User talk:Faendalimas/turtle phylogeny

Introduction

Ok for purposes of discussing what to do with this phylogeny rather than just delete it I have moved it to this temporary page. Please feel free to add comments wherever you see fit. Please try to keep some order to it so we can all follow. Section titles are just for clarity. Cheers Scott Thomson (Faendalimas) ^talk 15:56, 21 January 2018 (UTC)[reply]

General

I think this phylogeny is too big, takes up too much space and is too detailed for a page on turtles in general.

In say above I have no issue with a phylogeny being presented I just think we should cut it down.

One suggestion that came up was to only take it to family. I can agree with this as it is then also a pointer to the articles on the various turtle families, and more detailed partial phylogenies can be presented on those pages. This would break up the phylogeny reduce its size and be meaningful in terms of the topic of this page.

this phylogeny is a hybrid of PhylloCode and ICZN Code nomenclature. Without getting into arguments of which one is better. I do not think hybrid nomenclatures work.

Phylogeny of living turtles showing families

I suggest the following phylogeny based on Crawford et al. (2015)Cite error: The <ref> tag has too many names (see the help page)., with the additional family names as listed in the 2017 Turtle Taxonomy Working Group update.^[1] This uses the names in the primary source (Fig 2 in Crawford et al, 2015) and the secondary source (phylocode classification (p23) in TTWG, 2017). Jts1882 | talk 16:38, 21 January 2018 (UTC)[reply]

References

^ "Turtles of the World: Annotated Checklist and Atlas of Taxonomy, Synonymy, Distribution, and Conservation Status (8th Ed.). In: Rhodin, A.G.J., Iverson, J.B., van Dijk, P.P., Saumure, R.A., Buhlmann, K.A., Pritchard, P.C.H., and Mittermeier, R.A. (Eds.). Conservation Biology of Freshwater Turtles and Tortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group". Chelonian Research Monographs. 7: 1–292. 2017. doi:10.3854/crm.7.checklist.atlas.v8.2017. {{cite journal}}: Check date values in: |year= (help); Unknown parameter |authors= ignored (help)CS1 maint: year (link)

comment The general topology of the tree is fine, it is only molecular based which is problematic as molecular trees generally only sample 1-2% of known species, total evidence trees are better. However, that said. Since this is dealing with living species and for this group they use the linnean system, and the point that phyllocode has no nomenclatural standing we should be using the valid nomenclature. Hence Trionychia should be called Trionychoidea. With regard to the name Cheloides it is only used in Phyllocode, and has been in several papers discussing the Pan-Pleurodira when discussing stem pleurodires. Its not relevant here and has never been favored by many taxonomists. The labels that are currently red links should go, there is no need to label every node of a tree, this is a phyllocode issue, proponents seem to think you need to label all nodes, its overkill, plus they have low support and these families bounce around depending on the analysis. That is they have dubious support. I would leave them out. Stick to linnean names as they are are the only ones accepted under the code. TTWG 2017 acknowledged the existence of the phyllocode phylogeny but recommended against it. IUCN, CITES and all government agencies around the world use the linnean names only. Cheers Scott Thomson (Faendalimas) ^talk 17:08, 21 January 2018 (UTC)[reply]

I generally favour using the names used in the source for the cladogram (in this case Crawford et al, 2015), as this avoids taking a POV. However, the TTWG 2017 reference can be given for the names and the redlinks are not useful, so I've removed the redlinked names from the cladogram. What about Pelomedusoides and Americhelydia? Are they compliant? They do have wikipedia articles so I think they are useful and should stay.

What do you think about addin back some thumbnail images? I've have mix feelings about the use of images in cladograms as they often just make the cladogram larger, but in this case the shapes of the shell could be useful information. Jts1882 | talk 16:19, 22 January 2018 (UTC)[reply]

comment Further to this is that the changes outlined above would bring it in line with Wikispecies. I do think WM projects should be in agreement with each other where possible. Cheers Scott Thomson (Faendalimas) ^talk 17:16, 21 January 2018 (UTC)[reply]

Accuracy of this phylogeny

Chelidae

Now has 4 subfamilies, Zhang et al. 2017^[1], named Pseudemydurinae as the 4th subfamily containing the genus Pseudemydura.
Chelodina is sister to rest of Chelodininae
Flaviemys is sister to Myuchelys with Rheodytes and Elusor outside this, Elseya is sister to Emydura, which in turn is sister to rest of short necks. Spinks et al 2015.^[2]

References

^ Zhang, X., Unmack, P. J., Kuchling, G., Wang, Y., Georges, A. 2017. Resolution of the enigmatic phylogenetic relationship of the critically endangered Western Swamp Tortoise Pseudemydura umbrina (Pleurodira: Chelidae) using a complete mitochondrial genome. Molecular Phylogenetics and Evolution. Volume 115, October 2017, Pages 58-61.
^ Spinks, P.Q., Georges, A., and Shaffer, H.B. 2015. Phylogenetic uncertainty and taxonomic re-revisions: an example from the Australian Short-necked Turtles (Testudines: Chelidae). Copeia 103(3):536–540.

Copied here for purpose of commenting

Classification of turtles

Order Testudinata Klein 1760 accepted name is Testudines Batsch 1788, discussed in TTWG 2017 (annotations: 07:1, 10:4, 12:6, 17:1)

Genus †Pappochelys Schoch & Sues 2015
Family †Proganochelyidae Baur 1887
Family †Australochelidae Gaffney & Kitching 1994 sensu Lee 1997
Family †Proterochersidae Nopcsa 1928
Clade †Mesochelydia
- Family †Indochelyidae Datta, Manna, Ghosh & Das 2000
- Family †Heckerochelyidae Sukhanov 2006
Clade †Perichelydia
- Family †Chelycarapookidae Warren 1969
- Family †Sichuanchelyidae Tong et al. 2012
- Family †Solemydidae de Lapparent de Broin & Murelaga 1996
- Clade †Meiolaniformes
  - Family †Meiolaniidae Lydekker 1887
  - Family †Otwayemyidae Gaffney et al. 1998
  - Genus †Trapalcochelys Sterli, de la Fuente & Cerda 2013
  - Genus †Chubutemys Gaffney et al. 2007
  - Genus †Peligrochelys Sterli & de la Fuente 2012
  - Family †Kallokibotiidae Nopcsa 1923
- Clade Testudines Linnaeus, 1758 this name cannot be used for this clade, also it is not referable to Linn, it is Batsch' name 1788.
  - Suborder Pleurodira Cope 1864
    - Family †Apertotemporalidae Kühne 1937
    - Family †Platychelyidae Brän 1965 sensu Gaffney, Tong & Buffetaut 2006
    - Family †Dortokidae Lapparent de Broin & Murelaga 1996
    - Family †Notoemyidae Fernandez & Fuente 1994
    - Superfamily †Cheloides Gray 1825 sensu Gaffney, Tong & Buffetaut 2006 this name should be dropped it has little favor, even PhylloCode proponents now call it Pan-Chelidae.
      - Family Chelidae Gray 1825
    - Superfamily †Pelomedusoides Cope 1868 sensu Broin 1988
      - Family †Araripemydidae Price 1973
      - Family Pelomedusidae (African sideneck turtles)
      - Family †Euraxemydidae Gaffney, Tong & Buffetaut 2006
      - Family †Bothremydidae Baur 1891
      - Family Podocnemididae Cope 1868 (Madagascan big-headed and American sideneck river turtles)
  - Suborder Cryptodira Duméril & Bibron 1835
    - Infraorder Paracryptodira
      - Family †Pleurosternidae Cope 1868
      - Family †Compsemyidae
      - Family †Baenidae Cope 1882
    - Infraorder Eucryptodira Gaffney 1975a sensu Gaffney 1984
      - Family †Macrobaenidae Sukhanov 1964
      - Family †Eurysternidae Dollo 1886
      - Family †Plesiochelyidae Baur 1888
      - Family †Xinjiangchelyidae Nesov 1990
      - Clade Centrocryptodira
        Family †Osteopygidae Zangerl 1953
        
        Family †Sinemydidae Yeh 1963
      - Clade Polycryptodira Gaffney 1988
        Clade Pantrionychia
        Family †Adocidae
        
        Superfamily Trionychoidea Gray 1870
        Family Carettochelyidae (pignose turtles)
        
        Family Trionychidae (softshell turtles)
        
        Superfamily Testudinoidea Baur 1893
        Family †Haichemydidae Sukhanov & Narmandakh 2006
        
        Family †Lindholmemydidae Chkhikvadze 1970
        
        Family †Sinochelyidae Chkhikvadze 1970
        
        Family Emydidae (pond, box, and water turtles)
        
        Family Geoemydidae (Asian river turtles, Asian leaf turtles, Asian box turtles, and roofed turtles)
        
        Family Testudinidae (true tortoises)
        
        Family Geoemydidae
        
        Clade Americhelydia
        Family Chelydridae (snapping turtles)
        
        Superfamily Kinosternoidea
        Family Dermatemydidae (river turtles)
        
        Family Kinosternidae (mud turtles)
        
        Superfamily Chelonioidea (sea turtles)
        Sea turtle at Henry Doorly Zoo, Omaha NE
        
        Family †Toxochelyidae Baur 1895
        
        Family Cheloniidae (green sea turtles and relatives)
        
        Family †Thalassemydidae
        
        Family Dermochelyidae (leatherback sea turtles)
        
        Family †Protostegidae Cope, 1872

I think the non-linneaen names are better dropped. It only causes confusion as no valid nomenclatural references will use them. Scott Thomson (Faendalimas) ^talk 17:29, 21 January 2018 (UTC)[reply]

I was wondering about this listing. It seems to be a synthesis from Mikka's phylogeny and even then there seem to be errors (e.g. the indent for Meiolaniformes, which I changed). Any suggestions for a good source to use here for extinct forms. If've been looking at Anquetin (2012), but I assume there must be some more recent reviews.

What is the currrent thinking on "Casichelydia". If I understand correctly, this was coined by Gaffney (1975) for Pleurodira + Cryptodira so might be an option to replace the embedded "Testudine".

A few taxa are labelled extinct when they contain living families (e.g. Cheloides and Pelomedusoides). Jts1882 | talk 16:33, 22 January 2018 (UTC)[reply]

[TTWG-2017-1] "Turtles of the World: Annotated Checklist and Atlas of Taxonomy, Synonymy, Distribution, and Conservation Status (8th Ed.). In: Rhodin, A.G.J., Iverson, J.B., van Dijk, P.P., Saumure, R.A., Buhlmann, K.A., Pritchard, P.C.H., and Mittermeier, R.A. (Eds.). Conservation Biology of Freshwater Turtles and Tortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group". Chelonian Research Monographs. 7: 1–292. 2017. doi:10.3854/crm.7.checklist.atlas.v8.2017. {{cite journal}}: Check date values in: |year= (help); Unknown parameter |authors= ignored (help)CS1 maint: year (link)

[zhang2017-2] Zhang, X., Unmack, P. J., Kuchling, G., Wang, Y., Georges, A. 2017. Resolution of the enigmatic phylogenetic relationship of the critically endangered Western Swamp Tortoise Pseudemydura umbrina (Pleurodira: Chelidae) using a complete mitochondrial genome. Molecular Phylogenetics and Evolution. Volume 115, October 2017, Pages 58-61.

[spinks2015-3] Spinks, P.Q., Georges, A., and Shaffer, H.B. 2015. Phylogenetic uncertainty and taxonomic re-revisions: an example from the Australian Short-necked Turtles (Testudines: Chelidae). Copeia 103(3):536–540.

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