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- Eukaryota and Archea more closely related to each other than to bacteriaon GitHub
I’ve been reading about how Archaea and Eukaryota might be closely related to each other more than to bacteria
- Dotted lines?on GitHub
What do the dotted lines mean? What do the solid lines mean?
If you click on the grey oval with the word "Legend" above the tree, the page should show you a key to the visual elements used on the page. Branches that are placed entirely based on the taxonomy are dashed. The solid edges have some support from at least one published phylogenetic tree.
- Insectivora Wastebasket Taxonon GitHub
I remember reading in different places that Insectivora was a wastebasket taxon and the animals in that section were moved to different categories. Unfortunately I don't remember where I read that from. Is it possible to update the synthetic tree so Insectivora is removed and the families relocated?
Agreed. I think this has been discussed before. (Previously reported as #375.) But we can’t include any information without some kind of reference. Any chance you could find us a good modern taxonomic treatment in this area? NCBI claims that its Insectivora has Soricomorpha as a synonym (the name that CoL uses). It’s possible that NCBI has redefined the name to fit some improved hypothesis of monophyly. But it's also possible neither NCBI and CoL is up to date.
Understanding the situation is more work than I can do now, so any help would be welcome.
note that we have the Afrotherian mammals with common names including "shrews" and "moles" in Afrotheria (see https://tree.opentreeoflife.org/taxonomy/browse?id=746703) not in Insectivora (see https://tree.opentreeoflife.org/taxonomy/browse?id=796664 ). So the most egregious cases of Insectivora being a wastebasket are correctly dealt with. There may be some issues remaining, but I'm not aware of them.
There is the question of whether we should call the group "Insectivora" or "Eulipotyphla." I personally wouldn't mind using Eulipotyphla, because it conveys the fact that we aren't using the "old" definition of Insectivora. But NCBI uses Insectivora, so that is was is used in OTT. I don't really mind using "Insectivora".
- Species Concept?on GitHub
Which species concept is used in the synthetic tree for which groups?
Hi, The Open Tree project does not do any alpha taxonomy, so I think that it is hard to think of it as having any specific species concept implemented. We use a taxonomy that is assembled programmatically from other taxonomy inputs (and corrections from users). If you'd like more details on that process see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515096/
As a result, the species concepts used by many authors get incorporated (via the input taxonomies), and I am confident that their is a lot of internal inconsistency about what species concept is used as you browse across the open tree.
Is there a way to add something in the properties area that tells which species concept is used in each study in the Details section?
Not for any feasible level of programming effort.
I doubt there is a simple enumeration of species concepts. The intended design is that if someone cares that much about the details of a species definition, they would trace references, first to the source taxonomy and then to the sources it uses. Unfortunately few of the source taxonomies will tell you which 'taxon concept' (i.e. published description) applies to their use of a name, because a name (even when the authority is known) often gets reused for many difference 'taxon concepts', each perhaps with its own 'species concept', without any indication of the fact - an endemic horror in taxonomy. And then there is the issue that phylogenetic tree curation is not so carefully done that we're always sure a given sample belongs is assigned correctly to an OTT taxon (with its particular 'taxon concept'), even if the names match exactly.
What is your use case, out of curiosity?
- Annelidaon GitHub
I notice on the.synthetic tree annelids are not on there and when I.look for them on the database it thinks they are extinct
I tried to link to opentree.org because a website was required and it showed an error message
Here is the link I was trying to get to
Hi Danielle, thanks for reporting the issue. Annelids are not flagged as extinct in our taxonomy. The taxonomy page for them is https://tree.opentreeoflife.org/taxonomy/browse?name=Annelida (I do realize that the "e.g. extinct" text at the top of the page may make it look like they are flagged that way, but that is intended as explanatory note to show what the flags look like.
I think you can find most of them from navigating around: https://tree.opentreeoflife.org/opentree/opentree9.1@mrcaott24ott102965/Myzostomida--Clitellata
I think that they don't show up in the tree because the current tree does not put Myzostomida with the rest of the Annelids. Taxonomies vary on what goes inside Annelida. If you are curious about the details, there are a couple of Open Tree GitHub issues where this is discussed: https://github.com/OpenTreeOfLife/germinator/pull/112 and https://github.com/OpenTreeOfLife/reference-taxonomy/issues/238
The longer term solution is for the browser to show you the relevant part of the tree when a taxon is not monophyletic. This has been a long standing issue (see https://github.com/OpenTreeOfLife/germinator/issues/85 ). The good news is that we are pretty close to having a new tool for serving up the synthetic tree that would fix this. Unfortunately, it still needs a bit more testing before being deployed.
Thank you. I didn't know Annelida wasn't monophyletic. Thank you for teaching me. I think a Tree of Life should consist of monophyletic lineages and try and stay away from paraphyletic and polyphyletic lineages. I am not a professional taxonomist I just like to research this kind of thing. It's interesting to me.
Myzostomida is a genetic outlier and gets put in different places by different studies. I think Annelida could only be seen as nonmonophyletic if you believed both that Myzostomida is outside of it taxonomically (as NCBI says) and that Myzostomida is deep enough inside of it phylogenetically. Both of these claims are pretty weak, so don't call it quits yet.
- Is this project still active?on GitHub
I'm interested in this area and I am trying to determine if this project is still active. The latest links to the Blog area yield results which don't have a date and the last dated entry is for spring of 2016. If this effort is still being conducted, how do I find information about the project and what is currently being done?
Hi Philip, yes the project is still active (though not as many people are working on it as last year). We are seeking more funding and hope to continue to support it for years to come.
The software developers use an open chat at https://gitter.im/OpenTreeOfLife/public to discuss issues. So that is probably the best place for a short query, but using the email list is also fine. The lists are described at: https://tree.opentreeoflife.org/contact
all the best, Mark
- Allow the search for known familiar animalson GitHub
Like chicken, dog, horse, etc.
- New synthesis for Thecostraca?on GitHub
I realized that I had left some trees unrooted in the tree collection for barnacles. I fixed this issue, and would really like to know if it improved the synthesis tree. As of now, the placement of some taxa is incorrect, e.g. Tetraclita and Tetraclitella should be close relatives, but Tetraclita has been removed from the synthesis. Any chance you can re-run the synthesis, at least for the Thecostraca? Sorry I didnt catch this earlier, I only saw it when I started using the tree in depth.
Thank you, Christine
- 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.
@mtholder this seems low down on the radar, but has been picked up again by one of our users. Is there likely to be any resolution for this in the foreseeable future. Or could I author a patch in some way?
- 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.
Hi, Thanks for the comment. I agree that the age is an important thing to get right. I think you are referring to the tree that appeared https://www.scientificamerican.com/article/all-2-3-million-species-are-mapped-into-a-single-circle-of-life/ While that tree is based on work of this project, the age isn't. We are hoping to have age estimates for the nodes of the tree at some point, but currently our tree does not have age estimates.
- 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:
[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?
| 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).