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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)
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)
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cite journal}}
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ignored (
help)).I have the doubt. Template contains of the dubious clade Neomura. --
Krclathrate (
talk)
15:24, 22 March 2009 (UTC)
I thought the monophyly of Archaeplastida is contested. Shouldn't we separate Viridiplantae from Rhodophyta? -- kupirijo ( talk) 15:22, 1 August 2009 (UTC)
(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)
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)
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)
I would like to propose:
Zorahia ( talk) 15:45, 4 April 2016 (UTC)
Additional proposal:
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:
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{{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:
I created a new template for Opisthokonta, and I would like to make an additional proposal to the Template:Eukaryota:
A model with the debated changes (exclusion of some groups, change of colors):
Zorahia ( talk) 02:29, 13 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.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)
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)
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)
{{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).{{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.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)
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)
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)
![]() | This template does not require a rating on Wikipedia's
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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)
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)
{{
cite journal}}
: Unknown parameter |month=
ignored (
help)).I have the doubt. Template contains of the dubious clade Neomura. --
Krclathrate (
talk)
15:24, 22 March 2009 (UTC)
I thought the monophyly of Archaeplastida is contested. Shouldn't we separate Viridiplantae from Rhodophyta? -- kupirijo ( talk) 15:22, 1 August 2009 (UTC)
(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)
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)
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)
I would like to propose:
Zorahia ( talk) 15:45, 4 April 2016 (UTC)
Additional proposal:
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:
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{{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:
I created a new template for Opisthokonta, and I would like to make an additional proposal to the Template:Eukaryota:
A model with the debated changes (exclusion of some groups, change of colors):
Zorahia ( talk) 02:29, 13 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.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)
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)
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)
{{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).{{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.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)
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)
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)