Template talk:Eukaryota

Template name

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

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. (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. {{cite journal}}: Unknown parameter |month= ignored (help)).
• 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

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

(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

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)

Diaphoretickes

In Adl et al. 2012, Diaphoretickes does not include Excavata. Bikonta could be right here (I made the change). Then, AH/SAR could be replaced by Diaphoretickes. Franciscosp2 (talk) 19:02, 29 September 2015 (UTC)

Modifications proposal

I would like to propose:

• The creation of a specific template for basal Opisthokonta, to clean up the Eukaryota template; if possible, user Virion123 could cite the sources used in the recent changes on the template.
• The adoption preferably of the classification of Adl et al. (2012), more consensual; the adoption of other views (e.g., of Cavalier-Smith) should be pontual (we have Wikispecies for that); some groups (Opimoda, Varisulca...) above the supergroups are mainly based solely in genetic data, and are very unstable, so, I think they could be avoided.
• The choice or change of colors for the templates and taxoboxes of: Hacrobia, Opisthokonta, Eukaryota incertae sedis.

Zorahia (talk) 15:45, 4 April 2016 (UTC)

I can only repeat the points I made above. The purpose of the template should be to assist readers with navigation. It cannot accurately represent different views on classification, which for deep nodes in the tree of life are uncertain, unstable and subjective. I support choosing one system and using that, although I continue to think that there should be a warning message.

A serious problem with templates like this one is that they cannot have references embedded within them – because such references are likely to be in a different style than ones in the article in which the template is embedded, and citation styles are required to be consistent, and because they might duplicate references already in the article – yet the material should really be referenced. Peter coxhead (talk) 17:07, 4 April 2016 (UTC)

Additional proposal:

• To include in the templates of Opisthokonta (if created), Amoebozoa, Excavata, Heterokonta and Alveolata indications of the correspondence of the present taxa to the old (but helpful to lay people) groups or organization types generally learned in secondary school ("algae", "flagellates", "amoebae", "testate amoeba", "heliozoan amoebae", "sporozoan-like", "fungus-like", etc). I did that in the template of Rhizaria, and I think that the taxa cited are very heterogeneous and abstract to lay people and need similar indications (but I think that those indications are unnecessary in the templates of Archaeplastida and Hacrobia, that are groups more homogeneous). Zorahia (talk) 17:55, 4 April 2016 (UTC)

Hi, Zorahia. I haven't been paying much attention to these templates, but you asked for my input, so I had a look. From Peter coxhead's comments I gather that the Eukaryota template (which might be taken, by the casual observer, for some kind of hierarchical classification) is meant simply as a navigational aid. That's good, because as a snapshot of current classification it is a real dog's breakfast! :) Up near the root, we have Opimoda from Derelle et al, 2015...but, for some reason, we do not have their Diphoda. In place of it, we have Cavalier-Smith's old warhorse, Bikonta...but with Sina Adl's Diaphoretickes nesting inside it. Under that, among other groups, we have Hacrobia -- which has lately come apart at the seam between the "ha-" and the "-cr-" (see Burki et al., 2016). Clearly, anyone who mistakes the template for a handy synopsis of current classification is in for a headache. ;)

I agree with the notion of choosing a single system and sticking with it, with the understanding that the scheme used will sometimes be a few years out of date, and will always be at odds with other systems (a warning, as Peter coxhead suggests, is a fine idea). As you say, Adl et al., 2012, is probably the best candidate, but if paraphyly can be tolerated a case could be made for Ruggiero et al, 2015 (which Catalogue of Life has embraced). As it is, Wikipedia's templates and taxoboxes look like they were stitched together by a mad taxidermist.Deuterostome (talk) 20:28, 4 April 2016 (UTC)

Thank you Zorahia for initiating this discussion. This is I think seriously overdue.

Turning to the suggestion as to a new template to Opisthokonta this is probably a good idea. The current template is becoming increasingly difficult to use. Despite the suggestions elsewhere in this discussion I think that the classification as presented for this taxon is reasonably stable. It may not be perfect but I think it summarises most of the currently understood taxonomy.

That having been said the taxonomy within many of the groups is itself not stable. For example the relation of the comb jellies to the rest of the metazoa is a problem. There is a huge amount of work to be done in the nematodes also.

At levels that include the Opisthokonta the taxonomy is much less stable. The classification and re classification of the amoeba confuse me on a regular basis. The removal of several problematic groups from the Eugleoids I think has improved that taxon. It has probably dumped a lot of the problems in another taxon as well.

Concerning references the current template system does not manage references easily. If you have a suggestion on how to include these in a new template I am all ears.

There is a lot more to be done in sorting out the taxonomy. While Ali et al is probably the best reference overall this should not preclude newer work which cleans up the taxonomy being included. I look forward to reading other's views on this matter. Virion123 (talk) 08:48, 10 April 2016 (UTC)

A few further thoughts. Aside from some method of including references in this proposed template, another addition that I would like to see is the estimated divergence dates. There are reasonable estimates for the branching order for most of the major groups but there is no way of including this in the template at present.

Concerning use of Adi et al. The situation here is unlike that for viruses where the ICTV produces an update every 2 years down to species level. Adi et al produce an update from time to time - there is no fixed schedule. Some of the work is dated very quickly. Cavalier-Smith's work in general I tend to treat with a degree of caution. He is almost always right but he does change his mind frequently and this makes following him a nightmare. There are a number of others who have done and are doing significant work on this area of taxonomy and ignoring their work entirely seems more than a little unfair.

There has been comment here over leaving the bikont taxon alone. In taxonomy unless there is good reason to change the name of a taxon, the first name is the senior (preferred one). The Amorphea was a new taxon in 2012 which acted as a more inclusive grouping. The Varisulca is I suspect something of a rag bag from which at least one new taxon will emerge. At the moment its is a useful holding group with at least some justification. Most of the members in this group cannot currently be classified elsewhere. As the species in this taxon do seem to be more related to Amorphea than to the bikonts a taxon that includes Varisulca and Amorphea seems reasonable.

The relationships between the Apusozoa, Amoebozoa and the Opisthokonta are not clear. The Amoebozoa and the Opisthokonta are probably sister clades. The Apusozoa are probably in need of further division and reorganisation.

The Bikonts need some work also. The Myzozoa have more than two divisions - perhaps six. The Centrohelids do not yet I think have a settled place in the taxonomy.

In sum my thoughts on this matter are roughly as follows:

• It is a good idea to create a new template for the Opisthokonta as this taxon is now fairly stable. This would make editing the remaining template much easier.

• If possible the new template should include references. This is not usually needed for most templates but in this case the need is evident.

• If possible there should be a method of including divergence dates - between date X and date Y. The 1 million years ago template could be used in some fashion to do this.

• I would not rely on Adi et al for the entire taxonomy. This group does not do regularly scheduled updates unlike the ICTV and their view may become seriously outdated very quickly. That having been said given how often Cavalier-Smith changes his mind on the taxonomy some caution is also indicated.

• Wishing that the templates reflect only what was/is taught in secondary or high school is inconsistent with what Wikipedia is about. WP uniquely allows information to be updated unlike paper encyclopedias which have to wait for the next editions in X number of years. Teaching in school is also usually decades behind current scientific thinking. Biological taxons are what they are even if they do not make immediate sense to anyone. WP should report what is known rather than ideas that are now known to be wrong.

• It would be useful if there were a number of editors agreeable to working together who were interested in trying to improve this taxonomy. This area is complicated and discussion with other editors would be helpful. Virion123 (talk) 10:46, 10 April 2016 (UTC)

I meant to add that the addition of new colours would in my view be most useful. I would hope that any new colours that are proposed would not be too controversial. Having one colour for "Protists" given their immense variety does seem to me to be a bit daft. Virion123 (talk) 10:56, 10 April 2016 (UTC)

Another note I forgot to add: Ruggiero et al, 2015 admit their their classification of the protozoa is flawed. While their paper does have merits for taxonomy elsewhere, at the root of the eukaryotic tree I do not think this paper has anything useful to contribute. Virion123 (talk) 11:02, 10 April 2016 (UTC)

{{The Centrohelids do not yet I think have a settled place in the taxonomy.}} Depends on what you mean by "settled." ;) Fabien Burki and his collaborators seem to have confirmed that the centrohelids are basal to the haptophytes, and both groups together (Haptista) are sister to SAR ( http://rspb.royalsocietypublishing.org/content/283/1823/20152802 ). Meanwhile, Cryptista groups with Archaeplastida, so Hacrobia and the chromalveolate hypothesis are not looking too good. No doubt all this will all be vigorously disputed by someone with a hyphenated last name...but at the moment the paper still has no citations. :D

Since the principle of priority has come up, it should be noted that Cavalier-Smith has pointed out that Opimoda is a junior synonym of his podiates (TC-S et al, 2015). In any case, the group is not widely used, doesn't yet have a Wikipedia page, and a search in Google scholar search turns up just 6 uses of the term, including the original paper. Wikipedia is intended for a general readership, and it seems to me this doesn't serve them well. (Better not to root the tree, maybe?)

As for the general approach, here...yes, as the saying goes, "Wikipedia is not paper." I can see the disadvantages of yoking it to Sina Adl's timetable. The use of taxa cherry-picked from a variety of schemes looks a little eccentric, to me, but it seems to have been done thoughtfully (and since it's mostly a navigational tool, and not a proposed classification scheme, it doesn't violate WP:NOR).

I do sympathize with the potential user who does not already have a good grasp of the literature and is simply looking for a plausible (if not definitive) taxonomy. A while ago, I did some consulting for a company developing a line of educational posters about eukaryote diversity. They had tried to develop them in-house using Wikipedia as their main source, and quickly became hopelessly entangled in Wikipedia's internal taxonomic inconsistencies. They used Wikipedia precisely because of an earnest desire to ensure that their resource was up to date, and Wikipedia led them right into a quagmire. Deuterostome (talk) 13:53, 11 April 2016 (UTC)

Thank you Deuterostome. In particular thank you the Centrohelid reference. As you and I both know too well the taxonomy of this area is an ongoing mess. I loved you description of a mad taxidermist. the relations between the Apudozoa and the others are not clear. I think the amoeba and the opthiskonts are sister groups but given the mess that the aemobae are I am very reticent to say anything much about their relations. The excavata seem to more or less a fairly conherent group haveing had a few mvoed out. I suspect there will be more changes.

I think that anyone looking for a consensus view is simply not going to get one as such a view does not exist.

I hope that the current arrangement of the opthiskonsts is at least semi plausible - and subject to sudden unpredable and unforable changes. Virion123 (talk) 15:00, 11 April 2016 (UTC)

{{I think the amoeba and the opthiskonts are sister groups.}} The clade made up of opisthokonts + Apusozoa is sister to Amoebozoa. That group has been called Obazoa. See Brown et al., 2013: http://www.ncbi.nlm.nih.gov/pubmed/23986111 Deuterostome (talk) 15:34, 11 April 2016 (UTC)

Hi, thanks for the comments. I think that:

• In relation to taxa above the supergroups, care should be taken (personally, I would avoid them in the template, but maybe we could include a section "Altenative groupings" in the end of the template).
• In relation to Varisulca, Apusozoa, etc., I think these taxa could be included in the section "Eukaryota incertae sedis".
• In relation to the use of Adl et al. (2012), it could be only a basis, but of course we must use other classifications.
• In relation to the citation of sources, I think that citing in the end of the template (as we presently have for Eukaryota) the main sources (not necessarily all), and the link to Wikispecies (for alternative views) is sufficient. Similar things could be done for other templates.
• In relation to the inclusion of divergence dates, I think that they can be included in the Taxoboxes of each group (but not in the present Template:Eukaryota, which would be heavy). See, for example, Amniota (the taxobox has the date, but the template in the article end not). There is an article about it, Parfrey et al. (2011), [2].
• In relation to the inclusion of organization types (flagellate, amoeboid, algae, fungus-like, etc) in the protist supergroups templates (as in Template:Rhizaria)(not in the Template:Eukaryota), I think that, as Wikipedia is destinated for both specialist and lay people, they would be useful. Their use is not intended to say that these groups are natural, monophyletic, but only to "translate" the current academic classifications to the simplified versions still used in secondary schools (not because the teachers ignore the new classifications, but because pedagogical contents really need adaptations). I only fear that some people could think that the Templates would become heavy in informations (what you think?). Zorahia (talk) 16:59, 11 April 2016 (UTC)

I created a new template for Opisthokonta, and I would like to make an additional proposal to the Template:Eukaryota:

• Cleaning up the template excluding some redundant groups and ribogroups (Bikonta, AH, Alvaria, Opimoda) and including Apusozoa and Varisulca in Incertae sedis sections.
• Using different colors for the supergroups: Hacrobia, Heterokont, Alveolata, Rhizaria (SAR is a ribogroup, less relevant in my view). Zorahia (talk) 18:58, 12 April 2016 (UTC)

I agree with simplifying the template by removing Halvaria, AH, Opimoda and Bikonta. Halvaria puts a superfluous group between SAR and the three clades for which it is named. As for the "AH" clade, I can't see how it adds anything useful. The page it links to is a stub about an unnamed clade proposed by Burki et al. in 2008. Burki (as I mentioned above) no longer accepts Hacrobia, so I can't see the value of retaining his Plants+HC clade here. As for Opimoda and Bikonta, the root of the eukaryote tree is still a highly contended subject, so it seems better to avoid the subject until a consensus appears. The name Bikonta has fallen from favor in recent work, since it has become clear that the common eukaryote ancestor was biflagellate; and Opimoda, as noted above, has been criticized as a junior synonym of the podiates. Deuterostome (talk) 21:33, 12 April 2016 (UTC)

Simplified template

A model with the debated changes (exclusion of some groups, change of colors):

Zorahia (talk) 02:29, 13 April 2016 (UTC)

In my opinion, it's an improvement. A small point: under Amoebozoa, it's strange to see only Phalansterium as a representative taxon. It's not a particularly important genus, and its Wikipedia page is an out-of-date stub. Under Lobosa, I'd suggest Amoeba (genus), Difflugia and/or Acanthamoeba. Under Conosa, good candidates would be Dictyostelium, Pelomyxa and/or Entamoeba coli.Deuterostome (talk) 11:35, 13 April 2016 (UTC)

I am afraid I have to disagree with the above poster.

Kamera lens and the others in that wikipedia group are algae. They are related to the bikonts but their exact position has yet to be determined.

The Apudozoa appear to be a sister group to the Ameobozoa and Opisthokonta (which are probably sister groups).

The Hacrobia belong in the bikont goup. It is the internal divisions of this taxon that are the problem not its placement in the bikonts

The Varisulca will probably need revision but the members do appear to be basal to the Amebozoa and the Opithiskonta. Again this group will probably need revision but when this will occur I cannot say.

On the other hand the suggestions to revise the Amobezoa look sensible - at least for the moment. Virion123 (talk) 13:12, 15 April 2016 (UTC)

{{''Kamera lens'' and the others in that wikipedia group are algae. They are related to the bikonts but their exact position has yet to be determined.}}Records of "Monas lens / Kamera lens" are very old and very scarce, so any comment about where it belongs is speculative (see WP:NOR). I'm not aware of any real work on the genus since Woodcock's paper in 1916, apart from David Patterson's renaming of the thing in The Biology of Free-Living Flagellates of Uncertain Taxonomic position, 1991 (Paddy enjoys giving his taxa goofy names...Massisteria, Cafeteria, etc!) Frankly, I don't know why this marginal one-species genus is on the template at all.

{{The Apudozoa appear to be a sister group to the Ameobozoa and Opisthokonta (which are probably sister groups}}As I wrote earlier, Apusozoa and Opisthokonta are most likely sisters within Obazoa, and that clade is sister to Amoebozoa (citation above). The place of apusozoans within Amorphea seems pretty secure these days, so move the group there, by all means.

Re. Hacrobia...that hypothesis continues to deteriorate. This came to my inbox a couple of days ago: http://www.raccefyn.co/index.php/raccefyn/article/view/277 I'd be inclined to list Haptophyta and Cryptista separately within Diaphoretickes, but as incertae sedis, since there is no agreement yet about their placement.

The groups that make up Varisulca (a taxon that almost nobody but TC-S uses) cluster consistently with Obazoa & Amoebozoa in recent work, and I'm not aware of any controversy about that. I have no problem with placing them under Amorphea...if new work shows they belongs elsewhere, move 'em. Deuterostome (talk) 17:20, 15 April 2016 (UTC)

I think Deuterosome has summarised the position correctly. I was wrong to suggest that Kamera lens is an algae. I was taking this from the algae base. It could well be an excavate. It probably lies within the bikonts. The others in that WP grouping are also probably bikonts but the position is not clear. As to what these species are doing here, I do not have a problem with including weird ones. Firstly they would be even more forgotten about if they were not here. Secondly WP is an attempt to summarise all available knowledge - and this includes the weird stuff that text books leave out.

I suspect that the Apudozoa will be divided in the future. It is a bit of a mess. Mind you so also is Ameobozoa but perhaps to a lesser extent. I would be happy to go along with whatever Deuterostome suggests here.

Hacrobia: Thank you for the reference. This is another group that is a mess. I would go along with whatever whatever Deuterostome suggests here.

Re Varisulca: I agree with the comment about the lack of currency of this term. That having been said these species do seem to group together - this could be long branch attraction mind - and they do seem to map as a sister to Obazoa & Amoebozoa so the taxon does seem to have some use. At least for the moment.

To answer the original poster, I think that the new template if it includes the suggestions by Deuterostome would be a reasonable reflection on current thinking about these basal taxa. That having been said how long this remains the case remains to be seen.Virion123 (talk) 06:23, 16 April 2016 (UTC)

Turning now to the proposed collapse of the Opisthokonta protists. I love the new template. Thank you. However in the larger template I think that their omission is a mistake. Choanoflagates are recognised as the sister group to the metazoa to the exclusion of the others. For this reason I think that division should be included. The Filasterea seem to be the sister group to these two - at least for the moment. Again for this reason this division is probably worth including. The relationships within the Holomycota are I think not as settled as elsewhere as a larger grouping there is not unreasonable.Virion123 (talk) 06:41, 16 April 2016 (UTC)

I also note that the ref that Deuterostome has provided suggests that Excavates are not a single taxon. I do not think anyone will be surprised at that. The Opisthokonta and related taxa are fairly well worked out. The Bikont taxa are a mess. Virion123 (talk) 06:44, 16 April 2016 (UTC)

Now turning back to two points that were raised earlier (1) is there anyway to include references? and (2) is it possible to modify the template to include estimated dates of divergences? The first might be useful as the situation remains fluid and references might reduce the likelyhood of disagreements. The second would be useful - IMHO - because as it stands the template fails to give any sense of the rate of speciation. This it could be argued is not its function. That having been said I think this would add to it if this feature can be included.Virion123 (talk) 06:54, 16 April 2016 (UTC)

(1) Not in any way compliant with WP requirements to maintain consistency of citation styles with those already in the article and not to duplicate references.

(2) The function of navigation templates is navigation. The place to discuss other information is in the linked articles. The more information you put into this template, the more it needs references it can't have and the more it is likely to become out of date.

Peter coxhead (talk) 08:47, 16 April 2016 (UTC)

(1) Duplicated references are taken care of by WP itself. Consistency should not be a problem either.

(2) It is a misconception to imagine this template is "in date". The current version is probably the best that can be done at the moment. Even as it stands there are adjustments that could be made.

(2a) Estimates of the deep divisions in the eukaryote have only recently become available. When these templates were first formulated these estimates were not available and probably could not have been done as the data, software and hardware was simply not available. Just because this was not available several years ago does not mean that it cannot be done now. One method that might work could be taxon (2 million years ago - 1 million years ago) where the upper and lower bounds are the 95% confidence intervals. The advantage of using these templates is that they link directly to a page of geological eras. This in turn provides background to the state of the Earth when these divergences occurred. Virion123 (talk) 11:38, 16 April 2016 (UTC)

Diaphoretickes

Concerning the Cryptista et al. This reference - Burki F, Kaplan M, Tikhonenkov DV, Zlatogursky V, Minh BQ, Radaykina LV, Smirnov A, Mylnikov AP, Keeling PJ (2016) Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proc Biol Sci - is probably as good it is gets at the moment. The authors suggest that centrohelids and haptophytes (collectively Haptista) are sister taxa; Cryptista (Cryptophyta) and Archaeplastida are sister taxa; and that Haptista and SAR are sister taxa. This would help to sort out the confusion - at least for a while - in this area. I would be interested to hear others thoughts on this especially Deuterostome's. Virion123 (talk) 11:54, 16 April 2016 (UTC)

I think it may be fairly safe to say that the haptophytes are sister group to SAR. This is on the basis of the shared similarities between these groups and the plastid which was derived from a red algae. While other groups may have derived their plastid also from red algae there are significant differences between theses. This would support Burki et al in grouping the haptophtes as a sister group to SAR. This similarity was the basis for the chromoalveolate taxon - which it has to be said may need revision. Virion123 (talk) 12:10, 16 April 2016 (UTC)

Another group that is difficult to place are the katablepharids. These are an usual group of algae with uncertain placement. Possibly sedis incerta in Diaphoretickes (?) Virion123 (talk) 12:14, 16 April 2016 (UTC)

A second group that is not easy to place are the rappemonads. Suggestions are welcome.Virion123 (talk) 13:12, 16 April 2016 (UTC)

I would like to read the other interested editors thoughts on the organisation in this ref - Burki F, Okamoto N, Pombert JF, Keeling PJ (2012) The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc Biol Sci. 279(1736):2246-54. doi:10.1098/rspb.2011.2301. Like all such papers the organisation it proposes is subject to change without notice but it seems to give a fairly consistent taxonomy and covers all the main groups and quite a number of the less well known ones. Combined with the revisions to the Opthiskonta template I think this taxonomy would cover all the main groupings rather well. Admittedly it does not include the rappemonads. These could be included as sedis inserta along with several others. This would probably be the best (temporary) solution. Virion123 (talk) 13:27, 16 April 2016 (UTC)

The revised template would like something like this:Virion123 (talk) 13:45, 16 April 2016 (UTC)

Another question is whether the template should follow this reference - He D, et al. An alternative root for the eukaryote tree of life. Curr Biol. 2014;24:465–470 - which suggests that Discoba and potentially its parent Excavata - are sister to the Amorphea + Plants. My own feeling is that this grouping should be confirmed by another group before using it in WP as a guide as Excavata is quite possibly polyphetic which would mess this suggestion up.Virion123 (talk) 12:53, 16 April 2016 (UTC)

A few quick thoughts (no time to respond in detail to all the points raised). First, as far as I know, the katablepharids (Roombia, etc) are cryptists. Is there evidence against that? I don't recall any controversy about it. (Heck, with those ejectisomes you can tell some of them are cryptists just by looking at 'em) Second, for reasons of visual consistency, I'd be inclined to put Haptista next to SAR, and Cryptista (cryptomonads/cryptophytes and katablepharids) next to Archaeplastida. And third, I strongly agree with Peter coxhead about keeping the template simple. The guidelines on Wikipedia:Navigation templates and Wikipedia:Categories, lists, and navigation templates are pretty clear: the navboxes are for helping users get around within Wikipedia, not for supplementing the articles by giving additional information. Deuterostome (talk) 14:25, 16 April 2016 (UTC)

Thank you Deuterostome. I am sure you are right about the placement of the katablepharids. It is a group I know little about.Virion123 (talk) 15:11, 16 April 2016 (UTC)

I have revised the subtemplate following Deutrostome's suggesions. I do not know if there is a designated taxon for these divisions. If there is not perhaps colour coding might be of use? Virion123 (talk) 15:30, 16 April 2016 (UTC)

The picobiliphytes and telonemids now need to be included also.Virion123 (talk) 15:32, 16 April 2016 (UTC)

This reference - and there are not too many on the telonemia - suggests that this group are relations of the centroheliozoa. Burki F, Inagaki Y, Bråte J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen KS, Pawlowski J, Shalchian-Tabrizi K (2009) Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol 1:231-8. doi:10.1093/gbe/evp022.

In the absence of evidence to the contrary I will put telonemia in with the Hapista.Virion123 (talk) 16:09, 16 April 2016 (UTC)

Two other groups that belong somewhere in this taxon are the goniomonads and Palpitomonas. The goniomonads may be part of the Cryptophyta taxon but I am not familar enough with this species to comment further. Putting these into the sedis inserta seems reasonable for the moment.Virion123 (talk) 15:50, 16 April 2016 (UTC)

I have changed the background colours to suggest the taxons relatedness. Please feel free to change the colours to something more pleasing. It would be better to have a larger taxon for these groupings but I do not think such a taxon has been agreed to date.Virion123 (talk) 16:00, 16 April 2016 (UTC)

Halvaria should be on the template. I forgot to include this. Rhizaria acquired a plastid from a green algae after diverging from the other members of the SAR group and the taxonomy should reflect this. Virion123 (talk) 16:02, 16 April 2016 (UTC)

The picobiliphytes have been renamed the biliphytes. They are also known as Picozoa. They seem to be related to the Cryptista but the connection cannot be said to be certain. I will put these in the sedis inserta grouping at least for the moment. Virion123 (talk) 16:09, 16 April 2016 (UTC)

The branching order in Haptista seems likely to be Telonemia as the basal clade with Centrohelids and Haptophytes as sisters. This is by no means certain and I think just leaving them in one taxon is the best option for the moment.Virion123 (talk) 16:21, 16 April 2016 (UTC)

On further investigation both Goniomonas and Palpitomonas have been placed in the Cryptista/Cryptophyta taxon. Palpitomonas appears to be basal with the Katablepharids being the next to branch leaving the Cryptomonads and Goniomonas as the crown groups. Given the inherent instablity of these taxa it is probably best - at least for the moment - just to list them rather than try to introduce new taxon levels. Virion123 (talk) 16:52, 16 April 2016 (UTC)

Overall template discussion

Assuming that these changes to the template are agreed, then the deepest branches in the template will be The Opthiskonts/Amoboza/Apudomonas (Amorphea) + Varisulca, Excavata and Diaphoretickes with Kamera lens being a sedis incerta group. As well as being reasonable close to generally accepted taxonomy - at least for the moment - this should help with navigation.Virion123 (talk) 16:16, 16 April 2016 (UTC)

The other changes needed here would including Obazoa (Apusozoa, breviates and Opisthokonta) as a sister taxon to Amoebozoa with Amorphea being the taxon containing both of these. The Apusozoa and Opisthokonta are sister taxa. Varisulca is the sister taxon to Amorphea. The relationship between Excavata, Diaphoretickes and the Variscula/Amorphea are to be left undecided. Hopefully that summaries the changes agreed and needed. Virion123 (talk) 16:34, 16 April 2016 (UTC)

Below is approximately what the new template would look like. It is missing a few taxa (eg Halvaria, Obazoa) but the overall layout is correct. As noted before please feel free to make better colour choices. Virion123 (talk) 17:16, 16 April 2016 (UTC)

Another thought. It might perhaps be better to place Diaphoretickes and Amorphea/Varisulca beside one another if the eukaryotic root does lie with the Excavata or between the proposed Diaphoretickes and Amorphea/Varisulca clade. On the other hand it may be too early to make this call.Virion123 (talk)

The position of Kamera lens is at least a little odd here. It seems highly likely that this species belongs in the Diaphoretickes - it has been suggested that it may even be a member of the SAR group - so I think that putting in with the Diaphoretickes is sensible. Like much of these difficult to place taxa its' position is subject to revision.

I have now made all the proposed changes to the template. This has been done in stages to make for easier editing. I think the final template looks reasonable but probably could use some colour adjustments. Virion123 (talk) 18:46, 16 April 2016 (UTC)

There is one more taxon that could be included - that between Breviata and Amorphea. Given the instability of the these taxa I think it is reasonable - at least for the moment - to leave Breviata within the Apudozoa. Virion123 (talk) 18:55, 16 April 2016 (UTC)

Hi, Virion. A few thoughts, before running out the door!

• Where you've placed Cryptophyta you probably meant to write Cryptista. Cryptophyta comprises the same taxa as Cryptomonada (they're synonyms...a classic case of overlap between ICZN and ICBN/ICN), so it makes no sense to have one nesting inside the other.
• Like Zorahia, I don't see the reason for inserting Halvaria between SAR and the three groups from which its acronym is formed. The group doesn't provide access to any information not already included in SAR and its subgroups (apart from the name itself), so it serves no navigational purpose. Taxonomically, it's a little confusing, since schemes that include Halvaria will typically use Harosa for SAR, and heterokonta for Stramenopiles.
• I have a similar objection to including Obazoa. The group (a red link...no article) has no navigational value, and only clutters the template.
• Where you've written Sedis incerta you should use the standard plural Incertae sedis (there are three taxa there)
• Would it be possible to have fewer red links in the template? They're inconsistent with the guidelines: Wikipedia:Navigation templates#Navigation templates provide navigation between existing articles. Deuterostome (talk) 22:39, 16 April 2016 (UTC)

As ever thank you Deuterostome. I have now changed the Cryptista. I find that particular part of the taxonomy very very confusing. Incertae sedis is now also corrected.

Re red links; WP is built on red links. Given the fluidity of these taxa I would be amazed not to find at least some red links. My answer to anyone complaining about red links is to ask them to do something about them. If you can comment you can create a page. It just takes a little more work.

Re Halvaria. There is a BIG phylogenetic gap between the Rhizaria and the others in SAR. The Rhizaria aquired a green plasmid sometime after the SAR group formed and this is one of the distinguishing features of this group. If the page this links to needs rewriting then WP allows you to do just that.

Re Obozoa: This one is a little more problematic. Personally I rather like including it. It cleans up the taxomomy nicely. That having been said unlike Halvaria the evidence for this group and the likelyhood of it remaining as a taxon seems rather lower. A man with a hyphenated name could well suggest replacing it. I would prefer to leave it for the moment and see how the rest of the taxonomy at this level develops in the future. It can always be revised.Virion123 (talk) 06:04, 17 April 2016 (UTC)

Other thoughts: I presume that leaving Breviata in the Apudozoa is acceptable - at least for the present. And I would appreciate suggestions or indeed aesthetic changes to the colour scheme. Has anyone ideas on consistent and accepatble changes to the colour scheme? Virion123 (talk) 06:09, 17 April 2016 (UTC)

Another thought: Podiates or optimoda? Podiates does have priority and I am not sure how much currency Optimoda has.Virion123 (talk) 06:16, 17 April 2016 (UTC)

Correction to template. Obazoa is the taxon containing the Opthiskonts, the Berviates and the Apudozoa. It is the sister taxon to the Amoeba and these two taxa together form Amorphea. This has now been corrected. Virion123 (talk) 06:33, 17 April 2016 (UTC)

A few other thoughts. The root of the eukaryote tree seems likely to lie somewhere between the Opimoda/Podiates and the Excavata. The position of the Diaphoretickes is not clear. This latter group could branch with either. I think that at least for the moment it is best to leave this as a trifurcation as this remains debated - at least for the moment. Also given the uncertain relations between Cryptista and Halvaria these are best left as seperate groups. Halvaria seems to be related to the SAR group and Cryptista to the plants. The branching order is not presently clear so I think the current organisation seems reasonable - for a while.Virion123 (talk) 06:54, 17 April 2016 (UTC)

The Biliphytes almost certainly belong to the Cryptista taxon. Moving them there gives a rather satisfying result of having only Kamera lens and the rappemonads as incertae sedis. Kamera cannot be further classified until additional studies are done. The rappemonads are only known from DNA sequences and even the desribing authors admit that they had trouble placing them in a group. They are algea and clearly belong in the Diaphoretickes somewhere. Virion123 (talk) 07:37, 17 April 2016 (UTC)

Use of colours. I have removed the rather arbitary colour choices. There was nothing wrong with these but I am not sure they hadd much now that the taxonomy seems a little clearer. The Archaeplastida and and Crypista have been given the same background because it is likely they are closely related. The taxobox colour Chromalveolata is a bit more difficult as Chromalveolata is no longer recognised a valid taxon. I have used it for the SAR group and the Hapista as these seem to be related. Those taxa with designated colours - Fugni, Animalia etc I think should probably be left alone for consistency. If any editor feels that additional colours would help here I would have no problem with that. Virion123 (talk) 07:56, 17 April 2016 (UTC)

{{Re Halvaria. There is a BIG phylogenetic gap between the Rhizaria and the others in SAR. The Rhizaria aquired a green plasmid sometime after the SAR group formed and this is one of the distinguishing features of this group.}} Assuming you meant to write plastid rather than plasmid, only one small Rhizarian lineage, the chlorarachniophytes, has a plastid acquired from green algae. The rest, apart from the oddball Paulinella, are colorless. It's hard to see what that has to do with Halvaria. Perhaps you meant to talk about the red secondary symbionts in some (but not all) alveolates and stramenopiles? It is still not known whether these resulted from a single event, or serial endosymbioses (the lack of plastids in basal alveolates like the ciliates, and also in certain basal stramenopiles, raises some doubts about the single event hypothesis).

But, leaving that aside, my understanding is that these navboxes are simply intended to give users a broad, well-traveled road on which to travel between WP pages (in this case, pages featuring major eukaryote groups). The more detours, country lanes and cul-de-sacs they include, the more confusing the tool becomes. That said, I don't really have much of an investment in these templates, so I'll get out of the way and let you and Zorahia work it out! :) Deuterostome (talk) 13:17, 17 April 2016 (UTC)

Thank you again Deutrosome. You are correct in the spelling correction. I am aware that most of the Rhizaria are colourlkess. If my reading of the literature is correct there is evidence that the green algae plastid was then lost again in most of the Rhizaria. As we both know it is quite possible that these taxa may once again be subdivided but at the moment I think there is some taxonomical validity for this. I know quite a bit about the alveoltaes and I am well aware of the problems with the problems with the myxozoa-ciliate divergence problems. I would be amazed if there was not more than one such event in the myxzozoa given thie life style. However the green algae seems to be unique to the Rhizaria and at the moment seems to be pretty basal which would I think argue for the validity of this taxon. At least for the moment. Any insights you have into how the ciliates developed their weird DNA system would be very helpful as that has me very confused.

I look forward to Zorahia's input here. I hope the current arrangement is satisfactory - for the moment.

While I can agree that overloading the templant may not be a good idea, I think that the table should indicate at least some of the current thinking on the txonomy. If the sole purpose of the template was purely navigation, then a simple rectangle with a list of taxon in alphabetic order would suffice. I think and I hope others will agree that the current template is somewhat better than a simple listing. Once we are agreed that a more complex template is better than a list, then it is the details that we disagree on.

I note your 'lack of investment' in the template. For me I have found it a useful if rather time consuming exercise. I have learned a lot about some of the more unusual taxa and had a chance to bring my knowledge of some of other taxa up to date. Deuterostome's input also here has been most useful. The end result of the template reorganisation has suprised me in its simplicity which has one benefit of this exercise. I hope others will also be surpised by its relative simplicity. Virion123 (talk) 06:23, 18 April 2016 (UTC)

One question that seems to have been overlooked: Opimoda or Podiates? I am happy with either. Podiates has priority but does not seem to be much used. Suggestions/opinions please.Virion123 (talk) 06:27, 18 April 2016 (UTC)

• {{If my reading of the literature is correct there is evidence that the green algae plastid was then lost again in most of the Rhizaria.}} Perhaps you're thinking of conjectures about red plastid loss in Rhizaria (a supposition that is essential to the survival of the chromalveolate hypothesis)? As far as I know, everyone agrees that the green plastid in the chlorarachniophytes arose independently in that particular lineage by secondary symbiosis. Even TC-S -- who always stresses the rarity of symbiotic events -- agrees that the chlorarachneans, euglenids and one branch of dinoflagellates "acquired green algal chloroplasts by secondary enslavement substantially after the origins of their parent phyla and did not have as great an evolutionary impact as chromophytes"(Multiple origins of Heliozoa from flagellate ancestors, 2015). There was some early speculation about a common ancestor for the green symbiont in euglenids and chlorarachneans, but I don't think anyone still backs that horse.
• Not sure what you mean by the ciliates' "weird DNA system." Do you mean their nuclear dimorphism?
• I agree that editing WP is a fun way to learn and keep up with the literature, as long as we remember that this is not our little sandbox, but a general-purpose encyclopedia.
• Re. Podiates or Opimoda, I'd vote: neither. I liked the simplicity of Zorahia's layout, with Amorphea directly under Diaphoretickes (and really don't see why it's essential to place the proposed Varisulca under a higher taxon before there is broad agreement...it'll all get sorted out in a year or two ;) ) Like Unikonta, the podiates have an unproven synapomorphy embedded in the name (cortical pseudopods, presence of myosin II). As far as I can tell, the name is used only by TC-S and his collaborators. Opimoda is not in general use either, as I noted above. Deuterostome (talk) 12:16, 18 April 2016 (UTC)

I would like to give priority in the template for the "supergroups" of Adl et al., 2012 (Archaeplastida, Stramenopiles, Alveolata, Rhizaria, Excavata, Amoebozoa, Opisthokonta - each one with his own color), which in general have well defined synapomorphies. For me, most of the other ribogroups are near meaningless and unstable (I think Eukaryote#Phylogeny and Wikispecies are better places for them).Zorahia (talk) 16:36, 18 April 2016 (UTC)

I would along with the different colour idea.

The Cryptista and Halvaria seem to be fairly solid also. The only ribogroup in the Bikonts (I am using the older names as they are easier to spell - a cheat I know) is the SAR group which is accepted by Adi et al. Kamera lens and the Rappemonads are almost certainly Bikonts.

Turning now to the Unikonts the Apudozoa do come out in multiple analyses as the sister group to the Opithiskonts. The Ameobzoa have been similarly identified as the sister group to this Apud/Opthis clade.

The Excavates seem to be basal in all the more recent work.

The Varisulca are the only clade whose position is debated. This group seem to go with the Amoboazoa and others but the clade itself is likely to undergo further revisions.

Because there is considerable support for the arrangement given above - with the possible exception of the varisulca - I think the current arrangement is probably the best that can be done at the moment. I might add that I have reviewed most if not all of the current literature on these groups. Virion123 (talk) 09:23, 23 April 2016 (UTC)

All right! Zorahia (talk) 01:23, 25 April 2016 (UTC)

Update

Brown MW, Heiss AA, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida KI, Hashimoto T, Simpson AGB, Roger AJ (2018) Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. Genome Biol Evol doi: 10.1093/gbe/evy014

Brown et al created a new taxon CRuMs for collodictyonids, rigifilids and Mantamonas. The remaining taxa await further studies. Virion123 (talk) 12:17, 24 January 2018 (UTC)

Extinct incertae sedis

The box includes an Incertae sedis line at the bottom. This includes the extant species Parakaryon myojinensis, but then 6 extinct species, Acritarcha, Charnia, Gakarusia, Galaxiopsis, Grypania, Leptoteichos. Gakarusia, Galaxiopsis and Leptoteichos are red links.

This choice of extinct species seems silly. Red links serve no purpose in a navbox. Charnia is one of a large number of Ediacaran genera that could be listed here. I've changed "Acritarcha" to Acritarchs as this is a (possibly miscellaneous) group, not a single genus. I suggest replacing Charnia with Ediacaran biota, and dropping the three red links. Bondegezou (talk) 11:12, 23 November 2018 (UTC)

• Strong support. I think the red links can be kept for informative purposes, but Charnia (or Rangeomorpha) should be replaced with the Ediacaran biota as suggested. --Pinoczet (talk) 21:30, 18 February 2021 (UTC)

Charnia has been replaced with Rangeomorpha, which seems sensible enough. I still think the red links to Gakarusia, Galaxiopsis and Leptoteichos are pointless and against navbox policy. Bondegezou (talk) 09:14, 19 February 2021 (UTC)

OK, I've re-jigged the others. See what people think. Bondegezou (talk) 09:21, 19 February 2021 (UTC)

@Bondegezou: Seems reasonable. Still, Rangeomorpha belongs to a broader category—the Ediacaran biota or "vendobionts"—as you noticed. --Pinoczet (talk) 10:49, 19 February 2021 (UTC)

You're right, but it's complicated. I think now Ediacaran biota is too broad as that includes organisms that are covered by other groups. Vendobionta is questionable, AIUI, but would fit better... except Vendobionta just redirects to Ediacaran biota. We could have Rangeomorpha and Erniettomorph?

Editors: what would be better here? Ediacaran biota; Vendobionta (which links to the same place); or both Rangeomorpha and Erniettomorph? Bondegezou (talk) 11:26, 19 February 2021 (UTC)

I think either "Vendobionta" or "Ediacaran biota" would be appropriate here. See also: Ediacaran biota#Morphology, the subsection Non-Vendobionts. --Pinoczet (talk) 13:30, 19 February 2021 (UTC)

Use of obsolete / obscure names

Our job here is just to help readers navigate among Wikipedia articles. When a name is in common use like Holomycota, we must use that, not some obscure name which someone proposed earlier but found no favour. This is obviously different from a purely scientific or administrative function where other choices might be made by rule. Chiswick Chap (talk) 06:24, 10 April 2023 (UTC)

"Holomycota" and "Nucletmycea" are names for clades, and as such not covered by the nomenclature codes, and hence there are no priority issues. So we can, and should, use whichever is better known. Peter coxhead (talk) 06:45, 10 April 2023 (UTC)