User talk:Jmv2009

Jmv2009 -

There is a lot of conflicting information out about which taxa is the base. It is possible to refute Porifera and Ctenophora article for article. I suggest it might be more accurate at this time to express this something like this:

"At the present time there is no definite answer as to which taxa is the base taxa for all other animals. There have been reports that Porifera are the base taxa, which has been the traditional view, but there has been recent research that indicates Ctenophora may be the base taxa."

I have been in touch which several researchers and there is some information due to come out but the papers are currently embargoed that would tilt towards Porifera. Until the final consensus is in (which may be the twelfth of never) it might be worthwhile to provide a text indicating that this topic is a little squishy at the moment and also provide alternate versions of the clade diagram next to each other to reflect this.

There was a good paper that discussed the problem with statistical methodologies being used in that one method may provide strong results and another method may provide just as strong support. In addition, the choice of which samples to use complicates matters. Several papers have been published where the same data has been reanalyzed by a different methodology and different results where reached. And then there is the problem on Long Branch Artifacts. The farther back in time you go the more likely there could be a problem with LBAs due to variable rates of evolutionary change for genes that were not known, were not taken into account, or just didn't fit a notion.

So, I believe it might be a good idea to indicate that there is some discussion going on at this time as to which is the oldest, which would add authenticity to the Wikipedia entry.

As an aside, one of the reasons I favor Porifera is the discovery of fossil specimens of sponges or sponge like animals (they really do look like sponges) and of spicules in the fossil record that are older than 760 mya. That is a lot older than I am. I have not seen any records of Ctenophora in the fossil record that old. The fossils were found in Namibia. However, to stay pure at this point I believe e it would be better to indicate there is a discussion going on and there is no definite answer yet.Yerginml (talk) 18:32, 28 October 2017 (UTC)

Marc Yergin

Dear Marc, thank you for your comments. Briefly before your comments, I had already added the alternative Porifera-sister hypothesis to the article. Now, I added even more hedging. Furthermore, I resurrected the Diploblast article, which encompasses the sister-Porifera hypothesis. Please feel free to add more refs to that article. Also see the Animal article for more such discussion. More sources are always welcome (especially secondary ones!). Strictly speaking, we should actually not even be acting on primary sources, let alone embargoed papers. But let's see whether the tilting towards Porifera is actually over the vertical position. Then, there is still the possibility of a Porifera-Ctenophora clade. In the Whelan paper, when the genes which were likely to causing long branch attraction (fast evolving ones?) were removed, the Ctenophora-basal hypotheses got more basal, not less. The main problem of a late divergence date of the Ctenophora was not resolved by improved Ctenophora sampling. However, the divergence date was pushed earlier (to ~350 Million years ago). Also 760 Million years ago may not mean much, see ^[1] Jmv2009 (talk) 07:55, 29 October 2017 (UTC)

Jim -

The 760 mya wasn't from phylogenomic data - It was from finding a fossil that was 760 mya old. Blew me away when I read the following article:

Brain, C.K., et al (2012) The first animals: ca 760-million-year-old sponge-like fossils from Nambia. 108(1/2) Art #658 8 pages.

It has a really nice photo of the fossil that looks remarkably like extant sponges from today. Like I said, it really did blow me away.

This is my first venture into commenting on Wikipedia articles. I am impressed by how nice the discourse has been. If you ever need help with an article or information on sponges/porifera please do not hesitate to contact me. I still like the old saw that I heard more than 50 years ago in a zoology class (my first one): "Under the most carefully controlled conditions a living organism will do whatever it dam well pleases." I guess it holds as well for the historical record as well. When that embargoed article is out I'll let you know. Marc

It is true that it appears that actual fossils in that era occur way after the from molecular clocks apparent origination date.Jmv2009 (talk) 18:54, 1 November 2017 (UTC)

Hi, you've removed from Eukaryote both refs and the mention of ?Megavirus? with ref to a paper "Symbiosis in eukaryotic evolution" which doesn't even mention the word megavirus. Why? If something is a hoax then fine, but if not, then surely we at least have to mention it and say it's discredited by x, y, and z. What's going on? Chiswick Chap (talk) 20:06, 12 November 2017 (UTC)

It does not mention Megavirus, but it does mention "giant viruses". I took them to be the same concept, but maybe I'm wrong?Jmv2009 (talk) 01:16, 13 November 2017 (UTC)

Perhaps they are, perhaps not. Seems a flaky basis for decisions. Assuming you're right for the moment, why would that justify total removal rather than saying that there was once a theory about Megaviruses but now that's discredited? Why would you not say that? Chiswick Chap (talk) 08:08, 13 November 2017 (UTC)

I don't know. I had recently put that cladogram in (copied from Proteoarchaeota), and it seemed a bit much, too much clutter, and not very well supported/too speculative. There is also room for hypothesis about the nucleus in the rest of the article. Thanks for your comments.Jmv2009 (talk) 17:24, 13 November 2017 (UTC)

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Howdy, Could you include a reference for the update you made to Template:Taxonomy/Ichthyosporea (edit | talk | history | links | watch | logs)? I know not all the taxo templates have them, but the previous version did, so to avoid any confusion it'd be good to have one here. Thanks. Nessie (talk) 01:43, 27 February 2018 (UTC)

@NessieVL: The taxonomy (and templates below) should be well references in the articles themselves. In this case the Ichtyopsorea article. Please let me know if something is missing there.Jmv2009 (talk) 17:07, 22 May 2018 (UTC)

A discussion is taking place as to whether the article Zoosporia is suitable for inclusion in Wikipedia according to Wikipedia's policies and guidelines or whether it should be deleted.

The article will be discussed at Wikipedia:Articles for deletion/Zoosporia until a consensus is reached, and anyone is welcome to contribute to the discussion. The nomination will explain the policies and guidelines which are of concern. The discussion focuses on high-quality evidence and our policies and guidelines.

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Zoospoia was redirected to opisthosporidia due to aphelida getting associated with eumycota.Jmv2009 (talk) 20:31, 8 July 2018 (UTC)

Hello. This is a message to let you know that one or more of your recent contributions, such as the edit you made to [[:Zoosporia]], did not appear constructive and has been reverted. Please take some time to familiarise yourself with our policies and guidelines. You can find information about these at our welcome page which also provides further information about contributing constructively to this encyclopedia. If you only meant to make test edits, please use the sandbox for that. If you think I made a mistake, or if you have any questions, you may leave a message on my talk page. Thank you. Souvik Nova (talk) 20:14, 20 May 2018 (UTC)

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@Souvik Nova: I did not do such thing.Jmv2009 (talk) 09:27, 21 May 2018 (UTC)

You are found messing with tags and instead of giving a warning you repeated it. Dont mess with tags. You can easily move your page into Zoospore Page and you keep editing. You can contact me through email too. If you have done a good work on a article I will nominate it for good article and you will get a barnstar or wikiproject award. Souvik Nova (talk) 09:37, 21 May 2018 (UTC)

@Souvik Nova: Please explain. Please give the example. I don't know what you mean by "messing with tags and instead of giving a warning you repeated it", as the statement does not make sense. The only thing I can think of was that there was an edit conflict, and I discarded the interfering edit.

Note: Souvik Nova was blocked shortly after this for abuse and sockpuppetry.Jmv2009 (talk) 16:26, 22 May 2018 (UTC)

Thanks for creating Zoosporia, Jmv2009!

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Hi, I noticed a few things about some of your recent edits to the tree diagrams in various articles' phylogeny sections.

Firstly, the maximum likelihood trees that we use widely are phylogenetic trees; cladistics people (not me) are very picky about the term cladogram, and in a phylogeny section the tree article is clearly the right thing to link.

Secondly, it's really helpful to other editors if the tree diagrams are constructed tidily with equal indents for each level; I'd appreciate it if you could help to make sure that any diagram we edit is made a little easier to maintain with each edit.

If I'm allowed to mention one more thing, it is that we should try to construct well-formed trees with binary forks; when the state of play is so flaky that this can't be done, I'd suggest that we say explicitly that the tree is not yet fully resolved (as of 2018, or whatever). Having a tree with half-a-dozen individual fossil species listed with no structure, next to a well-resolved branch of living species, is not ideal, and on the whole I'd like to remove all such lists from phylogenetic trees.

Hope all this makes some sort of sense. The goal, surely, is to provide diagrams that make the text easier to understand, and give readers a quick and reliable overview of a group's evolution; for that, they must be clear and concise. All the best, Chiswick Chap (talk) 11:47, 3 June 2018 (UTC)

Thanks for your comments. Please describe what in your opinion the difference is between a phylogenetic tree and a cladogram, so I can take it into account. Often the timeline is included in the trees/cladograms as well. On maybe a seperate note, is it correct that we should use cladogram templates?

When you mention equal indents on each level: I assume you are talking about the code behind the screan: That appears very hard to maintain, as often branches merge and unmerge as they are recognized from paraphyletic to monophyletic, and vice versa. Also, parts of cladograms are sometimes transfered between other cladograms. On the other hand, it is nice to have, so feel free to do it. Or better, write a bot.

I strongly disagree that we should remove fossils from the trees, even though the phylogeny may not be that clear, as it improves our understanding of the evolution (why are people studying fossils otherwise anyway?).

On a side note, it is especially the fossils that make it clear that any clearly paraphyletic grouping is impossible to maintain, because fossils will invariably lead to ridiculous discussions when maintaining paraphyletic groupings with fossils. There are still a 20 odd places on wikipedia were paraphyletic groups are used. See e.g. the monkey article, where the literature speaks of monkeys for the ancestral common group, but somehow they are still regarded as two groups (while it should be at least three, if you include the ancestral groups.) Inevitably, the paraphyletic groups are discarded or accomodated eventually.

About always bifurcating: Sometimes there is no info. If there is info, I usually bifurcate, probably on too weak evidence. Jmv2009 (talk) 12:03, 3 June 2018 (UTC)

Hm. All our trees of phylogenetic relationships in our phylogeny sections are, plainly and necessarily, phylogenetic trees, presumably and we hope maximum likelihood ones too; if they happen also to be cladistic hypotheses, that might be interesting but it's not what we should be getting into. On maintaining the indents, it's simply good practice to format articles properly; "transferring" without formatting is, frankly, laziness. Nobody is asking for all fossils to be deleted, simply for them to be inserted properly rather than listed without any decent indication of phylogenetic position, combined with no discussion above the tree about how well resolved it is. Chiswick Chap (talk) 22:13, 3 June 2018 (UTC)

Hi, I'm Boleyn. Jmv2009, thanks for creating Gloeomargarita lithophora!

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The higher taxonomy of plants is a muddle, I know, but when you made the taxonomy template for Charophyta show its rank as a division and made it a parent taxon, you created a mess lower down, with many inconsistent rank orders, since Charophyta now had multiple divisions as subordinate taxa, sometimes way down the classification. I've changed the subordinate taxa to "cladus", but please do not change taxonomic hierarchies in this way without considering and fixing the full effects of your changes. Peter coxhead (talk) 20:24, 18 August 2018 (UTC)

@User:Peter coxhead: It appears that with you, you mean me personally, rather than generally. That's a bit too much honor. In any case, please note that I did not change the hierarchy of the Charophyta. See e.g. which was before the first edit I made on Charophyta. Jmv2009 (talk) 22:47, 18 August 2018 (UTC)

Sorry, I meant Template:Taxonomy/Charophyta, which you did create, and which recently caused problems when you made this edit, which meant that, e.g., Template:Taxonomy/Horneophyta showed two divisions – both Horneophyta and Charophyta. In taxonomy templates, it's best to leave the higher ranks as clades where there is no widely agreed set of ranks. Peter coxhead (talk) 08:36, 19 August 2018 (UTC)

@User talk:Peter coxhead For me, taxonomic ranks are not determined by biology but by history, so inherently arbitrary: It's arbitrary based on past assessments, extinctions, etc... In Rugiero et al (2015), they introduced the notion of "superphylum" for Charophyta/Streptophyta. We could go with that, but wikipedia doesn't support it yet. So from my part, feel free to change any taxonomic rank, if you feel it is appropriate (I trust you).

Yes, ranks are utterly arbitrary, we agree. Their usefulness is to provide a recognisable ordering in a classification, which is why multiple occurrences of the same rank in a hierarchy needs to be fixed.

Actually, the automated taxobox system does handle the ranks "superdivisio" as well as "superphylum". So this may be a good solution that can be sourced. I'll think a bit more about it. Peter coxhead (talk) 19:39, 19 August 2018 (UTC)

See Talk:Charophyta#Rank for my latest thoughts. Peter coxhead (talk) 06:21, 20 August 2018 (UTC)

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Hi, I'm really rather unhappy about how you are going about editing several animal phylogenies; the current shifting status based on single research articles is quite unsatisfactory, and I think entirely unencyclopedic.

It is quite wrong to change one slot in a phylogenetic tree and add a ref to a list without explanation. What is required is to write a sentence justifying the change, with its own ref, which should really be a secondary (review article) source - citing a primary research paper for a rather recent change is not good enough (see WP:SCIRS) because the very next primary paper on the topic will very likely refute, contradict or modify the change, which is precisely what Wikipedia does not want. So, I believe that what is wrong is not details of editing so much as the total approach.

It may help to reflect, what I am sure you know already, that the domains of research and of encyclopedias are very different - one favours the primary, one doesn't; one aims to be up to the minute, the other aims to summarize what is reliably agreed by multiple scientists. Wikipedia cannot, and must not attempt, to track every minute shift in opinion as soon as one team publishes a primary research paper. Hope this is clear. All the best, Chiswick Chap (talk) 20:06, 27 October 2018 (UTC)

@Chiswick Chap Thanks for letting me know. Apparently there are now two papers with respect to choanozoa (which has been updated, as well as apoikozoa), adl et al 2018/2019 ref article and Brunet and King 2017. See also discussion at Template_talk:Taxonomy/Animalia on updated nomenclature. Are you only referring to the choanozoa issue or is this a wider complaint? It's true, there have been a couple of significant refutations: Sponge-sister vs Ctenophora-sister. Trochozoa/Lophotrochozoa. Placozoa-Cnidaria sister relationship is probably still very controversial, which is why all the refs. On the diaphoretickes side, there's picozoa, cryptista, glaucophyta placements with respect to archaeplastida. How to deal? Just leave it all fully unresolved? I also got a comment recently from somebody who didn't like anything but bifurcations, but sometimes there is just no info. Edit: That was you as well! See previous talk on this page. But maybe you were only talking about extinct species, as they are much harder to resolve. Also holozoa/ichtyosporea placement is under discussion with alternate hypothesis.Jmv2009 (talk) 20:23, 27 October 2018 (UTC)

It's wider. We really must not try to rely or follow primary research. This applies to all biology articles. "Two papers" may be a tad better than one but if they're still primary they're still not the right kind of source. How to deal? Wait for reliable secondary sources. While things remain "controversial" they are pre-encyclopedic. If you want to do up-to-the-minute research, a lab is the place, not Wikipedia, I'm afraid. If you'd like to discuss this more widely we should do it at WikiProject Biology or some such place. Chiswick Chap (talk) 20:37, 27 October 2018 (UTC)

@Chiswick Chap Thanks for you comments. I can appreciate the goal, but honestly I have not seen many articles which meet that standard. It's always this primary ref says this vs this primary ref says that. And often of 5 yrs+ old at that. Often very taxonomic system oriented, not resolving further. If we have to wait for also the rather arbitrary taxonomic levels to catch up... BTW, why is the Adl 2018/2019 review article previous not a secondary source? Jmv2009 (talk) 20:51, 27 October 2018 (UTC)

This not an "arbitrary" matter but a keystone of policy. The undoubted failings of other articles, like the speeding motorist's excuse that others were also breaking the law, is no excuse for not doing things properly. I happened to be in the way when you made a series of what seemed to me to be unjustified and poorly structured changes, that's all.

If that's a review article then it should be fine. If so, please use it to support a sentence or two of paraphrased description to explain the change. Please do not just make uncited, unexplained, or primary-sourced changes, especially on recent and admittedly controversial matters, to articles, especially to major ones like Animal. I'd be really grateful, by the way, if you could write an explanatory sentence for Animal as the current state with a string of half-a-dozen citations for the phylogeny is unacceptable. Chiswick Chap (talk) 21:02, 27 October 2018 (UTC)

tnx. The choanozoa issue is not even interesting, as it is only semantics/naming.

As per the short discussion at Template_talk:Taxonomy/Animalia, I broadly agree with Chiswick Chap about primary sources (e.g. there was at one time far too much use of Cavalier-Smith's papers). On the other hand, I'm very aware that deep phylogeny remains a fast moving subject, and by the time good secondary articles appear they tend to be out of date. However, the Adl et al. (2018) paper at doi:10.1111/jeu.12691 is a synthesis of primary research with a wide range of authorship and so, I believe, presents a system we can legitimately use. Personally, I'm still digesting it. There are two different issues: what are the main clades that should be recognized, e.g. in taxoboxes, and what names should be used for these clades. Peter coxhead (talk) 22:13, 27 October 2018 (UTC)

@Peter coxhead@ Chiswick Chap There is indeed a lot to digest in Adl et al. 2018/2019.

a) Renaming of Plantae/viridiplantae/green algae to chlorobionta (specifically discussed)
b) Not recognising Mesostigma/Cholorybus/Some spirotaenia (still) as basal plantae, is still in streptophyta. No Streptofilum.
c) hedged acceptance of placozoa - cnidaria sister relationship
d) largely unresolved chlorophyta
e) largely unresolved archaeplastida (makes sense)
f) no tsar
g) unresolved phragmoplastophyta
h) unplaced syssomonas, corallichtrium in holozoa (specifically discussed)
i) no Ancoracysta Twista Haptista sister relationship
j) Ancyromonas vs Malawimonas as sister of Amorphea + CRuMs
k) Disolvement of excavates. (finally)
l) acceptance of CRuMs, no more Varisulca
m) unresolved metazoa (porifera vs eumetazoa/diploblast, parahoxozoa vs ctenophora)
n) Still lots of insertae sedis genera. It will be interesting to see how many of them are sister to a major group!

Please review these cases, and make suggestions on wikipedia actions, if you would.

Some pet annoyances of me, which are not going to fly:
m') acceptance of eumetazoa (vs diploblasts) nomenclature (Diploblast should have date-priority. Even though on the face of it is paraphyletic, I would argue tribloblast were always seen as having emerged within diploblasts. So diploblast was always implicitly read as "2+ germ layers", rather than literal two.)
o) Just use "green algae", if necessary "green algea, incl land plants", already instead of "chlorobionta". Again, on the face of it, it is paraphyletic. But is has long been very well understood that land plants emerged deep in water plants (i.e. green algae) tree. I don't see "chlorobionta" really being used. Jmv2009 (talk) 07:05, 28 October 2018 (UTC)

Well there are certainly some knotty problems in all that. The issue that I'd like fixed today is that Choanozoa is now called "a phylum of eukaryotes" and placed as what until yesterday we called the Apoikozoa, a clade containing the whole of the Animalia, i.e. not at phylum level but above kingdom. Well it can't be both; and we have two articles, one named Choanozoa which you have now wikilinked into the tree at Animalia in the kingdom position, and Apoikozoa which you have effectively unlinked. This isn't right, whatever view we take of the phylogeny. Either we put everything back as it was, or you need to rename Apoikozoa to Choanozoa (superkingdom), or you could merge the Choanozoa and Apoikozoa articles. Right now it's just a mess. Peter coxhead - which way would you fix this? Chiswick Chap (talk) 07:33, 28 October 2018 (UTC)

@Chiswick Chap@Peter coxhead Ok, it's now a clade. I actually also proposed to move Apoikozoa to Choanozoa, which is now a placeholder. See Template_talk:Taxonomy/Animalia I don't have the privileges to do it. The idea was to wholesale replace apoikozoa with choanozoa accross wikipedia.Jmv2009 (talk) 07:53, 28 October 2018 (UTC)

Well if you're merging the two articles you don't need special privilege, just merge and record in an edit comment where any materials came from. Alternatively submit a move request. All of this is about consensus, which must be based on reliable (secondary) sources, you can't get away from it. Chiswick Chap (talk) 08:03, 28 October 2018 (UTC)

Both articles have substantial page histories that need to be preserved, which makes it slightly problematic. However, most of the material that should now be at Choanozoa is currently at Apoikozoa, and Apoikozoa should become a redirect to Choanozoa. Peter coxhead (talk) 08:10, 28 October 2018 (UTC)

yes Jmv2009 (talk) 08:14, 28 October 2018 (UTC)

So, as you've both seen, I reverted Choanozoa to the redirect to ApoikozoaApoikozoa, on the grounds that the material added was basically just copied without attribution from Choanozoa; then I swapped them over and did some tidying.

@Jmv2009: please can you check the links to Choanozoa, because some seem to be meant for the old Cavalier-Smith sense. Peter coxhead (talk) 09:29, 28 October 2018 (UTC)

On a related point, I've started to resolve the chaos around animal phylogenetic trees in various articles. These must not be constructed by WP:SYNTH, i.e. by patching together branches from multiple primary sources (even worse if those sources aren't even named, but wrong either way actually). Further, if a tree is labelled 2011 then later additions don't fit, it must be one or the other. Further, if you want to use dashes for uncertainty, not unreasonable, then explain that. Further, if images are added, they must be commensurate in size with all the rest. In short, it's a mess, and we need to replace all these trees with new ones, using a single reliable secondary source in each case. I do hope this is clear: it's a core part of Wikipedia policy, and editing without it is disruptive. Chiswick Chap (talk) 09:20, 6 November 2018 (UTC)

Taxonomy templates are required to have a consistent hierarchy of ranks. Your two recent edits put multiple templates and pages into Category:Taxonomy templates showing anomalous ranks, which I've now fixed by undoing your edits. Homo is a genus; Australopithecus is a genus. One cannot have the other as a parent. If it were accepted in reliable secondary sources that Homo is paraphyletic with respect to Australopithecus and genera should be monophyletic, then this could only be fixed by merging Australopithecus into Homo as the latter name has priority.

Changes to taxonomy templates that will affect major articles like these two must be discussed on the articles' talk pages and consensus reached first. Peter coxhead (talk) 18:12, 3 November 2018 (UTC)

@Peter coxhead The paraphyly of Australopithecus with respect to Homo (not the other way around) is actually a foregone conclusion. See e.g. and . Blame Mayr (1950) Suggestions?

Well, the conclusion is the same: if and when there's a clear scientific consensus to merge Australopithecus into Homo in secondary sources acceptable here, and also consensus among editors that this is the case, then the Australopithecus articles can be moved and their taxoboxes adjusted accordingly. Until that happens, nothing can be done to the taxoboxes, although all appropriately sourced views can be discussed in the relevant articles.

As it happens, only one of your three sources actually suggests not using the genus Australopithecus, so I don't see any consensus to change the nomenclature. Peter coxhead (talk) 20:26, 3 November 2018 (UTC)

Making a more general point, taxoboxes, like other infoboxes, exist to summarize article features, in this case the taxonomy. Ideally taxonomy templates should repeat the main reference used in the article to support the placement in the parent taxon. Regardless, the taxobox, and hence the taxonomy template, must be consistent with the article, otherwise it doesn't do its job. This is the problem with your rangeomorph edit. Peter coxhead (talk) 20:33, 3 November 2018 (UTC)

@Peter coxhead It indeed looks like they are sticking to the genus in genus nomenclature for now. Can we just follow that not only in the articles, but also in the taxoboxes parent assignment, despite the taxonomic rules? This is arguably due to Paleoanthropologists violating taxonomic rules, which we should follow as being the consensus?^[1]

A little background: Australopithecus is more seen as kind of a sequential genus, australopithecus genus evolving into homo genus. This doesn't work when Australopithecus would not be otherwise extinct, but it also doesn't work when it otherwise is, which is what discussion is about. Logically, the taxonomic levels should inform about sequential-ity, not e.g. diversity.

Sure, I understand the argument perfectly. But you must accept what Wikipedia is about. We report what reliable secondary sources say. I can only repeat myself: when the scientific consensus in reliable secondary sources is to move Australopithecus to Homo, we will follow. What you or I think is logical is completely irrelevant to what goes in articles. What you or I think about paraphyletic taxa is completely irrelevant to what goes in articles.

(By the way, there are no "taxonomic rules" that say that genera can't be paraphyletic. Nowhere does the ICZN forbid paraphyletic taxa. The circumscription of a taxon is explicitly a matter for taxonomists to decide. All the ICZN does is to determine the name of the taxon, given its circumscription, position and rank. If the PhyloCode had the status of the ICZN, it would be a different matter. But it doesn't.)

Peter coxhead (talk) 22:07, 3 November 2018 (UTC)

@Peter coxheadThat's all fine and dandy and correct. But how, in our taxobox system, do you acknowledge established paraphyletic relationships? How do you show that Homo actually did emerge in Australopithecus? How do you show chronogenus relationships as in this ref and this ref ^[2]? It appears not to be possible/acceptable to acknowledge.

N.B. This is not consensus yet, but actually the likely course of action is not to move A. to H. but to add more genera (A. will become a higher level taxon, I guess). H. could also more to A, in theory, as A. is more inclusive. "Virtually all systematists and taxonomists agree that we should only give names to monophyletic groups. However, this evogram shows that this guideline is not always followed. For an example, consider Australopithecus. On the evogram you can see a series of forms, from just after Ardipithecus to just before Homo in the branching order, that are all called Australopithecus. (Even Paranthropus is often considered an australopithecine.) But as these taxa appear on the evogram, "Australopithecus" is not a natural group, because it is not monophyletic: some forms, such as A. africanus, are found to be closer to humans than A. afarensis and others. Beyond afarensis, for example, all other Australopithecus and Homo share "enlarged cheek teeth and jaws," because they have a more recent common ancestor. Eventually, several of these forms will have to have new genus names if we want to name only monophyletic groups."^[3] Jmv2009 (talk) 07:47, 4 November 2018 (UTC)

The short answer to your question is that no system of nomenclature can convey all the complexity of a cladogram/phylogram and even diagrams find it hard or impossible to capture the true complexity of evolution, including hybridization, splits and re~merges of lineages, horizontal gene transfer, etc.

By the way, as I noted before, since even the PhyloCode leaves species nomenclature to the traditional codes, Homo cannot move to Australopithecus, because of priority. Peter coxhead (talk) 08:33, 4 November 2018 (UTC)

We are only looking at 70 distinct evolution levels right now. Even if hundreds of levels were resolved, they could all be given named, etc. After all, also all the genes are progressively being given names as well. I agree with the complications arising from hybridization, splits, and re-merges of lineages, horizontal gene transfer, etc, but we are not discussing that here. We are discussing straightforward phylograms without additional complications. Incorporating established paraphyly/chronospecies do not change the bifurctating or multi-furcating structure if not resolved. I actually added a section on the complications and limitations in cladistics. See if you like it. Jmv2009 (talk) 10:16, 4 November 2018 (UTC)

@Jmv2009: "straightforward phylograms" don't solve the problem. It's always difficult to know what other editors know when communicating via talk pages. It occurs to me that you don't seem to know that genera cannot all be made monophyletic, regardless of how straightforward the phylogram is. If that is the case, see the explanation here. Peter coxhead (talk) 11:47, 4 November 2018 (UTC)

Thank you for your comments. I assume you are referring to fig 14. Did you recall my comments diversity: "Logically, the taxonomic levels should inform about sequential-ity, not e.g. diversity.", because that is what the fig appears to be about.

For Fig 14:

It would be fixed this way, because of the preference of monophyletic groupings rather than based on other criteria. Am I missing something here? It appears your "can not" should be interpreted as "Don't want to". But that just means rejecting the strict cladistic method. Cladistics can indeed not account for the alluded sexual intercourse; It does not work as long as hybridization is active among the lineages. It only works properly for deeper phylogeny.

This is the way it could be fixed for hominini, in due time:

This is what this ref is talking about: ^[4]

Especially with these hypothetical on-off extinct side branches, very little diversity is expected. Nevertheless, these Australopithecus species, e.g. anamensis, can not belong to the same genus as afarensis if status quo for genus homo is to be maintained. Normally, every step would be a different taxonomic level. The exception is with a "chronogenus", which is very close to paraphyly.Jmv2009 (talk) 16:43, 4 November 2018 (UTC)

Yes, of course it can be "fixed" if only terminal nodes are classified into genera which is precisely the point I was making. But if you look at the papers you referred to earlier that discuss the Australopithecus/Homo issue, some include extinct species as interior, non-terminal nodes. And these species cannot be placed into monophyletic genera. In the approach you outline, a high price is paid by having so many monospecific genera, which I very, very much doubt will ever be accepted.

Anyway, we'll have to wait a few years to whether the consensus changes. Peter coxhead (talk) 14:15, 4 November 2018 (UTC)

Regular cladistics works like that though. Moreover, at first sight, one would say that when an author tries to claim they have found a direct ancestor to e.g. humans, one would be correct to be skeptical. However, I think make a good point for this SPECIFIC case: For recent fossils, the likelyhood of finding fossils which have a direct ancestral relationship may increase if there are plethora of fossils AND the number of simultaneous lineages is reasonably assessed to be likely limited AND the lineages are sexually propagating. But then you still have the chronogenus issue. For deeper phylogeny, most individual fossils that you find probably will have gone extinct without having found a more recent fossil to which it is the direct ancestor. Things change again when you start to group fossils, but that is the regular paraphyly discussion again.Jmv2009 (talk) 16:43, 4 November 2018 (UTC)

Earlier you wrote I actually added a section on the complications and limitations in cladistics. See if you like it. The problem is the same as before: whether I agree with what you wrote, or whether I like it, is irrelevant. What matters is whether you are paraphrasing what reliable sources say. As you have written it, without enough references, it just reads like an opinion piece, and isn't acceptable in terms of WP's policies. Peter coxhead (talk) 14:26, 6 November 2018 (UTC)

Your insistence on labelling Glaucophytes as blue green algae is perverse, contrary to common consensus and just generally confusing. The term is generally applied to Cyanobacteria, while Glaucophytes are eukaryotic algae. Plantsurfer 16:10, 18 November 2018 (UTC)

Absolutely; in English blue-green algae = Cyanobacteria, not glaucophytes. Peter coxhead (talk) 17:45, 18 November 2018 (UTC)

I corrected it, although see Cyanobacteria 'modern usage' Calling bacteria algae is confusing! tnx Jmv2009 (talk) 17:55, 18 November 2018 (UTC)

Calling bacteria algae is confusing, biologists agree. The term is deprecated for that reason.Plantsurfer 18:37, 18 November 2018 (UTC)

You cannot just change the rank at Template:Taxonomy/Embryophytes and Template:Taxonomy/Streptophyta, etc.; it messes up many taxonomy templates and article taxoboxes, leaving them with inconsistent ranks. The entire set of ranks needs to be considered, and made self-consistent with consensus, which requires discussion, signalled at least at WP:PLANTS and WT:TOL. Peter coxhead (talk) 08:34, 3 February 2019 (UTC)

I've opened a request for comment/discussion at Wikipedia talk:WikiProject Tree of Life#Request for comment: new classification scheme for eukaryotes. Peter coxhead (talk) 09:51, 3 February 2019 (UTC)

Major changes to the logic of the article, including changing the taxobox from a paraphyletic group to a monophyletic taxon, need to be discussed and reach consensus first. Please now follow WP:BRD – you were bold, I've reverted, now we all need to discuss. Peter coxhead (talk) 16:27, 27 March 2019 (UTC)

I'd like to invite you to discuss the recent changes I made to the Bilateria article, relevant to your recent edits. You can join the discussion on the Bilateria article's talk page. BirdValiant (talk) 04:01, 27 August 2019 (UTC)

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This "warning" appears related to me adding a pdf preprint. However, it was a primary source listed together with a secondary source, which was allowed. Acknowledgement that the preprint only became available after the secondary sources used the result of a press conference and an exerpt/press release of the study. The primary source is useful as it partially clears up confusion about the reliability of the used test (false positives supposedly only in earlier versions of the test), and it makes it clear the shot noise / uncertainty associated of only 7 deaths was indeed not properly taken into account. Jmv2009 (talk) 03:40, 10 May 2020 (UTC)

It's an alert to make you aware, not a warning. To your second point: all sources on Wikipedia must pass the test for WP:reliable sources, namely, "reliable, third-party, published sources with a reputation for fact-checking and accuracy." As far as I am aware, preprint articles have not been subject to any of the normal scrutiny we would expect to qualify as a reliable source. If you feel otherwise, you are entitled to argue the case on the talk page or refer the matter to the reliable sources noticeboard, What you are not entitled to do is re-insert material that is challenged based on a faulty perception of the challenge (not a RS). If you do intend to edit-war to re-insert your preferred content, then the alert that I've provided you with will prove relevant. --RexxS (talk) 18:44, 10 May 2020 (UTC)

The issue here is that it is not just a preprint (or in this case, in a broader sense, their work), as their work has been viewed as significant by secondary sources. In that case, it is useful i.m.h.o. to provide the primary source as well, whether it has been formally reviewed or not. This is especially useful to get an accurate assessment of the limitations of the results. So the main reason for including it is not to support the results, but rather the opposite. Jmv2009 (talk) 19:05, 10 May 2020 (UTC)

When the work has been reviewed by secondary sources, we use the analysis done by the secondary sources, not our own opinion about what are accurate assessments of the limitations of the results. You can't use primary sources to contradict what secondaries state. --RexxS (talk) 20:10, 10 May 2020 (UTC)

My thought was only for the reader to be able to assess the reliability of an important (not reviewed) source that secondary sources appear to be running with. In my view that is the purpose of providing the primary sources together with the secondary sources. You always need to consider any finding as potentially faulty, and providing the primary sources helps in that regard. Jmv2009 (talk) 04:04, 11 May 2020 (UTC)

I tried, sorry. Nice secondary source Jmv2009. Let's not make an edit war out of this. More sources will come anyway. Iluvalar (talk) 17:55, 11 May 2020 (UTC)

@Jmv2009 and Iluvalar: I don't doubt for a moment your good intentions, but please think about for a minute. If it's important for readers to see this preprint, why shouldn't it be important for readers to see every primary source that secondaries are based on? We have WP:MEDRS for a reason, and it won't benefit anybody to see a coach and horses driven through it. I'm struggling to keep potentially unreliable sourcing out of these articles, and I'm sorry for being heavy-handed, but I really draw the line at preprints. Preprints are not reviewed, and there's a bright red disclaimer at https://www.medrxiv.org/ saying "They should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information." It's not fair to our readers to point them to raw research without the usual filter of a secondary source's review. Please let's stick with the secondary sources. --RexxS (talk) 19:16, 11 May 2020 (UTC)

Except that I presented them ALONG the primary source, which appears to be coveres by WP:MEDRS. And except that the secondary sources did some review/assessment on them already, despite their (in this case actually pre-preprint) status. But yes, they did not go through the usual reviewing channels yet. Jmv2009 (talk) 20:36, 11 May 2020 (UTC)

You mean you presented a preprint, which isn't even a reliable source for any Wikipedia medical content, along with the three other sources already supporting the sentence. MEDRS doesn't give you license to do that. You also mean that the secondary source did some analysis of the preprint, which means that we can report conclusions of the secondary source on the issue. It doesn't mean that we include primary sources just because the secondary source made use of them. Surely, it's not too difficult to grasp that you don't use preprints for any purpose whatsoever in medical articles? --RexxS (talk) 21:23, 11 May 2020 (UTC)

Hi. I strongly apologise to bother you, but if you do not mind, I would like to ask a question. I really appreciate your contributions to the article Plastid. I suggest slighty rephrasing the sentences regarding the Paulinella chromatophore to clarify that although it does not belong to the clade closely related to the Gloeomargarita, the term plastid is also applicable there, especially since it is considered a chloroplast. Thank you. --Pinoczet (talk) 21:15, 24 January 2021 (UTC)

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Caught by a colocation web host block but this host or IP is not a web host. My IP address is 2001:470:d076::/48 in block 2001:470::/43, which is a going through a legitimate Hurricane Electric ipv6 tunnel. Per WP:IPBE and per Wikipedia:Unblock_Ticket_Request_System this is the proper way to request an unblock. Although there is a ticketing systems for "appeals", which we do not need yet. I have been using this IPv6 range for a long time for regular editing. My ISP does not support ipv6 on these provisioning lines yet, which is why I have for a long time resorted to using this legitimate tunnel. Refer to https://tunnelbroker.net. BTW, Why does this block need to be a hard block, so that even logged-in users can not use this? Requesting permanent or long term unblock. Jmv2009 (talk) 20:40, 15 June 2021 (UTC)

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HE's service is blocked as an open/anonymizing proxy, per WP:PROXY, and globally as m:NOP. It allows users to change IP addresses at will, and is heavily abused. ^{!ɘM γɿɘυϘ}⅃ϘƧ 21:48, 20 June 2021 (UTC)

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I just want you to know that I do not revert it because I think your concern is invalid. If there is something not clear for you, then certainly we can try to make the text clearer. But, as explained in the talk page, just adding a word that has no technical meaning seems counterproductive, not the solution. Dominic Mayers (talk) 19:09, 21 October 2021 (UTC)

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I am aware. The specific pages on these specimens do not exist (yet). Jmv2009 (talk) 07:15, 27 March 2022 (UTC)

(Responding over on your talk page so you can delete whenever you choose.)

Good luck with your neighbour :_ . Thanks for you comments, your actions in the end result in improvements and clarity. Jmv2009 (talk) 19:25, 27 April 2022 (UTC)

Thank you. That's kind of you, and thanks for being gracious about my insistence about "simian" vs. "monkey" terminology. I was dreading a battle, or another battle, to include the one my criminal neighbors have been waging against me (still going on at this very moment, unfortunately, in ways so severe it would make people think I was suffering paranoid delusions, were I to detail them; fortunately/unfortunately, though, this abuse is quite real). Anyhow, thanks to you too, for your obvious commitment to scientific rigor. --Dan Harkless (talk) 09:52, 3 May 2022 (UTC)

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When you modified the Homo cladogram, did you have a particular source in mind? Per WP:SYNTH, you aren't allowed to come up with your own cladograms. Hemiauchenia (talk) 03:36, 23 October 2023 (UTC)

It is (mostly) Dembo 2016 based, simplified. I should indeed add some local references in the cladogram if there are updates.