Wikipedia talk:WikiProject Tree of Life

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WikiProject Tree of Life (Rated NA-class)
WikiProject icon This page is within the scope of WikiProject Tree of Life, a collaborative effort to improve the coverage of taxonomy and the phylogenetic tree of life on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.
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where to put base pair count?[edit]

Greetings, I have noticed that there is not a specific location for genetic base pair count. I've taken to putting it where the info helps but as the amount of DNA sequencing increases there will be more users, like me, interested in knowing and contributing to the base pair info. Where best to put this info? I've started here: and here: thank you for considering my issue worthwhile for discussion. DennisDaniels (talk) 18:32, 25 July 2016 (UTC)

It should go in List of sequenced eukaryotic genomes for sure, and perhaps List of model organisms as well. I'm not sure it generally belongs in most articles on organisms with a known base pair count (of which there are an ever-growing number), unless the genome is notably large or small.
It doesn't belong anywhere in mouse, which is about the entire genus Mus. It might be appropriate in house mouse and even more so in laboratory mouse (it's pretty annoying that the NIH press release about the sequencing doesn't give the species). Nevermind, missed I missed that mouse has a section on laboratory mice.
For plants, it could perhaps appear next to chromosome counts in a description section. A fair number of plant articles do have chromosome counts (which have been important in understanding plant speciation). I'd rather see chromosome count added to plant articles first, followed by BP counts, rather than BPs being added without chromosome number.
Ideally, notable model organisms would have a section on their use in research, and genome information would go there. In practice, such sections are rare. The house mouse article mentions research, the genome being sequenced and laboratory mice in the lead, but there's nothing in the body of that article on these subjects. House mouse ought to have a summary of some the material in laboratory mouse. Plantdrew (talk) 19:49, 25 July 2016 (UTC)

Taxoboxes and taxa lists with unresolvable reference links[edit]

Today, I went looking for Johnston, 1865 with regard to the taxobox in Serpulidae.

This reminded me of an earlier one: Louis, 1897 in the list for Diadematidae at Pedinothuria (which The Banner recently unlinked).

For those of us who are not sufficiently trained in biology, these tags are a bit of a mystery. Is there a central authority where these initial identifications of taxa can be looked up, using just these (name,year) tags? I recognize a few famous names among the tags, Agassiz (which someone figured out was Alexander, not Louis), Linnaeus, Mortenson; and, in general, someone has taken care to point most of the links to their respective scientists' articles, but no other references are left behind to substantiate these identifications. I see via Google searches that this system is widely used, but have not yet stumbled upon the key.

While I'll accept a response of "go away, we'll take care of this", but I would like to help and also to point out that the "Louis, 1897" one had been tagged as needing disambiguation all the way back in November 2011 with the only resolution being to unlink it nearly 5 years later.  —jmcgnh(talk) (contribs) 04:51, 7 September 2016 (UTC)

In the case of plants, yes, there is a single authoritative list, namely the International Plant Names Index. In the case of animals, sadly there isn't. Individual groups have sources which are pretty standardized (e.g. the World Spider Catalog for spiders), but practice varies widely among sources as to how fully the authors' names are given.
Authorities in taxoboxes should always be referenced, but sadly very often aren't. (We're better at this in WP:PLANTS, I think, but even there it's still far from universal.)
A problem with expanding authors is WP:OR; I've sometimes found incorrectly added links based on research done by an editor. When it's not clear, the form in the source should be used and left unlinked. Peter coxhead (talk) 08:24, 7 September 2016 (UTC)

BioRxiv support in citations[edit]

This project's feedback would be appreciated in this discussion, as this could greatly (and positively) affect biological citations! Headbomb {talk / contribs / physics / books} 21:54, 7 September 2016 (UTC)

Reptiliae or Aves?[edit]

Are birds reptiles? The issue has been raised here. It seems to me that a decision on this matter should be reached by a wider forum, such as this one. --Epipelagic (talk) 05:42, 21 September 2016 (UTC)

"Are birds reptiles?" is a different question from what classification system should be used. English words in common use, like "reptile" or "bird", have different meanings depending on the context. Sometimes they are used to refer to currently recognized taxa, sometimes they are used more generally. So the answer is "no", if you mean the usual English usage, but "yes", if you are referring to clades.
Compare "Are birds bony fish?" to which there are also diametrically opposed answers. The obvious answer is "no"; in normal English usage a bird and a fish are very different kinds of animal. The less obvious answer is "yes", if by "bony fish" you mean the clade Sarcopterygii, since all tetrapods belong to this clade.
The real question is what taxon at the rank of Class should be used for birds, and this is difficult to answer based on reliable sources, since modern systems tend to be clade-based and not interested in traditional Linnaean ranks. Peter coxhead (talk) 09:06, 21 September 2016 (UTC)
The problem as I see it is that to a lay person (or someone with dated taxonomical knowledge such as myself), having an animal listed in two classes simply looks wrong. It looks like a mistake has been made and perhaps reflects badly on the project. DrChrissy (talk) 16:40, 21 September 2016 (UTC)
I agree that in a single taxonomic hierarchy there should never be two taxa at the rank of Class. So long as relevant articles discuss alternative taxonomies, I'm not sure it matters which taxon is labelled "Class". Personally I favour a conservative approach until there's a strong consensus for change in secondary sources, but that's just my view. Peter coxhead (talk) 17:51, 21 September 2016 (UTC)
If that's the way most experts are doing it nowadays, we should follow their consensus. We don't have to like it. I don't. The way I see it, just because birds are a branch off the reptile tree doesn't mean they are reptiles. To me, anyway, this is a gross abuse of the meaning of the term "reptile". But who am I to object? We are mere Wikipedians, not experts, even if you are one in real life, our content comes from the sources, not from us. Within reason, of course. There are times when we make judgement calls when the experts don't agree or the sources don't say something that article needs to say. But by and large we try to just pass information along unless the case is exceptional. Chrisrus (talk) 04:21, 22 September 2016 (UTC)
@Chrisrus: you have the same right as every other English speaker to discuss the uses of the ordinary language word "reptile". It's only the scientific classification that depends on experts. I commend this expert view. Peter coxhead (talk) 08:31, 22 September 2016 (UTC)
Ok, but also, the word on that article is "Reptilia", not "reptile". Maybe reptilia doesn't mean "reptile". Chrisrus (talk) 23:27, 22 September 2016 (UTC)

A restatement of the problem[edit]

There are two self-consistent classifications using "Class Reptilia".

1. The traditional one, in which it is now known that the class is paraphyletic, since it excludes birds (Class Aves). Birds are not a subgroup of Class Reptilia in this classification.

2. The modern phylogenetic sense, in which Class Reptilia is monophyletic and includes birds. The precise details of the clades and names differ from source to source; one recent system due to Benton (2014) is at Reptile#Taxonomy, in which birds are a clade within Order Saurischia.

These two are mutually inconsistent, and cannot be combined in a single classification, as is the case at Bird as of now, based on the classification shown as of now at Template:Taxonomy/Aves, which has the rank "Class" for both Aves and Reptilia. Other parts of the taxonomy templates also show muddled and inconsistent hierarchies. One system at least partly based on (2) is shown by Template:Taxonomy/Neornithes. However, Neornithes cannot be a subclass since it lies below a suborder.

One "fix" would appear to be to make Neornithes and Aves clades in the taxonomy templates, and then make Neornithes the parent of Template:Taxonomy/Aves. However, the problem then is that it doesn't provide for the subdivisions within birds. If the order is Saurischia, then the traditional infraclasses, superorders, orders and possibly even families of birds are at far too high a rank. However, what reliable secondary sources provide lower ranks for these? None that I can find.

It seems to me that Aves has to be treated at the rank "Class" until ranks are provided for the divisions below Aves. This means that in the classification of Aves, Reptilia cannot be treated as a class, although it can elsewhere. Peter coxhead (talk) 09:27, 22 September 2016 (UTC)

Remove Reptilia. As long as we want a reasonable taxonomy tree, we must accept that once we have a taxon on a certain level, we treat any parent taxon on an equal or lower level to exclude it. And if we include Reptilia, then we would also need to include Theropoda, which is a suborder. And, of course why yes Reptilia and not Sarcopterygii (lobe-finned fish), which is also a class and would be paraphyletic if it excluded tetropods (which birds are)? עוד מישהו Od Mishehu 17:01, 27 September 2016 (UTC)
Remove Reptilia from the taxobox on all bird articles.
First, as noted above, why do we have two orders? We are under no obligation to have two taxa at the same level, and doing so doesn't seem to be common practice among experts or on other articles.
Second, the way the bird taxobox is presented is confusing to readers. Listing birds under reptilia wasn't meant to say that birds are reptiles, just where they come from, but that's not clear. I.e.: just because a branch stems from a limb doesn't mean that, for example, frogs are fish. It might be clear if we drew them a picture, but the ranking in a taxobox is understood by many readers that we're saying birds are reptiles, which is just wrong. Chrisrus (talk) 04:25, 28 September 2016 (UTC)
Leave Reptilia out. My gut feeling would be to revise the familiar taxon, keep and use it in a monophyletic sense, but looking it up at NCBI for example [1] we see it is accepted to have a paraphyletic definition. It should be clarified in the Reptilia lead that this is NOT a modern taxonomic class, since it is not monophyletic. In short, 'reptiles' is relegated to a descriptive common use only, like 'ducks' or 'monkeys'. We have a lot of clades we can include: Tetrapoda, Amniota, Sauropsida, Sauria, Archelosauria, Archosauria, Dinosauria, Saurischia, Theropoda, Coelurosauria. There's no need to resort to one that lacks a clear consensus meaning. Wnt (talk) 10:50, 1 October 2016 (UTC)
Allow only one "class" in infoboxes until sources actually say there are two classes for birds. I've never read that anywhere. Every reliable source I've read distinguishes birds as "Class: Aves". There is a recent edit request I'm handling that shows that having two classes for birds in the species boxes is very confounding for our readers. That situation should not continue. Where is the discussion that led to the consensus that put two classes for birds in template {{Taxonomy/Aves}}??? "Class: Reptilia" should be removed without further ado.  Paine  u/c 18:13, 1 October 2016 (UTC)
It appears as if one editor, rather than a community consensus, decided to alter the species boxes, as seen in the discussion at Template talk:Taxonomy/Aves#Class vs. Clade. I have altered them back the only way I know how, which is by changing the parent of the Aves class to Sauropsida. At present, that seems to be more in agreement with reliable sources, although cladistically it still may be controversial. In any event, this discussion needs a wider audience and participation before any further change is made.  Paine  u/c 21:39, 1 October 2016 (UTC)
I just handled it better - allow users who follow the immeduate parent using the taxobox to go through the reptile part of the tree. עוד מישהו Od Mishehu 19:10, 4 October 2016 (UTC)

Semi-protect all taxonomy templates?[edit]

With a unanymous agreement to implement, I did it. עוד מישהו Od Mishehu 17:40, 4 October 2016 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Should we disallow anonymous and new users from editing the taxonomy templates? Tecchnically, this would be done using MediaWiki:Titleblacklist, with the "noedit" and "autoconfirmed" tags (see MediaWiki talk:Titleblacklist for a desciprtion). here have been no useful edits to these templates by anons or new users, and vandalism on one of these templates causes damage to several articles, which can be confusing to readers (see, for example, how Tyrannosaurus looks with this taxobox version). עוד מישהו Od Mishehu 12:35, 30 September 2016 (UTC)

I agree. It is very difficult to figure out in which rank the vandal edit has occurred, and it affects every taxon below the rank... Such vandalism can stand for days before it is noticed. FunkMonk (talk) 12:44, 30 September 2016 (UTC)
I agree strongly. I check Category:Automatic taxobox cleanup most days; most errors are due to vandalism. Peter coxhead (talk) 01:29, 1 October 2016 (UTC)
Yet more vandalism at Template:Taxonomy/Serpentes – see here. Roll on protection Peter coxhead (talk) 21:01, 2 October 2016 (UTC)
Large number of pages in Category:Automatic taxobox cleanup this morning due to vandalism at Template:Taxonomy/Theraphosidae. Peter coxhead (talk) 13:18, 4 October 2016 (UTC)
I agree, makes perfect sense. The templates can be tricky even for users with good intentions. Micromesistius (talk) 02:14, 1 October 2016 (UTC)
Agree. No constructive edits will be lost in this area. William Avery (talk) 07:52, 2 October 2016 (UTC)
Agree. The content in taxoboxes is unlikely to change quickly unlike article content. Seems sensible to protect these. DrChrissy (talk) 21:21, 2 October 2016 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Pronunciations for Latin taxon names[edit]

Please see a proposal at Wikipedia talk:Manual of Style regarding pronunciations for Latin taxon names. Thanks! Kaldari (talk) 05:15, 24 October 2016 (UTC)