Talk:Neomura

Variations of the Theory

"The current mainstream system of classification is the three-domain system. The common consensus is that Archaea and Eukaryota evolved on a seperate branch from Bacteria, with the root of life lying somewhere in between. This branch is Neomura. However, Cavalier-Smith has postulated that Bacteria is in fact paraphyletic to Neomura, meaning that Neomura evolved from Bacteria. According to this theory, Neomura is a group which evolved from Gram-positive bacteria, this transition being marked by twenty evolutionary adaptions, which accompanied, or derived from, two other important adaptions: the development of histones to replace DNA gyrase, and the loss of peptidoglycan cell walls to be replaced by other glycoproteins."

This is confusing because it's worded too technically. Rather than seeming to contradict what has just been said, you should start out by simply saying that Cavalier-Smith theorizes that the Archaebacteria and Eukaryotia arose from the Neomura which arose from the gram positive bacteria bacteria. You can then go on to say that the Bacteria are paraphyletic without the Neomura, but this phrasing used is rather awkward. I can't correct it without the article handy. I just can't seem to see what the second sentence is saying, so it's impossible to correct. I would simply like to see this clarified first, inserted into the article later. I don't have the article handy, but will try my best to read and understand as much as possible. KP Botany 19:00, 2 June 2007 (UTC)

It's not correct to say the Archaea and Eukaryota arose from the Neomura; they each are part of Neomura. (It's like saying that Primata evolved from Mammalia.) If the hypothesis that Archaea and Eukaryota form a clade is correct then there are three alternative sub-hypotheses: either both evolved from stem Neomura (Cavalier-Smith's hypothesis, but there may be others), or Eukaryota evolved from Archaea (making Archaea paraphyletic), or Archaea evolved from Eukaryota (making Eukaryota paraphyletic). (The last doesn't seem very likely.) Lavateraguy 21:22, 2 June 2007 (UTC)

I'm not debating what is the current hypothesis, I'm debating whether or not you've said or presented them. What you just said here does not in any way come through from this paragraph in the article, as there is no mention whatsoever that there are three alternative sub-hypotheses! I'm not actually getting what is being said here at all by this paragraph, so there's no point in debating any substantive issues--it has to be written so the reader can undertand what is being said, regardless of what is being said.

So, what is C-S saying about Archaea and Eukaryota? That they belong in clade together, called Neomure, that evolved from the gram-positive bacteria, which, together with the rest of the bacteria form a crown group? Is that all? Who offers the latter two hypotheses, the alternatives to both evoving from Neomura? Are these dismissed or discussed by C-S or by someone else (does Woess mention any of this)?

Please don't debate the issues of various theories with me, although I'm not sure that's what you're doing, but rather clarify this text to get across what C-S is saying in his paper. KP Botany 21:48, 2 June 2007 (UTC)

And now we're left with less than we started with. Hmmm. I think we need a professional. Werothegreat 18:30, 3 June 2007 (UTC)

It's not less if what was there was difficult for the reader to follow. An encyclopedia is written for its readers--if it's wrong, it's not more, if it's not written for the general audience, it's not more, if it can't be followed accurately, it's not more. We always need the assistance of professionals on articles, particularly in areas outside of the multicellular eukaryotes when it comes to organisms. You, Werothegreat, however, read enough T C-S to rewrite this one little section--give it a try. KP Botany 19:37, 3 June 2007 (UTC)

Wikispecies link?

Why is there a wikispecies link? They're still mucking about in 4-eukaryote-kingdom-land. There is no Neomura article in wikispecies. Werothegreat 01:53, 17 July 2007 (UTC)

They have both Cetartiodactyla and Artiodactyla articles. They don't explain that only let write articles from one source. If a taxon exists it must have an article for explaining what it is. 83.45.216.23 17:45, 17 July 2007 (UTC)

What? Artiodactyls are mammals. We're talking about the supergroup that contains Archaea and Eukarya. There is no page on wikispecies for it, so there is no need for a wikispecies link at this time. Werothegreat 01:49, 18 July 2007 (UTC)

I don't see the difference between having two incompatible proposed clades at ordo level and at superdomain level. 80.30.232.210 18:10, 18 July 2007 (UTC)

It isn't incompatible. There just ISN'T A PAGE FOR IT ON WIKISPECIES YET. So there is no point to have a wikispecies link to a page that does not exist. Werothegreat 17:46, 19 July 2007 (UTC)

Origin of eucaryotes

The section "History of Taxon" implies that the first stage in the evolution of eucaryotes was the incorporation of aerobic bacteria into some species of archea to form mitochondria. AFAIK it is generally agreed that the first stage was the incorporation of spirochetes into some species of archea to form micro-tubules. Sorry, can't give a ref (most annoying as I was looking at one earleir today). Philcha (talk) 23:12, 20 January 2008 (UTC)

There's more than one hypothesis about the origin of eukaryotes. You might be thinking of Margulis'. (Margulis et al, The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists, PNAS 97(13): 6954-6959 (2000). This has the problem that there are no living primitively amitochondriate eukaryotes - the earlier opinion that there were arose from overlooking vestigal mitochondria in some taxa, combined with long branch artefacts in 18S RNA cladograms.) Cavalier-Smith proposes the existence of non-mitochondriate stem eukaryotes, but, IIRC, he doesn't postulate a symbiotic origin from these. (The problem with his hypothesis is that he has Neomura as a relatively young clade deeply nested in Eubacteria, as shown in the tree in the article, and has to explain the apparent existence of older red algae. Eukaryotes arising from symbiosis of an Archaean and a Proteobacteria is, I think, Woese's hypothesis.

It was not my impression that symbiotic origin of organelles other than mitochondria and plastids (and the "cyanelle" of Paulinella) was generally accepted. Lavateraguy (talk) 23:40, 20 January 2008 (UTC)

The spirochete hypothesis has been pretty much discredited. The actiniobacterial absorption of an alpha-proteobacteria is the industry standard. Werothegreat (talk) 12:58, 19 February 2008 (UTC)

Image concern

Is there any specific reason that an image of a leech is what represents this clade? It seems rather silly to simply place a picture of any arbitrary organism simply for illustrative purposes. Tan | 39 02:13, 22 June 2008 (UTC)

I myself was wondering why, of all possible members of Archea and Eukarya to carry the torch, the honor falls to the almighty leech. The choice really sucks. - 96.255.251.122 (talk) 02:32, 21 April 2012 (UTC)

Question about Neomura as a Taxon Superdomain

Hi. I think this article should explicitly specify whether the Neomura taxon is simply an artificial\conventional taxon, or, contrarily, it is based on a natural (real) taxon as well. --Faus (talk) 13:27, 17 May 2012 (UTC)

Integration of sources

Looking at this article in 2017, it is striking that comments from 5 or more years ago above remain valid issues for the article. Is Neomura valid? What is the evidence? Who (if anyone) other than Cavalier-Smith is for it, and why? Who is against it, and on what evidence? The list of "Further reading" needs to be integrated into the text, to answer all these questions as well as possible. The inclusion of Cavalier-Smith's own work in that sad afterthought of a list is frankly absurd—if the article isn't going to explain C-S's views on the Neomura, what is its purpose? At the very least, the article needs to discuss the key viewpoints against C-S. Chiswick Chap (talk) 09:44, 27 February 2017 (UTC)

This paper from 2014 is the latest I've found so far. They say that "[w]e also provide evidence that eukaryotes branch close to the last archaeal common ancestor." So while not specifically supporting Neomura as a taxon, they do argue that Archaea and Eukaryota are much more closely related than either is to Bacteria. But to sort out the article properly, more papers need to be found and looked at. Peter coxhead (talk) 13:16, 27 February 2017 (UTC)

My understanding is that there is a widespread consensus that Neomura is a clade (with some recent work having Eukarya nested with Archaea), but little acceptance of Cavalier-Smith's proposal that Neomura is deeply nested within (Eu)Bacteria. The problem with Cavalier-Smith's proposal is that it relies on a limited number of traits (even if a case for a high weighting can be made) and has to account for branch lengths within Neomura being comparable to branch lengths in (Eu)Bacteria. Lavateraguy (talk) 16:43, 27 February 2017 (UTC)

This review article from late 2015 is paywalled, but this abstract suggests that it contains relevant information. A recent presentation of Cavalier-SMith's hypothesis can be found (open access) here. Lavateraguy (talk) 16:52, 27 February 2017 (UTC)

Sounds like good progress; and the arguments against or for partial acceptance need to be stated and cited. Chiswick Chap (talk) 19:20, 27 February 2017 (UTC)

I can access the 2015 review. It defines Neomura as a "hypothetic clade composed by Archaea + Eucarya that would have evolved from single-membrane-bound, Gram-positive bacteria." So as Lavateraguy says above, there is pretty strong support for a clade combining Eukarya and at least some Archaea (perhaps not all), but no enthusiasm for Cavalier-Smith's idea that it is nested within Bacteria. The most popular view right now seems to be something like this:

	Bacteria C1 C2 Eukarya Archaea 2 (Lokiarchaeota or clade including Lokiarchaeota) Archaea 1

In addition the mitochondrion goes across from Bacteria to Eukarya. I guess C1 could be called "Neomura" although its origin is different from Cavalier-Smith's hypothesis, but C2 is the more interesting clade on this view as it's where eukaryogenesis occurred. Note that Archaea are paraphyletic w.r.t. Eukarya on this view. One of many open questions is the nature of the last common ancestor of Bacteria and Archaea/Eukarya. Peter coxhead (talk) 20:06, 27 February 2017 (UTC)

Good stuff! Looking forward to seeing it in the article. Chiswick Chap (talk) 20:14, 27 February 2017 (UTC)

On my to-do list there are about 90 spider articles that Plantdrew found that need taxobox fixes, so if you wait for me you'll be looking forward for some time. :-) Peter coxhead (talk) 20:51, 27 February 2017 (UTC)

A question is how tied the name Neomura is to Cavalier-Smith's hypothesis. I'm quite happy to use the name even if the etymology turns out to misleading - compare Basilosaurus (a whale), and various other taxa whose names reflect previous misinterpretations, but others might disagree?

I'm sure it needs more work (such as addition of references), but I've restructured the article so it's not so closely tied to the derived bacterial origin hypothesis. Lavateraguy (talk) 22:15, 27 February 2017 (UTC)

• I think it's pretty clear now that Neomura is a failed hypothesis. I've revised the article accordingly, and removed the taxobox – we only use these for taxa with a reasonable degree of acceptance. Peter coxhead (talk) 08:38, 1 August 2017 (UTC)

T C-S's 2020 defence and elaboration of neomura hypothesis

An article published online January 2, 2020 is a recent defense and extensive elaboration of the neomura hypothesis.

• Cavalier-Smith, T.; Chao, Ema E-Yung (2 January 2020). "Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)". Protoplasma. doi:10.1007/s00709-018-01442-7.

HTH. DCDuring (talk) 16:44, 18 October 2020 (UTC)

"DOI not found" (a search for the title finds a copy on ResearchGate, which I grabbed rather the seeing whether the publisher's copy was paywalled or not). Lavateraguy (talk) 15:13, 19 October 2020 (UTC)

One-domain hypothesis

There's yet another variant of the hypothesis I can think of: that the eukaryotes emerged from within the archaeans (which seems to be the consensus now), and that the archaeans in turn emerged from within the bacteria, making the traditional taxa Archaea and Bacteria both paraphyletic. Neomura would simply be a synonym of Archaea (including the eukaryotes) in this view. (Admittedly, I really like this idea aesthetically.) Is this possibility still a viable hypothesis? --Florian Blaschke (talk) 00:00, 6 February 2023 (UTC)

In fact, Archaea §§ Relationship to bacteria​ and Relation to eukaryotes does suggest that this proposal could be correct. --Florian Blaschke (talk) 00:55, 6 February 2023 (UTC)

Neomura the taxon vs neomuran hypothesis

I feel that this article wrongly conflates the taxon Neomura, which is accepted as a clade by most experts, with the neomuran hypothesis, which is generally rejected. So I think the taxobox should be added back, and perhaps we should limit information about the neomuran hypothesis to a single section. --Grey Clownfish (talk) 07:24, 1 November 2023 (UTC)

The terms Neomura, neomurans, etc. have been widely used, but with different meanings. In one usage (Cavalier-Smith's original), Archaea and Eukaryota were seen as clades/taxa, with Neomura being the clade/taxon comprising both. This seems to be discredited now. In another usage, Neomura can be treated a synonym of Archaea, with eukaryotes having evolved within Archaea, so the remaining archaeans form a paraphyletic group. (Both ideas are discussed and sourced in the article.) More recently, the sister archaeans to eukaryotes have been identified. Where is Neomura in the 28 April 2023 cladogram at Archaea#Cladogram? Or the cladogram at Asgard (archaea)#Phylogeny? What would be the subordinate taxa listed or referred to in a Neomura taxobox? Peter coxhead (talk) 10:57, 3 November 2023 (UTC)

In that case, should Neomura be merged into Archaea? Because if prokaryote archaea are paraphyletic, so Archaea is redefined to include eukaryotes, then Neomura is a synonym of Archaea.

However, it appears that Wikipedia tends to follow the three-domain hypothesis. Archaea does not include eukaryotes in this scheme. So merging Neomura into Archaea would contradict this. So I don't see why Neomura can't be a clade consisting of Archaea and Eukaryota in Wikipedia's taxonomy.

Yes, I think prokaryote archaea are probably paraphyletic. But at the moment, Wikipedia's taxonomy doesn't reflect that for whatever reason. --Grey Clownfish (talk) 04:34, 4 November 2023 (UTC)