Wikipedia talk:WikiProject Tree of Life

PhyloCode

Faendalimas has objected to some of my recent additions of PhyloCode names to the turtle groups of Pleurodira and Chelidae. diff stating they are considered invalid by the ICZN and workers on living turtles. I understand that PhyloCode is controversial among zoologists, but PhyloCode definitions such as "Pan-Chelidae" and "Pan-Pleurodira", are widely used by fossil turtle workers to refer to the stem-groups of these taxa. I think these clade names are useful for distinguishing stem and crown group taxa and I don't see a good reason for removing reference to them, but I would like to know others opinions. Hemiauchenia (talk) 21:17, 4 July 2021 (UTC)

Hemiauchenia If you wish to utilise them alongside the nomenclature used for living and fossil turtles, I have described both living and fossil turtles by the way and fossils do use ICZN also, that is fine but there was no need to delete the ICZN nomenclature and replace it with PhyloCode which does not get used for living species which are included in these groups, all fossil turtles on Wikispecies are named using ICZN code btw. In the end PhyloCode is not an accepted means of nomenclature across almost all of the 2.2 million described species of life. Cheers Scott Thomson (Faendalimas) ^talk 10:04, 5 July 2021 (UTC)

Need help with sexual system

One editor suggested I make an article on sexual systems. [Link to draft here].

There are clearly a good amount of sources on this topic. Like there is [this source], [this] and [this.]

There is even an entire book on sexual systems [right here.]

So it’s not like there is a lack of sources on this topic. It’s just there isn’t a proper definition of sexual system as a matter of fact some call them breeding systems or mating systems.

And I think one of the definitions in there clearly makes no sense.CycoMa (talk) 14:12, 27 July 2021 (UTC)

Actually I made an article on Sexual system. It just needs help with expanding and needs.CycoMa (talk) 22:09, 29 July 2021 (UTC)

Reliable sources list

Howdy. Do you guys have a list of resources or list of reliable sources? I'm trying to figure out what websites are generally reliable, so I can add them to my CiteHighlighter user script. Also, I was AFC reviewing today and marinespecies.org was used as a citation, and I have no idea if it's reliable. Thanks. –Novem Linguae (talk) 13:40, 5 August 2021 (UTC)

I don't know of a single list. Lists of resources tend to be in the individual project pages for mammals, bird, plants, etc. In this particular case, WoRMS (www.marinespecies.org) is definitely a reliable source and has its own template ({{Cite WoRMS}}). —  Jts1882 | talk  16:06, 5 August 2021 (UTC)

Wikipedia:WikiProject_Tree_of_Life#Taxonomic_resources is probably a good baseline for reliable sources? --Elmidae (talk · contribs) 16:12, 5 August 2021 (UTC)

Ah, I feel silly for missing this. This will work. Thanks! –Novem Linguae (talk) 20:30, 5 August 2021 (UTC)

Deuterostomia vs Xenambulacraria

Recent genetic research has provided strong support that Deuterostomia is not monophyletic[1][2][3][4][5][6][7][8]. Does this mean that we should remove the Deuterostomia from Scientific classification? I think it is too early to choose between the Deuterostomia and Xenambulacraria hypotheses, but for a neutral point of view it would be more correct to show Bilateria as the parent taxon of Ambulacraria and Chordata. HFoxii (talk) 06:28, 17 August 2021 (UTC)

Global Species List Working Group

I have begun writing a page for the Global Species List Working Group which is the organisation under the umbrella of the IUBS that is developing methods and moving us towards a single global list of species for all end users of taxonomy, hence I thought this would b a relevant organisation to this project. For purposes of full disclosure yes I am a member (Secretary) of the organisation and one of its principal authors of the publications we do. Second reason I am writing this is to make this clear. I will be grateful for any comments people have, this is an important project for many sectors of the biological community, and clearly particularly so for any Wiki Projects directly dealing with names of species, animal or plants. Its not finished yet I still have a lot I wish to add to this. Cheers Scott Thomson (Faendalimas) ^talk 21:15, 1 September 2021 (UTC)

new IUCN update

An FYI...the latest IUCN red list update has been published. I'll slowly start updating tomorrow.....Pvmoutside (talk) 02:16, 5 September 2021 (UTC)

Pvmoutside What has changed? Have you a link? According to this page any changes won't be published until 9 Dec 2021. The latest birdlife spreadsheet here is still dated Dec 2020. - Aa77zz (talk) 07:44, 5 September 2021 (UTC)

Table 7 (2020-2021) here says it was last updated on 4 September 2021, Maculosae tegmine lyncis (talk) 10:05, 5 September 2021 (UTC)

Looks like the next one is indeed 9 Dec 2021 but that the first update of the year was late (yesterday). The new list doesn't include any birds so it might be that they only update birds once a year in synch with the Birdlife checklist. —  Jts1882 | talk  10:34, 5 September 2021 (UTC)

Ya, no birds, but plenty of other stuff.. See -2 changes....Pvmoutside (talk) 12:22, 5 September 2021 (UTC)

I presume that you meant to link to -2 changes but somehow didn't?

—Trappist the monk (talk) 00:40, 6 September 2021 (UTC)

One of the things that I have been considering is a prospective bot task to replace old-form IUCN urls in {{cite iucn}} templates with new-form urls from the IUCN API (about 13000 articles). I have been holding off because there is a discrepancy between the citation that IUCN renders at the assessment url and the citation returned from the API. For example, this url https://www.iucnredlist.org/species/11389/115102240 has this citation

Powell, R. 2016. Leiocephalus herminieri (errata version published in 2017). The IUCN Red List of Threatened Species 2016: e.T11389A115102240. https://dx.doi.org/10.2305/IUCN.UK.2016-3.RLTS.T11389A71739645.en. Downloaded on 05 September 2021.

but, the API returns this:

{"name":"11389","result":[{"citation":"Powell, R. 2016. Leiocephalus herminieri. The IUCN Red List of Threatened Species 2016: e.T11389A115102240. https://dx.doi.org/10.2305/IUCN.UK.2016-3.RLTS.T11389A71739645.en .Downloaded on 5 September 2021"}]}

The API citation is missing the errata information. I have raised that issue with IUCN who say that the two citations should be the same and have said that they will fix the problem. The prospective bot might also address the issue of Polbot-created articles raised at this archived discussion (the number is now 15400ish articles).

All of that aside, would a variant of the prospective bot task be useful in doing this new IUCN update?

—Trappist the monk (talk) 00:40, 6 September 2021 (UTC)

if you can get the bot to work, it would be great.....Pvmoutside (talk) 17:24, 6 September 2021 (UTC)

I have a preliminary version of the prospective bot code. Here are a pair of example edits:

Hokkaido – this edit replaces a plain-text IUCN citation with a {{cite iucn}} template (the rendered citation)

Acacia confusa – this edit updates the {{speciesbox}} |status=, |status_system=, and |status_ref= parameters. Interestingly, the pre-edit version of this article had a reference for Acacia richii (a redirect to Acacia confusa). It seems to me that the {{speciesbox}} should not have a status reference that links to an IUCN assessment of a different 'name'. Even if the article has redirects from a bunch of different 'names', the name of the article and the name derived from the {{speciesbox}} or the {{taxobox}} and hence, the name that |status_ref= links to at IUCN should all be the same. Am I misguided in this thinking?

For {{speciesbox}}, the script gets the species name from |taxon= or from |genus= + |species= or from |name= or (as a last resort) from the article title. For {{taxobox}}, the script gets the species name from |binomial= or from |name= or (as a last resort) from the article title. There are about 150 articles with {{subspeciesbox}} and four with {{infraspeciesbox}} in Category:Cite iucn maint. For the time being, I am going to ignore those two infoboxen. I would have made it so that {{taxobox}} also assembled a binomial from |genus= + |species= but the documentation at {{taxobox}} wants editors to write the abbreviated binomial in |species= (H. sapiens instead of sapiens). Seems silly to me; if we want the abbreviated form, the template can make that without any difficulty. I may still make it possible for the bot task to assemble a binomial from the {{taxobox}} |genus= + |species= parameters.

The script compares the current infobox |status= against what it read from the IUCN API. If they are the same, the script does nothing with the infobox. Is that the correct thing to do? If the script does nothing, an old, possibly out-of-date |status_ref= value may linger (forever). On the other hand, the script could unconditionally update |status=, |status_system=, and |status_ref= but that might run afoul of WP:COSMETICBOT because it is possible that the only thing that will change is the value assigned to |access-date= in {{cite iucn}}. Opinions?

—Trappist the monk (talk) 22:04, 7 September 2021 (UTC)

We definitely should not be adding IUCN statuses applied to names that are redirects from heterotypic/subjective synonyms. IUCN recognizes some species that are lumped into other species by the various taxonomy databases we follow for different branches of the tree of life. The IUCN status for a lumped species simply doesn't apply to the broader species concept into which it was lumped. Hypothetical example: IUCN recognizes a species endemic to Borneo and assesses it as critically endangered; an authoritative database for the group lumps the Bornean species into a species distributed from Japan to Sri Lanka; we cannot assume that the CR status applies to a more broadly distributed species concept. In the case of homotypic/subjective synonyms it is safer to assume that the species delimitation used by IUCN and another source is the same (although the genus concept would be different). Polbot created many stubs for IUCN assessed species back in 2007, and there are a lot of Polbot stubs that are regarded as synonyms in other databases. I am certain there are cases where a well-meaning editor has moved a Polbot heterotypic synonym to a currently accepted name without removing the conservation status; I don't know how to find these cases.

It seems unlikely to me that you'd need to look at anything besides |binomial= for the name in a manual taxobox. If the binomial doesn't match anything on IUCN, but either |name= or |genus=+|species= do match IUCN, something is wrong. If you're interested in generating a list of articles where binomial doesn't match IUCN but another parameter does, I'd be happy to look into those.

Personally, I'm fine with bots making cosmetic edits. But I'd argue that change the access date isn't entirely cosmetic; there will be a difference in rendering output. With a relatively dynamic source such as IUCN, as a reader, I do want to know how recently the source was checked. But I'm not sure I understand your alternatives in this case. Your script replaces a plain-text citation at Hokkaido (and in this case doesn't involve parsing the status in a taxobox). Plain-text citations would be replaced without regard to whether |status= has/hasn't changed; you're only proposing to refrain from running the script on pages where the only change would be updating |access-date= in articles that already cite IUCN via {{cite iucn}}? Do I have that right? Plantdrew (talk) 03:13, 8 September 2021 (UTC)

If I understand your first paragraph, I think that you are saying that the script did the right thing when it replaced an IUCN reference to Acacia richii in the Acacia confusa infobox. That sort of replacement would seem to be a beneficial side-effect of updating the status parameters.

Alas, the manual taxoboxen name parameters are sort of optional. That is why the script starts at |binomial= or |taxon= and works its way down the ladder to the article's title. At the moment, I don't think that I need another list. In my testing, articles in Category:Cite iucn maint seem to have something that the script can use to fetch data from the IUCN API.

I am the author of User:Monkbot/task 18 so I am sensitive to editors perceiving anything that I do as cosmetic – I don't need that kind of drama. In this case, I think that my script is similar to the scripts that audit date formats where those scripts sometimes only update the |date= parameter in a {{use dmy dates}} template; an invisible change from the reader's perspective. Still, some editors get their knickers in a twist about that ...

The primary purpose of this script is to replace old-form IUCN urls with current-form urls. The script can replace plain-text references with {{cite iucn}} templates and it can update status parameters in certain infoboxen – after all, it's already there fiddling with old-form urls – it doesn't have to do these other things but why shouldn't it? Often, the only {{cite iucn}} template in an article is in the infobox |status_ref= parameter. That parameter should, I think, always be updated to definitively state how recently the source was checked. But this is a case where it is possible that the only change to the article will be the {{cite iucn}} template's |access-date= so I expect that somewhere sometime knickers will twist.

—Trappist the monk (talk) 18:28, 8 September 2021 (UTC)

@Trappist the monk: I did this a few years ago, and updated all/most of the straightforward cases where |status= had changed. The <ref> maintenance was the worst part, and caused the most exceptions. At that time (perhaps it has decreased since), a non-trivial fraction of pages used <ref name="IUCN Status">...</ref> elsewhere in the body (<ref name="IUCN Status"/>), sometimes to re-cite the current status (which has changed), sometimes to cite the status as of a certain date (which is fixed), sometimes to cite the geographic footprint (which may or may not have changed), etc., so you have to inspect those pages more carefully to decide how to handle the new & old ref (or save them for the end of the run).

I'd also suggest that, when naming new |status_ref= to append the year to the ref name (e.g. <ref name="IUCN Status 2021">), which might aid future maintenance when having to move refs around.

You might also find Category:Taxonomy articles created by Polbot (32,226) useful for finding relevant Polbot pages.   ~ Tom.Reding (talk ⋅dgaf)  11:13, 8 September 2021 (UTC)

Hadn't thought about <ref>...</ref> tags. Thanks for that. Yeah, that's a puzzler. I'll go away and think about how to handle that. I did take your advice to name the reference in |status_ref=; since I have the access date from the new {{cite iucn}} template, I use that: <ref name="iucn status 8 September 2021">{{cite iucn|...}}</ref>; pretty sure that is sufficiently unique to not break anything.

—Trappist the monk (talk) 18:28, 8 September 2021 (UTC)

Looks awesome! A couple questions, will your bot pick up new iucn listings for pages not previously listing any, whether they be new listings or listings not previously determined....and will it "correct" manual listings not entered the way it likes?Pvmoutside (talk) 15:06, 8 September 2021 (UTC)

No, not in the plan. will it "correct" manual listings not entered the way it likes? From the tone of that question, I get the impression that you are about to complain about something. Let's not beat-around-the-bush. What is your complaint?

—Trappist the monk (talk) 18:28, 8 September 2021 (UTC)

Reviving WikiProject Zoo

Hello, WikiProject Tree of Life members, I am reviving WikiProject Zoo as I feel many of the zoo articles are lackluster. If anyone is interested in helping out, please do so. -- PaleoMatt (talk) 17:24, 5 September 2021 (UTC)