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Polypodiozoa

Should this be added to this template? Lavateraguy ( talk) 16:55, 21 October 2010 (UTC) reply

This template badly needs citations. -- 24.5.147.203 ( talk) 22:26, 21 April 2012 (UTC) reply

Citations and Updates

I was looking into these phylogenies, and I've found some recent review articles that could be cited, and which also suggest improvements to this template.

The first is a review article from 2011, [1], which has been fairly highly cited since then (98 times), which summarizes recent results and gives a 'consensus' phylogeny. I've copied the cladogram below. * means the node has 'broad consensus'. Overall it agrees well with what's in the template. Here are the places with important differences:

  • everything under Lophophorata is placed differently in the cladogram below (which has a new category 'Polyzoa')
  • everything under Xenacoelomorpha is placed differently in the cladogram below

Minor differences (probably can be left alone):

  • Chaetognatha is in Protostomia by article, but it falls easily into the 'disputed' category.
  • cladogram is a little more precise about the Panarthropoda

Also, there seems to be some confusion elsewhere over whether Lophotrochozoa and Spiralia are different. I have not understood the relation yet.

I found another 2013 review article which attempts to describe current consensus on the more ancient metazoan divergences [2] from March 2013, cited 9 times since then. As you can read in the article, although this is the current consensus it is still somewhat uncertain. Probably the template's small amount of detail is enough, but in case we want more detail the cladogram is below. This would clarify the Mesozoa, Parazoa and Radiata in the template. I'm not sure if combining the two cladograms would count as 'original research', since how to do so is a tiny bit subjective.

Finally, here is yet another article which confirms the the last two above [3] from April 2014, 2 non-self citations since then. It does have one difference: It groups the Ctenophora and Cnidaria together. Otherwise it looks identical. I did not find any other more relevant articles.

I will let this sit here until I have time to work on it again or read the articles more closely, and then maybe I'll update the template. Ahalda ( talk) 20:07, 13 August 2014 (UTC) reply

I've updated it now. Another issue I didn't notice before has to do with the monophyly of the panarthropoda/Cycloneuralia, and specifically whether tardigrada should be included in panarthropoda. The 2011 paper says this is still uncertain. Hwoever I found a 2014 review by the same author on panarthropoda [4], which says the best evidence suggests it is monophylic. Therefore I have left that part as it is. On the other hand, a different 2011 publication (including Edgecomb as author again) claims that Cycloneuralia is paraphyletic. [5] Therefore I have removed it. Ahalda ( talk) 17:32, 14 August 2014 (UTC) reply


This template does not match at all with the cladogram in metazoa Jmv2009 ( talk) 15:59, 28 March 2015 (UTC) reply

It looks to me like there is only one inconsistency, in the placement of Ctenophora. That makes sense, since the metazoa page was recently updated based on some 2014 publications on the placement of Ctenophora. I looked into moving Ctenophora in the template, but I think we should make other changes as well: The subkingdoms Mesozoa, Parazoa and Radiata look to me to be obsolete. They are probably paraphyletic, and their wiki pages say they are only use informally/historically now. Ahalda ( talk) 16:19, 24 April 2015 (UTC) reply

Dendrogramma

Shouldn't Dendrogramma be added to this table... although I'm not certain where! Bondegezou ( talk) 11:15, 19 July 2015 (UTC) reply

The Dendrogramma article itself considers it a Cnidarian. Shouldn't Dendrogramma be removed from this table? Ypna ( talk) 11:07, 23 June 2016 (UTC) reply
Done. Yes, they found more and got some DNA from them. Bondegezou ( talk) 11:23, 23 June 2016 (UTC) reply

Porifera placement

Animal#Ctenophora.2C_Porifera.2C_Placozoa.2C_Cnidaria_and_Bilateria argues for a rather different phylogeny than this template shows. Any thoughts on whether we should reflect that? Bondegezou ( talk) 10:24, 21 July 2015 (UTC) reply

Add Nephrozoa?

Rouse et al. (2016) [6] uses Nephrozoa for a clade including deuterostomes and protostomes, but excluding Xenacoelomorpha. "Nephrozoa" was first introduced in:

Jondelius, U., Ruiz-Trillo, I., Baguñà, J. & Riutort, M. (2002). The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes. Zoologica Scripta, 31(2):201–215.

Should we add Nephrozoa? Bondegezou ( talk) 17:30, 4 February 2016 (UTC) reply

Obsolete taxa

Why does this navbox have an obsolete section? From experience it is more normal for these navboxes to only show what is accepted, not what isn't accepted. Ypna ( talk) 11:36, 23 June 2016 (UTC) reply

I suppose there is some value in it; some of these taxa are still often treated separately (e.g. Sipuncula). Maybe I could at least condense the section. Ypna ( talk) 11:42, 23 June 2016 (UTC) reply

Major groups within phyla

I find the new "major groups within phyla" section confusing. Can it be made more visually distinct so it doesn't just look like another phylum? Bondegezou ( talk) 09:23, 24 December 2016 (UTC) reply

Well one possible way would be to have a different background. I might experiment with this to see what it's like. --Jules  (Mrjulesd) 12:43, 24 December 2016 (UTC) reply

Mesozoans

"The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians" (2016) "The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution" (2017) Can someone edid the template accordingly? — Preceding unsigned comment added by 91.238.142.39 ( talk) 10:53, 6 June 2017 (UTC) reply

Agreed. We should move Orthonectida from Mesozoans to Spiralia, parallel to Gnathifera and Platytrochozoa, based on Kirill V. Mikhailov, Georgy S. Slyusarev, Mikhail A. Nikitin, Maria D. Logacheva, Aleksey A. Penin, Vladimir V. Aleoshin, Yuri V. Panchin (2016), "The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians", Current Biology, 26, 1768–1774. However, the syntax of the table has defeated me: can't work out how to do it! Bondegezou ( talk) 10:45, 7 June 2017 (UTC) reply

> Both Orthonectida and Dicyemida should go to Rouphozoa, based on the second of the cited above papers.

I moved mesozoa to sister of Rhoupozoa Jmv2009 ( talk) 07:51, 8 October 2017 (UTC) Is that correct? reply


Ctenaphora basal /epitheliozoa/Eumetazoa/Parazoa

The latest research [7] [8] [9] suggests ctenophora are the basalmost animals, actually with "full" support, as opposed to [10], which is substantially less resolved, especially in the surrounding clades. Of course this has been a discussion since the Ryan et al(2013) paper, but it really seems like ctenophora is basal. Feel free do discuss.

This leaves us with the naming of the Porifera + Parahoxozoa clade. The closest thing to this clade I know of is parazoa. Before ctenophora basal, it was already realized that the higher animals emerged within Parazoa. With this knowledge, in Cladistics you can either take the stance of rejecting parazoa as a valid clade or you can include the emerged clade (dramatically increasing the scope). This is a normal process when groups turn out to be paraphyletic stem groups. For lack of a better available name, the last option can be taken. Before ctenophora basal, including the emerged clade would have resulted in parazoa as synonymous with metazoa, rendering parazoa obsolete or superfluous. However, after ctenophora this is not the case anymore.

Also eumetazoa, now without ctenophora, which originally did not include placozoa, can be used closer to its original meaning, and become equivalent to the planulozoa rather than e.g. the Parahoxozoa/Epitheliozoa.

The Epitheliozoa hypotheses and Eumetazoa hypotheses (see placozoa) both more ore less hold true, as long as ctenophora is removed from the discussion there.

Jmv2009 ( talk) 12:27, 21 October 2017 (UTC) reply

Porifera not monophyletic

Re: recent edit disputes, Sponge#Relationships_to_other_animal_groups says Porifera probably not monophyletic, so we should reflect that. Bondegezou ( talk) 11:44, 1 March 2018 (UTC) reply

As it stands [1] whether or not Porifera is monophyletic or not is ambiguous regarding this navbox. I don't believe it is a navboxes function to specify whether phlya are monophyletic or not: in many cases this is unknown or uncertain. For example, did the Nematomorpha evolve from the the Nematoda, or the other way around? It is certainly a possibility.
Navboxes are primarily for navigation between articles, not cladograms: readers should view the article for these sorts of details. And I feel edits such as [2] give undue weight to the sponges, again without specifying whether the group is monophyletic or not; it practice it just add cladistic details to a single phyla without making monophyly clearer.
Also, as it stands the navbox already has extensive complexity: I think the best thing to do would be to try to add to this complexity unless it is wrong in some way. Adding cladistic breakdowns of phyla should be avoided. --Jules  (Mrjulesd) 17:59, 1 March 2018 (UTC) reply
I am more sympathetic to a cladistic approach, but concur with your concerns over undue weight and complexity. Bondegezou ( talk) 11:00, 2 March 2018 (UTC) reply

We need to talk about Xenambulacraria.

Where is the scientific consensus for the obsolescence of Deuterostomia? I am not seeing it. On the Bilateria, Deuterostome and Nephrozoa, and now in this template, someone has taken it upon themselves to "update" the foundation of animal phylogeny with cutting-edge research. This is inappropriate for two reasons, as I've detailed already on the talk page of the Bilateria article.

1. Wikipedia is supposed to reflect the scientific consensus. Our job here is not to push one particular scientific hypothesis over another, but instead, we must reflect the state of the field. Can anyone provide compelling evidence that there has been a widely-accepted paradigm shift in the understanding animal phylogeny? I have yet to see it.
2. The source that is constantly given for Deuterostome obsolescence, Philippe et al. [11] openly admits the following, in the Discussion section, p. 1824: "Although the majority of our analyses recover a monophyletic group of chordates plus protostomes, the support values are very low, meaning there is no solid evidence to refute the traditional protostome and deuterostome dichotomy." (emphasis mine). Further, they admit that "more refined methodologies (e.g., [30]) are required to adequately test the deuterostome monophyly." Therefore, it is far too soon to use the Philippe et al. paper to radically change the the traditional Protostome–Deuterosome dichotomy.

As I have not seen any broad scientific consensus, and as the study that has been used to justify this radical change readily admits that it is too soon to make radical changes in our understanding, I am reverting this template to again reflect the traditional Protostome–Deuterostome dichotomy. BirdValiant ( talk) 18:09, 13 September 2019 (UTC) reply

I think you are misrepresenting the discussion section somewhat. The authors are not casting doubt on their own "Xenambulacraria" hypothesis. The point of doubt is that the authors are not able to confidently resolve Chordata as sister to either group, leaving the conservative position (if we consider Philippe et al. to represent of the current scientific consensus) as a three-way split at the root of Bilateria: "All possible relationships between chordates, protostomes, and Xenambulacraria are observed in different analyses". -- April Arcus ( talk) 19:06, 18 April 2021 (UTC) reply
With the benefit of a few years time, we are now in a position to assess the scientific community's reaction to Philippe et al. Of 22 citing articles on PubMed.
1. Laumer et al. (doi: 10.1098/rspb.2019.0831) calls it an "ongoing controversy" "not addressed here".
2. Andrikou et al. (doi: 10.1371/journal.pbio.3000408) seriously considers the hypothesis, citing two authors in support of the idea that "excratory organs of the ambulacraria, chordata, and protostomia might not be homologous", but noting that more follow-up work is required.
3. Hartenstein & Martinez (doi: 10.1007/s00441-019-03096-6) takes no position.
4. Natsidis et al. (doi: 10.1038/s41598-019-55573-1) accepts Xenambulacraria as a prior, without comment: "We next applied our method to the two clades of deuterostomes: the Xenambulacraria (29 echinoderms, 2 hemichordates and 7 xenacoelomorphs) and the Chordata (2 urochordates and 29 vertebrates)"
5. Bezares-Calderón et al. (doi: 10.1098/rstb.2019.0376) shows a four-way split between Xenacoelomorpha, Ambulacraria, Chordata, and Protostomia.
6. Marinković et al. (doi: 10.1098/rstb.2019.0165) shows a four-way split between Xenacoelomorpha, Ambulacraria, Chordata, and Protostomia.
7. Martynov et al. (doi: 10.1371/journal.pone.0227173) comes out in support of Xenambulacraria.
8. Fleming et al. (doi: 10.1093/gbe/evaa015) calls the position of Acoelomorpha "disputed".
9. Yañez-Guerra & Elphick (doi: 10.3389/fnins.2020.00130) calls the position of Acoelomorpha "controversial" and goes on to note that "the xenacoelomorph luqin-type receptors are positioned within a branch that also includes ambulacrarian luqin-type receptors. Therefore, this may be additional evidence in support of the Xenambulacraria hypothesis.", citing Thiel et al. (doi: 10.1093/molbev/msy160).
10. Kon & Furukawa (doi: 10.1002/2211-5463.12832) accepts Xenambulacraria as a prior, grouping Meara stichopi (Xenacoelomorpha) as a sister to "Starfish + Acorn worm" (Ambulacraria), but disclaiming that "it should be noted that the Metazoan phylogeny is controversial".
11. Himmel et al. (doi: 10.1093/molbev/msaa065) notes that "among Eumetazoa, TRPS [transient receptor potential soromelastatin] genes are only present in some protostomes and lancelets", and that its absence in Xenacoelomorpha and Ambulacrarians could be parsimoniously explained by gene loss in a common Xenambulacrarian ancestor.
12. Odekunle & Elphick (doi: 10.3389/fendo.2020.00225) says "both phylogenetic positions are compatible with the structure of this review article." but picks the Xenambulacraria hypothesis on the basis of recency.
13. Kapli et al. (doi: 10.1038/s41576-020-0233-0) notes only that "Tools aiming to identify and eliminate sequences with [...] low phylogenetic information also exist"
14. Budd & Mann (doi: 10.1098/rsfs.2019.0110) takes no position.
15. Hulett et al. (doi: 10.1098/rspb.2020.1198) takes no position, but asserts that their work will allow future researchers to investigate the hypothesis on developmental grounds.
16. Schoch et al. (doi: 10.1093/database/baaa062) says that "The classification of major metazoan lineages generally follows the broad consensus of recent phylogenomic studies while taking a conservative approach to areas that remain contentious or unresolved (e.g. whether Xenaceolomorpha is the sister group to all other Bilateria or is a clade inside Dueterostomia).
17. Schrempf et al. (doi: 10.1093/molbev/msaa145) says "EDM (empirical stationary distribution mixture) models may help resolve open phylogenetic problems involving large data sets and distantly related species)".
18. Kapli & Telford (doi: 10.1126/sciadv.abc5162) states (in its abstract!), that "empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be ex- plained by systematic error. [...] the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives." This appears to be the wished-for follow-up study to Philippe et al. 2019, and deserves a journal club style discussion here.
19. Song et al. (doi: 10.1186/s12862-020-01714-4) says that "Acoels are part of Xenacoelomorpha, a group of worms that has been proposed to be the sister group of all remaining bilaterians. This view remains however challenged as they are also proposed to belong with the deuterostomes."
20. Natsidis et al. (doi: 10.1016/j.isci.2021.102110) makes no relevant comment
21. Kapli et al. (doi: 10.1126/sciadv.abe2741) affirms that relationships between Chordata, Xenacoelomorpha, and Ambulacraria can't be effectively resolved: "Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives".
22. Redmond & McLysaght (doi: 10.1038/s41467-021-22074-7) comments favorably on Philippe et al. (2019)'s methods.
My executive summary would be that (1) there are no citations openly critical of Philippe et al. (2019)'s methods or findings; (2) no persuasive direct support for either the Xenambulacraria hypothesis or a monophyletic Deuterostomia has been adduced in the last two years; (3) the approach adopted by Bezares-Calderón et al. and Marinković et al., in which a four-way split at the bilaterian root node with four monophyletic sister clades (Xenacoelomorpha, Ambulacraria, Chordata, and Protostomia) is depicted without taking a position on their interrelationships, is best aligned with Wikipedia's intention of presenting a conservative consensus position.
-- April Arcus ( talk) 21:06, 18 April 2021 (UTC) reply
Thanks for that review. Individual articles can comment on the uncertainty and debate, but I'd be fine with this Template going with 4 sister clades (Xenacoelomorpha, Ambulacraria, Chordata, and Protostomia). Bondegezou ( talk) 09:21, 19 April 2021 (UTC) reply

Bryozoa "sensu lato" - what should we make of it?

The template presents a view of lophophorate phylogeny including Ectoprocta ( Bryozoa) and Entoprocta in a larger clade called "Bryozoa sensu lato". However, the link for this clade redirects towards the article for Bryozoa as usually defined, "sensu stricto" (that is, not including the separate phylum Entoprocta, with the article contrasting the two phyla several times), and thus causing confusion as to the content of the phylum. Especially as the name Bryozoa is only used in the template for this larger grouping rather than for the usual phylum, here called by its alternative name Ectoprocta.

Where should the link point? Should it be moved towards the phylogeny section of Bryozoa, indicating the possible relation with Entoprocta in a larger clade of the same name? Should a separate article be created for the wider proposed grouping? Chaotic Enby ( talk) 09:10, 30 January 2023 (UTC) reply

Deuterostomia

Shouldn't Chordata be under Deuterostomia together with Ambulacraria? That is the structure shown in those three articles. Donald Albury 17:36, 10 May 2023 (UTC) reply

Deuterostomia is currently considered controversial. If anything the other articles should be updated. See the conversation on Xenambulacraria above. April Arcus ( talk) 05:48, 5 April 2024 (UTC) reply

References

  1. ^ Edgecombe, Gregory D.; Giribet, Gonzalo; Dunn, Casey W.; Hejnol, Andreas; Kristensen, Reinhardt M.; Neves, Ricardo C.; Rouse, Greg W.; Worsaae, Katrine; Sørensen, Martin V. (2011). "Higher-level metazoan relationships: recent progress and remaining questions". Organisms, Diversirt and evolution. doi: 10.1007/s13127-011-0044-4.
  2. ^ Dohrmann, Martin; Wörheide, Gert (2013). "Novel Scenarios of Early Animal Evolution—Is It Time to Rewrite Textbooks?". Integrative and Comparative Biology. doi: 10.1093/icb/ict008.
  3. ^ Shua, Degan; Isozakib, Yukio; Zhanga, Xingliang; Hana, Jan; Maruyamac, Shigenori (2014). "Birth and early evolution of metazoans". Gondwana Research. doi: 10.1016/j.gr.2013.09.001.
  4. ^ Edgecombe, Gregory D.; Legg, David A. (2014). "Origins and early evolution of arthropods". Palaeontology. doi: 10.1111/pala.12105.
  5. ^ Rota-Stabelli, Omar; Campbell, Lahcen; Brinkmann, Henner; Edgecombe, Gregory D.; Longhorn, Stuart J.; Peterson, Kevin J.; Pisani, Davide; Philippe, Hervé; Telford, Maximilian J. (2011). "A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata". Proceedings of the Royal Society B. doi: 10.1098/rspb.2010.0590.
  6. ^ Rouse, Greg W.; Wilson, Nerida G.; Carvajal, Jose I.; Vrijenhoek, Robert C. (2016-02-03). "New deep-sea species of Xenoturbella and the position of Xenacoelomorpha". Nature (530): 94–97. doi: 10.1038/nature16545. Retrieved 2016-02-03.
  7. ^ Whelan, Nathan V.; Kocot, Kevin M.; Moroz, Tatiana P.; Mukherjee, Krishanu; Williams, Peter; Paulay, Gustav; Moroz, Leonid L.; Halanych, Kenneth M. (2017-10-09). "Ctenophore relationships and their placement as the sister group to all other animals". Nature Ecology & Evolution. doi: 10.1038/s41559-017-0331-3. ISSN  2397-334X.
  8. ^ Shen, Xing-Xing; Hittinger, Chris Todd; Rokas, Antonis (2017-04-10). "Contentious relationships in phylogenomic studies can be driven by a handful of genes". Nature Ecology & Evolution. 1 (5). doi: 10.1038/s41559-017-0126. ISSN  2397-334X.
  9. ^ Ryan, Joseph F.; Pang, Kevin; Schnitzler, Christine E.; Nguyen, Anh-Dao; Moreland, R. Travis; Simmons, David K.; Koch, Bernard J.; Francis, Warren R.; Havlak, Paul (13 December 2013). "The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution". Science. 342 (6164): 1242592. doi: 10.1126/science.1242592. ISSN  0036-8075. PMC  3920664. PMID  24337300.
  10. ^ Simion, Paul; Philippe, Hervé; Baurain, Denis; Jager, Muriel; Richter, Daniel J.; Franco, Arnaud Di; Roure, Béatrice; Satoh, Nori; Quéinnec, Éric (3 April 2017). "A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals". Current Biology. 27 (7): 958–967. doi: 10.1016/j.cub.2017.02.031. ISSN  0960-9822.
  11. ^ Philippe, Hervé; Poustka, Albert J.; Chiodin, Marta; Hoff, Katharina J.; Dessimoz, Christophe; Tomiczek, Bartlomiej; Schiffer, Philipp H.; Müller, Steven; Domman, Daryl; Horn, Matthias; Kuhl, Heiner; Timmermann, Bernd; Satoh, Noriyuki; Hikosaka-Katayama, Tomoe; Nakano, Hiroaki; Rowe, Matthew L.; Elphick, Maurice R.; Thomas-Chollier, Morgane; Hankeln, Thomas; Mertes, Florian; Wallberg, Andreas; Rast, Jonathan P.; Copley, Richard R.; Martinez, Pedro; Telford, Maximilian J. (2019). "Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria". Current Biology. 29 (11): 1818–1826.e6. doi: 10.1016/j.cub.2019.04.009. ISSN  0960-9822.
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