Template talk:Eukaryota

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Template name[edit]

The template name is not descriptive. It does not link to article about life (how it functions, ideas about its origin and change, or its properties). Rather, the template links the five kingdoms of Margulis, with modification to reflect the discovery of the Archaea and the breakup of the Protista. That it, it links major groups of living things, rather than articles about life itself. --EncycloPetey (talk) 04:44, 25 February 2009 (UTC)

Is there a better name to describe the level above the three domains? We also have an article called Life which isn't just about taxonomy but which to a certain extent is. Maybe "living organisms"? Kingdon (talk) 17:35, 25 February 2009 (UTC)
I do not know if there is a name to describe what the three domains are. I chose "life" because that is what the domains categorize. I originally thought about also including Non-cellular life, making the first division cellular vs. non-cellular, but I do not think non-cellular life is widely accepted. So maybe this could be titled "cellular life"? EncycloPetey, you have accurately summarized what this template contains. Do you have any suggestions for better names? --Scott Alter 20:19, 25 February 2009 (UTC)
Not really. If I had, I would have suggested them. --EncycloPetey (talk) 03:50, 26 February 2009 (UTC)

Classification[edit]

I have serious doubts about the classification in this template. The omission of smaller groups (Mesomycetozoea and Nucleariid spring to mind but there are others) is understandable and perhaps even desirable, but more serious problems are: (1) omission of red algae, (2) inclusion of the rather dubious taxon Chromalveolata, (3) last I heard Excavata was pretty controversial too.

The simplest fix is just to delete the template; I'm not sure we need yet another navigational tool when we already have taxoboxes and various links within the bodies of articles. But if we want the template, I think it is a mistake to base it on a classification which is contradicted by evidence (there are some cites at Eukaryote or I can go into more details). Kingdon (talk) 18:35, 25 February 2009 (UTC)

The reason why I made this template is to expand on the taxonomy navboxes. This navbox project started with {{Mammals}} and Category:Mammal families navigational boxes. These navboxes link all extanct species of mammals to each other (see Wikipedia:WikiProject Mammals/Article templates/doc). I have been slowly expanding the schema upwards with {{Chordata}}, {{Animalia}}, and {{Life}}.
My goal is to have a navbox containing the domains and kingdoms, linking the highest level of taxa together in their own template. I don't really care what this template is called, or which classification scheme is used. I did not intentionally include or exclude any groups, and I did not mean to create controversy. I did not use any evidence to create this template, rather I briefly went through Biological classification, Life, Three-domain system, and Kingdom (biology) to get ideas. None of these articles make it absolutely clear as to the currently accepted model, so I just threw this template together. Ultimately, my goal would be to link all species of life through taxoboxes, and this navbox is needed to create the link at the highest level. --Scott Alter 20:09, 25 February 2009 (UTC)
There is no currently accepted model. At least, not a fully fleshed out one. Kingdon (talk) 13:44, 26 February 2009 (UTC)
A tool that helps / encourages the user to explore the family tree of life seems a reasonable idea. And a template is a useful tool if some aspects are controversial and / or subject to rapid change, because updates are visible wherever it's used. However I think this template's approach has some drawbacks:
  • It tries to squeeze a quart into a pint pot. In adddition to omitting red algae, it omits plants, although it includes animals and fungi. Although I'm no expert on single-celled eucaryotes, AFAIK there are a lot of such clades, and squeezing all these into "other opisthokonts" seems "rather anthropocentric" (this article is a fun read: Bonner, J. T. (January 1999). "The Origins of Multicellularity". Integrative Biology 1 (1): 27–36. doi:10.1002/(SICI)1520-6602(1998)1:1<27::AID-INBI4>3.0.CO;2-6. Retrieved 2008-09-03.  ).
  • After all the hard work its creation and maintenance require, most readers won't look at it, as it appears at the bottoms of articles that are sometimes long and complex (e.g. about a whole animal phylum).
  • A good article about a fairly high-level taxon, e.g. a phylum, should include in the main text a discussion of the family tree a few levels up and down, with cladogram(s).
I'd suggest trying a few Wikiprojects, except that in my experience their members concentrate on their favourite genera and families, and have little interest in higher-level taxa, possibly because these require more research per 100 words.
I'm sorry that I can't make any more positive suggestions about possible approaches. At present I'm improving my knowledge of high-level animal taxa (mainly phyla) by working on the relevant articles, and the whole tree of life is way beyond my knowledge at present. --Philcha (talk)
My original intent of this template was to keep it to the kingdom level of classification and higher, and have separate templates for each kingdom. There are currently templates for {{Animalia}}, {{Fungi classification}}, {{Archaea classification}}, and {{Bacteria classification}} for the phyla and lower-level classifications. We could simply this template by moving everything phylum and lower to kingdom templates. Then, the templates could be "managed" by people interested in each specific kingdom. With this simplification, maybe we could put links to Archaea and Bacteria back in to this template. Currently, there are no links via navboxes between Archaea, Bacteria, and the Eukaryotes. And by the way, plants is linked in this template, as "Plantae/Archaeplastida" in the first row. --Scott Alter 23:46, 18 March 2009 (UTC)

I have the doubt. Template contains of the dubious clade Neomura. --Krclathrate (talk) 15:24, 22 March 2009 (UTC)

Archaeplastida monophyly[edit]

I thought the monophyly of Archaeplastida is contested. Shouldn't we separate Viridiplantae from Rhodophyta? --kupirijo (talk) 15:22, 1 August 2009 (UTC)

Well, if you do that you need to separate Glaucocystophyceae because it is less studied (and more central to many of the doubts, as I recall the situation). I'd probably leave the template as it is: although Archaeplastida may not be proven, if any alternate hypothesis (or refinement of Archaeplastida) has the potential to replace it, it isn't a hypothesis which has gathered much study/evidence to date. Kingdon (talk) 01:18, 5 August 2009 (UTC)
I think that Eukaryote#Phylogeny is pretty much up to date. It's certainly true that the monophyly of Archaeplastida is contested; I personally find Nozaki et al. (2009) more thorough and more convincing than some of the other papers, but this is just my view. The reality is that there is NO agreed phylogeny and hence classification for eukaryotes at present. I don't like the template, because it suggests that there is a consensus when there isn't. Not sure what should be done about it though. Peter coxhead (talk) 22:25, 7 January 2011 (UTC)
I've added a warning note to the template. Peter coxhead (talk) 22:30, 7 January 2011 (UTC)

Template:Eukaryota_classification[edit]

(copied from Arcadian talk page) I think you were wrong to remove the disclaimer I added to this template. In the section Eukaryote#Phylogeny there are five cladograms shown. (One could add a few more from the plethora of papers around, but it seems to me that five is enough to make the point: there is no consensus.) The template more-or-less corresponds to the first two cladograms (full references for all cladograms are in the article). It does not correspond to the next three, none of which show an "AH" grouping, as they keep the Chromalveolata+Rhizaria together. If there is any kind of consensus in very recent papers (2009 onwards) it is probably against the template's splitting off of Hacrobia, which is supported only by older papers. Hence I think it is quite misleading to show the template as though it is an agreed consensus classification when it is not. I certainly don't wish to enter into an edit war over this, but I think there are good reasons for a warning of some kind at this point, rather than a different template. Why do you think a warning is inappropriate? Would you prefer a changed template? Peter coxhead (talk) 17:59, 8 January 2011 (UTC)

Chromalveolata+Rhizaria are kept together in this template. And support of Hacrobia isn't limited to older papers (see PMID 20418156 and PMID 20031978 for two 2010 papers). Please be more specific: in what precise ways does the current template contradict consensus? --Arcadian (talk) 18:11, 8 January 2011 (UTC)
1) The template doesn't contradict consensus because there is none at present, other than as noted in Eukaryote#Phylogeny, namely that SAR and unikonts are valid groupings. I repeat that this is my main point: there is not sufficient consensus to support the template. (By the way, I think that, as per the spirit of Wikipedia:RS#Academic_consensus, a claim of consensus has to be supported by sources, not a claim that there isn't consensus.)
2) The template shows unikont vs. bikont as the deepest division. This is supported by some papers, but not by others. It's not supported by PMID 20333181 or PMID 19698794, for example.
3) The template shows the chromalveolates split between AH and SAR clades. This is not supported by the above two papers, NOR by the Cavalier-Smith paper (PMID 20031978) which you cited (I can't access the full text of the other paper you cited at present). Hacrobia is a clade, but within Cavalier-Smith's Chromista, not a clade which joins Archaeplastida/Plantae before the pair join SAR. Maybe I wasn't clear in my comment above: when I wrote "the template's splitting off of Hacrobia" I meant splitting off Hacrobia from the rest of Chromalveolata/Chromista. The internal structure of the bikonts shown in the template at present is supported by only a small number of earlier papers, and is most definitely not a consensus position. It's in Burki et al. 2007 (PMID 17726520) but is NOT in the later paper by more-or-less the same group, Burki et al. 2009 (don't have a PMID for this but it's at [1]), which shows (p. 234 and the discussion around it) a clear chromalveolate clade with Archaeplastida/Plantae as sister.
But actually I would argue that you're not responding to the reason I gave for adding a warning to the template. I can only repeat it. There are five cladograms in Eukaryote#Phylogeny. Each of these is supported by a full reference to a paper from which the cladogram is re-drawn. If you look at these cladograms, they do not show agreement with each other beyond the points made above (SAR & unikonts as clades). They do not all agree with the template. The template does not represent a consensus. It is misleading to present it as if it were a consensus. What is wrong with a statement saying that it is not? Peter coxhead (talk) 19:43, 8 January 2011 (UTC)
These navigation templates do not represent phylogenies. They exist only to make it possible to reach various topically-related articles quickly. They aare arranged to link to major articles, regardless of the phylogeny. Your arguments pertain to aspects of phylogeny, and so don't pertain to the content or function of the template, but rather to articles about eukaryotic phylogenies. The community does not need consensus to navigate. --EncycloPetey (talk) 05:07, 10 January 2011 (UTC)
The template is not headed "Eukaryote navigation" but "Eukaryote classification". A normal Wikipedia reader (not an experienced editor) is surely entitled to believe that the template represents what its title says? All I want is a single warning sentence to say that the classification of the eukaryotes is currently uncertain. I'm not objecting to the existence of the template or wanting to change it (there's no consensus in the literature to do so). What is wrong with a warning sentence? No-one has yet told me! Arcadian reverted the sentence I added and asked for reasons, which I think I've more than adequately given. Peter coxhead (talk) 01:36, 11 January 2011 (UTC)
I have renamed the template to "Template:Eukaryota". --Arcadian (talk) 13:05, 11 January 2011 (UTC)

Consistency[edit]

For a person reading this template, like I like to do, it seems reasonable to assume that the rightmost taxa that have their own tab, such as Plantae sensu lato aka Archaeplastida, or Animals or Amoebozoa, are kingdoms. (Useful for trying to find a reasonable answer to the question, “How many kingdoms of life are there?”) Such taxa include Heterokonta and Alveolata. However, two groups' respective Wikipedia pages list them as phyla, as does Brown algae for Heterokonta; listing Heterokonta and Alveolata as phyla rather than kingdoms is also more consistent with the fact that Brown Algae apparently diversified rather recently, only about 150-200 million years ago, according to Brown algae. (the first Chordates emerged perhaps 600 mya. For that reason, could the Heterokonta and Alveolata tabs be removed and the two groups simply listed after the Halvaria tab, the way many other subgroups are listed after a kingdom tab.--Solomonfromfinland (talk) 10:21, 22 May 2013 (UTC)

As noted in the discussion above, this is simply a navigation template, and does not attempt to show a consistent classification. I would still like there to be some warning note about this, but I was over-ruled in the discussion above.
The classifications used for different groups within Wikipedia are inconsistent, because reliable sources are inconsistent. To reconcile them would involve WP:SYNTH.
There is at present no reasonable answer to the question "How many kingdoms of life are there?" or indeed the question "Are brown algae a phyla or a kingdom?" since (a) the deep phylogeny of the eukaryotes is still highly uncertain (b) researchers in this field (other than Cavalier-Smith) don't seem to be interested in classification and are content to produce trees showing clades. Indeed it's possible that there may never be answers to such questions; rather they may slowly become to be seen as irrelevant as clade-based classifications replace the traditional Linnaean ranks. Peter coxhead (talk) 10:04, 23 May 2013 (UTC)