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- Download in Newick format dysfunctional on GitHub
Starting from a few weeks ago, I cannot download a subtree anymore in Newick format. There seems to have been also some change with the download URL recently. I need to download regularly the vertebrate subtree (https://tree.opentreeoflife.org/opentree/default/download_subtree/node-id/ott801601/Vertebrata) and luckily I have an old version of the tree, which works for my script, but it will become outdated with time :-(
hmm that is odd that it changed a few weeks ago. we did change some of the back-end software on Monday. I'll try to figure out what is going on. There is a limit on the number of tips that can be downloaded from the web services. But if you have the entire vertebrate tree via a previous download, that seems like a poor explanation...
and thanks for the bug report!
Still gives my nothing when I try to download the vertebrate subtree in newick format :-( Maybe you have changed the limits? I manage with smaller subtrees, but e.g. also the amniota phylum fails. The downlaoded filecontains only the string "NEWICKNOTFOUND"
Confirmed, this tree won't load, while I'm able to fetch the https://tree.opentreeoflife.org/opentree/opentree10.4@ott913935/Primates">primate tree as Newick successfully. Could be a problem with larger clades, or perhaps a "poison pill" (funky Unicode taxon name)?
It's working again, thanks. If I reference this tree in a scientific publication, how should I cite it?
Great. General guidelines for citation of parts of the project are at https://tree.opentreeoflife.org/about/open-tree-of-life Studies that inform parts of the primate tree can be found in the "Supporting trees" panel for the relevant view of the tree at https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott913935/Primates if you want to cite the original publications.
- Incorrect synonymy (Orchamoplatus)on GitHub
The taxonomic name reconciliation service considers Orchamoplatus to be a synonym of Orchamus. Since Orchamoplatus is a genus of Hemiptera, and Orchamus is Orthoptera, this is likely incorrect. A google search did not turn up any evidence that there was even an Orchamoplatus genus in the orthoptera, although Hemiptera:Orchamoplatus was originally called Hemiptera:Orchamus, so possibly that is the source of confusion?
Other reference: https://core.ac.uk/download/pdf/5103593.pdf
- Trox in Insecta:Psocoptera:Trogiidae, should be in Insecta:Coleoptera:Trogidaeon GitHub
The members of the beetle family Trox are found in two places: Insecta:Psocoptera:Trogiidae and Insecta:Coleoptera:Trogidae.
As far as I can tell, there is not genus Trox in the Trogiidae, so all members of that genus are beetles and should be in Trogidae.
- Phylogeny of chelicerata.on GitHub
This study new phylogenic tree with 10p% bootstrap suplort
Great! Feel free to add the tree in the curator so it can be included in the synthetic tree https://tree.opentreeoflife.org/curator Contact me if you have any questions!
I cannot make a GitHub account. When I try, it says the password has been compromised to athird party breach.
Sounds like you are trying to use a password on a list of known hacked passwords. Try creating your account with a different password:
Thank you. I will try to add the tree now.
I added the study but I don't know how to add the tree. I mentioned this in the notes section but I searched for it later and couldn't find it. Hopefully someone else finds it and knows how to add the trees from the study.
I am sorry I couldn't add it. The good news is that people who know what they are doing can add the tree, I put the DOI url on the study somewhere. I can add it here, https://doi.org/10.1093/molbev/msu235
The title of the study is Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal
I think I tagged it as Arachnida
- Study showing possible eukaryotes treeon GitHub
I am searching for molecular studies to attempt to resolve eukaryotes phylogeny. The more phylogenies that are incorporated, the more data we can incorporate into the synthetic tree, hopefully resulting in more accuracy.
- Study shows sponges diverged first. LBA is implicated to be why Ctenophores showed up as basalon GitHub
- Mollusca Infoon GitHub
This link brings you to a page detailing the various hypotheses as to how the various mollusca Claude’s are related. Please give it a read. http://comenius.susqu.edu/biol/202/animals/protostomes/spiralia/trochozoa/mollusca/mollusca-description.html
- Vascular Plant phylogenyon GitHub
Here is a phylogenies tree of vascular plants. It’s good to have more data. I am not correcting anything, just showing a phylogeny that, if not already incorporated, could be incorporated. https://www.researchgate.net/figure/Cladogram-of-extant-lineages-of-vascular-plants-based-on-Pryer-et-al-2001-2004fig1266864861
- New study I found about systematic errors in molecular phylogenies and how people minimize those errorson GitHub
- Here is a study comparing similarities and differences in possible Molluca phylogenyon GitHub
I was curious about Mollusca phylogeny and found a study i will link to which gathered various morphological and molecular trees to determine the many differences that exist in phylogenic trees of Mollusca
- Monoplacophora is polyphyleticon GitHub
perhaps it would be a good idea to make the tree monophyletic
Hi Danielle, Thank you for your comments! Have you seen how to upload trees into the curator? More information is here: https://github.com/OpenTreeOfLife/opentree/wiki/Submitting-phylogenies-to-Open-Tree-of-Life It is the best way to update the relationships in the tree. Contact me if you want any information or help on how to do that! email@example.com
I added a chelicerata study to the database but I don't know how to add trees, and I tried searching for the study and had trouble finding it
I added a chelicerata study to the database but I don't know how to add trees, and I tried searching for the study and had trouble finding it
- Servers down?on GitHub
Hello, I am currently unable to access your webpage or download anything through R. Just wondering if the server is down or any other issue? Have double checked this with multiple devices. Thanks, Mike
Thanks for reporting this. The server is being very slow for me too. I'll try to diagnose the issue. I can
sshinto the front-end and the back-end. But something is definitely not working as intended...
seems to be more responsive now. I did try to restart apache, but it is acting more like a general network latency problem with wherever the server sits (as opposed to something that I fixed).
- 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
I think you should take a look at this
- 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
- 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/Evolutionaryhistoryof_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 |