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Species & subspecies abbreviation scheme

There is no link from this taxobox to any article explaining the species & subspecies abbreviation scheme, yet articles including the example on the template is using abbreviations. How is the reader suppose to understand in the example that species 'M. virginiana' means 'Magnolia virginiana'. Subspecies are abbreviated yet more, potentially baffling readers even more. Regards, SunCreator ^(talk) 15:39, 19 October 2010 (UTC)

I'm not sure what you'd expect or where you'd expect such a link to point to. This is pretty standard abbreviation and widely assumed to be easily understood. The genus is indicated directly above the abbreviation and the full binomial is usually below. I could maybe see an argument for avoiding abbreviations on the Simple English Wikipedia, but not here. Rkitko ^(talk) 00:26, 20 October 2010 (UTC)

The concern was in reference to a question brought up here. Long story short, some abbreviations (such as C. p. picta) may be confusing to those who don't know much about taxonomy.--NYMFan69-86 (talk) 01:07, 20 October 2010 (UTC)

Selected taxonomy, unranked clades versus Linnean

Do you have some support for this taxonomy? I am working on the algae articles, and I would like to see:

• Domain: Eukarya
• (unranked): Archaeplastida
• Kingdom: Viridiplantae
• Division: Chlorophyta

rather than:

• Domain: Eukaryota
• Kingdom: Plantae
• Phylum: Chlorophyta

as you chose for this taxobox, for taxonomic upkeep, organization, and reality in the artifice reasons.

There is a Wikipedia:WikiProject Algae, with a talk page, although with few participants. If you are going to create automatic taxoboxes, though, I would like for the included taxonomies to be discussed on the project talk page and alerts posted at the appropriate community portals.

Please raise a discussion about your choice at the project page and post a link to other pages. --Kleopatra (talk) 21:15, 23 October 2010 (UTC)

ITIS has Clorophyta as a division under Planta. Also, if you consider the articles for Viridiplantae and Plantae, I think you will find little support for changing kingdoms. It should however be a small matter to put in Viridoplantae and Archaeplastida as unranked units above Plantae. Notice however that the automated taxobox only shows the major ranks above the first major rank (i.e if you are working in a genus, it will show every super-, infra- etc up to family level, but only major taxa above that). The idea is to avoid overlarge taxoboxes. Petter Bøckman (talk) 21:36, 23 October 2010 (UTC)

ITIS is not a robust source for "algae" taxonomies, and it should not be the default choice. Even AlgaeBase is difficult when it comes to higher level taxonomies of "algae," and wikispecies uses an unfortunate mixture of "Cavalier-Smith" and "not C-S," for an unexplained reason.

The higher level taxa and unranked clades, kingdom, division, class, etc., are important in algae taxoboxes due to the way they separate out and/or combine algae from/with plants and/or combine them with funky and related non-photosynthetic organisms. It's not acceptable to automatically remove fundamental information from a taxon page. The taxobox is designed to give "information at at glance," and part of this is to let users know that fungi are not plants and red algae are closely related to plants, but brown algae are not as closely related.

If you want to discuss this further, let's move it to a community page. --Kleopatra (talk) 21:55, 23 October 2010 (UTC)

From what I understand (I'm not an algae expert by any means), you initial post has tow separate topics: 1) what taxons to use, and 2) the number of taxonomic levels in the taxobox. The first question should be discussed at the Algae project page (editing the automated taxonomic system is a bit fickle, but fully possible, even I managed with some help). The second question is universal to all taxoboxes, not only those of algae, and belong here. The idea of including only major taxa above the first major taxon har been discussed before, last time in connection with Domains, [1]. Basically, the accepted argument is that someone reading about a low level taxon like a genus or family is not looking for detailed information higher up. Someone reading a high level article do, on the other hand. If you can convince people that someone reading about e.g. Volvox need information about Archaeplastida and Viridiplantae, then you will have a case. Petter Bøckman (talk) 22:34, 23 October 2010 (UTC)

For some algae, the higher level taxa are more important, meaningful, and therefore more appropriate than families, orders, and, sometimes, classes. Knowing the genus without knowing that the taxon is closely related to land plants, while another genus is distantly related, is a flawed provision to a glance at the description of the taxon. Most algae are generally not animals, although some are closely related, and most are not land plants, although a few form a clade with them, and those that aren't have some strange higher level affinities, and the constraints on their taxoboxes should reflect their deep time evolutionary divergences, not an artificial constraint on the ease of programming automatic taxoboxes.

That Dasycladus is a member of the family Dasycladaceae and order Dasycladales adds almost nothing the reader's knowledge of the genus. However, knowing that Dasycladus is related to the sea lettuces, and is in a group closely related to the land plants, is important and fundamental information. The taxoboxes don't give detailed information about groups higher up, they merely gives link, and, yes, with algae, due to the limited knowledge many people have about them, information about higher up taxa is fundamental.

Algae are not as familiar to the general reader as plants and animals. I hope to make their article pages more useful by editing in a way that acknowledges this unfamiliarity.

However, I don't think I raised the issue of the number of taxa to use. I'm more concerned that green algae taxonomy be consistent. Thanks. --Kleopatra (talk) 22:57, 23 October 2010 (UTC)

I fully see the point of algae being a group people know little about (I am a biologist myself, but I must confess my knowledge of algae is limited to a few local species and dividing them into green, red and brown ones). As such, i understand the need for some higher taxa. On the other hand, I also see the need for units that I recognize as a layman, like green algae. Now, you will probably argue that green algae are paraphyletic, and then we have opened yet another can of worms (Linnaean vs cladistic taxonomy). I'm a zoologist, and we have had the same argument over reptiles vs sauropsids popping up ever so often. After a bit back and forth, the consensus (though weak), is that the common reader would expect to find reptils under Reptilia (even down to the birds close relatives like Velociraptor) rather than under the largely unknown Sauropsida. Thus, we use formal Linneaen systematic in the taxobox as a mean for navigating, and reserve a more detailed cladistic taxonomy for the text. Personally, I'd list the various algae Chlorophyta, Rhodophyta and Phaeophyta as subdivisions of (blatantly paraphyletic) Protista, and keep such notions as "Kingdom Chromista" in the text. Then again, I'm a zoologist, and traditional zoological taxonomy isn't that far off.--Petter Bøckman (talk) 07:43, 24 October 2010 (UTC)

Oh god no. Protista is dead. I think we'd be doing ourselves a real disservice to keep that in the taxobox. At WP:PLANTS we dumped the old classification systems and are still in the process of updating all our taxoboxes to the APG III system, which uses unranked clades. This, I think, is a vast improvement. In taxonomic cases, I think it's less about what the reader would expect and more about what's accurate, correct, and clearly supported in the literature. After all, wouldn't the reader expect the article to be titled Brontosaurus not Apatosaurus (and many other similar cases). I really think the Reptile consensus will change, but it's a shame it can't be updated to reflect the current literature now. Rkitko ^(talk) 13:00, 24 October 2010 (UTC)

No, I'm not going to argue about green algae being paraphyletic, they are. That doesn't mean it can't be an important article on wikipedia, and it doesn't mean the term "Green algae" can't be used. I don't even have any plans or see any need to change it at that level for categorizing the "green algae." A paraphyletic categorization exists already and can remain for some paraphyletic groups without increasing confusion for the reader and for editors. The brown algae are a clade, as generally defined, and that term also can be used. The terms must be defined correctly within their articles so as not to mislead or misinform the general reader, but there's no issue that I see with using well-established vernacular names as titles and categories for an encyclopedia.

This does not exclude including an unranked clade in the text. Using reptiles versus sauropsida does not change the phylum, domain, or kingdom of the reptiles, and the reptiles taxobox includes the unranked amniotes. So, your example is a taxobox similar to what I support, and, by the way, what is already being used at the higher level in the green algae.

This fossil algal, however, has an automatic taxobox that is not what is supported at the higher levels in the wikipedia taxobox it places the organism in. I would like to know what the community consensus for this automatic taxobox making the change is. And, if the automatic taxoboxes are going to be randomly selected taxonomies without discussion by the community, I would like to know what the support for this is. --Kleopatra (talk) 08:16, 24 October 2010 (UTC)

I also confess a relative ignorance of algae, but I just wanted to mention in your above proposal that you included the domain. Previous discussions have concluded that rank unnecessary to include in taxoboxes except for in Bacteria and Archaea articles where the domain is rather important. I think if you work with the automatic taxobox and shape it into what you (and others) decide is the best taxonomy, then it will be an improvement! I'm just really unaware of how accepted Viridiplantae and Archaeplastida are. What does the literature mostly use? Rkitko ^(talk) 13:00, 24 October 2010 (UTC)

It's necessary for wikipedia, because wikipedia has classified prokaryotic cyanobacteria as eukaryotes on a large scale, and green algae as prokaryotes on a small scale. The damage requires long term mitigation, and this includes keeping the obvious: that multicellular green algae are the eukaryotes. I don't see its great utility in plant and animal articles, but "algae" is a garbage term for a grand hoard of distantly related organisms.

The clades Archaeplastida and Viriplantae are well-supported, although I've used only the former as a name. However, if I start a discussion on what names to use, rather than going with what is in use right now, I might as well resign from editing article space and devote my life to wikipedia and talk space. I'm organizing the articles so I can get some experts on board to editing and adding images to them, as in the Smithsonian project example, while rewriting what I can.

For now, I'd like to organize the green algae according to the existing higher level taxonomies in the chlorophyta and charophyta articles. I would like the automatic taxoboxes (or rather their bot operator) to be constrained from being the one to choose which taxonomy to use in the case of algae mixed taxonomies. If support has already been given to the automatic taxoboxes for this taxonomy, I would like a link to the discussion, so I can make sure I contribute in the future. --Kleopatra (talk) 21:26, 24 October 2010 (UTC)

Huh? Which cyanobacteria articles were mislabeled? Was this a bot-generated article problem like the Anybot issue? Examples? And I don't think it's fair to say that because we've had some mistakes in the past that it's obvious we must include the domain on the eukaryotic articles. I think if you're going to do that, I would insist on a wider WP:TOL discussion about that very point (including domain in eukaryotic taxoboxen). And I know the automatic taxobox is still kind of new and we haven't really gotten much time to use it, but I thought a point of clarification is necessary here. We the editors set up Template:Taxonomy/Foobartaxon pages (e.g. what I did with Template:Taxonomy/Welwitschia). No bot will be choosing the taxonomy, as far as I know. There will be bots and toolservers, if approved, to help the conversion from taxobox to automatic taxobox, but we still control them. And if there's ever a mistake, it's a much easier fix because all you do is edit the appropriate Template/Taxonomy page to correct it and the hierarchy takes care of the rest! (e.g. if new research reveals Stylidiaceae to belong to a different order other than Asterales, I would just edit Template:Taxonomy/Stylidiaceae to change |parent = Asterales to whatever was now correct and all daughter taxa would display the new classification.) Since I've done some editing with the automatic taxobox, I'd be more than willing to help you organize and set up the Template:Taxonomy/Foobar pages to the correct arrangement. We can discuss that at WP:ALGAE, though. Cheers, Rkitko ^(talk) 21:47, 24 October 2010 (UTC)

I apologize for offending people. I will leave the green algae articles alone for others to edit. --Kleopatra (talk) 21:50, 24 October 2010 (UTC)

Now I'm really quite confused. I don't believe you've offended anyone here. And I, for one, was really pleased someone was going to give those article attention. Is there something I said above that dissuaded you from pursuing this objective? I certainly hope not. Cheers, Rkitko ^(talk) 22:14, 24 October 2010 (UTC)

I would like to edit articles. I am trying to use existing taxonomies and phylogenies wherever possible, and, due to the high flux in algae taxonomies, this is often possible where they are not wrong or unsupported in the literature.

This automatic taxobox, for some reason, opted for a higher level taxonomy that is not the one used in the higher level taxon's existing article. I would like to know the automatic taxobox's support for the chosen taxonomy. I asked a question about this, and I am now reduced to discussing and defending other issues without my question being answered.

I would like people to be able to access, read and edit wikipedia algae articles and get useful information from them.

I cannot organize and clarify and create a single taxonomy in the green algae articles while an automatic taxobox is using a different one, when I just started at the highest level of what wikipedia articles are already using, which isn't what the automatic taxobox is using. It seemed that if automatic taxoboxes are being adopted, then I should know where the discussions about their taxonomies are being held, so I can participate or learn what is being done, before I move on to editing those articles in a different way. And now, it seems that my trying to find that discussion will lead to other things I say or do or might be thinking being questioned. My question about the automatic taxobox has led me to doing not much else but discussing the automatic taxobox and defending my question and editing without my question being answered. I haven't edited anything in an outrageous way. I've merely used existing taxonomies, names, hierarchies, wherever possible, in an attempt to clean up articles to the level where others can edit. But, I don't have time to both edit and answer all of these questions. I simply wanted to know why the template chose this taxonomy over the existing higher level taxonomy and how I could participate in future discussion on this.

At this point, I would now like to return to editing articles, and to do this, it appears I must allow the automatic taxobox to be templated in whatever way it has been decided, without knowledge of the decision process, and this means that my editing green algae articles will not be in accordance with either the existing taxonomies or the automatic taxobox. I'm not going to waste my time with it. --Kleopatra (talk) 22:36, 24 October 2010 (UTC)

Ok, I get the issue now. The automatic taxobox is not a single person, entity, or group. It does not choose classifications. It appears that Martin (User:Smith609) was using the algae articles as testing ground for the automatic taxobox implementation back in June and July. I assume he just used the taxonomy presented in the article as it existed. If you want to change it, it's a simple edit. Go to Template:Taxonomy/Chlorophyta and change |parent=Plantae to |parent=Viridiplantae. I thought we were also discussing the merits of Viridplantae, but I'm so out of my league on that discussion that I'll leave it to the experts. Rkitko ^(talk) 23:14, 24 October 2010 (UTC)

No, he did not use the taxonomies in the articles as they existed. He created a different taxonomy for the automatic template for Chlorophyta than what is used in the Chlorophyta article. --Kleopatra (talk) 00:15, 25 October 2010 (UTC)

Algae taxonomy, continued

(Just a break because I'm lazy and don't like to scroll)

Now I think I'm starting to see what you want, Kleopatra! What you need to do is to edit the automatic taxonomy templates themselves. Don't be shy, that's what they are there for. Each box has has the following simple structure (Clorophyta as an example):

{{#switch:{{{1}}}

|rank=divisio

|parent=Plantae

|link=Chlorophyta

}}

The first line is just machine coding, no need to worry about it. The second line is Linnaean rank. If you leave it blank, the taxon will list as "unranked" in the taxoboxes, and it will not be a cut-off point for detailed higher ranks. The third line is the parent taxon. In this case it is obviously anchored wrong. If I remember my BIO 101 correctly, the plant kingdom (i.e land-plants) are a daughter group of the green algae, so this should clearly be changed. I can do it for you if you don't feel comfortable with editing the template. The fourth line is what article the taxon will link to. If I changed it to e.g. lumpfish, an automated taxobox for sea lettuce would stil read "Division Chlorophyta", but if you hit the Chlorophyta link, it would take you to lumpfish in stead.

I hope this explanation helps you get started. Petter Bøckman (talk) 07:34, 25 October 2010 (UTC)

Note: The template for the Chlorophyta link is at {{Taxonomy/Chlorophyta}}. The same naming convention is used for all the taxon link templates. Bob the Wikipedian ^{(talk • contribs)} 07:53, 25 October 2010 (UTC)

Also, if you wanted it to link to lumpfish with minimal visibility, you'd need to use the parameter link = lumpfish|Chlorophyta. :) Bob the Wikipedian ^{(talk • contribs)} 07:56, 25 October 2010 (UTC)

Monotypic genera

What should taxoboxes for monotypic genera look like? Should it look like its a genus article or should it look like it's a species article? ie, should it be:

 | familia = †[[Tyrannosauridae]]
 | genus = [[extinction|†]]'''''Tyrannosaurus'''''
 | genus_authority = [[Henry Fairfield Osborn|Osborn]], 1905
 | subdivision_ranks = [[Species]]
 | subdivision =
 * ''T. rex'' <small>([[Type (zoology)|type]])</small><br/><small>Osborn, 1905</small>

or

 | familia = †[[Tyrannosauridae]]
 | genus = [[extinction|†]]'''''Tyrannosaurus'''''
 | genus_authority = [[Henry Fairfield Osborn|Osborn]], 1905
 | species = [[extinction|†]]'''''T. rex'''''
 | binomial = '''''Tyrannosaurus rex'''''
 | binomial_authority = ([[Henry Fairfield Osborn|Osborn]], 1905)

I don't particularly care either way, but others seem to care enough to undo it either way I write it, so it would be nice to have some discussion. Thanks, ErikHaugen (talk) 17:15, 26 October 2010 (UTC)

I create articles using the first second style, its mainly a personal preference, but a number of the taxa listed in Category:Monotypic mammal genera seem to use that style.--Kevmin § 17:21, 26 October 2010 (UTC)

You mean you use the second, right? ErikHaugen (talk) 23:24, 26 October 2010 (UTC)

Yes I do, I just reread what I typed and realized the mistake! I apologize for the confusion. --Kevmin § 00:35, 27 October 2010 (UTC)

I would say a bit like both of those examples. Both the genus and the binomen should be boldface, and the authority should be given for each; I don't think subdivision= is appropriate, unless there are [more than one] subspecies. --Stemonitis (talk) 17:25, 26 October 2010 (UTC)

ok - I added genus_authority in the second one. Sounds like it is preferred? ErikHaugen (talk) 17:31, 26 October 2010 (UTC)

In general, the subdivision parameter is intended for taxa that have multiple subdivisions. When monotypic, use the appropriate subtaxon's parameter. Bob the Wikipedian ^{(talk • contribs)} 22:31, 26 October 2010 (UTC) Edit: this is from a zoological standpoint. Bob the Wikipedian ^{(talk • contribs)} 23:59, 26 October 2010 (UTC)

I prefer the second choice, e.g. Darlingtonia californica, Oreostylidium. This is how nearly all (if not all) monotypic plant genera articles appear. See Category:Monotypic plant genera. Rkitko ^(talk) 23:00, 26 October 2010 (UTC)

I prefer Version 1. It emphasizes that the article is about a genus, and the |species and |binomial sections of Version 2 are annoyingly redundant.
I'm not entirely convinced of the efficacy of the automatic taxobox project. Logistically, it's going to lead to massive numbers of new template pages to watch for sneaky vandalism, edit-warring, and plain old botches by editors who mean well but aren't much on templates. Accessibility-wise, it's going to make it more difficult for people to create articles on new taxa if they also have to create at least one new subtemplate for the article. J. Spencer (talk) 00:11, 27 October 2010 (UTC)

The |species= and |binomial= fields are redundant in all species taxoboxes. We should perhaps change that, but it can hardly be an argument in this specific case. I always use possibility 2. Ucucha 00:17, 27 October 2010 (UTC)

Exactly. Further, it's not just an article on a genus. It's an article on both taxa and we must emphasize that in the taxobox, bolding both the genus and the species parameters. I believe we had a discussion on the redundancy of species= and binomial=, but there was no consensus or there was support to keep both. Rkitko ^(talk) 00:23, 27 October 2010 (UTC)

Doesn't this go against the Wiki MoS? MoS states that the title should reflect the article subject. The taxobox for the article on Tyrannosaurus therefore goes down to the level of genus, becuase Tyrannosaurus is a genus. Otherwise the title would be Tyrannosaurus rex. At least this has been the philosophy at WP:Dinosaurs for a long time, and a change would require changing the taxobox of just about every dinosaur article there is. It's also inconsistent internally, at least for us. The taxobox would be visually different to a large degree between monotypic and non-monotypic genera, because we don't deal with species-level articles. Therefore we'd have a hodgepodge of articles using one format (for monotypic) with many using another (multi species), leaving any species that happens to be in a genus with another species without any binomial field in its taxobox. Why not stop at the genus level for all monotypic genera and only have to worry about one taxobox format? MMartyniuk (talk) 01:59, 27 October 2010 (UTC)

Also, isn't it redundant to list both a species parameter and a binomial parameter? The binomial is the species name. (And as long as I'm nitpicking the example, the author shouldn't be in brackets unless the species has been reclassified from another genus). MMartyniuk (talk) 02:00, 27 October 2010 (UTC)

And a follow-up question, how are synonyms handled if monospecific genera use the binomial field? In paleontology at least, people deal mainly with genera (for better or worse, since most dinosaurs tend to be split into monospecific genera rather than lumped). Take Pterodactylus for example. As the taxobox currently reflects only the genus, only generic synonyms are listed (there tend to be far fewer of these). It's an easy reference right up front, rather than scrolling to the very long and complicated table of species-level synonyms. If we are going with binomials for monospecific articles, could we add separate parameters for species-level synonyms and genus-level? That way we can keep the utility of listing synonymous genera at the top of the article (which are often redirects) and put a "See text" note for long and complicated species synonymy tables. MMartyniuk (talk) 02:08, 27 October 2010 (UTC)

I disagree with your first point, Marty. If a taxon is monotypic, how can we say for sure what characteristics are unique to its daughter taxon? On the note of redundancy, amen. And also amen to removing those parentheses on most taxoboxes. As far as genus synonyms/species synonyms, I typically include every synonym which has been published. In the nonexistant taxon Genius speciosus, let's say some controversy occurred, and it cycled through the names Paragenius speciosus, Anparagenius speciosa, and Paragenius speciosa. I'd include all four of those names, but leave out Anparagenius speciosus and Genius speciosa. Bob the Wikipedian ^{(talk • contribs)} 03:34, 27 October 2010 (UTC)

Not sure what you mean about listing unique characters of daughter taxa. Is the idea is that in the case of monotypic taxon species, we should always collapse down, rather than collapse up? For example, we have Ichthyornis dispar. I dispar is placed in a long series of monotypic taxa (Ichthyornis, Ichthyornithidae, Ichthyornithiformes, Ichthyornithes). In cases like this, the title doesn't really matter because they all refer to the same species. The MoS says we should use the most familiar name in the title. For most extinct animals, this is the genus name, not the species. Again, the content won't change, because all these taxa refer to the same species. This is more a question of, what should the title be? And, should the taxobox reflect the same subject of the title (the genus Ichthyornis) or one of its "synonyms" (I. dispar)? If the latter, doesn't this cause a bit of a logical disconnect? The article topic/title and the taxobox are referring to the same thing but by different names. MMartyniuk (talk) 04:42, 27 October 2010 (UTC)

Example: This doesn't involve a monotypic genus, but bear with me, because it does illustrate the concept. A few years ago, Irukandji jellyfish was monophyletic. When an Irukandji was discovered that caused paraphyly (polyphyly? I get them confused), we had the problem of resolving the article so it was actually about Irukandjis instead of about the two previously known species. To this day, that article still has problems as a result. The problem? The article had been written about the known examples and made several generalizations that didn't hold true when a new species was discovered. Had the article been written about the clade rather than the specific examples, the problem wouldn't have even existed in the first place. The only problem was this-- no one knew about the clade in general. How could we say that the size of the jellyfish ranged so broadly? Nobody would have guessed.

My point is this: You can write as much as you want to about Vampyroteuthis, but you're writing about V. infernalis, not Vampyroteuthis in general. Why? Because we don't know for sure what defines the boundaries of the genus...there could easily be a second or third species of vampire squid that no one's heard of yet. Therefore, I'd prefer to see the article with the title Vampyroteuthis infernalis with Vampyroteuthis redirecting to it. Bob the Wikipedian ^{(talk • contribs)} 05:54, 27 October 2010 (UTC)

I agree on the article titling. Excluding fossil genera, which seem to have different conventions, most of the information in a monotypic genus article pertains to the species, not the genus (e.g. distribution, life history, conservation). In this paper describing a (at the time) monotypic partridge genus [2], the authors have separate sections describing the genus and species (with information such as habitat belonging to species), and this is not at all unusual. Thus, I believe that articles on monotypic genera would be more precisely placed under the species name, as the species is what most of the article information would apply to. -- Yzx (talk) 06:17, 27 October 2010 (UTC)

Actually, this is usually done for fossil taxa too. A new monotypic genus will have separate diagnoses for genus and species, though the genus usually just has something like "as for the type species" and maybe a few generalizations. MMartyniuk (talk) 08:07, 27 October 2010 (UTC)