Talk:Archaea/Archive 5

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Number of phyla

This needs to be updated, as it is based research from the start of the 21st century, more than a decade ago. A lot has happened since then, especially the development of techniques for whole genome sequencing from a single cell in just the last three years [1] so hugely expanding understanding of at least the genetics of uncultivated microbes. This paper from 2016 says [2]

"Today at least 89 bacterial and 20 archaeal phyla are recognized by small subunit ribosomal RNA databases, although the true phyla count is certainly higher and could range up to 1,500 bacterial phyla"

So, we now know of 20 archaeal phyla. It doesn't say how many have been cultivated of those 20, but it says approximately 50% of archaea phila have no cultivated representatives. Does that mean that 10 of those 20 have no cultivated representatives, if so why does it say "approximately 50%" and why not "10 out of 20" or "9 out of 20" or whatever the number is?

And they now say that there could be up to 1500 undiscovered bacterial phyla, again doesn't say how many of those are archaea. So it needs a bit more research by someone, maybe some of you reading this know the answers to those questions or know where to go to find the information? So, I didn't feel I know enough yet to "be bold" and update the article though I may find out more. Anyway, clearly the figures in this article need to be updated, if someone is able to figure out what the new numbers are. Robert Walker (talk) 22:45, 9 January 2017 (UTC)

@Robertinventor: the general problem is that researchers who work on genome sequencing and molecular phylogenetics are typically not very interested in Linnean ranks. So you can find phylogenetic trees in the literature, but clear statements as to which clades are to be treated as phyla is a different matter. Peter coxhead (talk) 17:41, 10 January 2017 (UTC)

@Peter coxhead: Okay yes, I can see it is tricky. But I think something needs to be said. Wasn't very clear in my comment, it's not an idea to add anything new to the article, it's about this statement which is already there in the article in the section Concept of species:

"Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy.[17] Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, indicating that the diversity among these organisms remains obscure.[28] The Bacteria also contain many uncultured microbes with similar implications for characterization"

So, I think it's a good point and needs to be retained, but it cites a source from 2002, "Exploring prokaryotic diversity in the genomic era" which is way way out of date in such a rapidly changing field. It's not so important what counts as phyla - as - the proportions as in how many of the phyla have any cultured representatives - is it more than 8 by now? Also that range of estimates now is no longer 18 - 23, as after all there are 20 already known so lower number at least 20 and must go up to hundreds as the upper estimate (how many?) if you take the 1500 bacterial phyla as a possibility.

So - I'm looking for an update of that particular paragraph in the article. Could add some kind of disclaimer explaining that the concept of a phyla itself is somewhat fluid for archaea if that's the situation. But the idea is used by some researchers as the paper I just cited said there are 20 phyla. So it seems that one could say something. Hope that's a bit clearer. Robert Walker (talk) 20:20, 10 January 2017 (UTC)

sequencing or fingerprinting?

The article mentions, a few times at least, the word sequencing in what Woese did with 16S rRNA. At least in terms of current technology that wasn't sequencing, but maybe fingerprinting. (In the DNA fingerprint sense.) This was, pretty much, the beginning of sequencing technology, where he was sequencing maybe three, for or five base fragments, but without the ability to combine them into a whole sequence. The book The Tangled Tree (which I haven't finished reading) has much description for what Woese did, and what others were doing at the time. I am not sure that fingerprinting was the word used at the time, though, but it pretty much agrees with the current meaning. Gah4 (talk) 17:29, 13 May 2019 (UTC)

It seems that current terminology is closer to DNA barcoding, where DNA fingerprinting is meant to identify a specific individual, not just species. Gah4 (talk) 17:35, 13 May 2019 (UTC)

References

Asgard archaea superphylum

The Lokiarchaea have now been identified as part of the Asgard superphylum, a sister phylum to TACK, along with Odinarchaea, Thorarchaea, and Heimdallarchaea. The last is the closest to the eukaryates. See primary source and secondary source.

This is totally outside my area of expertise, so I won't touch the article itself. 2607:F470:8:1058:DDB9:1667:46AE:85EC (talk) 18:04, 30 January 2017 (UTC)

References

Added ref details to citations.Oceanflynn (talk) 15:49, 7 March 2017 (UTC)

Added ref details to citations.Oceanflynn (talk) 15:53, 7 March 2017 (UTC)

Recently I raised Asgard to the same level as TACK, which was acording to NCBI. However, NCBI does not mention the terminus Proteoarchaeota. However, in their 2015 paper "Complex archaea that bridge the gap between prokaryotes and eukaryotes", Spang, Saw et al. place Proteoarchaeota a level above TACK, and Lokiarchaeota (which acording to NCBI now has to be expanded to the whole Asgard group) as a sister group of TACK, i. e. 'Proteoarchaeota = { TACK, Asgard }'

Reflecting this in the taxobox needs to introduce a 3rd taxonomic level there, but I hesitate to do so because it might get too complex. On the other side we cannot drop contents of asgard group as long as this does not have its own lemma.

Any suggestions for correcting 'TACK = Proteoarchaeota' by 'Proteoarchaeota = { TACK, Asgard }' ? Ernsts (talk) 23:29, 5 May 2017 (UTC)

Changed Taxobox so that TACK and Asgard are both subgroups of Proteoarchaeota at same level. So Lokiarchaeota are shown as sibgroup of Proteoarchaeota which fits better to the sources.

Lokiarchaeota and its newly found sister groups ("Thorarchaeota" ,"Odinarchaeota", "Heimdallarchaeota") comprise "Asgard", which in consequence is a subgroup of Proteoarchaeota and therefor sister group of TACK. Ernsts (talk) 17:19, 7 July 2017 (UTC)

Phylogeny and ester/ether membrane

- Archaea Wikipedia article emphasizes the ether-linked membrane as one of Archaea key characteristic.

- If Bacteria and Eukarya has both ester-linked membrane, I would imagine that feature would be from a specific branch of Archaea, and that maybe Asgard had ester-linked membrane?

Those questions made me dig in a little, and I found:

• A mini-review article showing the Nov 2017 knowledge of Archaea phylogeny and genes of each branch.
• Asgard metabolism, including some Creative Common diagrams. :)

Asgard archaea in various environments

Asgard archaea Phyla

It's not my area of expertise either, so I ended up not getting a clear answer to the ester/ether membrane. But I ended up learning a lot, and I think the articles I mentioned could contribute to WP. —Arthurfragoso (talk) 06:37, 9 September 2019 (UTC)

References

Response to Headbomb

I reverted Headbomb's deletion of a citation to an article in InTech by Bernstein & Bernstein noting, in my edit summary,

The deleted citation is to an article cited, according to Google Scholar, by the Proceedings of the National Academy of Sciences and by The Transactions of the Royal Society. That ought to be good enough for Wikipedia.

Headbomb reverted my reversion, using as an edit summary:

intech is neither PNAS nor Transactions of the Royal Society.

and adding, on my talk page,

"I don't know what you searched on google, but that paper was not published in either venue."

Both claims contradict nothing I have written and do not address my point: that an article cited (not published) in such reputable journals can surely be cited by Wikipedia. What did I search on Google? I said Google Scholar, not Google, and my search key was simply the article title.

Would a different citation be preferable? We could use a later paper by Bernstein & Bernstein, which came up in my Google Scholar search and also makes the point:

Bernstein, Harris; Bernstein, Carol (2017). "Sexual Communication in Archaea, the Precursor to Eukaryotic Meiosis". In Witzany, Guenther (ed.). Biocommunication of Archaea. Springer Nature. pp. 301–117. ISBN 978-3-319-65535-2.

I have not replaced {{citation needed}} by this reference, however. The original citation was adequate, as evidenced by identical citations in reputable journals. What can be cited in PNAS can be cited in Wikipedia.

Peter Brown (talk) 19:18, 11 December 2019 (UTC)

If the InTech claim is endorsed in either PNAS or TRS, then cite PNAS or TRS. It is possible that the paper is good, but just got published in a crap venue. But you can also cite a paper that is crappy for a variety of reasons: you got fooled into citing crap, you are citing it as an example of crapiness, and/or you are citing crap to acknowledge prior works exist, without endorsing it. If other, actually reliable sources, make the same point, then cite those. Headbomb {t · c · p · b} 19:24, 11 December 2019 (UTC)

It is preposterous to maintain that what can be cited in both PNAS and TRS cannot be cited in Wikipedia. But have it your way. Peter Brown (talk) 19:47, 11 December 2019 (UTC)

Hardly so. I gave you a few cases where it's acceptable to cite bad papers in a good one. I also gave you a few cases where a citation to a bad paper slipped the reviewing process. It's also possible to cite the paper for part of its conclusions, but not others. We aren't in the business of guessing what happened. Unless clearly endorsed by a reliable publications, predatory venues are not reliable sources by definition. And when clearly endorsed, then cite whoever is endorsing, not the predatory venue. Headbomb {t · c · p · b} 19:57, 11 December 2019 (UTC)

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Issue with the Asgard link in the Cladogram

There's an incorrect link in the Cladogram for 'Asgard', which results in you being sent to Asgard of the Nordic fairytale variety. I've not been able to fix the link, but thought I would flag for someone with more experience in fixing the links in Cladograms.

Wikipeacheye (talk) 18:41, 16 December 2020 (UTC)

@Wikipeacheye: You're right, thanks - fixed now! Opabinia regalis (talk) 19:09, 16 December 2020 (UTC)

Issue that I can't confirm but

I think there is a problem in the Cladogram, I'm not an advanced editor and I don't have experience in Taxonomy but isn't Eurkaya a domain? If so, why is it included in Archaea as Archaea is also just a domain? I didn't change it because I'm not sure, so if anyone who knows Taxonomy pls help

11Jasejusttestingzapppp (talk) 06:38, 16 March 2021 (UTC)