 10 December 2022 (UTC)

Mil is the US unit, while thou is the more tradition UK unit (see Thousandth of an inch). But these are (or were) used in specialist fields and won't help people get a sense of size with a more familiar unit. There is no point in a conversion that won't help a significant number of readers. —  Jts1882 | talk  21:25, 10 December 2022 (UTC)

Yeah, electronics is a strange one. A lot of the older standards, like DIL still widely proliferate and are based on imperial, being developed, as they were, in the US. We, in the UK, probably didn't mind that too much and went with it. Not a good argument for lichen though. I'm all for ditching the conversion on this one. YorkshireExpat (talk) 22:02, 10 December 2022 (UTC)

Just to muddy the waters a bit, I am currently reading a popular science-level paleontology book (Fires of Life, by BG Lovegrove) where the author gives all μm measures as "x μm (y μin)". Never seen that before, but clearly there's more variety in usage than I thought. --Elmidae (talk · contribs) 16:37, 10 February 2023 (UTC)

Carabidae.org has left the building

Carabidae.org appears to have long been used as the authoritative reference for Carabidae taxa - we have ~7.4k active links to the site [1]. Unfortunately, and I don't know when that happened, they seem to have switched to a subscription model [2] which has disabled all direct links. As a consequence, what we've got now are 7.4k x 404 errors. Example subfamily, example genus, example species.

What to do? Many, possibly the majority of these articles (hard to tell without Quarry-ing, I suspect) are only sourced to this reference. Those would need to be switched over to CoL or some other database that would be expected to include all these taxa. In other cases the ref could possibly just be deleted if other sources are also given. In either case some bot assist would be needed due to the sheer volume. (Dropping a note at Beetle project) --Elmidae (talk · contribs) 13:11, 13 January 2023 (UTC)

It's been subscription for some time. I have some notes in a file that was last updated in June 2022 that says it is subscription. A lot of the pages are available on archive.org, e.g. brachininae so possibly a bot could convert to archived links. Shame it doesn't use a template as then we could just add the archive url.

An alternative source is the checklist at CarabCat, which is not the most user friendly interface. Fortunately, it's the source used by CoL so you can get most of the information there. —  Jts1882 | talk  13:43, 13 January 2023 (UTC)

is GBIF also a valid alternative ? Edisstrange (talk) 01:09, 14 January 2023 (UTC)

I don't see why not. They both use Carabcat as their source. It would be interesting to know how often CoL and GBIF update their records. —  Jts1882 | talk  15:08, 14 January 2023 (UTC)

CoL does monthly updates, but I'm not sure they comprise complete sweeps. --Elmidae (talk · contribs) 15:19, 14 January 2023 (UTC)

I suppose the real question is here, why would anyone pay €50 a year for a list like this? Also lol [3] the sole purpose of [Fominykh et al. 2020] was to describe new taxa in order to sell their paratypes. Is this actually something that happens? I would support using CarabCat as a replacement. Hemiauchenia (talk) 21:01, 15 January 2023 (UTC)

Describing the paper as "excellent" is an odd choice of words given the accusation. There is some market for biological specimens. I suppose the value for these wouldn't be as paratypes per se, but as specimens of a "new species" that have been definitively identified (i.e., identified by the describer of the species). Plantdrew (talk) 22:25, 15 January 2023 (UTC)

I don't think CarabCat is suitable because there seems to be no way to make hard links to individual entries, while this can be done for both GBIF and CoL. However, for both of those websites as well, the link consists of the ID (GBIF, CoL) and can't be generated from the taxon name without going through the search interface. Hmm. - Qbugbot linked to CoL during its runs, so presumably this has been solved? Maybe the bot could be employed to help in the changeover? Pinging @Edibobb: for his opinion. --Elmidae (talk · contribs) 09:40, 16 January 2023 (UTC)

I can fix these with qBugbot. It can get to it in March. CoL may be the best reference for Carabidae. I can add GBIF as well, if that would be useful.

Bob Webster (talk) 20:09, 29 January 2023 (UTC)

Cool, glad to hear it! Thank you! --Elmidae (talk · contribs) 20:43, 29 January 2023 (UTC)

I've submitted a Bot Request for Approval to replace the dead Carabidae.org references with Catalogue of Life references. I'd welcome any comments, criticism, or suggestions. Bob Webster (talk) 01:18, 8 March 2023 (UTC)

Thanks for doing this. One problem with replacing a carabidae.org reference with a CoL reference is that they may not contain the same information. For instance, the example genus article above, Eurylychnus, is a stub that lists nine species, citing the now dead carabidae.org page. CoL only lists eight species. However, the caribidae.org page is available on archive.org). Would it be possible to add the archive url and make the relevant citation status parameter changes to the existing citation, as well as adding a new CoL citation. That would keep the originally cited source and add a source where people can find the updated information. —  Jts1882 | talk  13:13, 8 March 2023 (UTC)

Correcting spelling of a genus name

I would like to correct the spelling of Palaeobalanus, a marine barnacle species (fossil). It is listed as Paleobalanus which is incorrect. Is this easy to do? Palaeobalanus (talk) 00:32, 20 February 2023 (UTC)

According to WoRMS, Paleobalanus is correct. Any change of name would need sources favouring that spelling.

Zoological names with Paleo- or Palaeo- prefixes are set at the spelling of the original description. They don't change when used in British or American English. This leads to apparent inconsistencies where genus Paleobalanus belongs to subfamily Archaeobalaninae. —  Jts1882 | talk  07:05, 20 February 2023 (UTC)

I am the author of the genus, and it was spelled Palaeobalanus in 1983 when I first published the genus. WoRMS is not always correct... Nonetheless, I will write to WoRMS and ask for the correct spelling to be used. Palaeobalanus (talk) 01:01, 21 February 2023 (UTC)

I note that the reference WORMS uses actually correctly spells the genus. [4]. Hemiauchenia (talk) 01:09, 21 February 2023 (UTC)

@Palaeobalanus: I've gone and fixed both instances where the erroneus spelling was used. Hope that sorts the issue. Hemiauchenia (talk) 01:11, 21 February 2023 (UTC)

Many thanks... Palaeobalanus (talk) 01:30, 21 February 2023 (UTC)

The Asoriculus/Nesiotites conundrum

This has been bothering me for approximately a year at this point, so I feel the need to lay out the confusing taxonomic history of these two extinct shrew genera and their conjoined Wikipedia article, Asoriculus:

• In 1855, the species "Sorex" similis was described by Hensel from remains found on Sardinia
• In 1864, the species "Crocidura" gibberodon was described by Petényi from remains found on mainland Europe
• In 1945 Bate erects the genus Nesiotites, with the type being the newly described Nesiotites hildalgo from remains found on the Balearic islands, and also including a newly described Corsico-Sardinian species, Nesiotites corsicanus, as well as "Sorex" similis within the genus as Nesiotites similis
• In 1959, Kretzoi erects the genus Asoriculus with the type species being A. gibberodon
• Later authors suggest that either Nesiotites should be subsumed into Asoriculus, or that Nesiotites should be restricted to species found on the Balearic Islands, and that the Corisco-Sardinan species should be re-assigned to Asoriculus (See introductory section of Rofes et al. 2012) As Rolfes et al. 2012 notes the autapomorphies of Asoriculus and Nesiotites with respect to their most recent common relative were minimal And most authors accept that the Nesiotites species originated from Asoriculus

Confusingly, the Asoriculus Wikipedia article was originally titled Nesiotites, but was moved in 2014 with the cited reasoning being Currently accepted name for genus; more commonly used [5], which I don't think is true, as Nesiotites is definitely the prevailing name used for the Balearic species. Many recent papers say that the taxonomy of the Sardinian-Corsican species are unresolved, and often refer to them as "Asoriculus" (eg [6])

I see two options here:

• Keep the article as is, as discussing both genera, which makes sense given their intertwined taxonomic histories and ancestor-descent relationship
• Split out Nesiotites into a separate article.

We currently have an article for N. hildalgo the most recent Nesiotites species, at Balearic shrew. I have honestly tried and I really cannot find significant material that would make the article anything more than a stub discussing it alone, so I think that if Nesiotites was to be split out that article should definitely be merged into it, as was done with the species of Hypnomys. I'd argue that it would be worth merging anyway into Asoriculus even if there was no split, but that's a separate issue.

I made a split request a year ago, but the talk page request never got any response. So I thought I'd try here. Many thanks. Hemiauchenia (talk) 18:09, 23 February 2023 (UTC)

Template:Taxonomy/Stegocephalia

Please, need help with a taxonomy template at Template talk:Taxonomy/Stegocephalia. Please help decide the best pathway. Thank you in advance! P.I. Ellsworth , ed. ^{put'er there} 22:58, 2 March 2023 (UTC)

Think this should be renamed to {{Taxonomy/Stegocephali}} soon. Would like to hear your opinion on the subject first. Thank you for your time! P.I. Ellsworth , ed. ^{put'er there} 07:54, 5 March 2023 (UTC)

Updated cyanobacterial classification

An updated classification of cyanobacterial orders and families has been published, based on robust phylogenomic tree.

"Using 16S sequences, coupled with genomic data, Strunecký et al. (2023) were able to lay the groundwork for a more modern understating of the relationships between the cyanobacteria. Strunecký et al. (2023) reconstructed well-supported phylogenetic inference, which served as a firm ground for their following taxonomic reasoning. In this paper, they erected 10 new orders and 15 families while revising many of the traditional ones. The excellent thing about the paper is that we now have some clear demarcations between families. Moreover, the most up-to-date list of the genera within the families and orders is included."

Petr Karel (talk) 10:29, 3 March 2023 (UTC)

AlgaeBase seems to have adopted Strunecký's classification, but WoRMS has not (WoRMS is supposed to be in sync with AlgaeBase). As the paper was very recently published, I'd give it a few weeks to see if WoRMS catches up. (Michael Guiry created a record for Anthocerotibacter on WoRMS on February 15th, 2 days after Strunecký was published, but the family/ordinal placement of Anthocerotibacter doesn't follow Strunecký). Plantdrew (talk) 16:58, 3 March 2023 (UTC)

Wikipedia's approach to taxonomy

I am trying to get a feel for how writers of Wikipedia articles about taxa approach the issue of what classification they use. I have not really understood the template system very well but it looks as if an automated taxobox is used by an author they will be importing the higher ranks with the taxobox. The data in the taxobox will represent the classification.

Presumably if an author wanted to make use of a different classification they could manually complete a taxobox with the higher ranks chosen by them to reflect the classification of their choosing.

I would like to be corrected on this if it is wrong and would also be interested in any discussions on Wikipedia's approach to classification which may be available. Gourdiehill (talk) 23:07, 5 March 2023 (UTC)

@Gourdiehill: at least in the areas in which I work, the relevant WikiProjects have discussed and agreed on a default taxonomy to be used in taxoboxes and article titles. This is necessary to ensure consistency among articles in the same area of the tree of life, and avoids the same taxon having multiple articles under different names. However, all well sourced alternative taxonomies should be always discussed in the text.

The automated taxobox system does allow alternative agreed taxonomies that could overlap. For example, bird authors and dinosaur authors use somewhat different approaches, which is why the taxobox at Bird shows a different set of parent taxa from the taxobox at Ornithurae, even though the latter says that Aves is an immediate child taxon. As another example, the taxobox at Reptile shows Reptilia as a class, even though it treats Aves as a child taxon, whose taxobox says it is a class. These variations are achieved by having things like skip taxonomy templates.

So if you want to know why a particular classification is used in taxoboxes, then ask at the talk page of the relevant WikiProject, where you can discuss possible alternatives. Peter coxhead (talk) 17:42, 6 March 2023 (UTC)

Yep, which taxonomy is used generally is agreed upon by the relevant WikiProject- generally, it is some combination of agreement of relevant taxonomy databases and "does this taxon/taxon change seem to be widely accepted in the field?".

For instance, the Mammals WikiProject uses the Mammals of the World (Wilson & Reed 2005) as the base, with any changes based on the agreement of the IUCN and Mammal Diversity Database (see here). Happy editing. SilverTiger12 (talk) 19:52, 6 March 2023 (UTC)

An author could use a manual taxbox ({{Taxobox}}) with "the higher ranks chosen by them to reflect the classification of their choosing" (as opposed to the higher ranks given in the taxonomy templates used by automated taxoboxes). But that isn't desirable. A big reason to use automatic taxoboxes is to keep classification consistent (and easy to update). We don't want to have a situation where different species in a single genus show different families in the taxobox. If an author thinks that the classification in the taxonomy templates is incorrect, they should get consensus to change the templates rather than using manual taxoboxes to override it.

Many of the WikiProjects have achieved consensus to follow a particular database or publication for which species/genera to recognize. There is often also a consensus to follow a particular source for classification at higher levels (family, order, etc.), which may be the same source used for species/genera, or may be a different source (flowering plants and fish use different sources for species/genera and families/orders). For some groups of organisms that have few editors interested in them, the classification may have been chosen by the editor(s) that do the most work on that group, without any formal discussion to achieve consensus. And there are cases where there is a detailed classification of higher level clades in the taxonomy templates that hasn't been discussed anywhere; the sources used for bird and mammal classification (from species to class) don't go into clades between the ranks of class and order, but there are taxonomy templates for various bird/mammal clades, that (as far as I am aware) have never been discussed. Plantdrew (talk)

The taxonomy templates should have a reference that supports the recognition of the taxon in question and its stated parent taxon. In practice, many templates lack a reference. Plantdrew (talk) 20:10, 6 March 2023 (UTC)

Indeed. I've tried to be strict in adding references in any taxonomy template I create or edit, but it does slow down fixing "obvious" errors and organising the taxonomy for whole groups. Perhaps we should start a category for unreferenced taxonomy templates. Unfortunately, I think they may be the majority. It might be possible to add a special parameter to taxonomy templates to indicate that a particular source is used for that taxon and its subordinate taxa, e.g. |taxon_ref=WoRMS (using a proper citation) in the {{Taxonomy/Gastropoda}} template or |taxon_ref=AGP IV for angiosperms. —  Jts1882 | talk  20:34, 6 March 2023 (UTC)

Taxonomy is usually referenced in the text of the article in question, which I think is usually enough. Hemiauchenia (talk) 22:20, 7 March 2023 (UTC)

@Hemiauchenia: the placement in the immediate parent is usually stated and referenced, but not all the higher taxa that are shown in the taxobox. I think it should be possible to find a reference for each of these via the taxonomy template hierarchy. If nothing else, the refs in taxonomy templates are a resource for editors. Peter coxhead (talk) 22:35, 7 March 2023 (UTC)

It would be possible, but it would be incredibly onerous to do so for something that ultimately does not direct affect readers. Automatic taxobox temples by design only document the immediate parent rank, with the taxonomy of the parent presumably documented by its own article. Hemiauchenia (talk) 22:40, 7 March 2023 (UTC)

I don't think anyone is suggesting going back through existing taxonomy templates and adding refs where absent, but I believe they should included when a template is created, and be added if the parent taxon is changed. Peter coxhead (talk) 23:09, 7 March 2023 (UTC)

Thanks for interesting responses to my question. I have been trying to understand the Catalogue of Life Checklist which seems to be an attempt at a single classification based on consensus views from experts in different areas. They do make the case for the advantages of a single classification. There are a series of six papers published in 2021 they have released called "Towards a global list of accepted species 1" (to VI). I presume they would hope Wikipedia adopts their classification. I am hoping to get round to reading more about it and perhaps editing some Wikipedia articles... — Preceding unsigned comment added by Gourdiehill (talk • contribs) 21:12, 7 March 2023 (UTC)

@Gourdiehill:, the problem with Catalogue of Life's classification is that it achieves monophyly by (mostly) ignoring extinct organisms, and changing the ranks of traditionally recognized groups that are inescapably paraphyletic. This goes for some other databases that to present a classification of all (extant) organisms. COL treats Osteichthyes as a "parvphylum" (traditionally it is a class, and is paraphyletic with respect to amphibians, reptiles, birds and mammals which are also traditionally treated as classes (and reptiles of course are paraphyletic with respect to birds)). Paraphyly of Osteichthyes is "solved" by elevating to parvphylum. COL "solves" the paraphyly of reptiles by splitting them into 4 (extant) classes and completely ignoring dinosaurs. For plants, paraphyly is "solved" by demoting 8 taxa traditionally recognized as divisions (or phyla) to classes, and ignoring anything extinct (actually, the paraphyly isn't solved at all, since COL recognizes a class Magnoliopsida corresponding to dicots and Liliopsida corresponding to monocots; dicots, in the loose circumscription adopted by COL, are paraphyletic with respect to monocots), Plantdrew (talk) 22:06, 7 March 2023 (UTC)

@Plantdrew

thanks for giving me some detail about that. I think their view is that it is not possible yet to build a correct classification and that an incorrect one which everybody uses is the best alternative. I will try and read up on the examples you refer to. Gourdiehill Gourdiehill (talk) 15:29, 8 March 2023 (UTC)

An incorrect classification is incorrect regardless of how many people use it. Peter coxhead (talk) 22:02, 8 March 2023 (UTC)

Exactly, which is why modern cladistics has abandoned most higher ranks. Hemiauchenia (talk) 22:10, 8 March 2023 (UTC)

Hi, not sure if anyone has mentioned this already in the thread but direct scientific references are more reliable than CoL. CoL is indeed a huge attempt at condensing all the taxonomic information, however it does not catch up very fast with the latest information. Not just fossil groups, but also extant groups that are being discovered or revised in the last 4 years.

In Adl et al. (2019) an alternative to CoL for eukaryotes (especially protists) is shown, called UniEuk, which has in its website a treemap of the different groups (here). But like I said, catalogues are unreliable when dealing with newly discovered organisms and newly-revised classifications.

This is the reason why Taxonomy of Protista utilizes many papers post-2019, even though it is largely based on the 2019 publication. It's all just a matter of trying to update everything to date. The only reason why there are many non-automatic taxoboxes with old classifications (at least in WikiProject Protista) is because they haven't been yet converted. ☽ Snoteleks ☾ 16:56, 16 March 2023 (UTC)

Since @Gourdiehill: brought up the series of papers I was involved in as part of the Global_Species_List_Working_Group the first paper in the series from 2020 is on Wikisource here. Ok with respect to Catalogue of Life, they are changing things significantly but for their release of CoL+ rather than the current iteration. The problem CoL has had is they are using roughly 180 checklists to develop their species list and there is problematic conflict resolution in this. The series of 6 papers released are also all available I can provide them to anyone interested went into the development of a governence system for a single global species list and ways to assess the quality of the various checklists on different organisms around the world. This system still being developed is being developed in conjunction with CoL and many other checklists.

@Peter coxhead: brought up the issue of fossils, and as a paleontologist I wish there was a better answer, unfortunately the vast majority of users of scientific names want them effectively excluded, at least the older ones that have no living relatives. We actually surveyed the international scientific community on this and the results of that is in press. However myself and several others have fought not to have this happen. In my own works I am one of the few vertebrate taxonomists that actually does phylogenies with all living and fossil material combined so I certainly am against this. But we do have to find a way to reconcile them. Unfortunately a number of fosssil groups have determined to use PhyloCode over ICZN and this also creates areas of conflict as the two systems are not entirely compatable and yield vastly different results in higher order classification. Most end users of taxonomy refuse to use PhyloCode as it is not accepted as a nomenclatural system by the IUBS and hence has no legislative support with respect to the work many users do in the fields of Medicine, Conservation etc. It takes up to 10 years to change the nomenclature in the legislative framework for CITES for example.

As for what Wikipedia should do, well it depends on what your role is as you see it. On wikispecies we are more and more following the recommendations of the GSLWG as it is becomming an industry standard (at request of IUCN and CITES also) and already has the support of legislative bodies around the world. Which is why when I add turtles to Wikispecies I always standardise the higher order taxonomy according to that standard. Which means this is what ends up in Wikidata also. Checklists that do not meet these Governance standards will in the end not be used in the development of the Global List of Species, which will in the end be managed by CoL+ once it is released. Wikipedia is an encyclopedia, ie review level taxonomy only, my suggestion would be follow the checklists because they are being reviewed using internationally accepted metrics, but its up to you all how you do it.We have a meetuing in two weeks to finalise the metrics that will be applied to this issue.

This is an onging problem and not one with a direct solution right now but it is in process. I thought you should all be aware. If anyone wants more info or any of our papers let me know. Cheers Scott Thomson (Faendalimas) ^talk 12:40, 9 March 2023 (UTC)

(Just to note that actually it was Plantdrew who brought up the issue of fossils and CoL above, although I have elsewhere stressed the importance of handling fossil taxa consistently. Peter coxhead (talk) 14:28, 9 March 2023 (UTC))

oops apologies for that yes I got you both mixed up cheers Scott Thomson (Faendalimas) ^talk 14:31, 9 March 2023 (UTC)

The series of six GSLWG papers can be found at this Springerlink search page. They are open access. I read three of them yesterday (I,II, VI) and it was interesting to see some of the problems I had generally recognised laid out clearly, along with additional ones that were completely new to me.

My general feeling about CoL is that it can be divided into its higher level taxonomy which is essentially just a cataloguing structure (which includes some archaic taxonomy concepts) and the group taxonomies which are modern phylogenetic taxonomies. The latter are only as good as the source databases. Some are very good, well-curated and updated regularly, while others are surprisingly outdated (e.g. birds and mammals) because they rely on generic sources rather than specialist databases. —  Jts1882 | talk  17:00, 9 March 2023 (UTC)

I actually try to avoid using CoL, because I have found it has serious limitations- outright excluding some widely recognized genera from its database (e.g., Nalepella). Edward-Woodrow (talk) 21:51, 9 March 2023 (UTC)

@Edward-Woodrow: It is important to remember that Global Lists such as CoL, same goes for Wikispecies, WORMS etc are syntheses of the available checklists upon which they rely. For CoL this is some 180 Checklists. If taxa are missing from those Checklists they cannot add them and to correct CoL in any lasting way requires that the CheckLists they rely on are corrected. The other point is the purpose of the lists in Question. As a taxonomist I almost never use CoL my own lists of the taxa I work with are far more detailed and precise as they need to be as I am actively working with those taxa. But for resource managers, Government agencies etc these Global lists are a good summary. Cheers Scott Thomson (Faendalimas) ^talk 00:57, 10 March 2023 (UTC)

As a fairly relevant aside, as I have pointed out to Scott on several occasions, the ICZN and the Zoological Code are equipped to accept definitive, discipline-specific, authority lists that are demonstrably achieved via consensus of large groups of appropriate taxonomic experts (under Article 79 in the ICZN Code). It is my own belief that this particular pathway is, at least in the near term, going to be a necessary "stepping stone" if we are ever to achieve stability in both nomenclature and in taxonomy in ANY discipline, let alone across all of biology. So long as it is possible for disputes to fester, unresolved, there will be problems; if, however, each discipline can achieve a consensus list of names, and a consensus classification, share and maintain these on the internet, and taxonomists working in those disciplines agree to adhere to those consensus schema, then we can finally have an easier time making sense of things (and waste a lot less time arguing). Oddly enough, despite the lack of authority, much of the content of Wikipedia and Wikispecies serves the same purpose, and helps contribute to stability, not unlike the proverbial tail wagging the dog. That's a major reason I commit to spending my time and energy here. Dyanega (talk) 00:13, 10 March 2023 (UTC)

Heya @Dyanega: yes we have had many discussions over LANs, I agree with you the section could be a major stabiliser of nomenclature. I tried at one time to start the idea of doing one for reptiles but the support for it under the current wording of Article 79 was low. It was felt the outcome did not achieve a value addition comparable to the workload it would require. Specifically in terms of the 5 year rule, time taken to ratify it and unclear means for updating. Note in Reptiles its biggest value would be a tool for quashing vandalism hence updates would be essential. These concerns led to my submissions on improvements to the wording of Article 79. Cheers Scott Thomson (Faendalimas) ^talk 00:37, 10 March 2023 (UTC)

Stramenopile or Heterokont?

We have since at least 2008 had this pair of articles covering what is now the same taxon with two different names, both rather familiar to biologists. Heterokont is the older name, so might have precedence, but its definition has shifted as genomics has come to bear and it seems that the newer name Stramenopile is becoming accepted as the name of the clade (e.g. "A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)", Derelle et al 2016). Suggestions for a merge have been made in 2008, in 2014, in 2021, and now again in 2023 from User:Snoteleks, so it is about time we merged the two. I actually don't care which direction the merge is in, but as I've just mentioned, it looks as if Stramenopile is probably the best name at the moment. The team's thoughts would be gratefully appreciated. Chiswick Chap (talk) 11:31, 16 March 2023 (UTC)

Thank you @Chiswick Chap. I support the transfer into Stramenopiles since it appears to be more in use by the latest classifications (such as "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes", Adl et al. 2019). The older Heterokonta name should still appear as a clear synonym both in the lead of the page, the taxobox synonyms and perhaps an entire section dedicated to the history of both names (maybe inside a bigger section on the taxonomic history?). This joining will definitely be good for every page that links to either of these, since it will stop confusing readers that might end up thinking they are two different clades. ☽ Snoteleks ☾ 12:05, 16 March 2023 (UTC)

I support as well, though it might be worthwhile to put a formal merge request on the appropriate page as well. - UtherSRG (talk) 12:14, 16 March 2023 (UTC)

I also prefere Stramenopiles: In Talk:Heterokont I wrote

A) The consensual position of many protistologists – taxon of no formal rank Stramenopiles Patterson 1989, emend. Adl et al. 2005 [syn. Heterokonta Cavalier-Smith, 1981 stat. n. 2017] (2018; DOI 10.1111/jeu.12691; PMID 30257078) (btw implicitly accepted by all recent systems using SAR)

B) Broadly accepted is also the last Cavalier-Smith's system – Superphylum Heterokonta Cavalier-Smith, 1981 stat. n. 2017 (stramenopiles) (2017; DOI 10.1007/s00709-017-1147-3; PMID 28875267 - Table 1) (btw implicitly accepted by all recent systems using Halvaria or Harosa)

Both respect the valid recent diagnosis of the clade/taxon. I would prefer A) because B) is formally a junior synonym and because Heterokonta is sometimes used with different diagnosis (=Ochrophyta/Heterokontophyta or =Xanthophyceae). But there may be other opinion – e.g. preferring the formal taxon with specified rank (superphylum). To be frank, I don't know the consensual position of phycologists; maybe somebody could add for better support of the final decision. --Petr Karel (talk) 13:27, 16 March 2023 (UTC)

I also can add a different recent cladistic proposal:

C) clade name Stramenopila C. J. Alexopoulos, C. W. Mims, and M. Blackwell 1996 [A. G. B. Simpson and M. Dunthorn], converted clade name (DE QUEIROZ, K.; CANTINO, P. D.; GAUTHIER, J. A. Phylonyms: A companion to the PhyloCode. Boca Raton, FL: CRC PressTaylor & Francis Group, 2020. ISBN 978-1-138-33293-5. Section 1, Registration Number: 103) --Petr Karel (talk) 13:43, 16 March 2023 (UTC)

This group is one of the few that have taken up use of a List of Available Names per article 79 of the ICZN, in there they seem to be using Stramenopile and as such this is the valid name, as this is an accepted LAN this name is accepted irrespective of any other inferred priority. So I also would support this nomenclature. Cheers Scott Thomson (Faendalimas) ^talk 13:50, 16 March 2023 (UTC)

OK, I think we agree that we should merge them, and in the direction Heterokont to Stramenopile. I'll propose that on their talk pages. Chiswick Chap (talk) 16:44, 16 March 2023 (UTC)

Yes, it's bizarre that the two articles have coexisted for so long. A merge is necessary.

I've always considered Heterokonta the proper name as it is older, hence with precedence and the senior synonym, and stramenopiles always seemed more like a vernacular name. But clearly the trend is towards stramenopiles, as without it the SAR supergroup makes little sense. The alternative is to consistently use the Cavalier-Smith names, so Heterokonta in Harosa, which he has recently redefined to include Telonema (i.e. =TSAR), Corticata for Diaphoretickes, etc. But there seems a reluctance to do this, even though his names would often seem to have precedence. Having recently waded though his 2022 classification and seen his frequent dismissal of names by others for not complying with the code, or not falling under the code when they do, or for basically coining a name without understanding the proper cell biology, I can't help wonder if this is a bit personal.

Anyway I'd support the move either way and stramenopiles seems the best choice. I notice that the Burki et al (2020) review uses Stramenopila (the phylocode name mentioned above) which sounds like a proper taxon name. Also, I can't find the ICZN list of names so would appreciate a link. —  Jts1882 | talk  17:59, 16 March 2023 (UTC)

It looks as if the Heterokontists have been in decline for some years, and that the Stramenopilists have been on the rise. Recent papers all seem to use S, with H in parentheses. Anyway, I've put the formal thingy at Talk:Stramenopile#Merger proposal. Chiswick Chap (talk) 19:26, 16 March 2023 (UTC)

Frankly I've also noticed Cavalier-Smith's personal vendetta against certain aspects of modern classification. In his 1998 "A revised six-kingdom system of life" he wrote much slander against preferring to use monophyletic taxa over paraphyletic taxa, saying that it's "dogmatic" and "confusing" (even though the terminology he used was only used by him and his vision was a subjective "balance" between cladistics and phenetics, as he himself writes). It's no surprise his classification is falling out of use, it's a very stubborn attempt to maintain paraphyletic groupings when the trend is the complete opposite. ☽ Snoteleks ☾ 23:36, 16 March 2023 (UTC)

Tom Cavalier-Smith (1942–2021) did seem to hold out for his views until his death. I assume he handed the text of the 2022 paper to the journal's editors while he was still alive, or we may start to wonder where some of that ghostly IP editing to Tree of Life articles is coming from ... Chiswick Chap (talk) 09:54, 17 March 2023 (UTC)

Ah, I hadn't realised he had died. The 2022 paper was submitted in late 2020 and accepted just after his death. That might explain the poor copy editing and apparent errors in the text. I wonder if his new names for the Rhodophyte-Rhodelphis-Picomonas groupings will stick? —  Jts1882 | talk  13:35, 17 March 2023 (UTC)

To be fair I think Rhodaria (Rhodophytes+Rhodelphis+Picomonas) do appear as monophyletic in other papers that aren't his own, so I think they will stick. Biliphyta won't, but only because it also contains glaucophytes, making it paraphyletic. ☽ Snoteleks ☾ 13:47, 17 March 2023 (UTC)

Another thing to consider for the merge is templates in the automated taxobox system. Most currently use Heterokonta. Only Bacillariophyta uses Stramenopiles. This raises a broader issue on the automated taxobox system, which currently uses Chromista, Hacrobia (both not generally supported), Harosa (instead of SAR), and Halvaria (is there an alternative for SAR+Alveolata?). These need to be updated, which shouldn't be too difficult as only a few templates need editing, but we do need to decide on what taxonomy to use and a good source. This has come up before with no consensus resolution, which means Chromista remains (it's easy to source). I would suggest Adl et al (2019) for the main framework, but iirc there was resistance to this when last discussed. —  Jts1882 | talk  17:17, 17 March 2023 (UTC)

As a cladist, I support the use of either Harosa or SAR, Harosa sounds better as a formal name but if the consensus is SAR I'd have no issue with it. But Hacrobia definitely needs to go away, especially after Alveidia has ceased to exist because of Provora, and Hacrobia is starting to get polyphyletic in a consistent manner (see: the CAM clade Cryptista+Archaeplastida+Microheliella).

Chromista needs to go too, because of the same reason: Chromista is paraphyletic because of Cryptista being closer to Archaeplastida. It's the same reasoning behind not using the kingdom Protozoa when it comes to Obazoa, Malawimonadida, Discoba or others; the kingdoms are just too paraphyletic. I also suggest Adl et al. (2019) for the main framework, as it is the main reference used for Taxonomy of Protista. What is the point of automated taxoboxes if they can't be updated according to the latest phylogenies? ☽ Snoteleks ☾ 17:32, 17 March 2023 (UTC)

The sooner Chromista goes the better. SAR on the other hand is a clade, and a much better-known name than Harosa. Chiswick Chap (talk) 18:11, 17 March 2023 (UTC)

@Snoteleks: I see you have started editing the automated taxonomy templates (e.g. {{Taxonomy/Bigyra}}). It would help if you added references. The lack of sources in the taxonomy templates is a major problem with the automated taxonomy system, which isn't exempted from Wikipedia guidelines on reliable sources just because the information is in a template. While updating the taxonomy we should take the opportunity to properly source the taxonomy. —  Jts1882 | talk  13:21, 18 March 2023 (UTC)

Yeah I know, I noticed that the reference (originally added by me) still keeps the name Heterokonta. I completely agree, the unreferenced taxonomy templates is a big issue. I always try to add references to those whenever I can, especially if I create them or need to modify them. ☽ Snoteleks ☾ 17:16, 18 March 2023 (UTC)

If following Adl et al (2019) should Bigyra and Gyrista be phyla?

I've created a new template {{Taxonomy/Diaphoretickes/displayed}} with |always_display=yes and used it as parent for {{Taxonomy/TSAR}}. This results in the taxobox showing Diaphoretickes and Eukaryota rather TSAR as the top rank. This should probably also be used for Haptista and Cryptista when they are removed from Chromista, but not for plants where it has been decided that Plantae or Archaeplastida should be the top taxon displayed. —  Jts1882 | talk  18:09, 18 March 2023 (UTC)

Now that's ingenious. Chiswick Chap (talk) 19:22, 18 March 2023 (UTC)

Excellent. And yes, I guess Bigyra and Gyrista are phyla. That brings into question what we should do with Ochrophytina since it is more widely known as Ochrophyta... ☽ Snoteleks ☾ 19:46, 18 March 2023 (UTC)

Cephalotaxus: Cephalotaxaceae or Taxaceae?

I noticed when Elmutanto (talk · contribs) was changing the taxonomy of gymnosperms based on the proposed classification scheme of Yang et al. 2022 (which I think may have been premature) that they changed the automatic taxobox classification of Cephalotaxus to Cephalotaxaceae rather than Taxaceae as it had been previously. I known reading the literature that "Cephalotaxaceae" is widely used, but does it have consensus amongst the major authorities? Regardless, I don't think we need a separate article on Cephalotaxaceae. given that Cephalotaxus is the only member of the family. Hemiauchenia (talk) 22:31, 20 March 2023 (UTC)

I will usually look to the literature and then see what the gymnosperm database at https://www.conifers.org/ are doing, with a preference to following the latter.--Kevmin § 22:38, 20 March 2023 (UTC)

Looking at their taxonomy, [7] they include Cephalotaxaceae within Taxaceae. Hemiauchenia (talk) 23:21, 20 March 2023 (UTC)

Then we should use Taxaceae. Chiswick Chap (talk) 08:54, 21 March 2023 (UTC)

Plants of the World Online also uses Taxaceae, so I agree that we should. We should (almost) never change classifications based on individual papers, but on the consensus of major taxonomic databases. Peter coxhead (talk) 09:23, 21 March 2023 (UTC)

Nearly all the usual database sources are using the Christenhusz et al (2011) classification, which remained unchanged in his 2017 Plants of the World. An article on Cephalotaxaceae is premature and probably not necessary even if ultimated accepted as a family. What is surprising is that orders Cupressales and Araucariales don't have articles and that they are still covered at order level in Pinales. That seems a much more pressing need if someone wants to wwrite new articles. —  Jts1882 | talk  16:12, 21 March 2023 (UTC)

Speaking of higher-rank classification of conifers, Elmutanto also created Cupressidae following the definition of Yang et al. 2022. Apparently the usual definition of this clade is just monotypic containg Cupressales. Should this be changed into something else? Hemiauchenia (talk) 23:57, 21 March 2023 (UTC)

Merging Nucleariid amoebae as a single page

As stated in Wikipedia:Requested_moves/Technical_requests, I'm proposing the merging of both pages Cristidiscoidea and Nucleariida into a single page Nucleariid. Here is my explanation. There are three completely different classifications of these organisms (that I know of):

1. As a single order Rotosphaerida. This one is the most extended among protistologists and seems to be the original classification (see this review of nucleariid amoebae by Galardón et al. 2022, and also Adl et al. 2019 and Siver et al. 2022).
2. As a new Kingdom Nucleariae with two phyla (Nuclearida & Fonticulida). This system appears to be partly sedimented within Wikipedia but I haven't found any mentions of it outside of the original paper which introduced it (see Tendersoo et al. 2018).
3. As a monotypic subphylum Paramycia with class Cristidiscoidea. This was Cavalier-Smith's take on the nucleariid classification (see his latest, post-mortem paper) and for that reason it's pretty widespread. However the subphylum itself belongs to the paraphyletic phylum "Choanozoa", a taxon that is not accepted by anyone else.

The informal name "nucleariid amoebae" agglutinates all amoebae in these groups. For this reason, I believe the title "Nucleariid" for a common page will avoid any controversial use of one name over the other. How many of you would support this? ☽ Snoteleks ☾ 13:54, 23 March 2023 (UTC)

Would we not then also have to merge Fonticulida and Parvularia? Chiswick Chap (talk) 14:03, 23 March 2023 (UTC)

I don't think so, from what it looks like Fonticula and Parvularia are two different genera. ☽ Snoteleks ☾ 14:36, 23 March 2023 (UTC)

Oh wait I think I see what you mean. The answer is Fonticulida would be moved to Fonticula. Since Parvularia is already a genus-level taxon page it doesn't need any changes. ☽ Snoteleks ☾ 14:36, 23 March 2023 (UTC)