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

Contents


[edit] Eukaryote phylogeny

I have been busily updating information on the eukaryote page (not controversially, like turning taxoboxes lavender), and I feel that the section that explains the eukaryote supergroups needs to be completely rewritten. I have added sentences explaining how the domain is divided into unikonts and bikonts, which pinpoints the eukaryote root, while there is a sentence saying "Otherwise the relationships between the different supergroups are mostly uncertain, and in particular there is dispute about where the root of the evolutionary tree belongs,..." I have also added that Cavalier-Smith has proposed that the apusozoa and centrohelida are bikonts, and that some canadian has published a paper putting the ebriids in the cercozoa, right next to a sentence saying "A few small protist groups have not been related to any of the major supergroups, notably the centrohelids, apusozoans, and ebriids." Can I please be given permission to rewrite the entire section? Werothegreat 20:53, 9 March 2007 (UTC)

Be bold. You don't need permission. If you're worried that you'll be deleting something potentially useful, then mention it on the article's talk page and copy the slab of text you've removed there, noting that you've rewritten it. —Pengo 21:28, 9 March 2007 (UTC)
Oh, heck, Wero, it's not as if eukaryotes aren't so confusing that anyone will understand. Post on my talk page when you get done with the rewrite, and I will try to look it over. Try to remember there is currently little consensus, but a lot of slacker acquiesence to some of the newer taxonomies, and reference everything because of that. If someone jumps on you about it, say that I encouraged you to do it (as no one else is tackling it and the article is dreadful). I'm not an admin or anything, but I know you're trying to get some things organized in this area, and I'll support your efforts, even if I think your results need tweeked. And I'll work with you on tweeking, if you can take the time to post on my talk page--very busy right now. KP Botany 03:40, 10 March 2007 (UTC)
Be bold, but you might want to take note of DOI:10.1016/j.tig.2003.12.003 here:

Trying to estimate the divergence times of fungal, algal or prokaryotic groups on the basis of a partial reptilian fossil and protein sequences from mice and humans is like trying to decipher Demotic Egyptian with the help of an odometer and the Oxford English Dictionary.

Dysmorodrepanis 07:40, 11 March 2007 (UTC)

[edit] Maybe of interest

Wish Shyamal 11:22, 12 March 2007 (UTC)

[edit] Proposed templates?

I'd like to set up an article-assessment template for this WikiProject, similar to {{Wikiproject MCB}}. It would be used to assess articles that are not yet covered by a daughter WikiProject. Are there any objections?

Also, is there a taxonomy stub? If not, may I create one for this WikiProject? Thanks! Willow 11:47, 13 March 2007 (UTC)

For stubs, ask over at The stub project whether such a stub is viable.
As for assessment, maybe it's wee bit overboard for such a broad project, though integration with subproject templates (like we at WP:PLANTS did with WP:BANKSIA and WP:CPLANTS's already existing templates) might greatly help. Circeus 13:17, 13 March 2007 (UTC)

[edit] Laminariales Families Confusion

Under the order Laminariales of the Brown Algae, there is some confusion as to which genera belong to which families, specifically Laminariaceae and Lessoniaceae. The specific genera include Macrocystis, Postelsia and Pelagophycus. They are listed on the pages of both families. I have visited various resources, and there does not appear to be any sort of consensus between them. Based upon morphology, I would think that Pelagophycus and Nereocystis are closely related, and Postelsia and Lessonia are closely related, and that Macrocystis is somewhere in between. Laminaria does not appear to resemble any of the previous as much as the previous resemble each other. However, I'm not an expert in algae. Could someone with experience in this field, who is very familiar with (or at least has a reliable resource describing) phaeophyte taxonomy please look at the family articles of Laminariales and make so much needed editing. Werothegreat 21:18, 14 March 2007 (UTC)

  • Also, the Laminariales page itself needs work. Half of it is just a list of various Laminaria species. Such information belongs on the Laminaria page. Werothegreat 21:23, 14 March 2007 (UTC)

[edit] Thing Found in Pond Water Tank

These arthropods were found in freshwater, with I believe Elodea plants and some snails. I think they're branchiopods, possibly fairy shrimp, but I'm not sure.




Werothegreat 18:16, 17 March 2007 (UTC)

Maybe a water louse (Asellus sp)?Sabine's Sunbird talk 23:33, 17 March 2007 (UTC)
No, it wasn't flat like an isopod. It was more like a shrimp, except it had the wrong kind of head, and it had these limbs on the hindquarters that moved very fast, as a blur. Werothegreat 00:04, 18 March 2007 (UTC)
Sounds like what we used to call freshwater shrimp then. I don't recall the proper name though. Sabine's Sunbird talk 00:35, 18 March 2007 (UTC)
I looked at the shrimp. This thing has too many legs to be a shrimp. Werothegreat 01:47, 18 March 2007 (UTC)
Freshwater shrimp is the common name in England, I finally found it's real name, Gammarus pulex. Or some relative. Check it out on Google Image. Sabine's Sunbird talk 01:54, 18 March 2007 (UTC)
That's it! Thank you. Werothegreat 19:05, 18 March 2007 (UTC)

[edit] Categories versus lists

Apparently a user has decided that living things should not be categorized by their nationality, but rather only listed by nationality. Instead of bringing this up for discussion on the lists versus category pages, the user is proposing categories for discussion (deletion) a number at a time.

I think it is important for members of this project to decide which, if either, is the most useful method for categorizing species. Are there reasons for categorizing by country, or not? If not, they should all be deleted at once. Are there reasons for lists that make them preferable to categories for topics of this nature, or vice versa?

Please, let's decide upon our own policy here and now, rather than allowing someone outside the project, who is devoted to deleting categories decide how organisms should be categorized or not--although we should be glad to let him/her do the work of deleting all the categories if we decide that's how to go.

Categorize flora and fauna by country category, or put flora and fauna by country in lists only?

KP Botany 00:08, 18 March 2007 (UTC)

This debate is a classic example of the List vs. Category debate. We've been accomodating both for a while now. I'm not clear what is the reason why we should have one and only one scheme. The provlem has more to do with the category scheme being poorly thought before it was implemented than it being inappropriate.Circeus 00:14, 18 March 2007 (UTC)
  • Weren't cats brought in to deal with the huge numbers of lists? It was before my time but I recall that was the reason.Sabine's Sunbird talk 00:33, 18 March 2007 (UTC)
  • Whatever. Personally I prefer lists because they're better presented, but if the category system is going to be used at all on Wikipedia for content (as opposed to for metadata), it might as well be used for species by country. Of course, we cannot have an overarching policy. Some countries have many endemic species, for example Category:Birds of New Zealand makes a sensible category (but the list is nice too (List of New Zealand birds)). Trying to add country categories to species with a more cosmopolitan distribution just gets silly. And as an aside, and as I know has been suggested before, we should be aiming to have lists (and categories) by ecoregion as well. —Pengo 00:43, 18 March 2007 (UTC)
  • What about lists of endemic species, rather than lists of species endemic, cosmopolitan and weedy? Is that more useful than a simply list? Ecoregion is useful, but a little harder to do with the resources available in botany. Unfortunately floras are done by political boundaries. KP Botany 03:16, 18 March 2007 (UTC)
What about categories of endemic species? There could be Category:Endemic Plants of North America, which would include both species and other categories, such as Category:Endemic Plants of the United States, which could in turn include such categories as Category:Endemic Plants of California. It is already a well-established (although not always followed) practice to place an article in the most restricted in a set of hierarchic categories.--Curtis Clark 03:30, 18 March 2007 (UTC)
Lists have an advantage in that they can have annotations and serve as more complete and useful references. Shyamal 11:40, 18 March 2007 (UTC)
Inasmuch as people will create categories anyway, they might as well be useful.--Curtis Clark 15:42, 18 March 2007 (UTC)

[edit] Wish list for articles, categories and lists?

Hi,

A few of us are working on systematically producing a large number of taxonomic Wikipedia pages (tens of thousands), and we'd appreciate any advice or guidance you have on their format, etc. They'll all have a proper taxobox (with synonyms), references and external links, but they'll also be image-less stubs; a reference-less, synonym-less example is Pyrodictiaceae. Our plan is to start at the top of the taxonomic tree and work down, as we've been doing for the Archaea, but we're also open to any suggestions about which segments of the Wikipedian Tree of Life we should fill in first.

A key question for us is how to categorize the pages. If you look at Category:Archaea, you'll see that we created subcategories for the different taxonomic ranks (such as Category:Archaea orders), but you all might have better suggestions for categorizing, say, the species of the Porifera.

Speaking of lists, it's also relatively easy for us to produce an initial draft of any taxonomic list you'd like. For example, it took about 12 seconds to produce the List of fungal orders. Please send your wish lists for taxonomic lists that you'd like to have added to Wikipedia. They won't be perfect, but they'll likely be pretty good.

Thanks very much for your help and suggestions, Willow 01:13, 18 March 2007 (UTC)

Can you please have a look at the above discussion? (Laminariales) I would really appreciate some help on figuring out which kelp goes in which family, as I have little to no access to reputable sources of information of this kind. Werothegreat 01:51, 18 March 2007 (UTC)

Is this helpful? I haven't proofread it yet, but I hope that it's useful. :) You may find that some genera are missing, though. Willow 02:32, 18 March 2007 (UTC)

It sounds like a good idea to me. However, what are you using to generate the lists? "This article lists the genera of the Phaeophyceae, the brown algae." is rather bold without being tied to a specific reference considering the current state of upheaval in the taxonomy of the Phaeophyceae. KP Botany 03:13, 18 March 2007 (UTC)

Hi KP Botany,

Thanks for your support and help! :) The Wikipedia lists and articles are based on the NCBI taxonomy files, which are admittedly imperfect but a good start; they're updated weekly, publicly available and provide references. You're right, the opening sentence is too bold, as I see now; I was trying to state the intention of the article, rather than its success. Perhaps we should soften it maybe like this: "This article seeks to list the genera of the Phaeophyceae, the brown algae." and provide a reference? Maybe a reference to the NCBI site (with access date) and/or reference(s) to the literature?

The Wikipedia pages are generated using my own program, which I've been called "Daisy" and which I wrote on a strange whim. As part of a wiki-game, I made some missing encyclopedic articles; since a quarter of those were taxonomic, it seemed like a Good Thing for Wikipedia to add more. Daisy can generate a list or the corresponding set of Wikipedia stubs for any branch of the taxonomic tree known to the NCBI; here's a list of the articles she's made already. These were uploaded and proofread manually, but Opabinia regalis wrote a program for uploading whole sets of pages automatically. She, David D. and TimVickers have all had excellent ideas for improving the pages. Looking forward to your ideas and insights as well — thanks! Willow 11:31, 18 March 2007 (UTC)

P.S. Systematic changes in the NCBI nomenclature can be made as well, if you'd define them for Daisy.

[edit] Archive please!

I think it's past the time this page was archived. It's taking altogether far too long for it to load on my computer. Werothegreat 19:11, 18 March 2007 (UTC)

Consider it done. --Stemonitis 19:25, 18 March 2007 (UTC)

[edit] Need help proofreading taxonomic references

Hi, so we've got a working system for generating the taxonomic references for arbitrary taxa, but we need help checking that the references produced are OK, i.e., proofreading them. It's described on my Talk page, if you have time to help out — thank you very much! :) Willow 22:42, 20 March 2007 (UTC)

BTW, this would be a good time to express your wishes about the categorization and other properties of the new taxonomic articles (see discussion above and on my Talk page). If we're going to add tens of thousands of new taxonomic pages, then those pages should reflect your wishes in their form and content. Any help with the proofreading would be most welcome as well; thanks! Willow 09:03, 24 March 2007 (UTC)

[edit] Schmidt Sting Pain Index

Can some of you knowledgable and discerning scientist Wikipedians take a look at this please? This article has currently been getting some coverage in popular "gee whiz funny link of the day... how goofy!" type blogs ( I hate it when this happens and the article in question is dubious... I think it gives a bad impression of wikipedia), but it seems to be mainly based on the idea that this one insect scientist guy wrote some goofy comments for an insect sting pain index one day. Ok, I agree that insect scientists are allowed to have senses of humour (WITHIN LIMITS, for the sake of us all), but I am concerned that 1) this scale is not really widespread and may be just one scale promoted by one guy without much acceptance in the insect expert community. 2) the pdf article linked which this wikipedia entry seems to be based on does not seem to say that Schmidt actually wrote those goofy comments. Its a bit ambiguous, but its seems to say that "the media" (without specifying what media) came up with the goofy comments to append to Schmidt's original dry scale (I think this may be another case where people exaggerate or misinterpret what an article is saying). I dont have any access to science journal databases, and am certainly no science or insect expert. But these concerns and quick scans of google books and google scholar led me to bring this issue to wiser heads. Thanks very much for checking this out. 88.109.1.60 16:39, 24 March 2007 (UTC)

[edit] Taxoboxes, vernacular names and automated parsing

We've been discussing the possible inclusion of multiple vernacular names in taxoboxes and how this might aid automated parsing; please see Template_talk:Taxobox#Space for "other" common names and comment there if you have a view. Thank you. Andy Mabbett 23:04, 25 March 2007 (UTC)

No, if any additional names go into the taxoboxes, it should be synonyms, not common names. And common names in the USA are not, as we've discussed many times, official. Too much information to add to something that is not designed to be its own list article, but merely a quick glance information tool. Taking away the original purpose of the taxobox (quick data table) to expand it to include a purpose that occludes the original purpose is pointless. KP Botany 03:47, 26 March 2007 (UTC)
Yeah, eventually if everything is in the taxobox, there is no need for the rest of the article. (What happened to Template:Smiley, btw?) I'm not even sure that synonyms should be in the taxobox.--Curtis Clark 05:54, 26 March 2007 (UTC)
As for Template:Smiley (and its little brotehr template:Emot), very normal TFDs, apparently.Circeus 21:08, 27 March 2007 (UTC)
Who is asking for "everything" to go in the taxobox? Andy Mabbett 10:10, 26 March 2007 (UTC)
As is said, discussion is taking place at Template_talk:Taxobox#Space for "other" common names; I've already addreessed KP B.'s points there. Andy Mabbett 10:10, 26 March 2007 (UTC)
Everything in the taxobox is fairly common around here, there is always another thing that should go in the taxobox. KP Botany 13:57, 27 March 2007 (UTC)

[edit] CfD

Just a heads up - Category:Biota by country is up for deletion. See Wikipedia:Categories_for_discussion/Log/2007_March_28#Category:Biota_by_country. Guettarda 12:59, 28 March 2007 (UTC)

[edit] Eukaryote Kingdoms

I hate to bring this up again, but I was skimming the brown algae pages, making edits, when I came across the Heterokontophyta page. Someone had took it upon themselves (some IP number) to change Chromista from an (unranked) to Kingdom status. I looked at it for a while, and thought how that was so much better than (unranked). It doesn't make sense to have an unranked taxon between domain and phylum when we have the perfectly reasonable kingdom classification. The same thing for the Rhizaria and the Excavata and the Amoebozoa (though someone along the way decided that all of the amoebozoa were a single phylum for some reason). The only reason I can think why haven't embraced monophyletic kingdoms is because (WARNING: Extreme opinion ahead) we're all too conservative and scared to move away from protista. And please don't say "But we've got to let people find information in many ways." There's a reason why taxa like Monera and Coelenterata are currently rotting away without a taxobox. It's a little sentence in their article describing how they're obsolete and paraphyletic. We could do the same thing with Protista, leaving a taxobox so that "people can find information in many ways." I propose a system something like this:

Subdomain Unikonta

Kingdom Amoebozoa
Phylum Mycetozoa
Phylum Archamoebae
Phylum Tubulinea
Phylum Flabellinea
Superkingdom Opisthokonta
Kingdom Metazoa
Kingdom Choanozoa
Kingdom Mesomycetozoa
Kingdom Eumycota

Subdomain Bikonta

Kingdom Apusozoa
Superkingdom Cabozoa
Kingdom Rhizaria
Phylum Radiolaria
Phylum Foraminifera
Phylum Gromida
Phylum Cercozoa
Kingdom Excavata
Phylum Metamonada
Phylum Loukozoa
Phylum Percolozoa
Phylum Euglenozoa
Superkingdom Corticata
Kingdom Chromalveolata
Phylum Alveolata
Phylum Haptophyta
Phylum Cryptophyta
Phylum Heterokontophyta
Kingdom Archaeplastida
Phylum Glaucophyta
Phylum Rhodophyta
Subkingdom Viridiplantae
Phylum Chlorophyta
Phylum Charophyta
Infrakingdom Embryophyta

Comments? Questions? Rants? Werothegreat 12:59, 30 March 2007 (UTC)

Is this system published anyware, or is it your original creation? I think the best option would be to choose one fairly widely accepted taxonomy from a published source, standardize the taxoboxes to follow it, and discuss alternate schemes in the text where needed. Dinoguy2 13:25, 30 March 2007 (UTC)
Yes, this is generally how we do it, except for the picking one "widely accepted texonomy from a published source" as there isn't one because of the turmoil in the taxonomy of the somewhat unfamiliar eukaryotes due to new DNA information and the somewhat controversial nature of environmentally skimmed DNA as the basis for phylogenies of the relatively unknown eukaryotic kingdoms.
Wero, you do understand that your "thoughts" about how much better something is don't really matter. As Dinoguy2 asks, is this from a published source? Please make it a routine habit to list the source of your taxonomies when you post them, in fact, you can just list the source, not even the phylogeny itself. KP Botany 15:59, 30 March 2007 (UTC)
All of the supergroups come from these two sources:
The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists (Adl et al. 2005)
<http://www.hisl.ent.msu.edu/discussion/Adl_et_al_2005.pdf>
The Root of the Eukaryote Tree Pinpointed (Cavalier-Smith, Stechmann 2003)
<http://www.cladocera.de/protozoa/stechmann_2003_cb.pdf>
They sort of shy away from the use of "phylum" or "kingdom" so I took the liberty of adding those myself, because it depresses me so much to see half of a taxobox say (unranked). Werothegreat 18:39, 30 March 2007 (UTC)
Do you understand that we can't use your unpublished phylogenies for Wikipedia taxonomies? PS You're going to have real issues should you venture towards the Plant Kingdom, so I suggest you not, as Linnaean taxonomies and ranks are not that popular here. Ranks are artificial constructs, they don't have a whole lot to do with nature, anyhow, other than species and below, sometimes genera. KP Botany 19:52, 30 March 2007 (UTC)
To put it more simply, taking groups and giving them your own rank and/or name, in the absence of a published reference you can cite for those ranks or names, is considered original research--a definite no-no in Wikipedia. MrDarwin 19:59, 30 March 2007 (UTC)
OK, I'll admit I was stupid to bring this up. Just one thing, though. Can we change Alveolata and Chromista to Chormalveolata? Both the sources I listed above use that taxon as a supergroup above its four phyla. We can leave it (unranked) if you like. Werothegreat 12:03, 31 March 2007 (UTC)
Not stupid, let's try "overcome by enthusiasm for the topic," instead. When you read deeply for understanding in a topic, scientist, amateur or student, things sometimes jump out at you. I'm certain there will be papers out within the next year or two, after doing a bit of reading myself, that justify your taxonomy. For now, how about adding the information from these papers to the Chromalveolate article in more detail, well referenced to both articles, and briefly with a wikilink to the Alveolate and Chromista articles, ditto with references? KP Botany 17:50, 2 April 2007 (UTC)

[edit] Rabbit identification

Hi, I took a shot of a rabbit in my yard [1] which I believe is a Desert Cottontail (given the physical similarity and the geographical area -- I'm in Thousand Oaks, California). On the other hand, I don't actually live in the desert. Can anyone help confirm before I upload this to Commons? Thanks. howcheng {chat} 19:46, 6 April 2007 (UTC)

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