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 2006-04 – 2006-10 Categorization; include in references; snakes; range maps; seasonality graph; common names; bioregions; brya;
19 2006-10 – 2007-03 various
20 2007-03 – 2007-06 various

Contents


[edit] Herrerasaurus

I've requested a scientific peer review of this article. The discussion is here, and all comments are greatly appreciated. Firsfron of Ronchester 06:58, 29 June 2007 (UTC)

[edit] Distribution maps

I have been working on some distribution maps for some species of birds and have been generating spot maps that are based on a number of sources (not all of them qualifying as equally reliable, but traceable and verifiable). I would just like to know if compilation of a map using data from multiple sources to generate a distribution map could in any way be construed as WP:OR (original research by synthesis). Thanks Shyamal 08:08, 29 June 2007 (UTC)

It's only OR if the synthesis is to advance a position, I can't see that a distribution map is likely to fall into that category. Assembling a taxobox is a synthesis of information, but it's just presentation, not polemics. Jimfbleak 12:05, 29 June 2007 (UTC)

[edit] Archive please

Can we archive please? The page is getting a bit long. Werothegreat 16:16, 29 June 2007 (UTC)

You may. I can't. KP Botany 22:31, 30 June 2007 (UTC)
Consider it done. --Stemonitis 05:37, 1 July 2007 (UTC)

[edit] Input needed at WP:RFD

I have listed infraspecies and infrasubspecies at WP:RFD as confusing redirects. Editors from this wikiproject are invited to comment at Wikipedia:Redirects for discussion/Log/2007 June 30. Thanks. Chick Bowen 22:01, 30 June 2007 (UTC)

[edit] confusion about what to do with eukaryotic higher level taxa flux

so i'm new here and i've started cleaning slime mould pages. i.e. the pages for
Myxogastria: plasmodial or syncytial slime moulds,
Protostelia: smaller plasmodial slime moulds,
Dictyosteliida: cellular slime moulds,
Acrasidae: similar life style to Dictyostelids, but of uncertain taxonomy

in particular. and the contradictory pages of higher level taxa they have been put in.

it's a tangled mess. so is there any consensus about this stuff? for instance there is: Dictyosteliida and dictyosteliomycota. there is slime mould and there is myxomycota. in each case one member of the pair sucks.

can someone sum up the discussion on these topics for me or do i have to read 20 archive files?

here's my ramblings on this tangle: User talk:Wikiskimmer/eukaryotic taxonomy, it's very confusing. i need a printer.

i cleaned up the slime mould page a fair bit. Wikiskimmer 21:38, 3 July 2007 (UTC)

YAY! I applaud your efforts. We need more people like you and me who like slime moulds and other fun protists. Werothegreat 02:08, 4 July 2007 (UTC)
O, I was just reading through some of your stuff... you should state that TRUE slime moulds belong to phylum/kingdom amoebozoa, and "pretend" slime moulds (slime nets, etc.) go elsewhere. Slime nets are chromalveolates. And acrasids (or percolozoans) are excavates, and plasmodiophorids (the phytomyxea) are rhizarians. Werothegreat 16:06, 9 July 2007 (UTC)

[edit] Bigfoot

Just to keep everything in perspective, I have written the following with our many excellent TOL editors in mind: User:Marskell/Think of the Children. Marskell 13:25, 4 July 2007 (UTC)

[edit] List of introduced fish in Australia

Hello. Would anybody in this WP be willing to help writing a lead section for this list? Thanks! Abbott75 ☺ 01:01, 5 July 2007 (UTC)

Y Done. Suggested format placed on talk page. Regards, AshLin 03:55, 9 August 2007 (UTC)

[edit] Anyone here

Posting contents of a mail below. Would hope that there is something Wikipedia related there. Shyamal 09:01, 12 July 2007 (UTC)

TDWG Annual Conference (http://www.tdwg.org/conference2007)
Bratislava, Slovakia, 16-22 September 2007
 
Call for Abstracts
 
** I will be away from my mail after 19 July. If you intend to respond
 to this call please contact me before then **
 
Symposium: Discovery, Integration and Use of Biodiversity Data
Session: Building biodiversity data content (Friday 21 September)
 
The idea of the session is to get away from the technical aspects of
 managing biodiversity data and to ask the wider community to tell us:
 
1) what is needed in terms of:
 
  - non-technical standards (standard lists, authorities, etc.)
  - on-line services
  - collection/specimen documentation standards
  - other data content standards
  - tools to help populate biodiversity, observational, ecological and
 conservation databases
 
2) what has already achieved (or is being worked on) towards these aims
 
3) how you can contribute
 
The schedule for the 2007 Conference is very busy and we have space for
 only five or six verbal presentations. We do have ample space for
 poster presentations and computer demonstrations.
 
My task is to ask the community for proposed presentations on the
 session theme, to integrate key verbal presentations into an interesting and
 thought-provoking session, and to encourage the submission of posters
 and computer demonstrations.
 
If you think you have something to contribute, please contact me at
 A.Rissone@nhm.ac.uk with Subject line "TDWG 2007: Building biodiversity
 data content", indicating whether you are proposing a verbal
 presentation (remember these are very limited), a poster or a computer
 demonstration.

[edit] Another new article

I've been working on infanticide (zoology) for two or three days, and it will probably be coming up for did you know soon. I'd appreciate anyone looking over it or adding more themselves. It's clearly not complete yet, but a few more examples should do it (particularly of parents killing their own young). Richard001 08:41, 13 July 2007 (UTC)

How morbid of you. What does this have to do with this wikiproject? This is about organisms and how they are classified... this belongs in a crime or sociology wikiproject... Werothegreat 17:34, 13 July 2007 (UTC)
Ah. I see after actually looking at the article. Interesting. Werothegreat 17:35, 13 July 2007 (UTC)
I've taken the liberty of removing the pipe to avoid similar future misunderstandings... Circeus 17:41, 13 July 2007 (UTC)
It would ideally be posted on an animal behavior project, but we don't have any animal project even so it's difficult to find the right project. This is the nearest parent project, though it's mainly concerned with taxonomy and classification. Biology could also be used but it has only recently been reopened and not that many people post there. Perhaps I should try rounding up some people from the various animal projects and see if we can put something together? Richard001 23:07, 13 July 2007 (UTC)
Go for it. Be bold. Werothegreat 00:32, 14 July 2007 (UTC)
This was a good default place to start, though, Richard. I'll look at it in brief, while echoing Wero's comment, "how morbid of you." I did study the topic in physical anthropology ages ago (for those unclear on the connection physical anthropologists also observe animal behaviour for clues to human behaviour, and to learn how to observe human behaviour), and in psychology--which is where I think you might post, as psychologists also study and observe animal behaviour. KP Botany 17:52, 14 July 2007 (UTC)

[edit] Mitochondria - Cristae shapes

Can someone PLEASE (who knows what they're talking about) detail the various shapes that cristae take (discoid, flat, etc.), describing their differences, and possibly the purposes for different shaped cristae, either in the eukaryote, mitochondria, or cristae articles, or even create a new one. I would have done this by now, except the whole subject confuses me, and I don't have any sources that clearly explain them. Werothegreat 14:53, 13 July 2007 (UTC)

Perhaps this would get better results at Wikipedia:WikiProject_Molecular_and_Cellular_Biology. AshLin 11:34, 30 July 2007 (UTC)

[edit] Ciliate article needs work

Ciliophora is one of the more important protistan phyla, and its article has no subsections. It contains a bunch of stuff about ciliates, a taxobox, and then a seperate section detailing classes and subclasses. And a bunch of thumbnails. I'm gonna need some help on this one. Werothegreat 16:07, 14 July 2007 (UTC)

[edit] conservation status in taxoboxes

Should the Taxoboxes section include how to use conservation status? I would appreciate some guidelines, and don't feel qualified to add it to the instructions myself. -- Donald Albury 13:05, 15 July 2007 (UTC)

WP:TX (the guideline/style guide covering them) links to it. That should be enough, shouldn't it? Circeus 16:04, 15 July 2007 (UTC)
Let's just say that things are not always obvious. I had looked for some guidance, but had not found that. -- Donald Albury 18:32, 15 July 2007 (UTC)

[edit] Template question

At least, I think it's a question about templates. I'm hoping someone here will either know the answer, or know where to find someone who can help.
I've been busy with a series of articles on vipers, many of which use a template (?) that makes it easy to create external links to entries in a particular online database. An example would be the first link in this external links section, the markup language for which looks like this:

  • {{EMBL species|genus=Bitis|species=gabonica}}

These links used to be for records at the Reptile database at the European Molecular Biology Laboratory (EMBL). At one point late last year, the EMBL stopped hosting this database, upon which the man responsible for it, Dr. Peter Uetz, went looking for a new home for it. In the mean time, the code behind this template at Wikipedia was changed to work with the Species2000 database, even though that's only a subset of the original EMBL Reptile Database. Finally, about two months ago, Dr. Uetz's database went online again here, but it seems that the folks at Wikipedia who maintain the EMBL template have not yet discovered this.
My question for you is therefore, how can I find out who maintains this template, or where can I find someone who can change it to query the Reptile database at its new location? Thanks! --Jwinius 22:04, 26 July 2007 (UTC)

Okay, it's been fixed, thanks to Shyamal. FYI, what needed to be changed was Template:EMBL species (and Template:EMBL genus). More information can be found at Help:Template and assistance can be sought at Wikipedia_talk:Requested_templates. --Jwinius 13:34, 1 August 2007 (UTC)

[edit] "Need taxobox" template

A new template, Template:Needtaxobox, is available for the purpose of tagging articles that do not yet have a taxobox. The "What links here" function can be used to comb through articles needing a taxobox. Badagnani 19:00, 31 July 2007 (UTC)

[edit] Chromalveolate Kingdom Color

Most high-level chromalveolate articles and many lower-level articles have had their taxoboxes changed to read Kingdom: Chromalveolata rather than (unranked): Chromalveolata. There have so far been no objections, and these changes have been standing for a while. I would like to take this one step further. I would like a unique taxobox color be chosen to represent the Chromalveolate kingdom, as Metazoa has pink, Plantae has Green, and Fungi has lightblue. Now, the last time I was bold and started changing taxobox colors right and left, there was an uproar and accusations of vandalism. I would like to avoid conflict this time by putting it to a poll. Post what color you feel it should be, and after a decent amount of time, say a week or two, or after we have sufficient nominations, we put it to a vote. Since this would take a lot of space, we could do this on the talk page of the chromalveolate article after we get started. Please remember, the following colors have been taken: pink, lightgreen, lightblue, khaki, brown (#e0d0b0), violet, lightgray, and darkgrey. Werothegreat 15:47, 2 August 2007 (UTC)

In the Catalan Wikipedia we did it time ago (see ca:Viquipèdia:Com entendre les taules taxonòmiques). If you choose the same colour, will be easier for us to move information from here to there :p Llull 19:15, 2 August 2007 (UTC)
Not that I have anything against lavendar, but if they've already chosen a color for those taxa on Catalan Wikipedia, I can't think of a good reason not to go with their color choice--nor am I going to try to. KP Botany 21:31, 2 August 2007 (UTC)
Not the color I would have chosen, but I have no objective objections. Implenting the change currently. Werothegreat 21:02, 3 August 2007 (UTC)
Thanks. KP Botany 21:05, 3 August 2007 (UTC)
I have changed all the higher taxa, and I have updated the eukaryote page and the taxobox usage page. Werothegreat 21:55, 3 August 2007 (UTC)
Thanks, I ran into one while looking something up, and it looks great to see these buggers discrimanted, even though no one but you and Cavalier-Smith know what they are. Oh, and apparently the Catalans. KP Botany 17:59, 7 August 2007 (UTC)
We are more than seven million people. Don't forget it :) (we never used Protista kingdom) Llull 21:06, 7 August 2007 (UTC)
Why not use the colour "coral"? It's easier to remember than six arbitrary hex characters, and much kinder to the eye as well... Verisimilus T 11:56, 11 August 2007 (UTC)
Hmmm. Coral is a little more orange, (a little harder on the eyes, in my opinion). Coral pink would be too close to the animal pink... How about lightcoral? It fits with the pastel scheme of the taxoboxes, and it is darker than the animal pink enough to be able to tell the difference. Any objections? Werothegreat 12:53, 11 August 2007 (UTC)
I think that they are colours too similar to the animal one. With the implementation of {{Taxobox colour}} template in the taxobox won't be the necessity of remember de colour code. Llull 13:44, 11 August 2007 (UTC)
Okay. What about:
#F0b070

It's got a similar hue and saturation to the existing colours, but is easily discriminated. It's also less garish than the current option (which is my main argument against sticking with what we've got). Verisimilus T 16:46, 11 August 2007 (UTC)

It's garrish, yet, but I think some unity around taxobox colors on the various Wikis is rather helpful, and it's just a color. I would really like to stick with a choice already made by another group of Wikipedia editors, unless it is really necessary to change it. It is readily distinguishable from other colors, it's already in use on another Wikipedia, it does not confuse with the other colors. KP Botany 19:32, 11 August 2007 (UTC)
As much as I like the idea of using the Catalá color (anyone who both rejects Protista and keeps their language alive is to be commended and emulated), the Chromalveolate color, as well as some of their other colors, are not likely to pass text-to-background contrast tests that either are or eventually will be a part of web accessibility standards in many countries. In the case of the Chromalveolate color specifically, white text might pass muster, and the changes to Taxobox might allow that to be more or less automatic, but it is something we need to consider. When I have a chance later, I'll find the tool and test all the color combos.--Curtis Clark 22:54, 11 August 2007 (UTC)
Then please test, Curtis, as I hate to discuss something that someone else has already hashed out, and I have no reason to consider, if they've already debated choosing a color for the Chromalveolates, that we can pick better than the Catalans can. Then, if it turns out that there are issues with the color, we'll revisit the issue with everyone. Or maybe they tested and that's how they wound up with this color. Thanks. KP Botany 23:03, 11 August 2007 (UTC)
Back to that taxobox color template, I really like the idea. Very nice. However, what about Rhizaria, Excavata, and Amoebozoa? Do they fall under the incertae sedis category? Werothegreat 23:54, 11 August 2007 (UTC)
I think that the best is to put them in a generic Eukarya colour (Eukarya that is not in one of the other four kingdoms). The other clades are too revolutionary and I think that we should wait few years for change it, waiting for new reviews. And wait years seems still more important in bacterial clades of neomuran article. Llull 08:15, 12 August 2007 (UTC)

Here are the results of using Colour Contrast Analyser for Web Pages. According to the program, "Text or diagrams and their background must have a luminosity contrast ratio of at least 5:1 for level 2 conformance to guideline 1.4,and text or diagrams and their background must have a luminosity contrast ratio of at least 10:1 for level 3 conformance to guideline 1.4." I've added the contrast ratios to each of the color combinations used in ca:Wikipedia, with the standard blue link color (left column) and the redlink color (right column). Note that every combination except the last fails with redlinks. --Curtis Clark 00:26, 12 August 2007 (UTC)

Blue link color Red link color
Animalia pink Passed at Level 2 (The contrast ratio is: 6.93) Fail (The contrast ratio is: 3.65)
Archaeplastida lightgreen Passed at Level 2 (The contrast ratio is: 7.50) Fail (The contrast ratio is: 3.95)
Fungi lightblue Passed at Level 2 (The contrast ratio is: 6.98) Fail (The contrast ratio is: 3.68)
Chromalveolata #FA7B62 Fail (The contrast ratio is: 4.08) Fail (The contrast ratio is: 2.15)
Eukaryotae #e0d0b0 Passed at Level 2 (The contrast ratio is: 7.02) Fail (The contrast ratio is: 3.70)
Bacteria lightgrey Passed at Level 2 (The contrast ratio is: 7.13) Fail (The contrast ratio is: 3.76)
Archaea darkgray Fail (The contrast ratio is: 4.57) Fail (The contrast ratio is: 2.41)
Virus violet Fail (The contrast ratio is: 4.60) Fail (The contrast ratio is: 2.42)
Viroides darkorange Fail (The contrast ratio is: 4.56) Fail (The contrast ratio is: 2.41)
Satèl·lits #FFA000 Passed at Level 2 (The contrast ratio is: 5.22) Fail (The contrast ratio is: 2.75)
Inespecífic lightyellow Passed at Level 3 (The contrast ratio is: 10.38) Passed at Level 2 (The contrast ratio is: 5.47)
But: when would redlinks appear? Surely the only thing that'll ever be wikilinked in the template is "Scientific classification"?
As I can't download the program, would you mind running it for #F0b070 too?
And at the hazard of broadening the debate, I did feel that the Virus colour was a bit dark, but didn't want to open that can of worms... Is it worth changing? It also appears very low classification with the purple "followed link" colour.Verisimilus T 08:53, 12 August 2007 (UTC)
That's a good point about the redlinks. Viroide is a redlink here, but not on ca:Wikipedia (it is Viroid here) and Satèl·lits is a redlink in both places, but neither would be linked in an actual taxobox, since the name only appears in its own article. So it seems that the only text colors we need to worry about are black, the blue unfollowed link, and the purple followed link. I'll redo the table later today.--Curtis Clark 13:58, 12 August 2007 (UTC)
Satèl·lits refers to Satellite (biology) (used in (ca:virusoide article), genetic information that needs a helper virus for its own reproduction. There we use different colours for viruses, satellites and viroids tables (the last two very similar because of they are very similar), but here all these entities are classified with the same violet colour. Neomurans, Mycoplasma laboratorium, transposons and other unspecific elements use the lightyellow there, but here you don't use taxoboxes for mobile genetic elements and you haven't needed a standard colour for this purpose. Llull 14:57, 12 August 2007 (UTC)

Here's the new table with contrasts added. The program also tests contrasts for the three types of color blindness; we should check that as well on any candidate combinations.--Curtis Clark 16:22, 12 August 2007 (UTC)

Animalia pink Passed at Level 3 (The contrast ratio is: 13.79)
Animalia pink Passed at Level 2 (The contrast ratio is: 6.93)
Animalia pink Passed at Level 2 (The contrast ratio is: 5.87)
Archaeplastida lightgreen Passed at Level 3 (The contrast ratio is: 14.91)
Archaeplastida lightgreen Passed at Level 2 (The contrast ratio is: 7.50)
Archaeplastida lightgreen Passed at Level 2 (The contrast ratio is: 6.35)
Fungi lightblue Passed at Level 3 (The contrast ratio is: 13.89)
Fungi lightblue Passed at Level 2 (The contrast ratio is: 6.98)
Fungi lightblue Passed at Level 2 (The contrast ratio is: 5.91)
Chromalveolata #FA7B62 Passed at Level 2 (The contrast ratio is: 8.12)
Chromalveolata #FA7B62 Fail (The contrast ratio is: 4.08)
Chromalveolata #FA7B62 Fail (The contrast ratio is: 3.46)
Eukaryotae #e0d0b0 Passed at Level 3 (The contrast ratio is: 13.97)
Eukaryotae #e0d0b0 Passed at Level 2 (The contrast ratio is: 7.02)
Eukaryotae #e0d0b0 Passed at Level 2 (The contrast ratio is: 5.95)
Bacteria lightgrey Passed at Level 3 (The contrast ratio is: 14.18)
Bacteria lightgrey Passed at Level 2 (The contrast ratio is: 7.13)
Bacteria lightgrey Passed at Level 2 (The contrast ratio is: 6.04)
Archaea darkgray Passed at Level 2 (The contrast ratio is: 9.09)
Archaea darkgray Fail (The contrast ratio is: 4.57)
Archaea darkgray Fail (The contrast ratio is: 3.87)
Virus violet Passed at Level 2 (The contrast ratio is: 9.14)
Virus violet Fail (The contrast ratio is: 4.60)
Virus violet Fail (The contrast ratio is: 3.89)
Viroids darkorange Passed at Level 2 (The contrast ratio is: 9.08)
Viroids darkorange Fail (The contrast ratio is: 4.56)
Viroids darkorange Fail (The contrast ratio is: 3.86)
Satèl·lits #FFA000 Passed at Level 3 (The contrast ratio is: 10.38)
Satèl·lits #FFA000 Passed at Level 2 (The contrast ratio is: 5.22)
Satèl·lits #FFA000 Fail (The contrast ratio is: 4.42)
Inespecífic lightyellow Passed at Level 3 (The contrast ratio is: 20.64)
Inespecífic lightyellow Passed at Level 3 (The contrast ratio is: 10.38)
Inespecífic lightyellow Passed at Level 2 (The contrast ratio is: 8.78)
New color #F0b070 Passed at Level 3 (The contrast ratio is: 11.28)
New color #F0b070 Passed at Level 2 (The contrast ratio is: 5.67)
New color #F0b070 Fail (The contrast ratio is: 4.80)
So... not only do we need a different chromalveolate color, we also need a new archaea color? This is becoming more trouble than it's worth. How about a more yellow shade of green for c-als, and a reddish lighter gray for archaea? I'm really reaching here. Werothegreat 02:37, 13 August 2007 (UTC)
Something like this?
Chromalveolata GreenYellow
Archaea #F3E0E0
Werothegreat 02:40, 13 August 2007 (UTC)

Inasmuch as there will always be the possibility of visited links in the colored-background parts of a taxobox, we also need new colors for Virus and Viroid. There are all kinds of pastels in the RGB color space, so if we were inventing this from whole bits, it wouldn't be all that difficult. If we want to preserve colors already in use, we might check out taxoboxen in some of the other Wikipediae for colors with an adequate ratio. I guess what I'd like to know next is the consensus: Are we bound by existing colors, or do we want to go for optima?--Curtis Clark 03:17, 13 August 2007 (UTC)

I don't know. This might be something we want to coordinate more with other Wikis, as one reason for going with the Catalan's color choice is having some consensus across wikis in a multi-lingual world. It's hand to be able to go to the Danish wiki and know I'm at least in the correct kingdom by the taxobox. KP Botany 03:44, 13 August 2007 (UTC)
I tend to agree in principle, but it's my understanding that EU countries have stricter standards for web accessibility that the US (WAI vs Sect. 508, and the latter only applies to the US Federal govt plus a few states, such as California), so maybe we can help them out and come up with an adequate-contrast set of colors that takes from the best of all the Wikipediae.--Curtis Clark 03:52, 13 August 2007 (UTC)

[edit] Adding a subsection to make it easier to comment

Most of the wikipedias use pink/lightgreen/lightblue/khaki. The only real exception is the french wikipedia, which uses the khaki exclusively for alveolates for some reason, and uses teal for the rest. My assumption is that if we change our taxobox colors, the rest will most likely soon follow. Werothegreat 12:55, 13 August 2007 (UTC)

I'd rather do it with a little consultation internationally though, if it turns out it is problematic all over, that we want to change everything, and that it's likely the others will follow through, and that European countries have stricter requirements. KP Botany 16:32, 13 August 2007 (UTC)

[edit] Four kingdoms after all?

It's swings and roundabouts... These guys seem to think that Protista is a kingdom. How do we avoid POV in our Taxobox colours? Verisimilus T 12:04, 24 August 2007 (UTC)

How quaint. Pananimalia and panplantae do make sense, but you can't really call a paramecium a plant, or a mushroom an animal. It doesn't quite work. And bacteria is paraphyletic. Why can't we just accept that life isn't that simple, and is not going to fit into cookie-cutter groups? Werothegreat 16:48, 24 August 2007 (UTC)
Because then all our taxoboxes would have to be the same colour, and what would we keep ourselves busy with then? Verisimilus T 18:39, 24 August 2007 (UTC)
I would rather have one color for everything (which the Germans do, coincidentally) than have a return of protista. Werothegreat 22:38, 24 August 2007 (UTC)
This does raise an interesting question which I suppose begs an answer: Is there really a purpose of having different colours at all, and if so, what precisely are we trying to achieve through them? Verisimilus T 12:55, 25 August 2007 (UTC)
I was just reading through this: <http://herba.msu.ru/shipunov/os/current/synat.pdf>. It's like I'm reading a paper from the seventies. He's grouping the cercozoans with the amoebozoans. That doesn't work. Werothegreat 16:55, 24 August 2007 (UTC)
Neither does your link! (-;
(Connection timed out) Verisimilus T 18:43, 24 August 2007 (UTC)
It works for me. I'm using Mozilla Firefox. What browser are you using? Werothegreat 22:38, 24 August 2007 (UTC)
Firefox too. Still not working now - maybe you have different access permissions or something? If you give me the title I'll find it in Scholar... Cheers. Verisimilus T 12:55, 25 August 2007 (UTC)
As for avoiding POV, this is a new development, just published. Whereas the six-supergroup system has lots of papers, Adl et al, Cavalier-Smith, lots of websites, etc. No one in their right mind uses Vegetabilia anymore. Werothegreat 22:41, 24 August 2007 (UTC)
It seems curious that Nature would publish something that's outdated... Classification isn't a subject I know much about, mainly because a cladistic approach renders it somewhat redundant on the phylum-scale. I'm interested to know more; is your principle objection with the paper mainly that it includes groupings which you consider paraphyletic?


I see no harm in including fungi in the same kingdom as the animals, as it does seem that fungi are a genuine stem-group to the animals. But then I'm a lumper, not a splitter. I have heard eminent scientists describe Paramecium as a plant (which has actually just led to a great deal of confusion, without my realising that you'd referred to it!). The level of diversity to be contained within a kingdom is always going to be a point of view issue, as it's entirely arbitrary. But the argument of "they seem too different to be grouped together" doesn't hold water - as the platypus illustrates.
Regarding the paraphyly of bacteria, there's probably got to be a degree of that - simply as older lineages are more diverse. As I look at it, the two sister species today as as different as the two sister genera were X million years ago, and so on up the tree of life. (It'd be interesting to do some maths and see how consistent "x" actually is) If kingdoms are real entities representing a certain degree of evolutionary differentiation, then every organism at a given point back in time (corrected for varying rates of evolution) would have the potential to found a kingdom, and there were (surely?) many many more than 4 or 6 organisms back then that managed an unbroken line of descendants to the present day? I wonder whether they've formed the blanket "Bacteria" kingdom, with inverted commas, as it's more useful than naming the hundreds of kingdoms that probably exist, but we're not very good at discerning yet. That's not the impression they give, but then there's very little discussion in the paper.
Whoops, I rambled a little there. The perils of becoming more and more interested in a subject...
Verisimilus T 12:55, 25 August 2007 (UTC)
I'm just feeling very torn, because the panplantae etc. does make some sense, but then he goes and proposes vegatabilia etc., which isn't even trying to be monophyletic, and I'm like, "But, no!" No, no, no, no. Linnaeus had some good ideas, but we've improved on them. Just like Edison had good ideas, but we're using flourescent lightbulbs now. Thanks for the start, but we've got it covered on our end. You can't go backwards. You have to go forwards. And really, the four evolutionary kingdoms are basically the three-domain system, except he's split up the eukaryotes into basically unikonts and bikonts. Don't make up new names! We have names! Unikonta, and bikonta! And he describes the Apusozoa as incertae sedis, when Cavalier-Smith believes to be basal bikonts, putting them in "panplantae." If ever I were to use the word "pananimalia," first, I would change it to "panzoa" to get lingual agreement (a latin root with a greek prefix? Please.) and then I would clump the choanaflagellates in there. The fungi would remain in Eumycota, which could be spread to "panmycota" to include the mesomycetozoa. And the only sense in which I'd use "panplantae" would be for the archaeplastids, and, wait a minute, we already have a word for those! This just gets better and better. You're a lumper, you say? Well, I've always been more of a splitter myself, if only to keep monophyletic groups. Werothegreat 12:16, 26 August 2007 (UTC)
"Pananimalia" is perfectly good Latin; it means "animal bread". --Curtis Clark 13:20, 26 August 2007 (UTC)
I don't see the linguistic problem with pananimalia. After all, the three greatest inventions of the last 150 years have mixed etymologies: auto (Greek), mobile (Latin); tele (Greek), vision (Latin); wiki (Hawaiian), pedia (Greek). Eugène van der Pijll 18:46, 26 August 2007 (UTC)

[edit] So... What should we do?

Well, I suppose it's become clear that there's little or no consensus in the scientific literature, on what to call the kingdoms, or even on what the kingdoms should be. Given the struggle one must go through to find consensus on anything in this place, it doesn't look like we stand much chance there. So: what do we do? The easiest way to avoid POV is to follow the Germans, and make everything the same unpleasant shade of wikipedia-blue. But I'm quite attached to the splashes of colour in articles, from a purely aesthetic perspective - and because I've nearly finished coding a bot to install my {{taxobox colour}} automater!

Emotional involvement aside, what do we aim to achieve with the colours? They're not adding information to an article, and in the vast majority of cases people don't need telling that something's a plant or an animal. In the event that it's not obvious, it often seems to be the case that the scientific jury is out.

So, much as it pains me, here's a suggestion for you to shoot down: Let's disable the colour parameter and make everything navbox-blue.

Verisimilus T 20:43, 26 August 2007 (UTC)

A measure of whether people notice: A common newbie-vandalism that I see is to change the taxobox color, perhaps to something the newbie thinks would better fit the article.
The colour automator is a wondrous thing, and if there were better consensus on the Kingdoms, that would be the way to go. But I reluctantly agree with Verisimilus. I'm not familiar with how the automator works, but perhaps setting all the choices to #ccf or whatever would allow us to easily reward ourselves with color when the Kingdoms stabilize.--Curtis Clark 22:51, 26 August 2007 (UTC)

I don't see what all the fuss is about. Unless we're going to take down the kingdom information from all infoboxes, what difference does colour make? Richard001 23:37, 26 August 2007 (UTC)

Correct me if I'm wrong, but we're going to keep the Kingdom field in the taxobox, right? If so, each entry will still have a kingdom listed that the color can corespond to. As for what to list, why not just stick with the system we have now, or revert to the 'traditional' 5-kingdom system until such a time as the taxonomy is sorted out and some kind of consensus is reached? Dinoguy2 00:18, 27 August 2007 (UTC)
I agree with Dinoguy2; in most cases (in terms of number of articles), the kingdom is simple. I see no reason why we can't have Animalia set to pink, Plantae set to lightgreen and only lump the difficult cases together into a default colour (without that colour necessarily implying monophyly). --Stemonitis 05:39, 27 August 2007 (UTC)
I agree with you two. Just how many taxa (as in "taxa having articles on WP or being interesting enough to likely get them in the foreseeable future") are actually affected by this? And in any case, we still have #e0d0b0 (I think) for the "Problematica" (basically "Kingdom incerte sedis").
The concept of strict monphyly is flawed at the kingdom level in any case. This may sound harsh, but it's what you get at the levels of horizontal gene transfer that apparently were still nothing unusual when plant and metazoan ancestors diverged... if you pick the right (or wrong) sequences, metazoans come out paraphyletic with viruses. The "tree" they use at TOLweb (see here) probably gives a good impression of the real deal. Dysmorodrepanis 15:46, 27 August 2007 (UTC)
Although I don't discount horizontal gene transfer, metazoans are paraphyletic with respect to some viruses because the viruses are metazoans, phylogenetically speaking. It has long been theorized, and for some groups of viruses there is good evidence, that viruses are replicating pieces of the genomes of cellular organisms, such that, for example, mammalian retroviruses are descended from mammals.
The advantage of monophyly as a hypothesis is that it can be falsified. Horizontal gene transfer can't be, since it can be invoked for any phylogenetic pattern.--Curtis Clark 16:35, 27 August 2007 (UTC)
I don't really see what the colours add either. And I'd just like to say that I don't care if the colours stay, go, or are simplified. —Pengo 07:42, 27 August 2007 (UTC)
Except most eukaryote groups have settled out. Many biologists (even that russian nut) recognize the difference between unikonts and bikonts, and that they are the only two branches of eukaryotes, and many more recognize the six supergroups of opisthokonta, amoebozoa, rhizaria, excavata, chromalveolata, and archaeplastida. All the incertae sedis fit into either bikonta or unikonta (most in bikonta). Werothegreat 21:44, 27 August 2007 (UTC)

Let's follow Verisimilus's suggestion and make everything navbox-blue for now. We can change it when the taxonomy gets sorted out, hopefully soon though I think much of the current system will get scrapped. Calibas 03:31, 28 August 2007 (UTC)

Let's not make any decisions based upon one article that appears to draw conclusions one cannot possibly draw from the sources it cites, at least not without some serious debate in the scientific community. This usually takes more than 10 days. KP Botany 04:14, 28 August 2007 (UTC)
I don't think any decision will be based purely on that article; the article is just one of many that have viewpoints inconsistent with one another!
I am almost bought by the suggestion of keeping the colours for established monophyletic groups (plantæ, anamalia... I'm not the one to make this list), and complementing this with a paraphyletic "eukaryote" colour for non-stable "kingdoms" where debate still rages - e.g. the Chromalveolata - as well as incertae sedis. Verisimilus T 09:06, 28 August 2007 (UTC)
Except debate isn't raging. Google rhizaria, excavata, or chromalveolata, and you will find many sites that recognize these clades. Sure, you'll get a couple that still recognize chromista, and the few 5-kingdomers out there, but most of the 5ker's admit that protista is not a valid taxon, and use the 5 for simplicity rather than any sort of phylogenetic justification. There is also the work of Adl et al, Cavalier-Smith, to name two. I'm sure there are others, though I can't name them off the top of my head. The only big incertae sedis I can think of are the apusozoa and the centrohelida, both of which are bikonts. All the old incertae sedis, the nucleariids, the ebriids, all fit into one of the six groups now. Nuclearida are choanozoans, and ebriids are cercozoans. Debate hasn't been raging for a while. Werothegreat 13:48, 28 August 2007 (UTC)
And is everyone agreed that the six groups are of equal ranking, i.e. kingdoms? If there is consensus for six groups, it does make a sound case for how to assign colours — if colours are deemed necessary. The nature paper I linked to, however, suggests to me that such a consensus is absent, at the moment at least (even if the paper is founded on bogus science).
Cavalier-Smith has made a name for himself by refusing to be bound by convention, a practice that, whilst bold, has made many sceptical of his claims; Further, by all accounts, he's not fond of people who disagree with him in print — I've not had time to read his papers, less still to get the thorough familiarity with all the unfamiliarly-named groups, but my instinctive reaction is to want wider support than C-S and someone else I've not come across before believing something I've read on Wikipedia! I think I'm slowly coming round to your argument, though - don't give up bludgeoning me with more reasons to believe you! Verisimilus T 16:26, 28 August 2007 (UTC)
The 6 groups being of equal rank is not the same as they being kingdoms. Merging fungi and animals into a kingdom Opisthokonta would be a big step from current practice. (It would also make taxobox colours by kingdom of little use, in that encylopedia users are not in general interested in the depths of eukaryote phylogeny - animal, fungus and plant are familar(ish) concepts to the man in the street, but opisthokont, chromalveotae and amoebozoan aren't.)
The evidence for the monophyly of each of the 6 groups is not unequivocal; in fact from the papers I've seen it appears weak. Lavateraguy 18:26, 28 August 2007 (UTC)
Verisimilus, we have hashed out the Cavalier-Smith issue with Wero, and he's aware of issues in the scientific community with C-S's organismal classifications, and is as mindful as possible of these concerns. Wero's a careful reader, and good at referencing. The issues are complex, and it wouldn't hurt to have someone looking over what he writes, and reading the C-S articles, and others, also. Wero deals more with articles that cite him than anyone else, so feel free to disagree specifically or elaborate any time you see an issue that requires this, as we are all aware of the need to handle citations by C-S with care and precision--it's a major, complex and very important issue in higher level classifications of organisms, and additional editors would be very useful--feel free to jump into the fire and the frying pan.
The issue isn't so much that people strongly disagree with C-S's conclusions, though, it's about the sweeping nature, overall, of the majority of conclusions. KP Botany 03:10, 29 August 2007 (UTC)

[edit] Cavalier-Smith

I'm meant to be reading a lot of other things at the moment, but if someone could post details of a couple of the more relevant references here, I'd be interested to cast my eye over them and see what I make of them! Cheers, Verisimilus T 08:34, 29 August 2007 (UTC)

Here's the Adl et al. article, which outlines the six major groups. <http://www.uga.edu/cellbio/pdfs/adletall2005.pdf>
Cogent Cavalier-Smith articles - <http://www.cladocera.de/protozoa/stechmann_2003_cb.pdf> <http://ijs.sgmjournals.org/cgi/reprint/52/1/7.pdf?ck=nck> Werothegreat 20:36, 29 August 2007 (UTC)
And please, don't anyone tell Verisimilus how long the average Cavalier-Smith paper is, until the hook is set. Thanks for posting links, Wero. KP Botany 05:01, 30 August 2007 (UTC)
Oh, I normally just skim through for important stuff, and focus on the diagrams. No one has the time to sit down and read an entire C-S paper in one sitting. Though the C-S Stechmann one is only two pages. Werothegreat 10:48, 30 August 2007 (UTC)

I love NCBI. This recent paper (from July!) gives further evidence for the monophyly of Rhizaria, Retaria (a clade within Rhizaria including the Radiolaria [sensus stricto] and Foraminifera), and Excavata. Also, the Nucleariids are found to be sisters to Fungi, so could be included in an expanded eumycetal kingdom, and all other choanozoa are sisters to Animals, which could be included in an expanded metazoan kingdom. Centrohelids (here called Heliozoa) and Apusozoa are still not including in one of the six supergroups, but Apusozoa are thought to be at the bottom of the bikont tree. <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17174576&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVBrief> Werothegreat 22:11, 30 August 2007 (UTC)

p.s., this was done using LSU rRNA. I'm still reading through recent articles... Werothegreat 22:12, 30 August 2007 (UTC)
Wow. Hear nothing for a couple years and ground-shaking work all within a year of each other (two were just published yesterday and last week!)<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17021930&ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum> Further evidence of mitochondrial endosymbiosis. <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16982820&ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum> Suggesting the Apusozoa are sisters to either the Opisthokonts or Amoebozoa, suggesting that one or both unikont groups derived from a biflagellate ancestor. Changes the definition of bikont and unikont.

<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17488740&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum> <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17726520&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum> These papers, published within the last seven days, together suggest that Chromavleolata is a sister group to Rhizaria. This blows the whole corticata/cabozoa dichotomy of bikonts (if this is even a valid clade anymore) out of the water. Wow. This is much better science than that four-kingdom crap. Werothegreat 22:25, 30 August 2007 (UTC)

Please note, that even though these papers propose some radical changes to the six-supergroup system, that all six supergroups remain monophyletic, and more evidence is provided for this. The proposed Rhizaria-Chromalveolata group does not disprove the monophyly of either group, merely advocates their melding.
 Werothegreat 22:29, 30 August 2007 (UTC)

Don't everyone comment at once... has this conversation sadly died? Werothegreat 20:18, 5 September 2007 (UTC)

Sorry, I've a lot on my plate, and haven't been able to catch up on the reading! I'll return shortly... Verisimilus T 09:46, 6 September 2007 (UTC)

OK, not to be a topic necromancer, but we really can't just let this discussion die. This is an issue that needs to be settled. Werothegreat 20:55, 4 October 2007 (UTC)

[edit] Necromancy

Okay, so there seems to be ample evidence for many of the higher-level groups, eg. Rhizaria. But, this still begs the question, where do we go from here? If we do decide that colours are useful, keeping fungi separate from animals seems to make a lot of sense for most readers. The bacteria and archaea groups don't appear too contraversial, either. I suppose the debate must be what we include in "plants" - if we're keeping animals and fungi seperate, perhaps restricting it to algae + land plants would be best. What other groups would we need - would Chromalveolata suffice? Verisimilus T 13:48, 27 October 2007 (UTC)

Recent evidence suggests that all of the choanozoa are split evenly on either side of the main branches of opisthokonta, i.e., animals and fungi. So, we can split all the unikonts into amoebozoa, "animals", and "fungi." That leaves Rhizaria, Excavata, Chromalveolata, and "plants" (I prefer the term Archaeplastida, but whatever). In this case, "plants" would mean land plants, green algae, and red algae, because they're all evolutionarily related. Some research also suggests that Rhizaria and Chromalveolata are close, but the four mentioned, no matter what their relations to each other, are pretty much settled as monophyletic groups. That gives us 7 major eukaryote groups (with some apusozoa and centrohelida on the side). Archaea is fine, and Bacteria is fine, as long as it is acknowledged as a stem group to Neomura (archaea and eukarya). As for colors, we have the green for "plants", the pink for "animals", the blue for "fungi", and the salmony-thing from the catalans for chromalveolata. Some possibilities for the other three could be lavender, light orange, and keep the protists khaki for one. Eukaryote brown can be used for apusozoa and centrohelida (which I believe is what they're colored now, anyway...) Werothegreat 10:25, 30 October 2007 (UTC)
Or wait, the salmony-thing didn't pass the test - nor did archaea-grey... Or does it even matter? Werothegreat 10:27, 30 October 2007 (UTC)
That sounds sensible. The salmony-thing (I assume you mean the bottom one on the final table) was close enough to passing (4.80 on a pass of 5.00) for common sense to permit its inclusion; I'm sure a slightly lighter version of Archaea grey could be suggested to make this compliant too, whilst we're making the changes. Lavendar and light orange (which precise colour do you mean - lightsalmon?) seem sensible for excavata and rhizaria; is the protist khaki a little similar to the generic eukaryote #e0b0d0? Probably not. Verisimilus T 13:09, 30 October 2007 (UTC)
Inasmuch as the foreground color is always black, they all pass.--Curtis Clark 14:01, 30 October 2007 (UTC)
The lighter pink color was meant for Archaea. The darker pink color (the one on the larger table) with the background word "Chromalveolata" is for Chromalveolata. I was thinking about #FFC8A0 for light orange, and that for Amoebozoa, and Khaki for Excavata, and Lavender for Rhizaria. —Preceding unsigned comment added by Werothegreat (talk • contribs) 19:16, 30 October 2007 (UTC)
D'oh. Oops! Verisimilus T 21:07, 30 October 2007 (UTC)


Well? The Archaea color change would have to be approved by the archaea group, so someone would have to post on the archaea wikigroup (if there is one, if not the archaea article) talkpage. As for amoebozoa and rhizaria, nobody really cares about them, so a vote here to change their colors would suffice. So, who's for changing amoebozoa to #FFC8A0 and rhizaria to lavender? Or against, if you like. Werothegreat 20:51, 2 November 2007 (UTC)

And the discussion dies again. *sigh* Werothegreat (talk) 18:57, 18 November 2007 (UTC)
Well, no-one's objecting, so let's press ahead! I've left brief notes on Talk:Archaea and Wikipedia talk:WikiProject Microbiology requesting comments be left here; I'll submit a bot request to remove existing "colour" declarations from taxoboxes, and an edit request on Template:Taxobox colour, when consensus has been reached (or after waiting a while for someone to reply...)
I might get you to check out my suggested edits to check that automatic colour detection will work appropriately!
Verisimilus T 20:27, 18 November 2007 (UTC)
Great! Let's sum up, shall we?
Animalia - pink
Archaeplastida - lightgreen
Fungi - lightblue
Chromalveolata - #FA7B62 (salmon-ish)
Amoebozoa - #FFC8A0 (a light orange)
Excavata - khaki
Rhizaria - lavender
Archaea - new color needed - possibly #F3E0E0 (a very pastel pink)?
Bacteria - lightgray
Virus - new color needed - Suggest #b9e
Incertae sedis/Eukarya - #e0d0b0 (a light brown)
Werothegreat (talk) 19:49, 19 November 2007 (UTC)
I still think the Chromalveolata colour is rather ugly. The suggestion of yellowgreengreenyellow seemed better, and also gives a nod to the close relationship of the group to the plants; I think that might be a more appropriate choice.
Verisimilus T 09:40, 20 November 2007 (UTC)
Hmmm. Yellowgreen seems to be too dark. I believe the color suggested was greenyellow... Werothegreat (talk) 21:00, 20 November 2007 (UTC)
Sorry - my misspelling; I thought it was a little dark, but blamed it on my laptop screen. Verisimilus T 09:53, 21 November 2007 (UTC)

So... shall we start? With the changing of the colors? Werothegreat (talk) 01:28, 23 November 2007 (UTC)

I'm ridiculously busy until Sunday, and it would be nice to keep the transition period to a minimum; I'll put in a bot request today, and we'll go when someone's been good enough to code one for us! Verisimilus T 10:16, 23 November 2007 (UTC)
So, any code yet? Werothegreat (talk) 16:52, 28 November 2007 (UTC)
No-one's shown much interest in my request yet. I hope I don't have to code it myself... Verisimilus T 19:00, 28 November 2007 (UTC)

[edit] Subsection for ease

Don't they usually take a while to respond anyway? Werothegreat 02:28, 1 December 2007 (UTC)

*sigh* RIP discussion. Whoa, deja vu! Werothegreat (talk) 22:33, 4 December 2007 (UTC)
Well, they've now archived my bot request twice; I may have to make a bot myself, which will be very time consuming - I won't have any time to consume until mid-January. So unless anyone comes forwards - it may be a long wait, I'm afraid! Verisimilus T 10:43, 5 December 2007 (UTC)
Very sad. Can we yell at anyone to make one for us? PM them or something? Werothegreat (talk) 00:38, 11 December 2007 (UTC)

Okay. In lieu of a bot, I'm going to start changing colors of higher level taxoboxes, in the hope that people will follow the trend and help out. Werothegreat (talk) 02:58, 20 December 2007 (UTC)

Okie dokie. I'll change guideline pages. Verisimilus T 11:09, 20 December 2007 (UTC)

Ummm... the whole don't-give-a-color-and-it'll-give-the-right-one thing is working for chromalveolates, but not for rhizaria, amoebozoa, or excavata. Can this be fixed? Werothegreat (talk) 15:38, 21 December 2007 (UTC)

Remember that you need to wikilink the kingdom entry. This will have the effect of bolding the text anyway on the article pages. Verisimilus T 16:02, 21 December 2007 (UTC)
Okay. But, the color for the excavates is the wrong color... it's supposed to be khaki... that's more booger... it should be the color that the protists used to be. Werothegreat (talk) 16:04, 21 December 2007 (UTC)
I've already noticed that and requested an update. I think I misspelt the original colour to something horrible! Verisimilus T 16:38, 21 December 2007 (UTC)
That's better. Lookin' good! Werothegreat (talk) 20:07, 21 December 2007 (UTC)

[edit] Wanted categories?

I created several wanted categories this morning, some of which duplicate existing names such as Elepids and Bovids. The duplicates should be merged, and one should become a redirect to the other, but which is better? Your input is requested... -- Prove It (talk) 22:15, 3 August 2007 (UTC)

[edit] Request for opinions

Greetings. Polbot is a bot that reads information from the IUCN and creates new stubs on plant and animal species. There is currently a request for opinions here regarding the linking of biologists' names. Any comments on that page would be welcome. – Quadell (talk) (random) 17:17, 7 August 2007 (UTC)

[edit] Animals project

Despite having some very specific animal projects, we have no central one to tie them together and allow for animal specific guidelines, discussions and assessments. Many animal related articles have to be assessed under the tree of life or even biology assessment scheme, despite being specific to animals. There are also other projects that could emerge from it in the future, such as one on animal behavior for example. With the project the pathway to improving zoology related articles is much clearer. If you are interested in creating this project please register your support and ideas here. All projects that come under the potential parentage of this one have been contacted. Richard001 09:13, 8 August 2007 (UTC)

Regardless of whether or not an umbrella project is created (and I personally support a way to standardize bio/zoology pages), the idea that sticks out with me is the concept of a project on animal behavior. As of now, there are not even stub or cat tags for ethology, and I feel it is important that some sort of project concerning this should be started. There are many species articles that inform the reader about an animal's name, habitat, size and shape, etc.--but that which intrigues and makes real the product of evolution and interests people not that concerned with systematics are the hows and whys of the way an organism interacts with its environment. Wikipedia seems somewhat lacking with regard to information like this. TeamZissou 09:41, 8 August 2007 (UTC)
I agree. Morphology, taxonomy, ethology & ecology of animals, amongt others, should be treated as centrally as possible with the inevitable forking/branching. Unfortunately instead of a Tree we have a weed approach with few articles being thrown up randomly by the WikiProjects. Snake scales has developed but Reptile scales has not. There is definitely a need for this WikiProject, not particularly from TOL pt of view, (WikiProjects are doing their bit, thank you very much) but to develop zoology in a general fashion. AshLin 11:45, 8 August 2007 (UTC)
I think this is a great idea, especially the animal behavior idea. I'd love to join such a project. Cheers, Corvus coronoides talk 01:40, 9 August 2007 (UTC)
I was wondering why there wasn't an animals project, nobody bothered to make one yet. I'll join. Calibas 02:23, 9 August 2007 (UTC)

I've started working on a draft at User:Richard001/Animals draft. Feel free to work on it - it's extremely skeletal at the moment and needs a lot of development. Richard001 01:44, 7 September 2007 (UTC)

[edit] Proposal Added

I think this is an excellent idea, so I've added the proposal to the WikiProject Council. If there is enough interest to handle a project of this size, I will start the skeleton and we can get working on it. J. Hall • (Talk) 18:10, 27 September 2007 (UTC)

[edit] Phoca vs. Pagophilus

Which is the proper Genus for Harp Seal? TNC and IUCN say Pagophilus, as does Phoca, but the article gives it as "Phoca", as does Smithsonian publications... Circeus 20:42, 10 August 2007 (UTC)

MSW3 agrees with TNC and IUCN. - UtherSRG (talk) 21:07, 10 August 2007 (UTC)

Another one: TNC says Bos and Bison are congeneric. Any thoughts? Circeus 22:25, 10 August 2007 (UTC)

Aren't these all questions of circumscription? If so, then there is no right answer, and each arrangement may be used by different sources. Fortunately, we are not constrained to a strict hierarchy, and we can explain how, depending on your generic concept, the scientific name can be either Phoca groenlandica or Pagophilus groenlandicus, and each of Phoca and Pagophilus can explain that the species is sometimes included in the other (or in this case, note at Harp Seal that it's sometimes split off into a genus of its own). There is fundamentally no such thing as a "proper genus", but at best a more likely or less likely hypothesis of relationships. --Stemonitis 14:33, 11 August 2007 (UTC)

[edit] Question on this Project

Hello I was wondering if I could join this project- and if the project includes nomen dubia or nomen nudum for taxoboxes. If I could get a response of what I could do for this project please contact me. Superraptor 16:06, 11 August 2007 (UTC)

Superraptor, you're welcome to join any project on Wikipedia that you want to join, simply by listing yourself as a participant on the project page. I think that sometimes nomen dubia are used as articles, in which case, if there is a taxobox, that is the name that would be in the taxobox, but I don't really know. It's easier for us if you just let us know what your interests are and someone can steer you towards a subproject or articles that might interest you. I didn't respond initially, because I assumed one of the animal folks would. Oh, wait, I see the big clue glaring at me. Try the folks at WikiProject Dinosaurs, and that is where I was thinking that nomen dubia might crop up. KP Botany 19:00, 12 August 2007 (UTC) PS With my apologies to anyone who catches the dreadful play on words.
Yep, this term comes up all the time at WP:DINO - Drop by, maybe you can join? :) Spawn Man 07:57, 15 August 2007 (UTC)

[edit] List of articles? (A articles, B articles, stubs, etc.)

In many articles, there are now headers in the talk pages detailing their importance (top, high, etc.) and their level of completeness (stub, FA, etc.). However, there is no overarching list compiling these. Such a list would make it easier for editors to focus on those top importance articles that are only stub or start class. How would one go about doing this? Werothegreat 12:34, 15 August 2007 (UTC)

Well, for each project currently analysed by WP 1.0bot, there is exactly such a list of articles (e.g. Wikipedia:Version 1.0 Editorial Team/Taxonomic articles by quality or Wikipedia:Version 1.0 Editorial Team/Arthropods articles by quality). It shouldn't be too hard to look through and find all the high-importance stub-class articles, or any other similar combination. --Stemonitis 12:56, 15 August 2007 (UTC)

[edit] Invertebrate paleontology

The article Invertebrate paleontology may benefit from additional contributions. Thanks! -- Jreferee (Talk) 20:10, 20 August 2007 (UTC)

[edit] Author (zoology)

A {{prod}} template has been added to the article Author (zoology), suggesting that it be deleted according to the proposed deletion process. All contributions are appreciated, but this article may not satisfy Wikipedia's criteria for inclusion, and the deletion notice explains why (see also "What Wikipedia is not" and Wikipedia's deletion policy). You may contest the proposed deletion by removing the {{dated prod}} notice, but please explain why you disagree with the proposed deletion in your edit summary or on its talk page. Also, please consider improving the article to address the issues raised. Even though removing the deletion notice will prevent deletion through the proposed deletion process, the article may still be deleted if it matches any of the speedy deletion criteria or it can be sent to Articles for Deletion, where it may be deleted if consensus to delete is reached. If you endorse deletion of the article, and you are the only person who has made substantial edits to the page, please tag it with {{db-author}}. NOTE: This redirect is linked fromAuthor (disambiguation). Not sure if this is the best way to handle the problem (a dictionary entry pointing to author(zoology) which is redirected to an unrelated article.) Spa toss 20:26, 20 August 2007 (UTC)

[edit] Species names in genus taxoboxes

Hi, I'm creating a bunch of taxoboxes for bacteria and archaea, and I had a question about the way that species should be listed in a genus taxobox. For example, please see Methylarcula or Thermococcus. I've been listing the species alphabetically, and including the full genus name. But I've noticed that others abbreviate the genus name when listing the species in the taxobox of a genus, e.g., M. terricola in Methylarcula. I'm also not sure how to handle the species with codes like Methylarcula sp. DT-12; should they even be listed at all? Does the alphanumeric code mean that they might not be a well-defined species? I should say straight away that I've no expertise with the modern taxonomy of microbes. Thanks for your help! :) Willow 13:41, 22 August 2007 (UTC)

These are unnamed bacterial isolates of the genus Methylarcula. I don't think the isolate number is italicized, but I'm not sure. This is how they are usually reported when it is a species that has been cultured and identified to a genus, but not given a species name, just like you posted, but, again, I believe without the isolate (and certaintly not the "sp.") in italics: Methylarcula sp. DT-12. They can only have an isolate "code" if they are a well-defined species.
Use the source article from which you got the Methylarcula isolates to decide whether or not they should be listed in Wikipedia. I don't have any bacteria articles handy, but I think that isolates to a genus, without the genus name are just called by the isolate, not italicized. For example, if I was discussing Quercus agrifolia and Quercus lobata I would eventually use Q. lobata, but for the Methylarcula sp. DT-12, in a later mention in an article on this genus, I would just refer to it as DT-12--again, not certain, and again, the article from which you obtained the initial information about the isolates will be the source to look at for style issues. In general, in species lists of bacterial isolates, I don't recall seeing the genus name abbreviated to an initial--again, check your source articles for this. Maybe someone else can help? KP Botany 01:49, 24 August 2007 (UTC)

[edit] Graphical fossil range indicator

In case you're interested, it's now possible to graphically illustrate a species' fossil range in taxoboxes, using my latest template {{fossil range}}. See Chitinozoan for an active demonstration. As with much of my work, it's likely to be buggy. Try to be kind when pointing out its flaws; your moans are gratefully appreciated on the template talk page. Thanks, Verisimilus T 19:33, 1 September 2007 (UTC)

I see you've added it to bird, but it isn't clear what it is trying to achieve. All I see is a scale using letters, but I only understand what they mean because I'm a dino-geek. The meaning would be lost on most people. EDIT, oh wait, I see, the green line is supposed to denote range. Although you'll forgive me for not getting it as the line suggests a range of birds from the Precambrian to the begining of the Ordovician! Sabine's Sunbird talk 00:07, 2 September 2007 (UTC)
As I mentioned on Taxobox usage, the lines appear too short for me, or misplaced, causing Therizinosaurus to be Paleogene and Archaeopteryx to be early Cretaceous! These graphical things should probably be removed at least until the formatting can be fixed... You admit it's buggy, shouldn't the bugs be worked out before adding it to prominant and featured articles? Where was the use of this app agreed upon? I missed that discussion. (The line on Bird appears from the Early Cretaceous to present for me, by the way. It should really extend into the Jurassic a bit). Dinoguy2 00:14, 2 September 2007 (UTC)
I just added it to Orchidaceae and it looks good to me. JoJan 08:17, 2 September 2007 (UTC)
The template does not display properly in Safari. In Firefox most of the ranges appear to match the dates listed in their format, though Tyrannosaurus is still off even in Firefox for some reason. I would recommend not spreading these around until they can be made to display correctly in all web browsers. Dinoguy2 08:38, 2 September 2007 (UTC)
I thought I had the template fixed in all browsers, but had assumed that Safari would be standards-compliant in the same manner as Firefox. Frustratingly, this is clearly not the case; this is a major issue which I'll work on today, when I get on a Mac. I've fixed the minimum-width issue on Firefox and am working on IE now.
I'd placed it on prominent articles as this was the quickest way to get some feedback, and raise awareness of the template. (WP:BOLD). I'm not planning on rolling it out exhaustively until I'm confident that it displays correctly on every combination of browser and OS... Verisimilus T 09:25, 2 September 2007 (UTC)

[edit] IUCN 2007

Ah... it's that time of year again. The kids are back at school, vandalism on Wikipedia is high, and the IUCN has published their updated listings. We should get a 'bot to update the taxoboxes.... - UtherSRG (talk) 16:31, 12 September 2007 (UTC)

I've created {{IUCN2007}} and updated Common Chimpanzee and Western Lowland gorilla. - UtherSRG (talk) 16:41, 12 September 2007 (UTC)

[edit] Genus article naming conventions

What's the standard when creating a genus article that exists for a different genus? Case in point is Tetracoccus, which already exists as part of Picrodendraceae, but there's a identically-named genus which is part of Dictyosphaeriaceae. Would it be Tetracoccus (Dictyosphaeriaceae)? Tetracoccus (algae)? Something else? Or is this a case of "make something up as you go"? Neil916 (Talk) 22:43, 22 September 2007 (UTC)

I'm not sure. Does anyone know of any other cases of identically named genera? If one was more well known it might be best to give the newer article the qualifier in brackets, otherwise they should probably both be given brackets and a disambiguation made. For what to put in the brackets, a more common name would probably be best as used with other articles, e.g. as in tui (bird). So in this case I would probably go with (plant) and (algae). Richard001 23:47, 22 September 2007 (UTC)

[edit] TOL peer review

It seems to me that there are enough animal/plant FA's going through to warrant a TOL peer review section. Anyone agree? -Ravedave 01:38, 23 September 2007 (UTC)

It would be helpful to those putting up FAs to get them reviewed by someone else with a background in biology. Even if your interest is paleontological and dinosaurian, you would be better at reading and giving editing tips on a plant article than an editor with no background in the life sciences. I would like to see one. KP Botany 02:01, 23 September 2007 (UTC)
Very good idea. How do we go about doing this? Werothegreat 11:04, 24 September 2007 (UTC)
Let's get Dave to put up the request for review page for all living things, as he suggested above. KP Botany 23:10, 27 September 2007 (UTC)

[edit] WikiProject Animals Created

Interest in a WikiProject Animals seemed high, so I've created the project (with most of the hard work done by the folks at WikiProject Plants. I still have to put together a todo list, but would appreciate anyone willing to contribute. Thanks, J. Hall • (Talk) 07:17, 28 September 2007 (UTC)

[edit] Wikipedia:Most_wanted_articles#Scientific_classifications

Wikipedia:Most_wanted_articles#Scientific_classifications has been updated using the 2007-09-08 data dump, and a section covering scientific classifications has been created that may be of interest to members of this WikiProject. --Sapphic 19:06, 8 October 2007 (UTC)

[edit] Synonyms and redirects

I have parsed the species taxoboxes in the August 2007 database dump, and created a list of all of the synonyms mentioned. In my opinion, all of these names should redirect to the corresponding article, as some of them are still encountered. For example, I have added a lot of images to articles from 19th century out-of-copyright prints, which were often labeled only with an obsolete synonym. However, 5555 of them are redlinks (as of last August).

This is a small sample of that list:

  1. Do you all agree that each synonym should be a redirect?
  2. Should I write a bot that creates the ~5500 redirect needed?
  3. Would it be useful to run the bot on lists of synonyms from other sources, to automatically create all redirects to existing articles for thoses synonyms as well?

One complication is that some binomials have been used for several different species. I only propose to create redirects if the synonym occurs in just a single taxobox; if there is not yet an article with that name; and if the synonym is not followed by the word "non". There will still be a few remaining cases in which the bot would make an inappropriate redirect, but that would happen as well if someone would create the redirs manually. See for example this correction. Eugène van der Pijll 20:38, 8 October 2007 (UTC)

It sounds good to me. The bot would probably make less mistakes than humans. Richard001 22:40, 8 October 2007 (UTC)
My bot was approved for this work, and I did a first run of about 25 redirects; see Special:Contributions/Eubot. If there is no objection, I will start to do larger runs in a few days. Eugène van der Pijll 23:32, 30 October 2007 (UTC)
How will your bot deal with common names which are used for more than one species? I sometimes find myself having to sort out Polbot's odd decisions, eg at Thornback ray/banjo shark. Totnesmartin 00:06, 31 October 2007 (UTC)
All redirects that I create are scientific names. I don't plan on adding redirs for common names by bot, exactly because of the problem of common names being, you know, so common.
(Note that the name "thornback ray" really is used for the banjo shark as well, eg. here, and that our article thornback ray should at least link to banjo shark. I have added that link, and a taxobox with an image.) Eugène van der Pijll 00:40, 31 October 2007 (UTC)
Yes, I should have linked to banjo shark - and thanks for the additions, I have no idea where to get pictures for the articles I create. Totnesmartin 13:04, 31 October 2007 (UTC)

[edit] Juvenile vs. adult

juvenile eastern newt
juvenile eastern newt
adult eastern newt
adult eastern newt

If a article has a good picture of a juvenile organism, and only a poor shot of an adult, which should be in the taxobox? --Cynops3 00:16, 12 October 2007 (UTC)

It's rather odd that we always use adult organisms as the 'standard' idea of what one should look like, given that it's just one stage in the life cycle, as important as any other. Many species spend most of their lives as larvae, and only a brief period as adults, yet you'd certainly be surpized to see a cicada larva rather than an adult as the lead image. If they spend the majority of their lives as adults, it makes more sense, and there's also the argument that adults are what we are more familiar with. Another one is that organisms are most distinct from each other when adults, e.g. fetus of a dog and human would not show the differences between them very well. I don't see much harm in using a juvenile though, especially if it's a better image. We should also be sure to avoid using males as the 'normal' case, an assumption that runs deep in Western society. Richard001 00:57, 12 October 2007 (UTC)
I'd use the juvenile in this case as the picture of the adult very poorly illustrates the subject. Richard001 makes some good points and I believe we should determine which to use on a case by case basis instead of making solid rules. Calibas 05:51, 12 October 2007 (UTC)

[edit] category defaultsort

I was about to do a category defaultsort on some animal-related articles, but thought I'd better ask here first. Would it be OK to do this? it would mean entering (for example)

{{DEFAULTSORT:Skua, Arctic}}

Making the Arctic skua under S rather than A, so that all the skuas are easier to find on the category page. this would be useful for categories which include many types of animal (eg geographical and habitat categories). This is of course the way it should be done for biographical articles - but why not for biology articles? Opinions please. Incidentally, this debate started here. Totnesmartin 15:00, 22 October 2007 (UTC)

UPDATE:I've done a basic version of it here and it works. Now all the gulls, plovers and gobies are together instead of scattered about the page. Totnesmartin 23:54, 23 October 2007 (UTC)
I don't like this for two reason: It's not always as clear-cut where the cut should be made, and as long as all articles are not done (not to mention the constant influx of new articles) you will end up with categories where some members are split, and other nones (much like what we had in some plant categories with some english names and other latin... At some point Category:Sapindaceae add all English-titled maples split and under "M", but all the latin ones under "A"! Circeus 05:09, 24 October 2007 (UTC)

That is rather awkward, however redirects can be categorised as well (without affecting the functioning of the redirect), so perhaps a solution lies there. Personally speaking, I think having all the plovers under G and all the Plovers under P makes perfect sense. On the other hand, you are right to say that there's not really a need for taxonomic categories to have it. In the end, the defaultsort tool would cause as many problems as it solved! Hand sorting it is then... Totnesmartin 10:50, 24 October 2007 (UTC)

I think that conclusion is partially correct, the DEFAULTSORT magic word probably isn't the sole solution, as different categories will regularly merit different sorts. Maintainers of a given category should feel free to sort the category as makes sense for that category. I believe that in Taxonomic categories the latin names should all be present (by categorizing the redirect, if need be). Sub-articles should be treated the same way that there parent is, with the sub-article term (e.g. Tilapia in aquaculture, the sub-article term is "in aquaculture") added to the end.
Another possibility is to create a disambiguation or list article and categorize it. We'd do a list article where the list of species is too long for complete inclusion in the article on the genus (or other higher level grouping with a single common name). We'd use a disambiguation page for unrelated things with identical common name, as in Whiting (fish). GRBerry 11:50, 24 October 2007 (UTC)

[edit] Wikipedia:Featured article candidates/Lambeosaurus

Lambeosaurus has become a Featured Article candidate. Suggestions for improvement or other comments from WP:TOL members would be welcome. I'd like to avoid groupthink and receive feedback from more of the community on FACs like this one. Firsfron of Ronchester 14:12, 30 October 2007 (UTC)

[edit] Distribution map request

Is there someone here who can create a nice distribution map from data? I'd like to have one on the article for Monosolenium, but can't generate it myself. It's an east Asian plant, and all the necessary distribution data can be found in the start of the section on Ecology. --EncycloPetey 23:59, 4 November 2007 (UTC)

[edit] Notice of List articles

Page(s) related to this project have been created and/or added to one of the Wikipedia:Contents subpages (not by me).

This note is to let you know, so that experts in the field can expand them and check them for accuracy, and so that they can be added to any watchlists/tasklists, and have any appropriate project banners added, etc. Thanks. --Quiddity 19:33, 5 November 2007 (UTC)

[edit] Taxoboxes for Livestock species and Categories

Is there some way we can make this less circular: See, e.g. Goat, the article is about the domesticated species (Capra aegagrus hircus), the taxobox puts it in Cat:Domesticated animals, however, the article is in Cat:Goats which is a subcat of Cat:Livestock, which is in Cat:Domesticated animals, which is unnecessarily duplicative. Also see, e.g. Chicken which is listed as domesticated and therefore in Cat:Domesticated animals but Cat:chicken is in Cat:poultry is in both Cat:domesticated birds and Cat:livestock both of which are in Cat:domesticated animals. This is a problem with any species that is categorized as livestock or poultry. Is there any way to make the taxoboxes more flexible with respect to categorization?--Doug.(talk • contribs) 19:29, 12 November 2007 (UTC)

[edit] Category:Syngnathidae

Category:Syngnathidae is orphaned. Maybe someone here will know what parent category (or categories) it belongs in. --BrownHairedGirl (talk) • (contribs) —Preceding comment was added at 14:34, 16 November 2007 (UTC)

Added to Category:Syngnathiformes. Thanks for the heads-up. — Dave (Talk | contribs) 15:00, 16 November 2007 (UTC)

[edit] Identification of a lily

Hi, I believe that the lily in this photo: Image:Bouquet of flowers apr07.jpg is that of the Easter Lily. Could someone please confirm? This shot of the stigma may be of use: Image:Large stigma.jpg Thanks, --Fir0002 02:12, 20 November 2007 (UTC)

Might have more luck at Wikipedia talk:WikiProject Plants. Calibas (talk) 03:05, 20 November 2007 (UTC)
Thanks for the tip - I'll give it a shot --Fir0002 21:09, 20 November 2007 (UTC)

[edit] Capitalisation of Common Names - Komodo Dragon vs. Komodo dragon

Stuck. Wikipedia talk:Manual of Style is the place to resolve this.

I notice bibliomaniac has reversed my change of the capitalisation of common names on the page on Komodo Dragons to "Komodo dragon" in spite of correspondence between us. As I said to him previously, either is acceptable, but I believe there are a number of reasons for choosing to capitalise the inital letter of each major part of the common name.

There is no hard and fast rule for most animals - there is no standard convention for common names, as there is for scientific names. But it has been the common convention with bird names for many years to capitalise the first letter of each major part of the common name - hence Bald Eagle, Common Crow, Black Swan. See, for example, the notes at: http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Tree_of_Life#Animals and http://en.wikipedia.org/wiki/WP:BIRD#Bird_names_and_article_titles.

This general rule - for some reason - has not always been applied to other orders of animals - I am not sure why.

However, the capitalising of common English names is becoming much more widely used, and so you will frequently see names written like: "Sign-bearing Froglet" (rather than "Sign-bearing froglet") and "Ornate Soil-crevice Skink" (rather than "Ornate Soil-crevice skink"), Alpine Cool-skink (rather than Alpine cool-skink) or Curl Snake (rather than Curl snake). None of these forms is "incorrect", but it is certainly becoming more standard to capitalise all major parts of the name.

There are good reasons for this. First, proper names are almost always capitalised in English. Secondly, it clearly shows that the last part of the name is separate from the first and to some degree classificatory - thus, Froglet, Snake, Monitor, Crow, Eagle, etc. In the case of the Komodo Dragon I think it usefully emphasises that we are not talking about some other sort of "dragon" (perhaps raising thoughts of dragons in mythology), and that it is a shortened form of the name of a real animal. For similar reasons, I think Tasmanian Devil is far preferable to Tasmanian devil, as the latter does not make it clear that it is a proper name and someone could easily think one was referring to some devil in Tasmania.

Finally, I think it is best to stick with one style to improve consistency and prevent confusion and I don't see why the convention should be limited to birds in the Wikipedia.

I think we need a rule or style, if not a convention, on the best way to list common names for animals and plants in the Wikipedia. At the moment, many articles contain a confusing jumble of both. For example, in this case, we find the following forms: Komodo dragon, Komodo Dragon, dragon and Dragon all referring to the same species, all in a single article

I would appreciate other readers' comments on my suggestion. John Hill 01:45, 1 December 2007 (UTC)

Well, there is an official Wikipedia position, clearly articulated in the Manual of Style and in the Naming conventions, and it disagrees with your preference for initial caps. That consensus was hashed out in a huge discussion at MoS, which can be found in the MoS talk archives. If you read those discussions, you'll discover why the situation at WP:BIRD can not be extended more generally. Basically, it boils down to the fact that there are "official" common names of bird species and that those official names are capitalised by definition. That argument was not and could not be made for other groups of animals. To be frank and with all due respect, this continual resurrection of the capitalisation debate is a bit tiresome. Can we not simply adhere to the MoS and NC (fauna) that say we don't capitalise routinely? — Dave (Talk | contribs) 02:28, 1 December 2007 (UTC)

Hi Dave:

Thanks for taking the time to reply and for pointing out that there IS a Wikipedia convention (which somehow, I had missed). Sorry if all of this has been thrashed to death previously - it is new to me. I still feel, however, that the names would be better capitalised for the reasons I have given above (clarity, consistency, less possibility of confusion, plus the fact that proper names are usually capitalised in English - and this capitalisation indicates that it is a proper name and not something else). "Tasmanian Devil," mangrove Jack," and "Water Dragon" (for example) are clearly names, while "Tasmanian devil," "mangrove jack," and "water dragon" are not.

For a good discussion of the problems and possible solutions, see: "Capitalizing the Approved Common Names of Species" (2003) by Ernest H Williams, Jr and Department of Marine Sciences, University of Puerto Rico, at: [1]

Whatever the case, we now have a really confusing mishmash in hundreds, if not thousands, of articles. For example I just looked up the article on the Snapping turtle which in the very first line gives the name as Snapping Turtle - and this sort of inconsistency is extremely widespread throughout the encyclopedia. I think we need to insist on one system only (and I won't keep on ranting if my preferred method is not the one chosen). Sincerely, John Hill 05:16, 1 December 2007 (UTC)

I understand your points. As you'll see from the archived discussion, those points all were made there. You'll also see what points were made by the prevailing side. In any event, I agree that we need consistency. I suggest only that that consistency should be informed by the existing guidelines. Hence, I maintain that among our tasks as editors is that we should change those articles, such as the Snapping turtle article to which you refer, to conform to exising guidelines. By the way, I notice that the reference you've provided is entitled Capitalizing the Approved Common Names of Species (emphasis mine). That goes directly to what I was talking about with the case at WP:BIRD, where the Ornithological Union has sanctioned approved official names and where the approved names are all capitalised names. We don't have a comparable situation in the reptiles, for example, or for most other groups of organisms. Cheers! — Dave (Talk | contribs) 14:02, 1 December 2007 (UTC)
There was, I suppose, a prevailing side in the MoS discussion, but the issue has not settled because there are heavy ToL editors that still prefer upper case and still employ it. (That would include myself.) The best rule of thumb I can think of for now: if you can show that at least a minority of sources employ it for a particular species, then it becomes a matter of editorial discretion. On this basis I've left caps in place on Giant Otter. Others should respect the original or primary author. Marskell 14:56, 1 December 2007 (UTC)
But doesn't this, in the end, amount to some combination of "preference trumps consistency" and "heavy editors needn't follow consensus"? I fear the consequences of such a position: endlessly explaining to new editors why our articles are a jumble of styles and thereafter engaging in the attendant rehashing of the various sides of the discussion.
  1. Recall that our readers do not read the sources, they read the article. Let me assure you that there is no publication in the world that leaves stylistic decisions to "a minority of sources". For example, in writing a chapter for a textbook, the overall textbook style prevails and I am not free to simply follow the style of a minority of sources.
  2. It leads to questions of who is and who is not a "heavy editor" and how do we identify "the original or primary author" of an article. Is it not a much cleaner solution for us to simply ask that all editors, heavy or light, follow the guidelines in the absence of some compelling reason to the contrary?
  3. How do we encourage all editors to take part in the consensus-building process if a an editor, especially a heavy editor, can at the end of it continue to do as he prefers and claim, perhaps, that preference is a compelling reason not to follow a guideline? It seems to me that a guideline that is applicable to a light editor, who makes 1 or 2 or 5% of the edits to our pages, also should be applicable to a heavy editor who makes 50 or 70 or 90% of the edits. After all, it is that heavy editor who, by sheer volume of his edits, wins the day. Consensus-building is the most important aspect of Wikipedia's existence. What does it say to a new editor who we are trying to bring into "the process of Wikipedia" if, after a process has run its course, a heavy editor's preference still deserves deference?
In the end, I suppose, it boils down to a question of for whom do we exist? If we exist for the convenience of readers, consistency matters. If we exist for the convenience of heavy editors, then consistency can afford to be relegated to a subsidiary level of concern. Let me assure you that I'm not attempting to say that you are doing any of these things but that they appear, to me, to be the logical consequence of the positions you espouse. — Dave (Talk | contribs) 16:15, 1 December 2007 (UTC)
I would not have typed "heavy editors" had I expected this misinterpretation. I was not suggesting a special entitlement, but only observing why the issue has remained unresolved.
Guidelines should be followed but also admit to exceptions, which is why they're guidelines. On this particular issue, I don't see that we're seriously compromising our presentation to readers. There are tens of thousands of ToL subjects, edited by thousands of people. Unless we turn a bot loose I can't ever imagine consistency on this; and a bot will only work until somebody else comes along and muddies things up again. The fact is a large minority of people are going to turn up and capitalize species names because they believe they are proper nouns or simply because it's what they're used to. I came to Bobcat and found it upper case; that's what I prefer, so I left it as it was. Ditto on Giant Otter. Marskell 16:39, 1 December 2007 (UTC)
Firstly, I apologise if you feel I've misinterpreted your contribution. If I did so, it was entirely unintentional.
I agree that there exist exceptions where we should not follow a guideline. This is touched on, for example, in Wikipedia:Manual of Style#National varieties of English where they suggest that the guideline should be followed "unless there is a compelling reason not to". My position is quite simple. I maintain that there are decidedly clear advantages to following the guideline in this case, among them that it helps the encyclopedia strive for consistency and that it encourages participation in the consensus-building process. Frankly, I can't see a single advantage in encouraging or suggesting to editors, especially those who make most of the edits, that they need not follow the guideline. In my opinion, simply saying that there will always be editors who don't follow the guidelines is not an acceptable reason for me to not follow the guidelines. Let's face it, 90% of edits are made by 10% of editors (I made that up but you know what I mean :-)). If we can recruit those 10%, or a significant fraction of them, to follow the guidelines, we will have a hope of approaching consistency. As long as a significant fraction of that 10% are permitted to think that the guideline doesn't apply to this case or that other because of preference or some other non-compelling reason, your pessimisn is well-founded. In a similar vein, I don't feel that I can justify not following a guideline because I prefer it, or I happened upon it, elsewise. In my opinion, doing so denigrates the consensus-building process. When editing an article, I will choose not to leave it in a style I prefer if the guidelines support another unless I can find a compelling reason to do so. But that's me, and I appreciate that others may not feel the same way. I guess, for me, it boils down to the fact that I can't see a single compelling reason not to follow the guidelines in this case while I see clear and significant advantages in following them. Of course, I am always amenable to instruction otherwise. — Dave (Talk | contribs) 17:29, 1 December 2007 (UTC)
I do see an advantage in not following the guideline on this one: it eases readability and understanding, and is appropriate because species names should be considered proper nouns. (IMO—others have disagreed.) When I typed "The otters form the Lutrinae subfamily within the mustelids, and the Giant Otter is their largest member," I found the upper case much preferable, for instance. At present, I actually don't change anything: if it's upper case I leave it because that's what I like; if it's lower case I leave it because of the guideline. Marskell 18:52, 1 December 2007 (UTC)
Fair enough. As you know, all of those arguments in favour of caps were discussed at length on the MoS talk page. In summary, then, you feel that the advantages you cite are compelling advantages that encourage you to ignore the guideline when editing articles that are already in violation. I understand your position and I thank you for sharing it with me and for making it clear. Needless to say, I disagree. I feel that the advantages of consistency and of encouraging respect for the consensus-building process are more important. To each his own, I suppose. Now, if you'll excuse me, I must run along. The Dog and Cat are making me miserable by whining for food and I really must go milk the Cows, slop the Pigs and water the Horses. Cheers! — Dave (Talk | contribs) 20:23, 1 December 2007 (UTC)
Dave's usage of upper case in his last sentence is not what I advocate. That's common noun usage and should be lower case; in a mild sin, I've cross-posted to his talk so the point is understood. Marskell 20:36, 1 December 2007 (UTC)
No, I understood that. It was simply my feeble attempt at humour and I see, now, that it was feeble indeed. I also meant it as a light-hearted way to demonstrate my own point, though. The articles for dog, cat, cow, pig and horse are all written in lowercase and do not appear to suffer from any readability concerns. In any case, I apologise for having been obtuse. It appears my wife is right -- I shouldn't quit my day job in an attempt at a career in comedy (neither of which are uppercased in their articles, either)! — Dave (Talk | contribs) 20:47, 1 December 2007 (UTC)
Bringing up (D)dog and (C)cat is understandable, funny bones aside. Just over a year ago, I was using that exact example with User:UtherSRG (by volume of edits, he's our most prolific fauna editor, and he approves upper case) when I was on the opposite side of the ledger. Do you really want to audit for every proper noun usage of dog and upper case it?, I was thinking.
That would be impossible, but I've changed my mind more generally: typing black bear to refer to a species ceased to make sense; it's the Black Bear, like this is Wikipedia—a proper noun. Editing birds makes it all the more clear and I think ornothologists are spot-on with capitalization, even if they appear a weird minority. If you audited across subject matter types, I think you'd find English remains significantly inconsistent on this. Marskell 21:04, 1 December 2007 (UTC)
Deary me! I didn't realise I was going to stir up such a discussion - but it is good to know that people do care so much - I am just sorry that I have taken so much of your time. I guess until the Powers That Be (who I guess are taxonomists and active biologists) make up their minds I will follow Marskell's maxim: I won't "change anything: if it's upper case I leave it because that's what I like; if it's lower case I leave it because of the guideline." I really do think upper case is really preferable and clearer and an increasing number of books and articles seem to be using it as a standard. Anyway, enough already! Season's greetings to you all and best wishes for the New Year (and thanks again for your thoughtful comments on my query). Cheers, John Hill 22:54, 1 December 2007 (UTC)

This discussion is probably pointless here and should instead take place at WT:MOS, since the style guideslines are not going to change one way or the other because of discussions at topical wikiprojects. — SMcCandlish [talk] [cont] ‹(-¿-)› 21:26, 12 December 2007 (UTC)

Ah, but it's actually so simple:
  • All Leading-letters Capitalized is always permitted
  • Leading element-only capitalization is OK except for birds (I think no other group has common-name standardization) though one would perhaps avoid it in mammals too (for many mammals, informal "standard vernaculars" exist as per IUCN etc)
  • In-Word Capitalization is best avoided; it never was very widespread and it can be misleading.
  • no capitalization for anything above species except when at the start of a sentence.
Did I miss something? Dysmorodrepanis (talk) 00:59, 22 March 2008 (UTC)

[edit] Taxobox-related CfD

A closed CfD had (apparently) the unintended consequence of renaming nearly all the "needing a taxobox" categories within the Tree of Life. There is currently a DR going on at Wikipedia:Deletion_review/Log/2007_December_12#Category:Articles_needing_an_infobox, for those that are interested. Justin chat 02:36, 14 December 2007 (UTC)

[edit] Last common ancestor/Most recent common ancestor

Hi there, a discussion is underway on the talk page of Last Common Ancestor on the correct definition and application of these terms. Could somebody with some knowledge of phylogenetics comment there please? Fred Hsu (talk) 05:07, 17 December 2007 (UTC)

[edit] Suggested change to taxobox categories

There is a current CfD discussing a potential change to Category:Plant articles without taxoboxes. There are two proposed changes: Category:Plant articles needing a taxobox and Category:Plant articles without infoboxes. The proposed changes include other taxobox categories, including animal-related taxobox categories. At present time there is no consensus, so input from the WP:TOL editors would be appreciated. . Justin chat 19:42, 18 December 2007 (UTC)

[edit] Template for disambiguating common names

Hello all. On a couple articles I have worked on, the situation arises where the common name does not have a one-to-one correspondence with a taxonomic unit. Either the word includes animals from several relatively unrelated groups (e.g. Guillemot can refer to either some Uria or any Cepphus) or there are several names for similarly related organsim (e.g. sea lions and fur seals are common names for relatively arbitrarily named organisms in the Otariidae family). Biologically, it is more meaningful to fully describe the appropriate taxonomic unit rather than the animals grouped under a common name. Anyways, on top of the sea lion page and the fur seal page I put the following leads:

Sea lion is a common name that does not refer to a single taxonomic unit. For a more comprehensive discussion of all eared seals, including the fur seals, see Otariid.

and

Fur seal is a common name that does not refer to a single taxonomic unit. For a more comprehensive discussion of all eared seals, including the sea lions, see Otariid.

I was wondering if there existed a template for this situation already, as it must be common (I shudder to think of Fish!). If there isn't, perhaps one should be created? Best, Eliezg (talk) 23:53, 21 December 2007 (UTC)

I've just created Template:Common name for. Hope it helps! Verisimilus T 11:05, 22 December 2007 (UTC)
The template is wonderful, thanks a bunch! Nicely pro-active. Eliezg (talk) 11:40, 22 December 2007 (UTC)
I've just read the first line of the article for Fur seal, which reads "Fur seals refers to nine species of pinnipeds in the eared seal (Otariidae) family which also includes the sea lions." Is repeating the same information directly above it actually necessary?? Verisimilus T 11:09, 22 December 2007 (UTC)
I guess the reasoning behind it makes more sense if you consider the sea lion article. A lot of people go there expecting to learn what a sea lion is, but it was a stubby little article for a long time since all the real substantive information on the family is in Otariid and in the separate species articles. Recently, someone tagged it with a {{Expand|date=December 2007}}, and understandably so. But strictly speaking, it could just be a disambiguation page (which is what it is in the German version). A template like this one would, perhaps, immediately direct a person to the appropriate biological category.
I guess the short answer to your question is: No, not really, but why not?
Incidentally, where do templates live in Wiki-space? Is there some place I could go see how it works? Thanks again, Eliezg (talk) 11:40, 22 December 2007 (UTC)
They do have a slightly convoluted syntax, but once you understand that, they're really quite easy to get to grips with. Help:Templates would be a good place to start, and that template itself is at Template:Common name for - click "edit this page" to view the code behind the template. Verisimilus T 13:15, 22 December 2007 (UTC)

[edit] Categorizing scientific discoveries by year?

For some time, Wikipedia has featured categorization of things by year. The ones I have tended to use on articles I have worked with are categories like Category:1914 architecture and Category:1966 establishments. Does it make sense to anyone besides me to have a category analogous to these, such as "2006 scientific discoveries" that could include species discovered/cataloged in that year? It would be generic enough to also include when scientific theories were first published, or when celestial bodies were discovered, et cetera. Right now there is a series of categories under Category:Years in science, but something about how it is titled does not seem to fit anything except list articles about years or months in science. Any thoughts? — Eoghanacht talk 16:17, 28 December 2007 (UTC)

It's probably my lack of imagination but I can't think when such categories would be useful. Could you maybe give a couple of examples? Verisimilus T 12:42, 29 December 2007 (UTC)
It provides a cross-reference by timeline of otherwise seemingly unconnected events. How useful it is on an absolute scale, I cannot answer, but at least it can be interesting. The tool would be there for others to use however they see fit. My main reason for thinking about it, is that animal species are routinely cited by authority and year [such as Simia hamadryas (Linnaeus, 1758) or Heosemys depressa (Anderson, 1875)]. It seemed natural to me to categorize by the year. Maybe in some cases (such as Linnaeus) to categorize by authority as well? — Eoghanacht talk 18:13, 31 December 2007 (UTC)
I'm not quite sure what you mean by cross-referencing; indeed the events are usually rather unconnected. The reason the year is included is so that the original description can be easily sought out if needed, not that there is any fundemental significance in when it happened to be described. If you think it would be an interesting project, though, then by all means feel free to go ahead with it - but it seems a lot of work to set up and maintain! Verisimilus T 23:16, 3 January 2008 (UTC)

I quite like the idea of Category:Taxa published in 1875, if we could untangle the question of whether the year applies to the current name or the basionym. Hesperian 05:26, 4 January 2008 (UTC)

See, that's the issue: taxa aren't published, names are. The category would need to be explicit, either Category:Scientific names published in 1875 or Category:Basionyms published in 1975.--Curtis Clark (talk) 14:23, 4 January 2008 (UTC)
Given that most articles aren't at the basionym, this doesn't work either. For some reason my mind keeps telling to put it at the singular... Personally, I'm not sure this is really necessary anyway (Most names are at best a pain to track anyway for plants, as far as I'm concerned). Circeus (talk) 14:30, 4 January 2008 (UTC)

What matters from a taxonomic purpose is when the species was first described. The oldest specific epithet has precedence, the first-described species in a family gives the family its name, etc. So the date of the first valid publication of a description of the species (ie, the basionym) is what matters most. Of course, this is probably amenable to lists as well. Guettarda (talk) 15:05, 4 January 2008 (UTC)

A quick look at Cronquist's big book shows that many, if not most, flowering plant families have conserved names, so that the date of publication of the conserved basionym won't necessarily have anything to do with when the family was recognized.
The good news about plant basionyms is that you can look them up in ipni.org. The bad "newses" are that (1) IPNI only treats nomenclatural synonyms (what zoologists call "objective synonyms"), and (2) it is sometimes wrong.--Curtis Clark (talk) 15:47, 4 January 2008 (UTC)

[edit] Bird identification

Hi,
I was hoping someone could help me identify the bird in this photo. It was taken in June 2007 in Swifts Creek, Victoria, Australia. --Fir0002 00:02, 7 January 2008 (UTC)

Image:MG 4456.jpg
Unknown bird
Image:MG 4460.jpg
In flight
It looks like a Restless Flycatcher Myiagra inquieta. Certainly a Myiagra, I'll go find a book after work to confirm. Nice photo by the way. Sabine's Sunbird talk 00:57, 7 January 2008 (UTC)
Thanks! I've uploaded another image which may assist you --Fir0002 01:26, 7 January 2008 (UTC)
If it is a restless flycatcher, those photos (especially the flight one) should go in the article. They're very good. Totnesmartin (talk) 12:33, 13 January 2008 (UTC)

[edit] ITIS

I noticed that there are about 500+ links in Wikipedia that use ITIS' old domain name www.itis.usda.gov instead of its current one www.itis.gov . I corrected the link on this project's page and on one article, but those of you in this project may wish to go through and check the citations and update the links. Simply deleting the usda part of the domain may restore the page that is referenced. The links can be found via by using the Special:Linksearch page. Caerwine Caer’s whines 01:10, 13 January 2008 (UTC)

It would probably be best to convert most or all links to the {{ITIS}} template. Any further changes in the ITIS website structure would then be easy to implement. Eugène van der Pijll (talk) 11:10, 13 January 2008 (UTC)

[edit] Wildlife of/biota of/biodiversity of

I think we need to do something about the inconsistent naming of articles on the biota of a given area. Some articles use biota, some biodiversity, some wildlife... At minimum there should be redirects from all the alternative names that could have been used. Richard001 (talk) 23:04, 20 January 2008 (UTC)

[edit] URN

i just noticed that norman platnick introduced universal resource names for spider families, genera and species in his World Spider Catalog. as this should be a neat way to identify species across databases, i would really like to include this information as soon as possible, and wanted to ask if somebody has experience with this, if there is something like that in other realms, so that including it in the taxobox would make sense etc. cheers --Sarefo (talk) 00:03, 21 January 2008 (UTC)

My understanding from the discussions on the Taxacom mailing list is that these are LSIDs; there has been some criticism in that AMNH does not yet have a resolver for them. I have no familiarity with them beyond what I've looked up on Wikipedia; I mention this because it might be of use to those considering including the LSIDs in Wikipedia.--Curtis Clark (talk) 03:31, 21 January 2008 (UTC)

[edit] Merging a branch of the tree of life

http://www.scientificblogging.com/news_releases/the_tree_of_life_loses_a_branch I'm guessing we should wait for some more papaers/literature to come out before acting on this. But a heads up anyways. -Ravedave (talk) 03:43, 22 January 2008 (UTC)

The underlying article is available on-line here[1]. -- Donald Albury 14:38, 22 January 2008 (UTC)
  1. ^ Burki, F.; Shalchian-tabrizi, K.; Minge, M.; Skjæveland, A.A.; Nikolaev, S.I.; Jakobsen, K.S.; Pawlowski, J. (2007). "Phylogenomics Reshuffles the Eukaryotic Supergroups". PLoS ONE 2 (8). doi:10.1371/journal.pone.0000790. 
Well, not really losing a branch, just that one of the branches is being attached to another. Still, we should wait until this becomes more accepted before we make the move, but we can mention it on the appropriate articles. - UtherSRG (talk) 15:33, 22 January 2008 (UTC)
Agreed: the paper doesn't make the current classification invalid, it just identifies monophyly where it wasn't necessarily expected. Worth mentioning in relevant articles (as a point of view for now until it is accepted or debated in the literature), but not worth initiating major changes on its strength alone. Verisimilus T 15:39, 22 January 2008 (UTC)
I've been making a number of changes in response to this paper (and others like Laura Wegener Parfrey, Erika Barbero, Elyse Lasser, Micah Dunthorn, Debashish Bhattacharya, David J Patterson, and Laura A Katz (2006 December). "Evaluating Support for the Current Classification of Eukaryotic Diversity". PLoS Genet. 2 (12): e220. doi:10.1371/journal.pgen.0020220. ). Not so much to write the articles to reflect this new result (I agree that would be premature), but to take out material which doesn't seem well-established. Sorry I don't have a full list of affected articles, but things like eukaryote, Evolutionary history of life, cabozoa, etc, were some of the more heavily affected. Kingdon (talk) 06:23, 29 January 2008 (UTC)

I tried to start some discussion on this article ages ago when we were actually doing major overhaul on the eukaryote classification. However, I won't initiate major change for this until they come up with a better name than SAR. It makes me think of SARS. Werothegreat (talk) 12:44, 19 February 2008 (UTC)

Well, yes, the name is one thing (has Cavalier-Smith gotten as far as he has due to a knack for catchy names? Probably best to leave that one as a rhetorical question). But in general it is dodgy to be rewriting textbooks and encyclopedias based on cutting edge research which hasn't (yet) stood the test of time. I'd recommend again the Parfrey et al paper that I cite two comments up, the gist of which is that the 6 supergroups are far from well-established. I'm as guilty as the next person of getting enthused by new papers, but we should temper that impulse to some extent. Kingdon (talk) 06:35, 21 February 2008 (UTC)
I would generally not rewrite anything at the base of the eukaryotic tree and the base of the metazoans if it is not supported by damn good multiple-line evidence and a consistent evolutionary scenario. One horizontal gene transfer event at the wrong time, and you can infer gene-trees all you want - if you choose the "bad" sequence (and you can't tell which ones are bad), you'll never get "good" phylogenies.
The new findings need to be discussed in detail and their consequences for taxonomy duly noted. That way, however the further research turns out, we will have to change but little in the article text and readers will have access to the cutting-edge information.
It is interesting to note that the change - if it turns out to be good - might even be easier accomodated in Linnean taxonomy than in phylogenetic taxonomy. Depending how the Chromalveolata and Rhizaria are defined in phylo-taxon, they could now collide (if one or both use apomorphy-based definition).
Rank-wise, the Rhizaria would become a phylum and included with the Stramenopiles in a chromalveolate superphylum, with the rhizarian ranks shifting down as required. Dysmorodrepanis (talk) 01:29, 22 March 2008 (UTC)

[edit] Reminder of the Philip Greenspun Illustration project

Hi. You may be familiar with the Philip Greenspun Illustration Project. $20,000 has been donated to pay for the creation of high quality diagrams for Wikipedia and its sister projects.

Requests are currently being taken at m:Philip Greenspun illustration project/Requests and input from members of this project would be very welcome. If you can think of any diagrams (not photos or maps) that would be useful then I encourage you to suggest them at this page. If there is any free content material that would assist in drawing the diagram then it would be great if you could list that, too.

If there are any related (or unrelated) WikiProjects you think might have some suggestions then please pass this request over. Thanks. --Cherry blossom tree 16:51, 29 January 2008 (UTC)

[edit] Taxobox colour for animals

Anyone interested in taxobox aesthetics may be interested in this discussion to change the colour of animal taxoboxes. Verisimilus T 17:15, 31 January 2008 (UTC)

[edit] Velvet worm translated

Hi all,

Just finished translating the velvet worm article from the rather more comprehensive German one, which is an Exzellentes Artikel (FA). It's taken me about 10 months of extremely sporadic editing and could definitely use some outsiders' eyeballs to correct any inaccuracies (I'm not a biologist) or general cockups. Images and/or illustrations would be particularly welcome to break up the interminable and pretty technical text! If any of you've got 10 minutes spare, please give it a read through and if you have any feedback, I'd love to see it on my talk page.

Much obliged, --YFB ¿ 19:46, 1 March 2008 (UTC)

The text is kind of interminable in places. I tried to concisify the hydraulic skeleton prose (I wasn't really sure whether/how to make the comparison to the water vascular system, but ended up putting it in with the weasel words "somewhat similar"). Images would indeed help to break up the monotony, but so would showing a bit wider perspective. One current example is the paragraph "Unlike the arthropods, . . . high air humidity". Bringing in comparative anatomy and ecology livens up the anatomy lesson by giving it a point. On the plus side, I found very few errors of spelling, grammar, etc, and your translation is certainly more comprehensive than what we had before. So thanks for doing this. Kingdon (talk) 16:31, 2 March 2008 (UTC)
Thanks, Kingdon. Your attempt at the hydraulic skeleton section is a great improvement - sadly I lack the expertise to be much help in bringing in comparisons etc., but hopefully now that I've provided the "raw" text of the German article some other contributors can make things a bit more palatable to the general public. Cheers for the feedback, --YFB ¿ 17:59, 2 March 2008 (UTC)
I've added another image I found on FlickR. JoJan (talk) 20:13, 2 March 2008 (UTC)

Great work on the translation. Were there any references in the German article which could be copied across? I'm struggling to verify some of the claims made in the Geological History section. Thanks, Verisimilus T 14:11, 3 March 2008 (UTC)

[edit] Who am I?

Thailand Feb 2008. The bad news is that there are quite a few butterflies to come.

A damselfly (something like that in India has the English name of "forest glory" Vestalis sp. fam:Calopterygidae ) and an Auchenorrhynchan. Try WP:ARTH or User:Dyanega. Shyamal (talk) 04:43, 5 March 2008 (UTC)
Thanks, will do Jimfbleak (talk) 07:16, 5 March 2008 (UTC)

[edit] cultivated status for cultivated plants?

What conservation status applies for cultivated plants (I refer here to cultigens, or other plants for which neither a wild status nor "extinct in the wild" applies)? For animals, DOM (domesticated) is the right status, but that doesn't work for plants because it adds the page to Category:Domesticated animals. My first idea on how to solve this would be to add "cultivated" as a possible status, which would be just like domesticated but which would add the page either to no category, or to a new one. Because domesticated is a wikipedia-specific category, and the Red List or NatureServe categories don't seem to provide anything equivalent, there doesn't seem to be an issue with consistency with an external classification. Another solution would be simply to rename Category:Domesticated animals to Category:Domesticated species (or domesticated taxa or ... I'm not coming up with a good name). I guess another solution is just to omit status for cultigens (which I suppose is closest to the status quo, although the discrepency between animals and non-animals seems a touch jarring). The subject came up for Nicotiana tabacum. Kingdon (talk) 15:05, 10 March 2008 (UTC)

Category:Domesticated taxa would do the job methinks. And indeed, the common tobacco-plant is DOM if one just applies the criteria we've always applied.
If we want to be naughty in the future, we could go as far as to add another category for extinct/critically endangered/endangered cultivars/cultigens/animal breeds. I mean, we got cultivar boxes, dog breed boxes etc, which are a sort of a taxobox equivalent. DOM, as it is used, always refers to the species-group taxon as a whole. Dysmorodrepanis (talk) 01:35, 22 March 2008 (UTC)

[edit] Linking (not parsing) EoL

The new Encyclopedia of Life can be used as a source for Wikipedia.

Pro: has info where WP might only have a stub

Con: taxonomic/systematic information is usually better on Wikipedia as of now, and looking at the bugs they introduced with large scale parsing of often-obsolete databases, this is not gonna change soon...

What could be done, then, is this:

  • make a EoL template yielding a standard "external link"
  • bot-add this template to any WP:ToL stub where info on the EoL exists.

That way, one gets a source of further info for readers. For editors, the EoL link is present if one wants to expand the article. Non-stub articles are usually better and more correct than EoL in its present state. If there really is a very cool EoL article alrady (like the EoL example articles, Kiwa hirsuta is one I think), this can be added manually.

What would need to be done is to check how easy it is to exclude EoL entries that only have bare-bones info. Because if only the name and systematic placement exist on EoL, it can add nothing positive. Dysmorodrepanis (talk) 01:46, 22 March 2008 (UTC)

I browsed through a handful of plant articles, and I'd generally tend to prefer other sources, like PLANTS or efloras. Doing some kind of bot-run (at least on wikipedia articles marked as stubs) might not be a bad idea, although I'm not sure I'd single out eol.org as opposed to other sites. Kingdon (talk) 03:28, 22 March 2008 (UTC)
The intro for Amanita phalloides on the EOL page actually comes from the wikipedia page..(egads, a loop of cross-referencing!!)  :) Cheers, Casliber (talk · contribs) 03:53, 22 March 2008 (UTC)

[edit] Animal kill?

On Talk:Fox hunting, editors are debating whether to keep or remove an image purported to be of a fox killed by hounds. The question has come up: what does such a kill look like? Would any wildlife biologists here care to respond? --Una Smith (talk) 15:31, 5 April 2008 (UTC)

[edit] This could be big

Anyone know about Cetartiodactyla? (note that the subject's page lists it as an unranked clade, but Laurasiatheria lists it as an order containing two now-suborders, Cetacea and Artiodactyla.

Here is my question: How should we take care of this?

If the proper solution is to list it as an order containing two suborders, there are three options:

a) list the order b) list the suborder c) list both

Otherwise, appropriate actions need to be taken to ensure that there are no conflicts in the related articles. Bob the Wikipedian, the Tree of Life WikiDragon (talk) 16:17, 17 April 2008 (UTC)

The proper thing to do is to follow Mammal Species of the World (3rd ed 2005), which lists Cetacea and Artiodactyla as orders and ignore, for now, Cetartiodactyla. However, MSW3 is the authority more on species than on orders. Anyone know a good modern reference for mammalian orders that we should be following? - UtherSRG (talk) 16:30, 17 April 2008 (UTC)
Doesn't the International Code of Zoological Nomenclature put out any publications? I should think that the codes they set should regulate this sort of thing-- or am I way off-base?Bob the Wikipedian, the Tree of Life WikiDragon (talk) 16:35, 17 April 2008 (UTC)
No, they don't make scientific decisions. They make the rules that dictate how things are named when a scientist makes a scientific decision. - UtherSRG (talk) 16:40, 17 April 2008 (UTC)
Oh. So who is responsible for maintaining the most up-to-date catalog? Anyone? Bob the Wikipedian, the Tree of Life WikiDragon (talk) 16:50, 17 April 2008 (UTC)
Many folks. That's why I asked the question in my initial reply. MSW3 (http://www.bucknell.edu/msw/) is the canonical listing of mammalian species, and it gives some information about higher ranks. On Cetartiodactyla vs Cetacea and Artiodactyla it silently lists the two orders with not a mention of the combined taxon. This is understandable to some degree as the various Order listings in the book were each written by different authors, so it is likely that one author wrote the Cetacea section, and another the Artiodactlya section. (I can't say which since I'm away from home until the end of May. I'll be bringing my copy of MSW3 with me next time.) - UtherSRG (talk) 17:02, 17 April 2008 (UTC)
Yeah, and artiodactyl specialists are likely to be different than cetacean specialists (Artiodatyla in MSW 3 is by Peter Grubb, Cetacea is by James Mead and Robert Brownell). However, MSW 3 makes no mention at all (as far as I can see) of this matter (not in the introduction either, which includes a brief section on the taxonomic arrangement).
However, it seems that recent publications mostly still use the two-order system (Cetacea and Artiodactyla). I think it is now too early to merge the orders, though it may well have to be done in the future.
Also, there are no institutions that make really official taxonomies for any group of mammals, as far as I know (though there are some quite commonly accepted reference works, of which MSW 3 is the prime example). The ICZN does not have any jurisdiction over matters of taxonomy, it only rules on nomenclature (that is, on the names that are to be used in taxonomy). Furthermore, the ICZN does not extend above the level of superfamily, so it does not have anything to do with orders. Ucucha 17:17, 17 April 2008 (UTC)
I don't know which authors are to blame, but MSW3 really dropped the bal in continuing to recognize a paraphyletic Artiodactyla. This is an example where MSW3 contrasts with the vast majority of current (primary) literature on the topic. Even most (but not all) paleontologists have come around to the idea that Cetacea evolved from within the Artiodactyla. The remainder at least recognize that they are sister taxa. The correct answer in this case: discuss the controversy. Either way the Cetacea+Artiodactyla clade exists (either at the level of order or at an above-ordinal rank) and that discussion should be discussed in the artice Cetartiodactyla. Right now, there's a political inertia to continue to recognize these as separate orders (much like "Aves" vs. "Reptilia"), and we are probably better off have our quick overviews treat them as separate orders. --Aranae (talk) 18:10, 17 April 2008 (UTC)
Everything looks OK to me. Cetartiodactyla discusses the differing hypotheses, evidence, etc, concerning the origin of the cetaceans. Laurasiatheria links to all three articles (reflecting the fact that there isn't consensus on how to name the orders and even if there is, there will be lots of older sources with older names). The key thing here is not to get bogged down in paragraphs and paragraphs of taxonomic minutia, and try to avoid taking sides until there really is a scientific consensus (especially, try to avoid taking sides in such a way that thousands of pages need to be updated whenever a new paper comes out). Kingdon (talk) 05:50, 18 April 2008 (UTC)

[edit] Software ideas

This is sort of off-topic, but I figured this is the best place to get the response I'm looking for. I'm going into software design, and I want to focus my software to a zoological aspect. I was wondering if anyone here has any ideas for a useful piece of software which has to do with zoology? Useful = something people would be willing to pay for. Bob the Wikipedian, the Tree of Life WikiDragon (talk) 16:56, 17 April 2008 (UTC)

This probably isn't the place for this type of discussion, but I toss out a quick answer before the discussion gets deleted. Biologists are stuck holding on to old computers because there's no motivation for programmers to upgrade (it's not a financially booming industry) so that their apps can run on new OSs. I think anyone who upgraded those programs (involves working with the companies) or created new apps that did the same thing could be sucessful (note that it's a limited market with limited funds, though). For example, the fact that PAUP won't run in OSX essentially requires most systematists to hang onto an old Macintosh (unless they want to go back to command-line interface). --Aranae (talk) 17:08, 17 April 2008 (UTC)

[edit] Long-standing template problems

Template:Clade is an immensely useful template, sadly however, it has problems (noted on the Template talk page) and no fixes have been attempted so far. It would be great if some of the concerns noted could be fixed. Just to make usage of the template easier, I have hashed up a visual editor and have made the code and binaries (M$ Windows only) available here http://code.google.com/p/claded/downloads/list . Shyamal (talk) 07:50, 19 April 2008 (UTC)

[edit] Fossil range vs. molecular divergence

I've been helping out with fossil ranges the past few days on all kinds of animal and bacteria articles, when it suddenly hit me that the fossil range was being used for two different purposes. In the dinosaur articles, "fossil range" refers to the first known fossil. In the extant articles, the "fossil range" does not refer to fossils at all! Instead, it is the estimated point of molecular divergence.

In response to this misuse, I propose adding a field to the taxobox for the molecular divergence. That way, this information does not need to be removed, as it is nice to be able to find it quickly. Otherwise, we need to remove all non-fossil-record-based fossil ranges. Either way, it will definitely take a little while to fix this big error, but I think it's possible, especially if a couple of us work hard for a one or two hours. Opinions? Bob the Wikipedian (talk) 13:45, 13 May 2008 (UTC)

I would be willing to take on this task myself, although as far as editing the taxobox code, I might need assistance. Bob the Wikipedian (talk) 14:25, 13 May 2008 (UTC)
I agree, those are two very different things. GoEThe (talk) 15:09, 13 May 2008 (UTC)
Of course, the fossil range should not be constructed to mean a divergence date estimate: the first is observation, the second is inference, and such different things should be separated.
I'm not quite in favour of adding a field about divergence date either. Those estimates (at least for mammals, I don't know about other groups) differ widely among studies,1 there is significant opposition to their use, and I do not think they are relevant enough to be placed in the taxobox. The taxobox should give a quick overview of basic information on the article's subject, not an exhaustive account. In my opinion, it should be limited to plain nomenclatural and classificational data and other noncontroversial things (such as the IUCN status and the fossil range), while all other information can be placed in the text. Ucucha 15:20, 13 May 2008 (UTC)
1 For example, the divergence between the rodent genera Mus and Rattus has been estimated to have been between 12 and 43 million years ago in different studies, and phylogenetic studies of related groups usually assume that they diverged 10 million years ago for calibration purposes (this is based on "paleontological data", which seems questionable since we hardly know the relations among Mus, Rattus, and their relatives, let alone the full relations among the fossil species; the first Rattus-like animals date from the Late Pliocene). Which divergence date estimate should then be used for the Murinae (note that the Mus-Rattus-split is not even the basal split among the Murinae)? Ucucha 15:20, 13 May 2008 (UTC)
I agree, divergence estimates are far too controversial to include in the taxobox. Stick with fossil range. Ideally, there should be a cite somewhere in the text for the earliest known (and last known, for extinct groups) fossil representatives so the range listed is verifiable. Dinoguy2 (talk) 21:42, 13 May 2008 (UTC)
Since divergence is something which could technically be in any life article, perhaps there is a sort of template someone could create. Maybe it would appear at the bottom, like the old fossil range diagram (is this still in use?). However, I don't know anything about making these, so I won't worry about that right now.
In the meantime, I'll begin removing (or moving, where appropriate) the information from taxoboxes. If I have any troubles determining whether it is fossil or divergence, I'll move it to the article's talk page for disambiguation. (Objections? The fastest way to stop me is to post on my talk page.) Bob the Wikipedian (talk) 22:05, 13 May 2008 (UTC)

Virtually the same discussion was had here a week or so ago. Hesperian 00:03, 14 May 2008 (UTC)

[edit] Wikipedia:WikiProject Tree of Life/taxobox usage (multi-template)

This page documents how to use the old multi-template version of the taxobox, and has therefore been redundant since late 2005. Would there be any objections to me deleting it? Hesperian 04:10, 14 May 2008 (UTC)

As for usages of the taxobox itself, there's one at Wikipedia:WikiProject Birds (family taxobox example) (and likewise for a handful of other wikiprojects), plus a fair number (<100) on talk pages and user pages. Does the existence of these stragglers argue for keeping something saying "this is obsolete" (perhaps in the doc for Template:Taxobox begin?). Has advice like "Extinct subgroups should be indicated with a dagger † (†) or the word (extinct)." been carried over to the new documentation (I didn't see it, nor did I look through the whole multi-template documentation for similar items)? Kingdon (talk) 15:11, 14 May 2008 (UTC)

[edit] Archive time!

Can someone please archive this page? It's getting unwieldly again... Werothegreat (talk) 23:54, 27 May 2008 (UTC)

[edit] Taxobox update

There is a discussion to add interproject links (such as Commons and Wikispecies) to {{taxobox}}. Your input will be welcomed. OhanaUnitedTalk page 05:18, 10 June 2008 (UTC)