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  • Myomorpha incorrectly synonymised with Sciurognathion GitHub

    If you type in "myomorpha" to the search box, it thinks you are looking for squirrels (Sciurognathi), not the same at all

    • yeah. This is not optimal, but when NCBI's classification does not recognize some subgroups (Myomorpha and Sciuromorpha in this case) of a higher taxon (sciurognathi), it lists the subgroups as synonyms. See https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=33553 which is why OTT treats these as synonyms). I'm not sure that we have an easy fix for this.
      Ideally the name Myomorpha would be stored with a taxon concept definition, so that searching for it could return a meaningful message. It would probably still dump the user to the same part of the tree (the parent taxon), but it would be less confusing. But we are pretty far from having taxon concepts under our names/IDs in OTT.

    • Hmm, this is worse in this instance, because (and I quote for wikipedia) "most researchers do not consider Sciurognathi as an equally valid group. In particular, gundis are thought to be more closely related to the hystricognathous rodents than to other sciurognaths. In spite of this, most texts continue to use these two suborders due primarily to a lack of a viable alternative. Alternatively, some texts group rodents into three suborders on the basis of the shape of the infraorbital canal. According to this taxonomy the rodents are divided into the suborders Sciuromorpha, Hystricomorpha, and Myomorpha."

      So it may be that NCBI is not using a monophyletic taxon, which will (presumably) vanish if a correct phylogeny is incorporated.

    • @mtholder in fact, myomorphs does exist on the OpenTree, it is simply not named. It is at https://tree.opentreeoflife.org/opentree/opentree8.0@mrcaott42ott55949/Dipodidae--Muroidea. What happens in this case?

    • If we had this taxon, it would get the name. The trouble is that the only thing that we know about the name is that NCBI lists it as a synonym. We could fix this with a "patch" to the reference taxonomy. @jar398 would probably need to help in authoring what that would look like. Then the names would not be synonymized in future versions of the tree, and this node would get its label.

    • Well, for this particular case, Myomorpha is named in e.g. Fabre (2012) which is referenced in OpenTree as a study that resolves this node. So can it simply to be added as a clade name to https://tree.opentreeoflife.org/curator/study/view/pg_2688 or one of those other trees? Or do you not take clade names from phylogenetic studies?

    • No. Currently the taxonomy creation is quite separate from the phylogenetic study curation. But thanks for pointing out that study. We have one ad hoc tree provided by taxonomic experts as a taxonomic input. That tree that is used a a source of names and structure. So having a study is helpful.

    • NCBI distinguishes pro parte synonyms from others, so there is the possibility of being smarter. This happens to be the same question as #341, and I've created https://github.com/OpenTreeOfLife/reference-taxonomy/issues/316 to track it.

  • Is Life only 3.5 billion years old, or older?on GitHub

    The latest research shows life may be 3.8, or even 4.1 billion years old, not 3.5 as shown in the Circle of Life. See here: https://en.wikipedia.org/wiki/Evolutionary_history_of_life This matters greatly since the earlier life began on Earth, the easier it presumably is to establish. This has profound effects on our expectations for life on other worlds too, as we ramp up our collection of Earth-like planets in the galaxy and beyond. Please consider updating the origin of life date in your model.

  • Inconsistencies in the Educational Tree of Life Timelineon GitHub

    Hello, congratulations for the website. In the Educational Tree of Life Timeline, however, there some mistakes. The audio of the entry "Domain Archea is Born" distinctly says: "Archea branched off the domain Archea about one point seven billion years ago". However, it should be "two point seven billion years ago". Indeed, in a much subsequent segment, the entry "Domain Eukarya is born" says "the first discovered eukaryotic fossil was dated at about 1.8 billion years ago", which is clearly incompatible with Archea branching off later (!) Also, in the segment before, the entry "Genetic Drift" is really a copy of "Domain Eukarya is born".

    | Metadata | Do not edit below this line | | :-- | :-- | | Author | Luca | | Upvotes | 0 | | URL | https://tree.opentreeoflife.org/contact">/contact | | Target node label | | | Synthetic tree id | | | Synthetic tree node id | | | Source tree id(s) | | | Open Tree Taxonomy id | | | Supporting reference | None |

    • Newick format from Mammalia not correct?on GitHub

      Hello. I've been trying to download the subtree for the Mammalia branch to prune using the R package ape. However, the downloaded .tre file seems to be off in some way - when I try to use other tree visualizers I get error messages about not having a valid Newick format. Is there a way to get a link to a working newick file for this branch? I'm happy to send over the file I have if that helps.

      | Metadata | Do not edit below this line | | :-- | :-- | | Author | Amy | | Upvotes | 0 | | URL | https://tree.opentreeoflife.org/contact">/contact | | Target node label | | | Synthetic tree id | | | Synthetic tree node id | | | Source tree id(s) | | | Open Tree Taxonomy id | | | Supporting reference | None |

      • Hi Amy, I suspect this has something to do with ape, rather than the newick string. Assuming that the file came from our https://tree.opentreeoflife.org/opentree/argus/ottol@244265/Mammalia">Mammalia page, I can open this with Dendroscope, with the DendroPy python package, and with the R phytools package, but ape does give me an error. I am not an ape expert, but I believe that we have found the tree importer from ape to problematic in the past - refusing to open files that are indeed valid newick. The cause might be monotypic nodes - nodes that correspond to taxa that only have one descendant.

        So, my first suggestion might be to try phytools instead of ape. Let us know how this goes.

      • Noted - thanks for checking this out - I'll look at in phytools later this week --> do you happen to know if you write a newick from Dendroscope or phytools if it will then open in ape (just curious) since phylogeny.fr conversion was having trouble with it as well - super odd!

        | Metadata | Do not edit below this line | | :-- | :-- | | Author | Amy | | Upvotes | 0 |

      • So I was able to load the tree into phytools and then write the tree as a nexus to read into ape - phytools drop.tip command was giving me problems and I had a working code in ape. I'm curious if you've ever encountered using the drop.tip command and having it fail to drop any? I'm using testtree <- drop.tip(OTOLTree, OTOLTree$tip.label[-match(testtips, OTOLTree$tip.label)]) to retain only the taxa in the object testtips defined as: testtips <- c("Ateles_geoffroyi_azuerensis_ott5857438", "Bos_taurus_ott490099", "Camelus_dromedarius_ott510752", "Cavia_porcellus_ott744000") which is the truncated example I used. But instead of returning a tree with 4 tips as it has done with other trees, the same tree with thousands of tips remains. Thoughts? I do think there is something funky in the nexus that was written out to begin with... the taxa towards the top are quite funky before getting to the expected taxa designations in the very last line pasted below:

        NEXUS

        [R-package PHYTOOLS, Tue Aug 16 07:50:02 2016]

        BEGIN TAXA; DIMENSIONS NTAX = 8698; TAXLABELS 'Artibeus sp. BOLD 'Artibeus sp. BOLD 'Artibeus sp. BOLD 'Canis sp. Belgium/36 'Canis sp. Russia/33 'Choeroniscus sp. BOLD 'Erinaceus sp. ''Ito 'Erinaceus sp. ''Odawara 'Hipposideros bicolor ''131 KHz''_ott619171' 'Hipposideros bicolor ''142 KHz''_ott619159' 'Hipposideros cf. pomona BOLD 'Marmota sp. BOLD 'Microcebus sp. d''Ambre_ott4117711' 'Microtus cf. arvalis BOLD 'Microtus sp. BOLD 'Molossus sp. BOLD 'Murina cf. cyclotis BOLD 'Mustela sp. BOLD 'Myotis cf. ater BOLD 'Myotis cf. muricola BOLD 'Myotis cf. muricola BOLD 'Neacomys sp. BOLD 'Nectomys sp. BOLD 'Nectomys sp. BOLD 'Neusticomys sp. BOLD 'Niviventer cf. confucianus BOLD 'Oecomys cf. rex BOLD 'Oecomys sp. BOLD 'Oecomys sp. BOLD 'Oryzomys sp. BOLD 'Oryzomys sp. BOLD 'Oryzomys sp. BOLD 'Oryzomys sp. BOLD 'Oryzomys sp. BOLD 'Otomys sp. ABTC 'Peromyscus sp. BOLD 'Peromyscus sp. BOLD 'Peropteryx sp. BOLD 'Pipistrellus cf. tenuis BOLD 'Proechimys sp. BOLD 'Proechimys sp. BOLD 'Rhinolophus cf. chaseni BOLD 'Rhinolophus cf. pusillus BOLD 'Rhinolophus sp. BOLD 'Sorex sp. BOLD 'Tupaia sp. BOLD 'undetermined Sciuridae ''chipmunks''_ott357544' Kanagawa''_ott348328' Shizuoka''_ott348324' 000_ott5338951' 500_ott5338950' Abditomys_latidens_ott3610454

        | Metadata | Do not edit below this line | | :-- | :-- | | Author | Amy | | Upvotes | 0 |

    • Oecanthinae additionson GitHub

      Hello. There are three species of Oecanthus that should be added: Oecanthus bakeri, Oecanthus belti and Oecanthus symesi. There are two species of Neoxabea that should be updated: Neoxabea cerrojesusensis is currently showing on the tree as Neoxabea sp. 1 LC-2014; Neoxabea ottei is currently showing as Neoxabea sp. 2 LC-2014.

      | Metadata | Do not edit below this line | | :-- | :-- | | Author | Nancy | | Upvotes | 0 | | URL | /contact | | Target node label | | | Synthetic tree id | | | Synthetic tree node id | | | Source tree id(s) | | | Open Tree Taxonomy id | | | Supporting reference | https://www.researchgate.net/publication/276420127_Two_New_Species_of_Neoxabea__Three_New_Species_of_Oecanthus__and_Documentation_of_Two_Other_Species_in_Nicaragua_(Orthoptera_Gryllidae_Oecanthinae) |

      • High Resolution Imageon GitHub

        Is it possible to get a high resolution of the image that appeared in Science Magazine (http://www.sciencemag.org/news/2015/09/first-comprehensive-tree-life-shows-how-related-you-are-millions-species)? It would be great to print and frame it. Also I would imagine the great breadth of variation that could be used in different representations of taxa. Any thoughts in this?

        Thanks, Nick

        | Metadata | Do not edit below this line | | :-- | :-- | | Author | Nick Payne | | Upvotes | 0 | | URL | https://tree.opentreeoflife.org/contact">/contact | | Target node label | | | Synthetic tree id | | | Synthetic tree node id | | | Source tree id(s) | | | Open Tree Taxonomy id | | | Supporting reference | None |

        • Hide Propertieson GitHub

          If I hide the properties they should stay hidden until I click show properties. I clicked the "Hide Properties" button. Then I clicked a node, and properties reappeared. Why? If I want to hide the properties, I want them hidden. I most certainly do not want to have to hide them every time I move through the tree. At

          | Metadata | Do not edit below this line | | :-- | :-- | | Author | Nicholas Beeson | | Upvotes | 0 | | URL | /contact | | Target node label | | | Synthetic tree id | | | Synthetic tree node id | | | Source tree id(s) | | | Open Tree Taxonomy id | | | Intended scope | |

          • Good point! The current behavior was chosen to ensure that a new user (esp. in a narrow view like a tablet) would always see meaningful data, beyond just the tree structure. This has come at the expense of other users who want to move through the tree without the clutter. I'm sure we can make this persist, once the user has made a choice.

            I've added this as an enhancement request in our bug tracking system, in case you want to track its progress: https://github.com/OpenTreeOfLife/opentree/issues/778

            | Metadata | Do not edit below this line | | :-- | :-- | | Author | https://github.com/jimallman">Jim Allman | | Upvotes | 0 |

          • Thanks Jim. This is a joy and wonder to me. Your group has done a truly marvelous thing. It is an intellectual triumph.

            | Metadata | Do not edit below this line | | :-- | :-- | | Author | Nicholas Beeson | | Upvotes | 0 |

          • This is fantastic - I've learnt a lot in just a few minutes browsing.

            | Metadata | Do not edit below this line | | :-- | :-- | | Author | Alan Fish | | Upvotes | 0 |

          • Would be nice if "i" also displayed a brief definition or description of each node

            | Metadata | Do not edit below this line | | :-- | :-- | | Author | Alan Fish | | Upvotes | 0 |

          • That's a good idea, Alan. Especially for people who want to keep the properties pan hidden, having a small popup when you hover over a node with some basic info would be helpful.

          • Awesome helpful to learn many things how can i join to this.

            | Metadata | Do not edit below this line | | :-- | :-- | | Author | Abhilash | | Upvotes | 0 |

          • Please make a way to download your entire database&site so I can make a home wiki if your page gets taken down. It should show like a MediaWiki or similar.

            | Metadata | Do not edit below this line | | :-- | :-- | | Author | AmbiguousUser | | Upvotes | 0 |

          • Related to that: https://github.com/OpenTreeOfLife/opentree/issues/403

            All the steps for setting up your own copy of the site are documented, and the data is all public. The problem is that the documentation is spread over several documents, and the procedure is bespoke (to put it mildly).