Wikipedia talk:WikiProject Tree of Life

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Archives for WT:TOL edit
1 2002-07 – 2003-12 Article names
2 2003-11 – 2004-02 Taxoboxes
3 2004-02 Taxoboxes
4 2004-02 – 2004-08 Bold taxa; taxonomy
5 2004-03 – 2004-04 Taxonomy; photos; range maps
6 2005-04 – 2004-06 Capitalization; authorities; mammals
7 2004-06 – 2004-08 Creationism; parens; common names
8 2004-05 – 2004-08 Templates; †extinct; common names
9 2004-05 – 2004-08 Categories; taxoboxes
10 2004-08 – 2004-12 Categories; authorities; domains; Wikispecies; ranks; G. species; capitalization; Common Names
11 2004-11 – 2005-05 Capitalization; common names; categories; L.; authorities; algae; cultivars
12 2005-03 – 2005-05 Ranks; common names
13 2005-05 – 2005-06 Hybrids; taxobox format; cultivars
14 2005-06 – 2005-07 Categories; food plants; identification; Capitalization
15 2005-07 – 2005-09 Synonyms; types; authorities; status; identification
16 2005-09 – 2005-12 Paleontological ranges; Rosopsida; Taxobox redesign; identification
17 2005-12 – 2006-04 Taxobox redesign; identification; APG; common names; capitalization
18 2006-4 – 2006-10 Categorization; include in references; snakes; range maps; seasonality graph; common names; bioregions; brya;

Contents


[edit] Cladistics coding

Did i once see a way to write in a bit of code and wikipedia would do some wizzy work and produce a taxonomy tree? Something similar to the <math> function. Did i see this, or was it just an experimental thing? chris_huh 18:38, 15 October 2006 (UTC)

I had a go at it here: User:Pengo/clad and had a rant about it here. But it's a pretty miserable attempt. The best thing is still is to make one from scratch in Inkscape or something. —Pengo talk · contribs 09:12, 17 October 2006 (UTC)
Wouldn't this be more of a wikispecies kind of thing? --SB_Johnny|talk|books 14:20, 17 October 2006 (UTC)


[edit] Category:Fauna_of_the_United_States_by_state_and_its_subcategories up for deletion

All US "fauna by state" categories have been nominated for deletion. I think this would be of interest.

Wikipedia:Categories_for_deletion/Log/2006_October_13#Category:Fauna_of_the_United_States_by_state_and_its_subcategories

Please see Category talk:Biota by country GameKeeper 13:40, 20 October 2006 (UTC)

[edit] Problems with the usage of sub-categories of Category:Biota by country

I am trying to get a discussion going on the Flora of <region>/Forna of <region>/Biora of <region> caregories.

Please see Category talk:Biota by country GameKeeper 13:40, 20 October 2006 (UTC)

[edit] Talk:List of regional bird lists

Please comment on the move and reversion jimfbleak 05:49, 22 October 2006 (UTC)


[edit] Protists and plants

What should one do with taxoboxes for groups where their classification is still not well agreed upon, such as whether or not Rhodophyta (and Glaucophyta) should be separated from the other protists and put with the plants? It's not exactly a new concept for the Rhodophyta, but the taxoboxes leave no allowance for it, and it is one of the issues people take strong stands on, whether the Rhodophyta are protists or plants. What can be done so that the taxobox reflects the level of ambiguity in the taxonomic placement? Can the boxes have a color slash, khaki above, green below? Should they reflect Wikipedia's current classification system--although I think the one article listed on the protist page does classify Rhodophyta with the plants, not with the protists? Should it be majority rules as primary and the secondary classification within the article? Can the boxes be stacked so both are represented by taxoboxes?

This issue should also be addressed with Angiosperm taxonomy--as has been brought up before. If Wikipedia is chosing APG II as the primary classification, certain groups should not be used in the taxoboxes.

Were these issues discussed and decided before?

KP Botany 00:20, 24 October 2006 (UTC)

Good question. As far as I can remember, this topic has not come up before. Would it be a satisfactory solution to assign two values to each parameter, separated by a slash? Something like "|regnum = plantae / Protista"? Or "|regnum = plantae | Protista"? (Or whatever the alternatives are, and this down the different levels) TeunSpaans 17:36, 24 October 2006 (UTC)
Yes, a good question, and also a sticky one. I remember when green algae, and even cyanobacteria, used to be classified as "plants", back in simpler times when there were only two kingdoms of living organisms. But my old introductory botany textbook, Raven et al.'s "Biology of Plants", classifies green algae as protists. I never did like this and since this is an old edition (1981) maybe they've changed their minds since then--I have the latest edition at home so will have to check.
It's possible that there's more support nowadays for defining plants to include green algae, as the latter are decidedly paraphyletic if the embryophytes are excluded, whereas green algae plus embryophytes comprise a pretty solid monophyletic group. This just helps to illustrate, once again, that classifications are opinions: the relationships are pretty objective and well-accepted, it's just how to sort them into groups and what to call those groups that causes disagreement. My recommendation is that if you're going to use a classification of any kind, however well-accepted, you ought to cite a reference for it. Who calls green algae plants, and who calls them protists? And why? There are some good subjects for an article right there. MrDarwin 17:50, 24 October 2006 (UTC)
I guess the issue is the taxobox itself, in part because I'm too biased from educational background to do these mixed groupings of the taxoboxes, and my bias towards monophyletic classification schemes. However, it makes Wikipedia confusing as it stands, to include a paraphyletic category in the taxoboxes.
What Raven et al. do in their latest edition is call the Chlorophyta protists, but include a cladogram that clearly shows they form a well-supported monophyletic clade with the embryophytes based on the apomorphy of [chlorophyll b, starch storage, stellate flagellar structure, and gene transfers], and that the Rhodophyta and Glaucophyta form a monophyletic groups with the viridophytes due to chlorplast endosymbiosis--they use 'viridophytes' only in pointing out that other biologists use it.
After thinking about it, the problem seems to be the meaning in the taxobox, because taxonomy today has a strong emphasis on monophyletic groups, but also because there are different levels of certainty attached to various ranks within the taxobox--although this is true of all of botany. Does its use in the taxobox imply anything?
Someone did just that, with the slash on one page between Protista / Plantae--this is probably more useful than using either one. I think it will work with a note attached that protists are not monophyletic, so including the Rhodophyta in the Kingdom Protista does not precude their placement in the Kingdom Plantae?
There are a number of other problems with the taxoboxes that have been pointed out before, in particular mixed classification schemes. Possibly each taxobox should use a single classification scheme and give a reference for the one used?
Also, the title of the box has a little '?' in it--a link to more information. However, in scientific nomenclature isn't a question mark used to denote that a taxon's name is presently undecided, or an organism is not certainly identified? If so, it should not be used at all as an information icon next to the name of a taxon--something someone else pointed out.
KP Botany 21:53, 24 October 2006 (UTC)
Now I'm looking at Judd et al.'s "Plant Systematics: A Phylogenetic Approach". They basically define "plant" as green algae plus land plants, but then go on to ignore pretty much everything except the tracheophytes. And yes, the taxoboxes are problematic--one reason why I stay almost completely away from them. MrDarwin 00:21, 25 October 2006 (UTC)
There are certainly situations where the community is simply split in half and there's really no way to pretend that choosing one over the other is anything but POV. The older taxoboxes had a bit more flexibility in them and I took advantage of this on a few occassions where, as an editor, I thought listing only one option in the taxobox was picking one side on a coin flip. Here and here are examples. Neither survived the transfer to the new (and superior) taxobox format. I think in most cases the community will pick a taxonomy to use in the taxoboxes and discuss the controversy in the text, but I do think there are a handful of situations where the taxobox should represent the controversy as well. --Aranae 01:08, 25 October 2006 (UTC)

For most of the protists and algae, the taxonomy is really variable. The problem with saying "| regnum = Plantae / Protista" is that it implies the rest of the classification is less controversial, but although a general outline has taken shape, a lot of aspects vary from author to author. Thus the taxoboxes should really be considered representative systems, since they don't have room to explain the others. In fact, in most cases the different possibilities aren't even discussed in the articles. They should be, but it's really hard to find good information on them, as most people just pick one system and stick with it.

The question of whether red and green algae should be considered plants has come up before. Really, it depends on what the currently favored classification is, which is difficult to tell. Reading journal articles about protists, I think it's better to call them plants; but few of these worry about what counts as a kingdom, except Cavalier-Smith, and his breakdown is not entirely standard (e.g. he argues in favor of paraphyletic groups, and for that matter does not use Protista at all). Josh 05:38, 25 October 2006 (UTC)

As these uncertaintes seem quit major, I think it might be wiser to leave the disputed taxons out of the taxobox. The taxobox has no required levels, see User:TeunSpaans/testtaxobox for an example. Thus, if regnum and order are disputed, we can leave them out and just have family and below. It is a possibility, I leave it to you to judge what is best. TeunSpaans 17:34, 25 October 2006 (UTC)
The regnum cannot really be left out, because it determines the colour of the taxobox: note that in User:TeunSpaans/testtaxobox it is clear you think that bears are animals from the pink taxobox. I'd prefer to make a choice; to make it a consistent one across all our articles (e.g. all out taxoboxes on green algae should follow the classification on our Green algae article, whatever choice we're making); and to annotate the really uncertain ones. See User:Eugene van der Pijll/taxoboxtest. -- Eugène van der Pijll 22:36, 25 October 2006 (UTC)

The color of the Kingdom It seems to me that if we are forced to change information, ie include information that is not accurate enough or too much in conflict, to meet the limited confines of the taxobox, it's the taxobox that must change, not what is included in the article--if we conform the information to the taxobox we are doing OR or inserting our POV. How about no color and a note when the kingdom is in dispute? I had not thought of this, but once TeunSpaans said it, although it irks me as an obsessive classifier, it seems the method least likely to misinform or confuse the user, or demand contortions of the editor, while indicating to both the need to look further in the article for more information as to why this is not classified at the kingdom level, namely scientists differ in how they define the kingdoms. We could also just make the color for the questionable placements protist/plantae be orange or something.

Also, please note, it is not necessarily in conflict on most classifications to say that something is both a plant and a protist, because the former is a monophyletic clade, but the latter is simply a grouping on convenience, usually, but not always, everything that isn't in one of the other groups.

I would still like to suggest that the question marks in taxoboxes be done away with as a link to more information about the taxobox. They have a meaning, as far as I know, in the nomenclatural codes for organisms, namely a level of uncertainty as to the correct placement, depending upon their location in the organism's name. Taxoboxes now simply indicate that all kingdom level classifications are in question. It could be an asterisk or a little 'i' like someone earlier suggested, but in this instance it really can't be a question mark. However, a non-colored box with a question mark in it, indicating uncertainty as to kingdom and linking to a discussion within the article of this uncertainty would be useful.

I think the taxoboxes are useful in giving information at a glance. However, I don't think they should be allowed to misinform at a glance, and others may be right that multiple taxoboxes decreases their usability. Not including misinformation, by removing the color, and tying the issue to a discussion in the text, would erase this issue, without interfering with the usefulness of taxoboxes. KP Botany 18:42, 26 October 2006 (UTC)

I agree that the taxoboxes should inform, not misinform. I also agree that changing the taxobox to a colour not yet in use (white? orange? grey?) for taxons unclassified at the regnum level seems like a good option. A third option I thought of, possibly identical to the note KP botany mentioned, is to create a link to the article where the dispute is explained, something like:

|regnum=[[Rhodophyta#Taxonomy|Disputed]]
This option could be implemented without a taxobox change, only the colour would be suggestive of a kingdom, but adapting the taxobox would be neater.
TeunSpaans 19:11, 26 October 2006 (UTC)

I just took a look at the taxobox, they do have a color parameter, so I think we don't need to change the taxobox. See User:TeunSpaans/testtaxobox2 TeunSpaans 19:19, 26 October 2006 (UTC)

Except the kingdom is not especially disputable. For instance, look at the two classifications listed on red algae; they're similar, but one has added new classes and changed some of the ranks. What phylum Cyanidiophyceae gets is as disputed as its kingdom. And yet the relationships are the same, and I'd hesitate to leave its entire position as uncertain, when only the ranks of the groups are. (Incidentally, if most specialists working in red algae consider them plants, maybe we should follow them without worrying how more encompassing systems treat them).

Also, an explanation about the kingdoms should be given on green algae, but if we footnote each variation in classifiction in each page about each genus, we're going to have a very difficult time adjusting and maintaining it. Maybe a better idea would be to change the link from "scientific classification" to something like "typical classification", to emphasize that some authors deviate from it. It would be easy enough to add a flag to do that, like we do for viruses. The question would then be at what point we stop using it - for instead, is APG solid enough that we can treat it as authoritative, and what about the minor variations for mammal orders? Josh 19:37, 26 October 2006 (UTC)

[edit] Archive

This talk page has been archived. Feel free to reintroduce any topic that needs more discussion. Also, someone else needs to list the topics of that archive in the archive TOC. pschemp | talk 14:42, 22 October 2006 (UTC)

Done. TeunSpaans 17:43, 24 October 2006 (UTC)==

[edit] scientific evidence

Citing temtbooks at each other seems, shall we say, a little medieval? Majority vote has nothing to do with it, either of people or of textbooks. The best evidence for the scientific consensus is recent review articles in peer-reviewed journals, or recent articles themselves if they give a good background.

  • For the higher categories in land plants, I think it's Yin-Long Qiu, L, et. al.

The deepest divergences in land plants inferred from phylogenomic evidence PNAS 2006 103: 15511-15516; published online before print October 9 2006, 10.1073/pnas.0603335103 [not open access, unfortunately, except for the abstract, but will be in 6 months. Perhaps we should add others to this page as they appear. I will, but I'm not going to do it retrospectively. DGG 02:05, 25 October 2006 (UTC)

The article you cite is not a review article, but original research according to its abstract. Review articles would be excellent evidence for the scientific consensus, though.
KP Botany 03:12, 25 October 2006 (UTC)
I repeat from yesterday: "The best evidence for the scientific consensus is recent review articles in peer-reviewed journals, or recent articles themselves if they give a good background." This one does. Be pragmatic. DGG 06:35, 26 October 2006 (UTC)
Review articles are different from including a "good background" of a subject, because a scientific review, by its nature, generally must include all valid conflicting theories:
"In terms of scientific literature, reviews is a category of scientific paper, which provides a synthesis of research on a topic at that moment in time. A compilation of these reviews forms the core content of a 'tertiary' scientific journal, with examples including Annual Reviews, the Nature Reviews series of journals and Trends." Wikipedia
I somewhat doubt that an article this dense on content also includes a good background anywhere near the level of a review in its 6 pages. Qiu's contribution alone to the topic would require more than 6 pages.
KP Botany 18:55, 26 October 2006 (UTC)

[edit] Project directory

Hello. The WikiProject Council has recently updated the Wikipedia:WikiProject Council/Directory. This new directory includes a variety of categories and subcategories which will, with luck, potentially draw new members to the projects who are interested in those specific subjects. Please review the directory and make any changes to the entries for your project that you see fit. There is also a directory of portals, at User:B2T2/Portal, listing all the existing portals. Feel free to add any of them to the portals or comments section of your entries in the directory. The three columns regarding assessment, peer review, and collaboration are included in the directory for both the use of the projects themselves and for that of others. Having such departments will allow a project to more quickly and easily identify its most important articles and its articles in greatest need of improvement. If you have not already done so, please consider whether your project would benefit from having departments which deal in these matters. It is my hope that all the changes to the directory can be finished by the first of next month. Please feel free to make any changes you see fit to the entries for your project before then. If you should have any questions regarding this matter, please do not hesitate to contact me. Thank you. B2T2 23:41, 25 October 2006 (UTC)

[edit] help on species name

I took this ptoto in Turkey this year, tr:Image:Resim14.jpg, but don't know their species name. Can anyone help on this? Thanks --Ugur Basak 11:18, 26 October 2006 (UTC)

[edit] a real tree

Taxoboxes are a nice navigation interface, but they are still purely textual and lack a "graphical" component for orientation ; it would be nice to have something maybe in the form of a tree, showing where a given group is located relative to the global tree (maybe showing the sister nodes at each parent node) or at least w.r.t. to the parent and child nodes, e.g.

Genus Balaenoptera   Genus Megaptera
                 \    /
                  \  / 
                   \/
       Family Balaenopteridae  Family2  Family3 ...
                             \   |      /
                              \  |    /
                               \ |  /
                                \|/
                             Mysticeti   Suborder2  ...
                                    \    /
                                     \  / 
                                      \/

— MFH:Talk 17:53, 27 October 2006 (UTC)

These textual representations rarely come across as very visually pleasing. Graphics almost always turn out nicer. Note Image:Hominini.PNG for an example including a highlighted section for the taxon of interest. --Aranae 19:26, 27 October 2006 (UTC)
I think you didn't get my point: I did ask for graphics, my ascii art was just to explain what it should be! — MFH:Talk 21:56, 28 October 2006 (UTC)
It would be useful to put trees in many of these articles. But is there some simply way of graphically coding them for some uniformity of presentation? Now, the trees all over Wikipedia are simply made for that particular article. KP Botany 20:16, 3 November 2006 (UTC)
As far as a free web interface making a simple tree graphic that doesn't involve actual data or any other computer program, you might try Phylodendron. The simplest input is a single line that contains a representation of your tree. The format for that line is (A,(B,C)); where A, B, and C are taxa on the tree and B and C are sister taxa. Unfortunately the output formats are a bit awkward, but I find that outputting the tree as a GIF image map and then right clicking and selecting view image produces a workable GIF file. You can certainly use a graphics program to convert any of the other outputs into a loadable image as well. --Aranae 21:37, 3 November 2006 (UTC)
Also note that you can label nodes by using [ ]. So the tree immediately above could be generated with: (((Balaeonoptera,Megaptera)[Balaeonopteridae],Family2,Family3)[Mysticeti],Suborder2); . Image:Hominini.PNG could be roughly reproduced with: (((((Homo,Pan)[Hominini],Gorilla)[Homininae],Pongo)[Hominidae],Hylobates)[Hominoidea]); . Note that you can vary the output type (vertical/horizontal or tree appearance). You can also incorporate branch lengths, but I'm not sure that will factor in much without running into OR problems. --Aranae 23:13, 3 November 2006 (UTC)
On the French wikipedia, there is a field in the taxoboxes for a graphical tree, showing the cladistic position of the taxon/clade. See e.g. fr:Solanaceae. This would also be a solution for some of the problems on ambiguous classifications. Unfortunately, the existing images are all in French... Eugène van der Pijll 23:25, 3 November 2006 (UTC)
Their taxobox is nicely done on this page. However, what are they using for the classical taxonomy? I'll go look, I guess, but if you know... And with the embedded link to the image, it's useful and attractive. What do others think? Does someone individually make the images? Do all the organisms have these? Again, I can go look around, but if you know the standard.... KP Botany 00:38, 6 November 2006 (UTC)

While not a much more pratical than generating images of varation of the family tree templates could be made to do this. THey currently woudl make the articles look a bit messey unless they were done as templates, and they take a bi of time to do by hand. However since what we need here can be a lot less flexable than the family tree templates It is possible that we could do away with the internal formatting and just provide the names. We could with relative ease create a template that simply took 14 inputs and formatted them into a tree, with one of them bolded or some such. The tree in the pimage above would look something like this:
Hominoidea
Superfamily
Hominidae
Hylobatidae
Family
Homininae
Ponginae
Subfamily
Hominini
Gorillini
Tribe
Homo
Pan
Gorilla
Pongo
Hylobates
Genus

It is also worth noting that it woudl not have to be this big. We could drop the borders and move all of the cells twards eachother, and if we built some slightly diffrent images we could compress it vertically as well, and get it to close to the same size as the image above. Dalf | Talk 23:38, 5 November 2006 (UTC)

And finally it is also worth looking at Double-sized IPA vowel chart which appears to use an image as backgroun in a table then superimpose a second table on top with text. We could do somethign like that as well in a template. Dalf | Talk 23:43, 5 November 2006 (UTC)

[edit] Josh's cladograms

I don't think taxoboxes really have enough room for legible cladograms, but they'd be great additions to the article texts. If the developers are OK with nesting template arguments, that might be a simpler and more flexible way to write them. Here's a quick example based on the drawing code from the family tree templates; it would still need some polishing, but is it a step in the right direction? Josh

Euglenids

Peranema



Eutreptia

Euglenales

Euglena


Phacus





Yes, it's a step in the right direction, and fine without the colors. Did you look at the fr:Solanaceae one? Making it a clickable, even an abbreviated form of a larger one, looks very feasible on theirs, in my opinion. KP Botany 17:03, 6 November 2006 (UTC)

The problem with the above two examples is that the data used is too clean. It's all nice and binary; each node has 0 or 2 children. This is not always the case. Simple binary trees are often easily understood through less graphical means, but the cases where the phylogeny is not so well defined (and the resulting trees have more than 2 branches from a node) are the ones that really need to be described graphically. For examples, take a look at the first and last images on Hominoidea#History_of_hominoid_taxonomy, or just the Strepsirrhini taxonomy, where we don't know which of the three infraorders is sister to the other two. - UtherSRG (talk) 17:26, 6 November 2006 (UTC)

Compare and contrast:

Euarchontoglires
    ├─Glires
    │    ├─rodents (Rodentia)
    │    └─rabbits, hares, pikas (Lagomorpha)
    └─Euarchonta
         ├─treeshrews (Scandentia)
         └─N.N.
              ├─flying lemurs (Dermoptera)
              └─N.N.
                   ├─†Plesiadapiformes
                   └─primates (Primates)
Euarchontoglires
Glires
Rodentia (rodents)
Lagomorpha (rabbits, hares, pikas)
Euarchonta
Scandentia (treeshrews)
Dermoptera (flying lemurs)
†Plesiadapiformes
Primates
Euarchontoglires
Glires

Rodentia (rodents)


Lagomorpha (rabbits, hares, pikas)


Euarchonta

Scandentia (treeshrews)



Dermoptera (flying lemurs)



†Plesiadapiformes


Primates






- UtherSRG (talk) 18:02, 6 November 2006 (UTC)

Two answers. KP, the diagram on the French page is expandable because it's an image, and I'm not sure you can do the same thing with templates. We could just use images, but the downside is we'd need a separate file for each article and they wouldn't be directly editable. Uther, it's not too difficult to make templates allow ternary or more complex nodes, as below. Josh

Arthropoda

†Trilobita


Chelicerata


Myriapoda



Hexapoda


Crustacea




I continue adapting the Euarchontoglires trees above, to get a feel for things. Josh, is there a way to pass in a style argument the way the familytree accetps one? I'm really starting to like your implementation, but I want some control over sizing. Sometimes we'll want the larger text (such as for smaller trees), while other times it would be most handy to have the smaller font. - UtherSRG (talk) 12:03, 7 November 2006 (UTC)

A word of warning: these graphical implementations don't work well in Opera. I don't know what the solution for that is, but it's something to bear in mind. --Stemonitis 12:26, 7 November 2006 (UTC)
Can you post an image of what they look like for you? - UtherSRG (talk) 12:32, 7 November 2006 (UTC)
Here's what the last two trees look like for me:
and a similar effect occurs in the Euglena example above. --Stemonitis 12:43, 7 November 2006 (UTC)
Hrm.... Looks like the outer tree doesn't align properly with the inner tree when there's a nesting. Josh? - UtherSRG (talk) 12:54, 7 November 2006 (UTC)
I guess the first version was working on a coincidental alignment. I've changed the template to avoid this; it requires a slightly different approach, labeling branches rather than the stem. Please let me know if the labels are positioned ok. I've also added a style parameter to the above. Josh

I'd also suggest that if there's any way that terminal taxa could line up, that would be preferred. As it is, these trees look like they are attempting to be phylograms or even chronograms with certain taxa implied to be extinct fossil taxa. --Aranae 22:06, 7 November 2006 (UTC)

It's possible but non-trivial. I could give the outer table a set width and push everything against the side; this would right-align the final taxa rather than left-align them, or I could also make parameters for the length of each line, so that you can manually align them. But these are clumsy, and I'd wait to see if someone familiar with div formatting can't come up with a better solution. Josh
Looks like we're getting closer.... Having the name on a line, though, means some interference to users who have a underscore for the links, instead of just the coloration. However, this is a user preference issue, and no underscore is the default. I'm going to be bold and move this into the regular template namespace. Bravo Josh! - UtherSRG (talk) 15:53, 8 November 2006 (UTC)
I think putting some space before and/or after the text would help, too. - UtherSRG (talk) 16:15, 8 November 2006 (UTC)
I thought the only time the terminal taxa should line up is if they are all extant taxa? If they're not all extant, they shouldn't line up, right? Yes, I think this would be a vast improvement to current taxonomic information presentations if it could be implemented throughout Wikipedia--a simple diagram that displays relationships, plus it is currently how scientists have been presenting information for a long time. Good work, Josh, thanks. KP Botany 19:15, 8 November 2006 (UTC)
Not all cladograms have lined up terminal taxa, KP.[1] - UtherSRG (talk) 19:26, 8 November 2006 (UTC)
Oh, yes, I didn't say that they all have lined up terminal taxa, I'm questioning whether terminal taxa should line up, paritcularly if terminal taxa are mixed extinct and extant. Your link doesn't work. KP Botany 19:36, 8 November 2006 (UTC) 19:32, 8 November 2006 (UTC)
Fixed the above link, but you're right, it doesn't show what you are looking for. How about this? [2] - UtherSRG (talk) 21:33, 8 November 2006 (UTC)
I'm sure I've seen cladograms such as these with solid lines, but also some with mostly solid lines and a small number of dashed lines to indicate hypothetical or proposed placements. I'll see if I can find an example.... - UtherSRG (talk) 19:23, 8 November 2006 (UTC)
Enlarge

How about doing them as .png diagrams like this one (right)? A bit more robust with respect to editing (and even more, vandalism), too, as the above examples would be very difficult for a casual editor to understand on the edit page - MPF 21:01, 8 November 2006 (UTC)

Definitely looks nice. -- Donald Albury 22:29, 8 November 2006 (UTC)
I agree it looks nice, but it's not something that any user who takes the time to research the information can easily modify. That makes it somewhat anti-wiki. Images are good for something that is static to a certain degree. Phylogenetic trees are revisable on a moment's notice, and any editor who is following the research journal should be able to update the cladogram, just as they can update the taxobox. - UtherSRG (talk) 02:44, 9 November 2006 (UTC)
Actually, Wikipedia articles should not be "revisable on a moment's notice, because the information isn't supposed to come from primary, but rather secondary and tertiary resources--otherwise it's that sin-above-all-sins, Original Research. It'll only be required to update them when new textbooks are written including the latest, or enough articles, or a major review article, but never with each new hypothesis presented in a new research journal article, so that won't necessarily be the big deal it would be if this were a primary science site. They are better, imo, with the clickable links in them, rather than the static picture. KP Botany 01:56, 10 November 2006 (UTC)
Erm... most textbooks are about 10 years behind the scientific journals. We should not be relying upon 10 year old information, we should be going with what's published a bit more recently than that. Perhaps not the first publication of an idea, but certainly not waiting for it to trickle down into textbooks. - UtherSRG (talk) 03:12, 10 November 2006 (UTC)
My botany, my plant phylogentic systematics textbooks, and my phycology text, even my almost worthless 5 year old genetics texts are all more up to date than articles in their areas on Wikipedia, so whether or not Wikipedia should be relying upon the latest confirmed information (and it should), it currently isn't. None of my books are 10 years old, and none of the science texts being used at any the schools in my area (Cal, Stanford) are 10 years old. But, yes, the general point is not the first publication of an idea.
But most papers in peer-reviewed scientific papers are either original ideas or refutation of an original idea, and in certain cases, confirmation of an original idea, outside of reviews of course--this is what peer-reviewed literature is for: oritginal research! In introductions you get confirmation of other research, but it's not the primary purpose of the article, and often requires contacting the primary researcher to find out whether or not they did anything for confirmation or just went with the reputation of the researchers on the other paper(s). KP Botany 17:07, 10 November 2006 (UTC)
Avoiding primary sources is not at all what's meant by original research. Original research is downloading characters off a public database such as GenBank, making your own tree, and publishing it on wikipedia. The majority of what's in the primary literature will not be dealing with controversies, but will be providing all new information. If there's a conflict with previous results it should be presented here as such. What's the point of an internet repository of knowledge if we handicap it with the caveat that it must be a decade out of date? I agree that if there's a new earth-shattering phylogeny we are usually better off going with the last "stable version" or waiting for independent confirmation, but to wait for the textbooks to catch up is excessive. --Aranae 03:30, 10 November 2006 (UTC)
I read the lengthy discussion on what is meant by Original Research and seriously, that is what Wikipedia thinks is meant: you don't use the first publication of an original idea out of a peer-reviewed research journal for a Wikipedia idea. Maybe I read it wrong. I'll review this issue.
And, as I pointed out in my other posts, there is no handicap for it to be a decade out of date, this is simply not required on Wikipedia, as review articles are an excellent source for background for scientific information in Wikipedia, and they're more up-to-date than textbooks. They're designed for us to use as a resource, the authors have been selected as authorities in their fields and invited to write a review of the literature on an important and current topic. Also, again, introductions and conclusions to scientific literature contain a lot of addition information, compiled background on an issue that is usable. I used to compile the latest information in the field for a molecular cell biologist and for most of my work I simply read hundreds of introductions and could write a clear-cut background paper on the current state of research in the field. The scientists writing the papers had already, for the purpose of their introductions and background material and for their research, already separated the wheat from the chaff.
Also, the way knowledge is being dispersed right now is a bit in conflict with waiting for the latest "stable version" as some of this isn't being published, but rather being presented at professional organizations, before it is being used. In angiosperm phylogenies, for example, most scientists are now using an enhanced APG II, such as that presented on Dr. Stevens' Mobot APG website. KP Botany 17:07, 10 November 2006 (UTC)
Pinophyta

Pinaceae




Araucariaceae


Podocarpaceae




Sciadopityaceae



Cupressaceae



Cephalotaxaceae


Taxaceae







Ginkgophyta



Cycadophyta


[edit] Amborellaceae cladogram

I added a cladogram to the Amborellaceae article, just an image, but I will try to use this code to make it a set of clickable links. Anyone want to jump ahead and do it for me, would be fine by me. It needs a branch for angiosperms as a whole, though. KP Botany 01:21, 15 November 2006 (UTC)

Can do... but I think we need to teach me how to do a div so that the text will flow around it like the image... - UtherSRG (talk) 04:39, 15 November 2006 (UTC)
angiosperms



eudicots

rosids



Cucumis (cucumber & melons)


Medicago and Gycine (soybean)


Malus (apple)



Populus (poplar)




Gossypium (cotton)


Citrus (orange, lemon, grapefruit)


Arabidopsis




Vitis (grape)

Saxifragales

Ribes (currant, gooseberry)

asterids



Antirrhinum (snapdragon)


Solanaceae (tomato, potato, others)



Asteraceae (lettuce, sunflower)



Vaccinium (blueberry)


Caryophyllales

Mesembryanthemum (ice plant)


Beta (beet)



Ranunculales

Eschscholzia (California poppy)


magnoliids


Persea (avocado)


Liriodendron (yellow poplar)



Saruma


monocots



Poaceae (wheat, maize, rice, others)


Musa (banana)



Asparagus, Yucca, Allium (onion)



Acorus (sweet flag)




Illicium (star anise)



Nuphar (water lilly)



Amborella


gymnosperms




Cryptomeria (Japanese cedar)




Welwitschia


Gnetum



Ephedra (Mormon tea)



Pinus, Picea



Ginkgo




Cycas


Zamia






Wow that's big.... Some of hhe hugeness is because of it tries to keep boxes somewhat square, and so text wraps instead of getting pushed to the right. Even a non-breaking space is forced to break. - UtherSRG (talk) 13:06, 15 November 2006 (UTC)

But it's so much more useful in this manner than a static, unclickable, difficult to change, image. Thanks. KP Botany 23:11, 15 November 2006 (UTC)


Unfortunately this tree only looks optimal in IE; it needs some more work to make it presentable in all browsers. See below for what it looks like in Opera (left) and Firefox (right). -- Eugène van der Pijll 23:31, 15 November 2006 (UTC)
Oh crap. So I can't use it. Thanks for checking. I guess I'll just make a new and cleaner image of the one I've uploaded and use it for now. KP Botany 23:35, 15 November 2006 (UTC)

Opera 9Firefox

[edit] Geographical categories

In the light of discussion elsewhere regarding geographical categories for flora and fauna, I think that guidance along the following lines may be appropriate.[3] With consensus, this would be an addition to the Category subheading on the project page.[4]

Geographical categories help readers find species by location. Regional categories are preferred over a large numbers of smaller categories. For example, country/state/province categories are useful for narrow endemic species, but don't add a country/state/province category if the species occurs in more than 4 or 5 countries/states/provinces; in those cases use larger regional categories (so a widespread species like Red Fox would be in Category:Fauna of the United States and Category:Mammals of Europe, but not in Category:Fauna of West Virginia or Category:Fauna of Lombardy). In some cases, a ecoregion category such as Piney Woods forests may be more appropriate than a country/state/province. The presence of a regional category makes the its subcategories unnecessary. The latter should be removed to avoid page clutter.[5]

--Walter Siegmund (talk) 17:15, 29 October 2006 (UTC)

Agree fully; I'd go even further in the Red Fox example and cut it to Category:Mammals of Asia, Category:Mammals of Europe, Category:Mammals of North America, as it occurs in virtually every country of all three continents. - MPF 19:33, 29 October 2006 (UTC)
Yes. Boar is another example of the problem. -- Donald Albury 19:35, 29 October 2006 (UTC)
There is some discussion of this here Category talk:Biota by country GameKeeper 19:43, 29 October 2006 (UTC)

Sounds like a great idea, but keep specific cats for those items that are indeed extremely localized...though, in most cases, this is rare. Ecoregions for such places as the United States are generally well accepted as are those for many other larger counties. We need to be careful to not have a supercategory such as Category:Fauna of the United States become filled with ten thousand articles. I recommend we do either what Wsiegmund suggests by using ecoregions or figure out a better way to create categories so they are based on a regional structure...ie: Category:Fauna of the U.S. Pacific Northwest , etc.--MONGO 07:04, 30 October 2006 (UTC)

The more I think about this, the more I think that categories may be the wrong way to handle it. Part of what we are trying to do is indicate range. Categories by political units doesn't work well for that most of the time, and categorizing by ecoregions isn't much better. (Another element in the current system is 'biota chauvinism', look at how many species our country/state/whatever has.) I have no clear idea of how to do this, but shouldn't we be looking at the possibility of developing range maps that provide two-way access; links to political units and ecoregions that the species range extends to, and links from political units and ecoregions to species with ranges falling in those areas. And yes, I understand that the development effort may be too much, and that maintenance of such a system might be too much, but can we kick the idea around a little bit? -- Donald Albury 13:27, 30 October 2006 (UTC)

Actually, it might not be a bad idea to have a map which links to all the ecoregions of the world. I don't know if it is entirely possible, but have a map on the text/explanatory section of Category:Fauna by continent, which has overlaid links to all the continent categories. Then, when you go to Category:Wildlife of Oceania (by clicking the map or the text), there is a map of Oceania, with links to all the subcategories (New Zealand, Australia, New Guinea etc.), and it goes down the line. This way, we can get rid of the political boundary categories, which have the disadvantage of getting out of hand, and gets rid of the confusion caused by ecoregions, as well as the confusion caused by US states etc., as not many people know them.
I know this idea would take a long time, but would those against deleting the politcal categories be willing to use this alternative (which would involve eventually deleting the political categories when all maps are done)? I would be willing to put a lot of work into this, but only if it eventually results in the cleaning up of the categories. We would need to vote on deleting political categories upon the completion of this project before anyone starts though, as it could waste time otherwise. Thanks. --liquidGhoul 13:51, 30 October 2006 (UTC)
Could you please reply at: Category talk:Biota by country#Using maps, the discussion is split, and I would like to keep it at the one place. Thanks --liquidGhoul 14:07, 30 October 2006 (UTC)

I think this whole project is being approached rather idealisticly and will therefore produce very little in the way of substance. You need to be far more systematic. The problem is that many of the enthusiasts involved in this geography project have no idea of the numbers involved. We want categories to remain small, right? Well, then why do people keep adding category tags like "Reptiles of Africa" to the articles that I'm working on? These people have no clue just how big such a broad category is likely to become. In such cases, it would have been so much better to create a number of more specific subcategories first and only to have added those tags to the articles. However, that requires foresight and thus knowledge of the subject. I would therefore like to suggest that these people simply not bother unless they first do the necessary research. After all, recategorizing hundreds articles will be tough enough, but thousands? --Jwinius 15:53, 30 October 2006 (UTC)

On the contrary, it would be much easier to go through Category:Reptiles of Africa and split it into Category:Reptiles of West Africa, Category:Reptiles of East Africa, Category:Reptiles of North Africa, Category:Reptiles of the Mascarene Islands and so on than it would be to search through all of Category:Reptiles. Every bit of categorisation is useful as long as the category itself is meaningful. Not creating a category because it may become large later is a poor approach, and involves creating many underpopulated categories early on, and they're a real pain to navigate. --Stemonitis 16:00, 30 October 2006 (UTC)
In other words, creating big categories first, populating them, waiting a while, then creating subcategories and recategorizing all the existing articles, over and over again, is preferable to thinking first and acting later... despite the huge numbers of articles that this will eventually involve? How can you call that practical? Also, remember that the articles won't categorize themselves and many editors will likely be less than impressed with this unsystematic approach. As the growing number of articles will eventually prevent you from ever achieving your goal without their cooperation, the project will surely fail. --Jwinius 17:16, 30 October 2006 (UTC)
That's the way it works now. When someone decides it's time to create a new sub-cat, they do, and re-cat the affected articles. I've done it a few times myself. There's no point in creating cats before they're needed, as empty cats will be deleted. Besides, the whole category structure is a work in progress, and is constantly being reshaped. It's better to adapt the structure to WP's needs as we go along than to try to create some master plan that almost certainly won't fit later needs. -- Donald Albury 20:10, 30 October 2006 (UTC)
I don't buy this argument. I've seen people come by and add tags like "Reptiles of Africa" to the articles I've created, but they always stop before they're finished -- kind of like they expect me to finish the job for them. I suppose that would be logical, since I know those articles inside out, but that doesn't mean I'm not going to help them. Why should I, if I can expect them to show up again later on and replace a few of those tags with "Snakes of Africa", expecting me to once more follow their example and do the rest? Now, if instead they had created a subcategory strait away, such as "Vipers of Africa", then I might have felt more cooperative, since it's not as likely that this one will be subcategorized any further. You could even place this category directly under "Reptiles of Africa" for the time being, since moving it to "Snakes of Africa" later on would not require the original tags in the articles to be changed. --Jwinius 22:01, 30 October 2006 (UTC)
And I don't see how laying out a detailed plan of future cartegories will help that problem. That's the nature of Wikipedia, some people add content without worrying a lot about structure, and some people take care of the structure. Me, I try to do a little of both, but there are different ways to help Wikipedia. -- Donald Albury 23:01, 30 October 2006 (UTC)
I agree completely with Donald. If Wikipedia really did become a repository of all human knowledge then even a currently empty category like [Category:Nematodes endemic to the Comoros Islands] could turn out to be too cumbersome. We cannot know in advance what categories will be sensible, although we may be able to guess in some cases, so we just have to accept that repeated re-categorisation will be needed. It's a boring chore, but it works - it keeps the categories to reasonable sizes whilst still being navigable and meaningful. --Stemonitis 07:52, 31 October 2006 (UTC)

[edit] Mixed-breed dog

Mixed-breed dog is up for a featured article review. Detailed concerns may be found here. Please leave your comments and help us address and maintain this article's featured quality. Sandy (Talk) 23:55, 3 November 2006 (UTC)

[edit] ID help, please

I know these are pine sawflies, but I don't know whether they're the European pine sawfly or the red-headed pine sawfly. Anyone know which? --SB_Johnny|talk|books 12:46, 8 November 2006 (UTC)

Hi, this seems to match the white form of Neodiprion lecontei on this page. Hope this helps Richard Barlow 15:21, 8 November 2006 (UTC)

Yup, that looks about right, thanks!
BTW: just made a wikibooks page (A Wikimanual of Gardening/Pine Sawflies) about pine sawflies (we don't have one here)... might be worth copying for a stub article here, but it's primarily how-to. --SB_Johnny|talk|books 15:35, 8 November 2006 (UTC)
Check conifer sawfly. - UtherSRG (talk) 15:49, 8 November 2006 (UTC)
Ah, ok :). I think I'm going to copy it over anyway though, since it's more specific. --SB_Johnny|talk|books 15:51, 8 November 2006 (UTC)
Here 'tis: Pine_sawfly. --SB_Johnny|talk|books 15:58, 8 November 2006 (UTC)
I'd suggest merging the two pages (particularly given the paucity of info we have!). The family Diprionidae (the existing conifer sawfly page) contains a few genera; ones I know of include Diprion, Neodiprion, Gilpinia, all of which include pine-feeding species which would come under the header 'pine sawfly', so it isn't realistic to split out one genus for a pine sawfly page distinct from the family page. - MPF 19:28, 8 November 2006 (UTC)
Maybe... I'm going to be working on at least one more conifer sawfly pages on wikibooks (spruce sawfly). I have plenty of info on several species, but it's more oriented towards how to kill them than what they are :). --SB_Johnny|talk|books 21:54, 8 November 2006 (UTC)
Oh nevermind, I see what you're saying. I think it's ok to have a few common-named articles on the groups for now, and hopefully an entomologist who loves talking about conifer sawfly species will come along one day and split them up :). Too bad the site Richard Barlow pointed meto isn't copyleft, because then we could at least have some pretty taxoboxes on stub articles that our readers could find. --SB_Johnny|talk|books 21:58, 8 November 2006 (UTC)

[edit] Information link

Hi, I think the taxabox is great! Just one thing though. The link leading to this page is in a form of a question mark (?) after the common name. I've had a couple of instances where first time readers of a Wikipedia article has asked me if the question mark indicates if the identity of the species pictured was in question. This seems to be especially confusing where the common name of a species is long and the question mark appears to be attached to the common name, as in this example. The taxabox info link is important, but I'd like to suggest either that it be moved to a different location in the taxabox and/or change the symbol. Instead of a ?, perhaps an i in a circle? Jnpet 05:42, 12 October 2006 (UTC)

Like this oneImage:Gfi-set01-info.png

Jnpet 06:42, 12 October 2006 (UTC)

Or even about? --SB_Johnny|talk|books 10:47, 11 November 2006 (UTC)





ⓘExample
Just a random image
Just a random image
Scientific classification
Species: Exampli gratia
ⓘ seems like a good idea, if "?" can cause confusion. It does not cause any for me, but there are now two separate reports that it does for some (see Template talk:Taxobox). See right what it would look like, approximately. Eugène van der Pijll 00:13, 16 November 2006 (UTC)





Yeah, i, or 'about' is good, too. I posted this comment on the Taxobox page:
"I don't understand why this hasn't been changed. A "?" in taxonomy means something, it means there is uncertainty about the taxonomic placement. Wikipedia cannot have every taxonomic box on article pages showing that the taxon's identity is in question.
I just got a newsletter blurb from one of my writers advising readers not to use Wikipedia as a resource because it indicates that Umbellularia californica is in dispute as a name, when in fact it is not!
I thought she was talking about the common name discussion, but, no she pointed out that the species name is in dispute, "See the question mark after the species name in the classification box on the right?"
KP Botany 23:51, 15 November 2006 (UTC) "
I don't like "about"; it's too long, and likely to run into the taxon name, if that is also long. The image of the circled "i" has the problem that it will link to the image description page. However, I've just found the unicode codepoint for "circled i". I don't know if this char is available on all computers, but if it is, it could be a winner. Except that it could perhaps be a bit larger. Eugène van der Pijll 00:16, 16 November 2006 (UTC)
Yes, I see the 'about' can be too long, although it is certainly the clearest, however an 'i' as suggested by the original anonymous poster should be fine, just as long as it isn't a question mark~ KP Botany 00:39, 16 November 2006 (UTC)
I'll check this on IE tomorrow; if it works, I'll change the taxobox template. Unless there are objections, so if anyone can't see the circled i in the taxobox to the right, please shout. Eugène van der Pijll 00:51, 16 November 2006 (UTC)
Looks good. Other comments welcome, of course. Eugène van der Pijll 08:51, 16 November 2006 (UTC)
Sounds like a good idea to me too —Pengo talk · contribs 10:00, 16 November 2006 (UTC)
Though I'm no too keen on using a unicode symbol. It seems unlikely to work on a large range of computers (especially older ones). Unknown unicode characters tend to turn into a question mark (back to square one) or an ugly rectangular block. Instead, how about using one of the graphics from commons:Info. e.g: although the anti-aliasing makes it a bit too blurry. A simple 'i' could work too (as suggested above). (and the unicode symbol suggested is not even a proper "info" sign, it's just a circled 'i'.) —Pengo talk · contribs 10:26, 16 November 2006 (UTC)
I'd rather use the image than Jnpet mentioned, above. But you cannot link that to an article; it will automatically link to the image description page. I don't like a plain "i"; that doesn't really suggest "explanation here" to me. Other articles depend on Unicode too, so unless there are many problematical browsers, I still prefer the circled i. Eugène van der Pijll 17:32, 16 November 2006 (UTC)
Surely there's a place on Wikipedia to check in multiple browsers? I know for some websites I did years ago the company had a means of "browser checking," that did that, just posted the websites and viewed them in various browsers. I'm fine with your arguments for the circled 'i', it seems you've thought it out beyond the scope of your posts. KP Botany 17:42, 16 November 2006 (UTC)
I have some other proposals, but I'm going to change it to a simple 'i' until a better solution is agreed upon. —Pengo talk · contribs 03:37, 18 November 2006 (UTC)
How about we just get rid of the link all together? There is ample information available through the headings links. Yes, the 'i' is terrible, and ⓘ is probably better, but is the help page needed at all when all the heading links already go to more information? —Pengo talk · contribs 15:42, 18 November 2006 (UTC)
I agree. The taxobox is created in a way which is very user friendly. I don't see why anyone would require extra information as to what info the taxobox presents. --liquidGhoul 15:46, 18 November 2006 (UTC)

Problem with plain 'i' It disappears on my new browser, I think it needs to be the circled one, maybe an asterisk? The original user friendly goals of the taxobox are met, imo, but some folks probably want more details. I didn't really think of that, that's it is fairly self-explanatory. KP Botany 23:08, 26 November 2006 (UTC)

[edit] Finding some copyvios, what to do?

I've been finding a few minor copyvios in plant pathology articles (like Phytoplasma), involving word-for-word inclusion of materials from the Encyclopedia of Plant Pathology. It's usually just a sentence or two... should I just add the book as a source? I just don't see why someone would bother typing something in without adding the citation (citations only improve the articles, right?). Should I bother with using <ref> tage, or just add it to the bottom? --SB_Johnny|talk|books 10:51, 11 November 2006 (UTC)

I would say that wherever possible, we should be using the <ref> tags. That way, it's clearer which individual statements are sourced and which are not. --Stemonitis 10:55, 11 November 2006 (UTC)

[edit] Can we come up with a common name policy?

I keep running across articles on plants and fungi that either use "corrective" common names for organisms, or couch regional common names in phrases such as "mistakenly called", "misleadingly called", etc.

The most recent example I've come across was in the Gymnosporangium article, where the common name "Cedar-apple rust" (and several other cedar-other rusts) were changed to "Juniper-apple rust". This was presumably done because the telial host of the fungus is in fact a species of Juniper, (as opposed to Cedrus), but the name of the rust is "Cedar-apple rust", and the common name of the most commonly implicated "cedar" (Juniperus virginiana) is "Eastern Red Cedar" (only a botanist or horticulturist would understand what you mean by "Eastern Juniper"... the term is not used).

It's really frustrating to go in to work on an article, only to have to waste time undoing this sort of thing.

I have discussed this a few times with the user who routinely makes these changes, and he feels strongly that there are "proper" and "improper" common names for plants. I, on the other hand, feel strongly that common names are part of the English language, and can't be "proper" or "improper", but rather are just words used to describe things that are found in the environment. Just as "Lorry", "Truck", and "Semi" are all names for the same thing, each just as proper as the other when used in one region or another, so are the various names for plants, animals, fungi, etc. The English language is wonderfully diverse, and an english encyclopedia should describe (from a neutral point of view) how the language is used, and discuss the things that English words are used for. It's not meant to be used as a tool for codifying the language, but rather a description of what the language is, how it describes the world, and above all what the things in the world are, whatever they're called.--SB_Johnny|talk|books 11:08, 11 November 2006 (UTC)

I absolutely agree. It is not Wikipedia's place to prescribe common names, merely to report which are used. If it might be confusing that "Eastern Red Cedar" is actually a juniper, then we should explain that calmly and encyclopaedically. Even where "official" lists of common names are produced, I deny that they are any more correct than other commonly-used names, and for organisms where such lists don't exist (viz., most), the concept of "correctness" doesn't even begin to apply. I would recommend that any such usage of "mistakenly" be replaced with "also". "Misleadingly" could actually be true, but it needs to be qualified with an explanation. If there were "proper" common names, we wouldn't need scientific names, whereas centuries of experience tells us that we do. --Stemonitis 11:18, 11 November 2006 (UTC)
I don't think "misleadingly" is appropriate either... in the Juniper/Cedar example, the only thing "misleading" about it would be that the common name doesn't match up with the binomial, but the binomials are a metalanguage all their own (I suspect the reason this particular plant is named "cedar" is because of the scented, rot-resistant wood, as most if not all plants called "cedar" have). "Eastern Juniper" isn't a name at all (at least I've never heard it used in the regions where it grows... it's a valuable timber crop here, or a nuisance tree in apple-growing regions), just something made up for the purpose of clarifying that the species is not a species of Cedrus.
The problem with a lot of these articles is that one or more common names are followed by parentheticals "(which is misleading, because...)", "(note that this is not actually..."), etc. It's not only POV, but frankly it's just bad prose. Maybe better to just keep this sort of thing out of the individual articles, and just wikilink "common name" where appropriate (and add more discussion about the problems with common names on that article. --SB_Johnny|talk|books 12:00, 11 November 2006 (UTC)
Common names have problems and, imo, should not be used at all as article titles. However, as to all these articles with POV comments about "misleading" usage of common names in the articles, they simply should be changed. But as long as common names are used as article titles, instead of as redirects to the scientific name, this issue will continue to arise.
Sometimes the point to show what is misleading in the name overwhelm all else. Turns out that most people I know (I live in the midst of a thousand or so acres of walnut groves) thought the English walnut was called that because it was traded all over the world by English merchant ships, not that anyone thought it was native to England. So an article saying the common name was "confusing" because the species was not native to England introduced an artifact of modern usage, limited knowledge of historic trade, and failed to add the possibly correct source of the common name.
Just change the articles, please, that don't contain neutral point of view, or that add nonsense, such as non-existant common names. Try to search for the actual etymology of the common names, also. They are culturally important. All of this is, of course, simply my opinion about the names, however here is an example of how I changed the Acer negundo article to reflect more neutral POV on common names while adding important, because they show the variety of ethnobotanical knowledge of the various cultures where the trees grow, cultural information about the names to the article that enriches the overall knowledge the article imparts to the reader.
It is called Manitoba Maple in Canada, and Ash-leaved Maple (also Ashleaf Maple, Ash Maple) or Box Elder (also Boxelder, California Boxelder, Western Boxelder, Inland Boxelder, Boxelder Maple) in the United States. The American common names come from the pinnately compound leaves of Acer negundo that are similar to those on the elder (Sambucus) and some species of ash (Fraxinus). The "box" in the name is thought to be because this maple's wood superficially resembles that of the box hedge (Buxus sempervirens). Additional common names include Cut-leaved Maple (because of the compound, or fully dissected, leaves), or Three-leaved Maple (because all new leaves from overwintering buds have 3 leaflets), or Sugar Ash (because the leaves resemble the ash, but it is a source of maple syrup). Its numerous and diverse common names attest to its familiarity to many peoples over a great geographic range.
This tree is familiar to many people. They knew it was a maple because of its syrup, in spite of its resemblence to the ash, they recognized the similarities between its wood and that of an important wood from elsewhere, the notice whether plants have compound leaves or entire leaves--all of this shows information about the culture of the people where the plant grows. This imparts actual verifiable and useful knowledge, whereas showing the impropriety of a name and stating its impropriety simply adds POV, so try to show the user who adds these non-neutral comments the difference between what is valuable, the explanations, and what is POV, the adjectives about propriety.
KP Botany 19:19, 11 November 2006 (UTC)
This has all been discussed at length in WikiProject Plants: [6][7][8][9]The consensus was in favor of scientific names for most plant articles, with common names used only in specific cases.--Curtis Clark 04:21, 12 November 2006 (UTC)
Yes, it has been, however there will continue to be problems with what common name to use (see the current fracas in Maize for example), as long as they are used anywhere, so I don't want to ignore that point. SB Johnny is, however, talking about the names in the articles. KP Botany 18:24, 12 November 2006 (UTC)
I wasn't really referring to article titles, I agree those should all just use the binomials except in the rare cases where there's no regionalism of the names (like oak, tomato, etc.).
The user involved has been asked repeatedly to stop doing this, but refuses to do so, because he really does feel that there are or should be "proper" common names, and that wikipedia should reflect this because the alternatives are deceptive. While I'm generally against having a policy for everything, it seems in this case that we need one in this case to bring an end to this once and for all. --SB_Johnny|talk|books 14:18, 12 November 2006 (UTC)
I suggest that you politely change the articles to a neutral POV in the way I did with the Acer negundo article or the Persian/English walnut article. It explains the roots of the common names, indicates the breadth of usage (although there should also be a comment about Manitoba Maple, its commonality in the Manitoba area or whatever), and provides useful cultural information.
If you do this, rather than continuing to discuss a point with someone who won't yield, you will show other Wikipedia editors the utility of using neutral POV discussions of common names within the articles and it will become a de facto policy. KP Botany 18:24, 12 November 2006 (UTC)

[edit] Generating large number of species articles w/ taxobox

Would there be much interest in seeing a large number of species articles being generated from the information on the IUCN red list. The generated articles would contain a taxobox with conservation status, a reference (to the red list), a stub notice, a category, and very little actual text. Example: Apron Ray.

I think populating the encyclopedia this way would give a good starting point for a great many entries, and make it easier for people looking to start articles on a species.

I'm quite time poor at the moment but am interested in doing this. The above example was hand made and not generated, but it would not be very difficult to generate such articles.

Thoughts? —Pengo talk · contribs 04:39, 12 November 2006 (UTC)

Stubs are better than redlinks, so I'm good with it. - UtherSRG (talk) 04:46, 12 November 2006 (UTC)
But stubs without useful informations are less useful than redlinks. Circeus 18:00, 13 November 2006 (UTC)
But they wouldn't be "without useful information" as they would have the Latin name, some common names, the family, and the geography. The point is to generate the pages with some useful information, the taxobox, common names, and the geography, from an existing database. At least with this, people could find out more information about the family, or learn the least bit of information on the plant. KP Botany 18:04, 13 November 2006 (UTC)
The IUCN entry also lists the countries where a species occur, doesn't it? When you could add that, the article would at least have some content. Ucucha 07:08, 12 November 2006 (UTC)
Yes. I'd like to do that too. —Pengo talk · contribs 08:49, 12 November 2006 (UTC)
What would be done about categorisation? How would you choose the name of the article? Also would you be able to create a list of the articles created, and add a link to the list of the talk page so that people could cross them off when they decide to add content to the articles. Thanks. --liquidGhoul 13:04, 12 November 2006 (UTC)
I'm all for it, especially in cases where we have photos. Use binomials for the common names, and use the first most-specific category that's under 200, as we've been doing for at least the past year or so (order when there's only a few articles of the order, family when the order gets too big, species if the family category gets overpopulated, etc.).
What's the "red list"? --SB_Johnny|talk|books 14:22, 12 November 2006 (UTC)
See red list. --Stemonitis 16:04, 12 November 2006 (UTC)
It looks rather useful. KP Botany 18:36, 12 November 2006 (UTC)

Categories could be chosen by finding the next higher taxon that already has a category.. I guess a new category could be created if there's a bunch of species (4 or more?) with the same genus or family. Common names are listed in the database, so for animals the first one listed would be put into Title Case and used (admitadly they're not all unique names. I guess I'd have to check for that). Alternatively we could stick to generating articles with binomial names and let someone choosing a name simply move the article? I wouldn't create an article if the any of the common names or binomial synonyms already exist.

By the way, when I ran Beastie Bot in June there were 33827 binomial names found in the red list (including least concern) that weren't found as wikipedia articles. So a bit less than that number would be a ballpark figure for how many articles might get created. —Pengo talk · contribs 15:20, 13 November 2006 (UTC)

Recently I used the IUCN database for the articles in Category:True vipers. One thing that I found rather unsurprising is that the entries in the IUCN database don't follow the ITIS taxonomy that I use for the viper articles. I'm not certain, but it may be that, because of the way they work, they don't keep to any specific taxonomies for the various groups of plants and animals. For snakes, I'd rather see new articles generated from ITIS information -- not the IUCN. Likewise, the amphibian folks may like to see some new articles generated as well, but then using taxonomic information from the AMNH. --Jwinius 21:55, 13 November 2006 (UTC)
Will this work, though? One underlying assumption about the IUCN data is that the taxa are important because they are listed, making it likely that an article about a particular taxon will be needed on Wikipedia. Is the underlying assumption true for AMNH data? (I don't know.) However, with plants there are just too many plants largely unknown to the English-speaking world. I can't see that Wikipedia will, at least in the near future, be a repository for articles about a couple hundred thousand species of angiosperms. Plant taxonomy is such a bit of a systematic nightmare these days, so the wrong taxonomy won't matter. However, particularly if the bot also generates a list of the articles it created it might be a great source of stubs for interested botanists to work on when they have time. KP Botany 22:01, 13 November 2006 (UTC)
Perhaps we should run several samples with a representative from a host of orders, have editors on that wikiproject evaulate whether the information is accurate and the bot won't be making more trouble than it's worth. With a thumbs up, the bot could run the whole database for that particular order (I'm assuming the bot can manage things on an order by order basis?). --Aranae 22:33, 13 November 2006 (UTC)
Jwinius is probably right, and I should look at using other systems for taxonomic info. As for whether the species is important: I've never seen a species (or taxon) article be deleted or being put under trial with AfD. I personally believe every species is important. Whether any particular article will be needed, referenced, or improved is another question, but an impossible one to answer until after the fact. And yes, Aranae is right in that I'd have to run it in order of .. er.. order.. or at least class. —Pengo talk · contribs 23:23, 13 November 2006 (UTC)

[edit] Wikipedia:Speedy deletion criterion for unsourced articles

This is a new proposed deletion policy that should interest ToL contributors. Many articles, especially about species as diverse as Moray eel or Tongue Orchid, lack references or sources and will fall under this speedy deletion policy if it gets adopted. Consequences could be enormous. We should follow this discussion closely and participate in it to discuss the consequences. JoJan 13:19, 14 November 2006 (UTC)

Yes. However, those articles still need sources. I think the proposed policy is reasonable. Perhaps a variant template for ToL articles so that they get added to a ToL Category, so that we can speedily source them, albeit at a rudimentary level? - UtherSRG (talk) 13:26, 14 November 2006 (UTC)
Existing articles are exempt (sp?) from the proposed speedy deletion rule. Eugène van der Pijll 14:30, 14 November 2006 (UTC)
There is serious discussion on the talk page about the grandfather clause. It looks like this proposed policy will include ALL non-referenced articles. I have no idea how many articles in ToL-range we're talking about, but I suspect there could be many. Only the original contributors know what sources have been used. If we want to source them, we would have to use references to sources we would have used. Besides we would have to check every fact first. That can be very difficult if one has no access to scientific journals, asking payment per view. There could be a tremendous task ahead. JoJan 15:26, 14 November 2006 (UTC)
It's not necessary to check every fact, a basic ref will do, and for many vertebrate groups at least it should be feasible to give suitable text. jimfbleak 15:41, 14 November 2006 (UTC)
In the worst case scenario, if this rule will be applied to existing articles, it would be trivial for a bot to add an external link to, say, ITIS or one of the other taxonomic databases automatically. This would be enough to save the article from speedy deletion. -- Eugène van der Pijll 17:26, 14 November 2006 (UTC)
Please, the proposal is deliberately restricted to apply only to articles created after it becomes part of the speedy deletion criteria. There has been discussion about the possibility that it may eventually be extended to articles that existed before the criteria is accepted, but it is also recognized in the discussion that it will be a while before the community of editors will reach consensus to do that, so it won't be coming soon. -- Donald Albury 01:02, 15 November 2006 (UTC)
It's a good idea, though, users should be able to immediately tie everything in the article to a source that they can verify for themselves. This is one area where I feel that Wikipedia falls down: a lot of editors don't use reliable sources. Part of this is simply because articles are being created by editors in subject areas where the editor's knowledge is not up to discerning the various sources. But dang, it's a lot more work for an editor. KP Botany 01:19, 15 November 2006 (UTC)

[edit] Breed disambiguation

Is there any naming standard for breeds/varieties? I see that list of breeds of cattle has X (cattle), X cattle, and X Cattle. List of breeds of horses also has all three. List of breeds of dogs is mainly X Dog with a few X (dog). Is there any standard? Rmhermen 14:57, 14 November 2006 (UTC)

[edit] Deletion

Folk, the list of placental mammals is up for deletion. - UtherSRG (talk) 10:54, 15 November 2006 (UTC)

Whatever would anyone consider deleting such a useful list for? Thanks for the alert. KP Botany 23:09, 15 November 2006 (UTC)

[edit] Wildlife Barnstar

There is currently a barnstar proposal at Wikipedia:Barnstar and award proposals/New Proposals#Wildlife Barnstar for a barnstar which would be available for use for this project. Please feel free to visit the page and make any comments you see fit. Badbilltucker 15:23, 15 November 2006 (UTC)

[edit] Transwikied ToL pages

Over the past few weeks I've transwikied some ToL pages that had contained how to sections, all are now on wikibooks and will be incorporated into other books (mostly b:Animal Care). The howto sections should probably be removed now, if anyone's interested in helping with the cleanup:

I'll mostly be doing the cleanup on the wikibooks side, if anyone wants to help dewikify the wikibooks versions, that would be great! --SB_Johnny|talk|books 11:55, 17 November 2006 (UTC)

[edit] wikifying describer year

Stemonitis and I had the idea of linking the year of description inside a taxobox like this: [[Species described in <year>|<year>]]. This would be a nice feature if one wanted for example to check out what other species were described in the same year. right now, when the year is just linked like this: [[<year>]], this is not really useful, because it will link to a very long list of events that are normally not interesting to the user following the link. Alternatively, this could be implemented as categories, analogous to Category:People born in <year>. If this feature would be deemed useful, it would probably be best to let a bot do the work of changing the existing taxoboxes. Alternatively, or additionally, there could be an extra optional field like binomial_authority_year, but that would lead to problems when first describers stand in parentheses. --Sarefo 01:25, 18 November 2006 (UTC)

Sounds good, especially if the bot could create the categories or lists. I can't say that I would find it particularly useful, but if it is useful to someone else, I am all for it. --liquidGhoul 01:54, 18 November 2006 (UTC)
I agree that the current format is rather useless, but I don't think [[Species described in <year>|<year>]] would be that much of an improvement. I imagine that eventually there would be many entries for each year: long lists of totally unrelated species all mixed up with each other. Ho-hum. On the other hand, if this were to be more specific, i.e. [[Bird species described in <year>|<year>]] or whatever, now that would be interesting! --Jwinius 02:15, 18 November 2006 (UTC)
Another suggestion in the same discussion, incidentally, was to link the date, where possible, to an article about the work in which the name was published. It seems to me perfectly reasonable to link a taxon to its original description; as an example, Carcinus maenas already does this (I hope that's not a violation of WP:POINT), linking the date 1758 to Systema Naturae. And while, yes, a category or list of names published by Linnaeus (even in individual works by Linnaeus) will probably be too big to be useful, for other authors it may be more reasonable. Wouldn't a list/category of species described by Darwin be interesting? Dana? Asa Gray? Lamarck? --Stemonitis 13:19, 18 November 2006 (UTC)

Just to see what this would look like, I've created two lists from the latest database dump, for two years chosen completely at random. See User:Eugene van der Pijll/Animal species described in 1758 and User:Eugene van der Pijll/Animal species described in 2006 for the results. (Note, these are just the raw output of a simple script; the format of the output can still be improved.) Eugène van der Pijll 14:05, 18 November 2006 (UTC)

I do actually find it very interesting, but there is a big problem of incompleteness for the more recent years. --liquidGhoul 15:47, 18 November 2006 (UTC)
True, these are only lists of species that currently have articles in Wikipedia. (Articles with information on the authority, I should say.) Data from other sources could be added, but it is hard to guarantee consistency in that case. Eugène van der Pijll 16:10, 18 November 2006 (UTC)
I don't see incompleteness as a problem. I'm pretty sure that outside a few exceptional groups (furry things and feathery things, usually) Wikipedia will never be comprehensive. The categories, should we make them, will inevitably contain only species/taxa about which we've already got articles, but that's OK, because they'll tend to be the most notable taxa (or so we hope). --Stemonitis 16:48, 18 November 2006 (UTC)

It's a simple concept with no simple solution. Do you want only to link for species themselves, or for higher taxa as well? Both get a year in the descriptor, and if you only wnat one and not the other, that will confuse editors. Other the other hand, if you utilize a category ([[:Category:Taxa erected in <year>|<year>]]) you can get a nice complete picture, but the listing won't be in any particular order. *shrugs* I'd like to see something done with the year, but I'm torn between the pros and cons of all the options. - UtherSRG 16:40, 18 November 2006 (UTC)

[edit] New guideline for fauna/flora of categories

I know this has been brought up a lot, but it has gotten nowhere, and I think I have come up with a solution which should work. I would like to create a guideline, which would be kept under the TOL project. If we create a guideline, it would make it muich easier to move, merge and delete articles in quicker time, and clean up this whole mess much quicker. It would go along the lines of:

"Categories related to the flora and fauna of a region should should be based on the common grouping of that region used by zoological/botanical publications. For example, if it is common to seperate a region based on political boundries (as in parts of Europe), categories should be seperated by countries. If it is common to seperate regions based on geographic features (such as New Guinea), categories should be seperated by geographic region."

I wouldn't like to apply this guideline to articles, as it would be too restrctive, and I don't particularly agree with it. I think the main arguments that occured with this discussion occured because people of different countries were relating it to their country/region. As an Australian, it could go either way, but Americans seem to prefer the use of political boundaries. The reason to have this, is that there are many regions which are represented by more than one category, and it creates over-categorisation, and under-population of some articles/categories. Thanks. --liquidGhoul 13:34, 18 November 2006 (UTC)

I would like to add on to the above. If it is passed, I would like to clean up the navigation to the fauna/flora by region categories. I suggest the following.
Category:Biology --> Category:Natural history --> Category:Natural history by continent --> Category:Fauna by continent
Category:Biology --> Category:Natural history --> Category:Natural history by continent --> Category:Flora by continent
Currently, the categories lead everywhere, and it is very complicated, and can lead people astray. If we keep the navigation of our categories simple, it will make Wikipedia more user friendly. I intend to create maps for all the categories we have, as I have done with Category:Fauna by continent. If we simplify the system, I can do this much quicker.
Oh, and if anyone disagrees with what I say, please speak up. If I get no objections, I will add the guideline myself in a week. Thanks. --liquidGhoul 14:23, 18 November 2006 (UTC)
I guess the experiment begins. :) --liquidGhoul 07:25, 26 November 2006 (UTC)
LiquidGhoul and I have today had an extensive discussion on this subject, and I think we largely agree on the following:
Categorisation of regions is complex and subjective. For example: should New Guinea be considered part of Asia or Australia? Should Australia and New Zealand be bundled with the Pacific Islands and called "Oceania", or kept separate? Should Hawaii be considered part of the United States for floristic purposes? And if so, does that make it part of the North American continent for floristic purposes?
Rather than make our own decisions on this highly complex and subjective topic, it would be much better, if possible, to let the scientists nut this out, and adopt whatever system that come up with. In the case of botany, a standard already exists: the World Geographical Scheme for Recording Plant Distributions effectively categorises the entire world into named geographical areas, intended for use in recording plant distribution. A brief look at the standard document will make it clear just how complex the topic is, and what a great amount of debate and compromise has gone into the standard. I think it would be best to adopt this, rather than try to come up with a categorisation convention of our own.
Hesperian 04:36, 27 November 2006 (UTC)
If people didn't pick it up, I support this. Is anyone aware of an equivalent for fauna? Thanks --liquidGhoul 04:46, 27 November 2006 (UTC)

[edit] Promeropidae

There is an inconsistency over Sugarbird (Promeropidae) that needs resolving. The family is categorized as Passerida, but listed under the Corvida page. One of these is clearly wrong, but I don't know which. Apologies if this is the wrong place to ask the question. JohnCastle 21:48, 21 November 2006 (UTC)

[edit] Stablepedia

Beginning cross-post.

See Wikipedia talk:Version 1.0 Editorial Team#Stablepedia. If you wish to comment, please comment there. ★MESSEDROCKER★ 03:35, 26 November 2006 (UTC)

End cross-post. Please do not comment more in this section.

[edit] Catgories for threatened taxa

Currently there are three automatically added categories for conservation statuses:

These are automatically added, e.g. when status = EN. They can currently be turned off on an article-by-article basis with "|category=off" or something like that.

I'd like to stop all of these categories from being automatically added, so they can be controlled more easily on an article-by-article basis. There are two or three problems:

  • "Species" is often incorrect. Some are subspecies. Occasionally they are genre (e.g. rhea (bird))
  • "Species" is too broad, and could be put into useful subcategories, like "Endangered plants" or "Critically endangered mammals".
  • Endangered ain't Endangered. Categories should perhaps be qualified with whose criteria they match. like Category:Endangered reptiles, IUCN Red list or Category:Endangered reptiles, ESA.

The main questions, if people are happy with the overall change, are:

  1. What should the categories be? I'm thinking (Critically Endangered|Endangered|Vulnerable) (plants|mammals|reptiles|birds|fishes|invertebrates|fungi)
  2. Should the categories be qualified with the organisation or act that categorizes it? (I'm not sure either way, suggestions welcome)

—Pengo talk · contribs 11:01, 27 November 2006 (UTC)

Folks should not be listing conservation status for non-species articles. This is wrong. If you see articles like this, simply remove the conservation status from the taxobox. Perhaps the existing categories should be renamed as "... species and subspecies...", but I agree that the categories are indeed too broad, but I disagree that we should distinguish between IUCN and ESA, etc, any more than we already do - we talk about the differences in the article, but side with the IUCN in the taxobox. We should do the same for categories - talk about it in the article, but categorize according to the IUCN status. - UtherSRG (talk) 12:27, 27 November 2006 (UTC)
Strongly disagree on two points:
  1. Banksia brownii is listed as "Endangered" under Australia's Environment Protection and Biodiversity Conservation Act 1999 (EPBC 1999) but, like most endangered Australian species, it does not appear on the IUCN Red List. It is not acceptable to remove the conservation status from the taxobox, as though IUCN is the only status that counts. It is also not acceptable to impose an IUCN semantics on terms such as "endangered", which may be defined in subtly different ways in different systems.
  2. EPBC 1999 is quite happy to gazette subspecies and varieties as threatened, endangered, critically endangered, etc. In such cases it is perfectly appropriate to list them as such in the taxobox. I can see no reason at all why "this is wrong".
Hesperian 13:07, 27 November 2006 (UTC)
It's not just EPBC — The IUCN also lists subspecies and varieties (and even regional populations) with the red list categories. Often the taxonomy is debated as to whether something is a subspecies or a species anyway, such as with the Chinese White Dolphin (Sousa chinensis or S. c. chinensis); or Wikipedia's recent 1,500,000th article Kanab Ambersnail (Oxyloma haydeni kanabensis or O. kanabense). So "... species and subspecies" seems like a reasonable label, which also excludes higher taxa. (Yes, I agree we should not have a conservation status on higher taxa than species, but rhea (bird) is tricky, as both species are listed as NT and neither have their own articles. A simple solution would be to break it into two articles, but simply removing the status from the taxobox works too.) (Correct me if i'm wrong, but) I think UtherSRG's point was that we should favour IUCN when both IUCN and other threatened-listings exist, not that we should remove other listings? ... and so far it's 2-nil against differentiating between IUCN and EPBC etc in categories names (I have no preference). —Pengo talk · contribs 14:18, 27 November 2006 (UTC)

[edit] Synonymy and the taxobox

Can somebody either merger synonym (botany) and synonym (zoology) or work a way to switch between them in the taxobox? Because it is now a disambiguation page (as it should have been, might I add), and the previous state was not much better anyway. Circeus 18:29, 28 November 2006 (UTC)

Now how did I know that I would find Brya's fingerprints all over this??? I agree that the two articles should be merged, maybe under the title "Synonym (taxonomy)" but I'm taking a break from Wikipedia so I'm not going to touch it. MrDarwin 18:50, 28 November 2006 (UTC)
Wow, go for it Circeus, but please use the language from the zoology text, as the botany one is almost incomprehensible. KP Botany 19:16, 28 November 2006 (UTC)
Te merger is complete now, and the taxobox link is fixed. I felt a need tokeep the two meanings clearly separate, further cleanup for jargonmight be needed (although I did some myself). Do you think other similar pairs (e.g. Valid name (botany) and Valid name (zoology), or are those terms too different in uses?) should suffer the same fate? Circeus 19:31, 28 November 2006 (UTC)
This one is not as straight forward, see Correct name (botany), which would also need to be added to the mix. --Peta 04:02, 6 December 2006 (UTC)
In fact the notable thing is that "Valid name" means something totally different in ICBN and ICZN.--Curtis Clark 04:35, 6 December 2006 (UTC)

[edit] Listing synonyms in the taxobox

I was excited to see the topic, but now I'm wondering if I misunderstood. I'm wondering if maybe we could also list binomial synonyms in the taxobox as well? I think it comes up in botany more than in zoology, but in florae like An Illustrated Flora of the Northern United States and Canada, there are often numerous sysnonymous binomials listed, and I think it would be a good addition to our taxoboxes. This would be particularly valuable for the plants that have different binomials in "horticultural" vs. "plant taxonomical" parlances, as well as giving the search engine something to grab at if someone were reading an old book that uses deprecated names.

I guess the problem with this is that it would require a lot of new fields if there were a lot of synonyms, though it could be kept to a minumum if we used piped links to authorities rather than separate fields for them. --SB_Johnny|talk|books 14:29, 14 December 2006 (UTC)

You mean like this? --liquidGhoul 14:35, 14 December 2006 (UTC)
Yup, just like that :). --SB_Johnny|talk|books 12:39, 15 December 2006 (UTC)

[edit] Protista

I was wondering what people here think about dropping the kingdom Protista, and treating them directly as basal eukaryotes. When we started not enough was known about their relationships to make that really practical, but now they most of them could be arranged in terms of a few unranked supergroups, following current systems like Adl et al. I know we normally prefer ranked taxa, but recently enough editors have been trying to move towards a clade-based system that it has made the current organization hard to maintain.

We wouldn't have to change other kingdoms, and could keep using lower ranks from phyla on down. The new organization would then look something like this:

  • Domain Eukaryota
    • Supergroup "Opisthokonts"
      • Kingdom Animalia
      • Kingdom Fungi
      • Several classes
    • Supergroup Archaeplastida
      • Kingdom Plantae
      • Phyla Rhodophyta, Glaucophyta
    • Supergroup Chromista
      • Phyla Heterokontophyta, Haptophyta, Cryptophyta
    • Supergroup Alveolata
      • Phyla Dinoflagellata, Apicomplexa, Ciliophora
    • Supergroup Excavata
      • Phyla Euglenozoa, Percolozoa, Metamonada
    • Supergroup Amoebozoa
      • Phylum Amoebozoa
    • A few unplaced orders

If people support this, I'd be happy to adjust all protist articles, taxoboxes, and categories as necessary. Josh 03:49, 4 December 2006 (UTC)

I'm not sentimental about taxa, so if it's supported by evidence and better reflects real clades, then I'm all for it. Can you point the uninitiated towards some literature on the changes/research/new understanding of these groups? How new is this taxonomy? —Pengo talk · contribs 22:24, 4 December 2006 (UTC)

The newer ones come from Cavalier-Smith (2002), who treats most of them as infrakingdoms of his paraphyletic kingdom Protozoa. This is fairly recent, but papers written since generally seem to accept them, including ones like Baldauf (2003) and Adl et al. (2005) which have done a lot to promote their use. The main variation is whether the Chromista form a separate group, but that's appeared in more-than-five-kingdom systems since the '80s and has never been solidly rejected, so I think it's safe to use. Josh

Ok, it doesn't seem likely anyone is going to object to using unranked supergroups. Since users like Kupirijo and WeroTheGreat had already started adding them, and others like KP Botany have expressed concerns about using the paraphyletic kingdom, I'll start switching the protist articles to that system. Josh 07:09, 8 December 2006 (UTC)

I think I'd like to think about this some more. My only concern is that users be able to find them by searching for them in the Protist Kingdom, as much as I abhor that. I want to restart WikiProject Protists. In general, if you can make it so people can still find them, I'm fine. But I don't want to use all Cavalier-Smith, as he's considered a bit of a, well forward-thinker. I suspect his work will prove the hardiest in the long run, but he's not in total accord with his peers on everything. I'm okay with it, but to repeat: users have to be able to find things the old way, if C-S is the only authority, other classifications must be explained, and overall you need to justify this change extensively from the literature. KP Botany 18:43, 8 December 2006 (UTC)
PS I'm still reading!! Everyone reads scientific literature a lot faster than I do, or has more time to. KP Botany 18:47, 8 December 2006 (UTC)

Cavalier-Smith treats these as ranked taxa, which is definitely a bit forward, but by now I think the supergroups themselves are mostly solid. A few editors have a lot of enthusiasm for them, which is why I wanted to switch to them, instead of letting a mix of phylogenetic-placed and kingdom-placed pages develop. But I guess I did sort of jump the gun here. Explaining alternative systems has often proven to be tricky, because it's not easy to find out what everyone uses, but I promise I'm not going to remove mention of the other systems. From the start, it's been very important to me that everything can be found in several ways, including old categories like algae, flagellates, etc. It's just our "primary" organization system I wanted to change. Josh 23:23, 8 December 2006 (UTC)

As several people have probably noticed, I have been changing the color of some of the taxoboxes. This was not to wreak vandalistic havoc on Wikipedia, but because I thought that having all non-animal-plant-fungi eukaryotes have khaki taxoboxes would be rather silly. If the majority feels all the "protists" should have khaki taxoboxes, then so be it, I will switch them back. However, I feel that since the three still accepted kindgoms have their own taxobox colors, then why not have the other supergroups, chromista, alveolata, rhizaria, etc. have their own taxobox colors, rather than be all lumped together just because they used to all be in kingdom protista. Werothegreat 21:24, 9 December 2006 (UTC)

It's a style change throughout Wikipedia. Don't you think that it should be discussed first? That's what this page is for. Also I want to get the Wikipedia:WikiProject Prokaryotes and protists up and running again, a proposal on that page would be useful. This has been discussed before, with no conclusion drawn, feel free, also, to find past discussions and throw your 2 cents worth in to try to bring participants to a conclusion. There are multiple issues here, and it is a matter in great contention in the scientific community, to assume that the Wikipedia community could easily meet a consensus when none exists in the scientific community, is probably unrealistic. Also, I think Josh's point that everything should be found in serveral ways should be considered with taxoboxes, rather than making them something different, show that protists can be defined in two ways, morphologically as protists, and phylogenetically with their nearest close relations in some cases, and as evolutionarily distinct branches in other. KP Botany 00:44, 10 December 2006 (UTC)
Would you go ahead and revert them for now, until we can reach some consensus on the issue? You also used multiple colors and colors that won't be distinguished on all monitors well. KP Botany 00:52, 10 December 2006 (UTC)
User:Werothegreat was asked to revert his changes to the taxobox colors, and didn't. It appears there may be about 100 that have various nonstandard colors that don't mean anything according to the taxobox information page, and there are eukaryotes that appear, because of User:Werothegreat's color choice, to be bacteria by color, something else by text. These have to be changed, so would folks check his list and change them. I put a vandal warning on his talk page, also. This is quite a bit of work to undo. KP Botany 20:17, 12 December 2006 (UTC)
My bad, other users changed most of them, I changed some. His whole edit list probably needs checked, though. KP Botany 20:29, 12 December 2006 (UTC)

Do you want them khaki or the eukaryote brown? Werothegreat 16:15, 15 December 2006 (UTC)

Animalia pink
Plantae lightgreen
Fungi lightblue
Protista khaki
Bacteria lightgrey
Archaea darkgray
Virus violet

The background colors are based on this table, eukrayote brown is not listed, although I've seen it on the eukaryote page. Since Protist is more refined, and they were already khaki, they should just stay where they were, until a decision is made to do otherwise. KP Botany 17:40, 15 December 2006 (UTC)

[edit] Access to journal

Hi everyone,

I was wondering whether anyone had access to the "Zootaxa" journal (ISSN 1175-5334). I want to find out how to differentiate some species in the Mixophyes genus, and this is the only reference to work off, as the species are brand new. I am specifically looking for the paper: "Species boundaries among barred river frogs, Mixophyes (Anura: Myobatrachidae) in north-eastern Australia, with descriptions of two new species" 1228: 35-60 (2006). My uni doesn't have a subscription to this journal, so it makes it hard :).

If someone could read it, and right up somewhere how to tell the difference between species (morphologically), that would be great. The abstract says there are morphological differences. Thanks. --liquidGhoul 11:53, 5 December 2006 (UTC)

I have been eyeing Zootaxa articles enviously for months! Some articles are free access and they are brilliant. Does anyone know how much it is and is some kind of Wikigrant available for this kind of thing:)Richard Barlow 08:43, 6 December 2006 (UTC)
This is the abstract, though it doesn't look like it has a lot of information (maybe you already found that). If you want, I can have a look at it (it's in the library of Naturalis). But I don't know when I will be able to go there. Ucucha 07:24, 10 December 2006 (UTC)

[edit] Proposed Veterinary medicine project

There is now a proposed project at Wikipedia:WikiProject Council/Proposals#Veterinary Medicine to deal with matters of veterinary medicine, a subject which currently has disproportionately low content in wikipedia. Any wikipedia editors who have an interest in working on content related to the subject are encouraged to indicate as much there. Thank you for your attention. Badbilltucker 22:07, 6 December 2006 (UTC)

[edit] Fly ID

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Another picture of same fly
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Another picture of same fly
Same place, similar fly
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Same place, similar fly

Would anyone be able to ID this fly pictured in Victoria, Australia and listed at: Wikipedia:Featured picture candidates/Image:Housefly white background.jpg? I think it may be Calliphora stygia, common brown blowfly or eastern goldenhaired blowfly, but it's not my field of expertise.[10][11][12]--Melburnian 09:28, 8 December 2006 (UTC)

[edit] Unranked phyla

User:Werothegreat (contribs) has been modifying some taxoboxes, changing their color and changing "regnum = Protista" to "domain = Eukaryota unranked_phylum = Rhizaria". This looks highly controversial to me but I'm underqualified to address this, please someone look in to this.--Steven Fruitsmaak (Reply) 18:31, 9 December 2006 (UTC)

This discussion took place on this page just a few sections up (section title = Protista). --Aranae 20:53, 9 December 2006 (UTC)

[edit] Undescribed taxa

Is there already a policy regarding undescribed taxa, and, if not, should we have one? I have come across a couple of examples of articles about species with provisional names (Tripteroides sp. No. 2 and Paramoera sp). They each deal with a good species and include a verifiable reference to back it up, but in each case the species has not been designated a name. I can see several ways of dealing with this (in order of increasing harshness):

  1. The articles are fine as they are, and can be moved as and when a name is published
  2. The articles should be merged in to the next taxonomic rank (genus in these cases) until a name is published
  3. The articles must be deleted because an undescribed species is either unverifiable or not notable (or for some other reason?)

I think I'm leaning towards option 2, but I'd like to hear what others think. --Stemonitis 12:01, 14 December 2006 (UTC)

Option 1, separate article, would be my preference: there is no need to treat undescribed taxa different from described taxa. In some cases, that may mean that merging with the next taxon is better; that's a decision that can be taken on a case-to-case basis.
I don't know if the titles are ok. "Tripteroides sp. No. 2" probably is a good article title; I assume that this insect is always referred to by this name, until it receives a final name? "Paramoera sp" is a more problematic name: this may refer to any species in the genus Paramoera, right? Is there a systematic way of naming undescribed species? I'm not a taxonomist, so an article undescribed taxon would be very helpful. (How can a species be undescribed if there are several articles referring to it?) -- Eugène van der Pijll 12:52, 14 December 2006 (UTC)
Here, "undescribed" means "not described formally", i.e. there is no formal name under the ICZN or ICBN or another code. Currently, many species have been known informally for some time before they get a formal name.
There are many "systems" for naming undescribed species: Genus sp. nov., Genus sp. nov. A (etc.), Genus sp. nov. 1, Genus sp. 1, etc. I think we should just use the name the source for the species uses. Ucucha 12:58, 14 December 2006 (UTC)
Thanks. There are many mentions of "undescribed species" in wikipedia, so this should be explained somewhere. I've started the article undescribed taxon, but as I'm not an expert, can you check if it's not total nonsense? -- Eugène van der Pijll 14:14, 14 December 2006 (UTC)
The next question (which I should probably have asked earlier) is what consequences this has for the taxobox. Clearly the "binomial=" field cannot be used, and I wonder whether a taxobox is at all appropriate for a taxon which has never been given a proper name. --Stemonitis 13:02, 14 December 2006 (UTC)
A taxobox is meant to inform the reader of the location of the organism in the "tree of life"; this is as useful for undescribed taxa as for other taxa, so why not include the taxobox? The full (temporary) name should be included, but preferably not under the header "Binomial name".
A question about Tripteroides sp. No. 2: it has a "binomial authority" of "(Mattingly, 1981)". Surely that cannot be right? It should probably be replaced with a link to undescribed species, like I did at Paramoera sp. Eugène van der Pijll 13:28, 14 December 2006 (UTC)

[edit] Advice on Beauveria bassiana (and A Wikimanual of Gardening/Beauveria bassiana

I imported this to wikibooks this morning to make a how-to page, and my research hit on a lot of things not in the article (and in fact contrary to it insofar as the safety claims are concerned. At least two extension service websites and one "medical Q&A" website noted that the organism was indeed capable of infecting mammals, including humans. However, these references were made "in passing" on the Extension sites, and the EPA factsheet doesn't address the issue at all. There are references on the wikibooks page (the {{Cite web}} template works the same way, so feel free to just copy them).

I still have a bunch of work to do in the wikibooks page, but I'll copy what I have so far into the edit history of the WP article (for the GFDL requirements), and maybe someone could have a look and see? I'd really just like some general pointers on how to re-incorporate additional research done on the wikibooks side back into the original wikipedia article as a matter of course, since I often come up with a lot of "encyclopedic" information along with the "how-to" stuff that I'm actually looking for. See the topic below too: would heavy-handed reorganisations following wikibooks standards be inappropriate for wikipedia?

Also, I'm wondering if someone with paid access to the New York Times could have a look at the article referenced for the potential use of B. bassiana for malarial mosquito control. In particular, I'd like to know if that article has any discussion of potential pathogenicity in humans. --SB_Johnny|talk|books 14:53, 14 December 2006 (UTC)

[edit] "Templatizing" TOL articles

I'm building a gardening manual on wikibooks, and most of the pages are imported copies of wikipedia articles. When I get them onto the wikibooks page, I first add a substituted template that provides an organizational structure for the page (e.g., b:Template:Weedprof or b:Template:Biocontprof). They provide headers, hidden editor's notes, and automatically add non-substed templates as well (for us that would probably just be the taxobox in most cases, though it could add the nutritional templates for food crops as well).

Having done this 100 or so times now, I'm wondering if applying something similar to the wikipedia TOL articles might not be a good idea too. When I'm taking the articles apart and fitting the information into the templated structure, I've noticed that every article follows a different structure. Worse still, there's often a paragraph about one thing, then a sentence on the end of a paragraph further down the page that should be part of the first paragraph's structure (nonsequitors abound).

What I'd suggest is maybe something like the following:

  1. A general description of the organism, using the standard essay style of mentioning all the points that will be discussed later in the article
  2. A physical description of the organism
  3. Taxonomy and other naming issues
  4. Life cycle, ecological relationships, etc.
  5. Economic importance and issues of cultivation or husbandry
  6. Evolution, history, historical "trivia"
  7. See also
  8. References
  9. Category

In the wikibook, using these templates has helped give the book a consistent, "professional" feel, which I think is certainly something we should be aspiring to on wikipedia as well. In some cases I've also come back and edited the wp article as well if the structure was just really out of hand, but I'm wondering if implementing a "standard templatization" regime on wikipedia would also be helpful in doing a wide-ranging (and long term...this is time consuming) cleanup of the TOL areas. --SB_Johnny|talk|books 14:53, 14 December 2006 (UTC)

I totally like this idea for plants. KP Botany 16:37, 14 December 2006 (UTC)
I'm sorry, but I can't see this being so useful for an encyclopaedia. In a gardening manual, you want to present the same sorts of information for all the types of plants you cover, but in an encyclopaedia, the contents are driven by what is important and what is interesting, which may or may not coincide with the template's suggestions. It's all well and good saying that a ToL article should contain description, ecology, economic uses, etc., but the order will vary widely from article to article. That flexibility is an advantage, not a disadvantage. --Stemonitis 16:47, 14 December 2006 (UTC)
As long as they're not mandatory, I don't see what the harm would be. On the plus side, it's nice to have an idea of where one might go when starting an article. Guettarda 18:01, 14 December 2006 (UTC)
I don't get the impression that SBJohnny is mandating their use, simply offering it as a suggestion. They could be handy when making new articles. There seems to be no intent, either to dictate the result of using them, like you can't change them around or add or subtract. I like the idea of a handy template, and if Stemonitis's only objections is their lack of flexibility he/she can not use them. And that's about as flexible as one can get. KP Botany 18:14, 14 December 2006 (UTC)
Sometimes suggestions end up mandates, but otherwise, I think it might be helpful to have a rough guideline. I'd like to suggest moving detailed discussion of taxonomy to the end, beside history. That makes it easier to discuss older systems, which may still be in use, all in one place; and it means information about the actual organisms isn't interrupted. Josh
"Sometimes suggestions end up mandates" -- ick, yes, that's the downside of any approach like this. I guess I was just thinking that having a "base structure" which we could use while cleaning up might be handy. In my experience on the books, having those blank fields at the top of the page and then thinking about where each part of the content goes really helps in putting related things together in an organized way. I'm certainly not suggesting we start adding templates saying THIS ARTICLE DOES NOT FOLLOW THE TOL-ACCEPTED TEMPLATES AND SHOULD EITHER BE REWRITTEN OR DELETED!!! (excuse the noisy melodrama there), but rather just coming up with some templates we could use as an aid to quietly improving articles that are in need of organisation.
BTW: I agree completely with Stemonitis... flexibility is key, and even if a template is used, there's no reason the template would need to be followed. The wikibook chapters have a much narrower purpose in mind: either how to grow a thing, or how to kill it, and it's easy to conficure and follow templates in that situation. Encyclopedia articles about living things might just be about what it is and where it lives, but in many cases what it is and where it lives isn't what people want to know (e.g. Cannabis, Wheat, E. Coli, Dog, etc.). I just think it might be helpful as a tool for cleaning up articles. I don't think it's something to add to the MoS :). --SB_Johnny|talk|books 21:57, 14 December 2006 (UTC)
I stand corrected on this, having come across attempted enforcement of all sorts of voluntary guidelines in the last few days. The template talk page or something should strictly say, maybe yell in all red, that's is voluntary, not mandatory, and that the article should always be guided by what's important and relevant, not by the template. But I want one for plants, and I want it now, and I want one for scientist biographies, also. Does the latter already exist? KP Botany 17:43, 15 December 2006 (UTC)
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