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  • I found a study on echinoderm phylogeny supporting Asterozoaon GitHub
    <p>I found a study supporting Asterozoa for Echonodermata Will add tree soon</p>
    • Download in Newick format dysfunctional on GitHub
      &lt;p&gt;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 (<a href="https://tree.opentreeoflife.org/opentree/default/download_subtree/node-id/ott801601/Vertebrata">https://tree.opentreeoflife.org/opentree/default/download_subtree/node-id/ott801601/Vertebrata</a>) and luckily I have an old version of the tree, which works for my script, but it will become outdated with time :-(&lt;/p&gt;
      • &lt;p&gt;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...&lt;/p&gt;
      • &lt;p&gt;and thanks for the bug report!&lt;/p&gt;
    • Incorrect synonymy (Orchamoplatus)on GitHub
      &lt;p&gt;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?&lt;/p&gt;
      • &lt;p&gt;Other reference: <a href="https://core.ac.uk/download/pdf/5103593.pdf">https://core.ac.uk/download/pdf/5103593.pdf</a>&lt;/p&gt;
    • Incorrect synonymy (Delia vs Dellia)on GitHub
      &lt;p&gt;The taxonomic name reconciliation service considers Diptera:Neohylemyia monticola a synonym of Orthoptera:Dellia monticola. It should probably be a synonym of Diptera: Delia monticola.&lt;/p&gt;
      • Trox in Insecta:Psocoptera:Trogiidae, should be in Insecta:Coleoptera:Trogidaeon GitHub
        &lt;p&gt;The members of the beetle family Trox are found in two places: Insecta:Psocoptera:Trogiidae and Insecta:Coleoptera:Trogidae.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt;
        • &lt;p&gt;Members of Omorgus and Afromorgus are also currently divided among Pscoptera:Trogiidae and Coleoptera:Trogidae; all should be in Coleoptera:Trogidae <a href="https://en.wikipedia.org/wiki/Trogiidae">https://en.wikipedia.org/wiki/Trogiidae</a> <a href="https://en.wikipedia.org/wiki/Trogidae">https://en.wikipedia.org/wiki/Trogidae</a>&lt;/p&gt;
      • Phylogeny of chelicerata.on GitHub
        &lt;p&gt;This study new phylogenic tree with 10p% bootstrap suplort&lt;/p&gt;
        • &lt;p&gt;Great! Feel free to add the tree in the curator so it can be included in the synthetic tree <a href="https://tree.opentreeoflife.org/curator">https://tree.opentreeoflife.org/curator</a> Contact me if you have any questions!&lt;/p&gt;
        • &lt;p&gt;I cannot make a GitHub account. When I try, it says the password has been compromised to athird party breach.&lt;/p&gt;
        • &lt;p&gt;Sounds like you are trying to use a password on a list of known hacked passwords. Try creating your account with a different password:&lt;/p&gt; &lt;p&gt;<a href="https://blog.github.com/changelog/2018-07-31-new-improvements-and-best-practices-for-account-security-and-recoverability/">https://blog.github.com/changelog/2018-07-31-new-improvements-and-best-practices-for-account-security-and-recoverability/</a> &lt;/p&gt;
        • &lt;p&gt;Thank you. I will try to add the tree now.&lt;/p&gt;
        • &lt;p&gt;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.&lt;/p&gt;
        • &lt;p&gt;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, <a href="https://doi.org/10.1093/molbev/msu235">https://doi.org/10.1093/molbev/msu235</a>&lt;/p&gt; &lt;p&gt;The title of the study is Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal &lt;/p&gt; &lt;p&gt;I think I tagged it as Arachnida&lt;/p&gt;
      • Ameobozoan relationships molecular analysison GitHub
        &lt;p&gt;I found a study that should shed more light on ameobozoan relationships.&lt;/p&gt;
        • Study showing possible eukaryotes treeon GitHub
          &lt;p&gt;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.&lt;/p&gt;
          • Study shows sponges diverged first. LBA is implicated to be why Ctenophores showed up as basalon GitHub
            &lt;p&gt;<a href="https://evodevojournal.biomedcentral.com/articles/10.1186/2041-9139-6-1">https://evodevojournal.biomedcentral.com/articles/10.1186/2041-9139-6-1</a>&lt;/p&gt;
            • Cepaea genus (Gastropoda, Helicidae) polyphylyon GitHub
              &lt;p&gt;I fond a study revealing that Cepaea is polyphyletic&lt;/p&gt;
              • Mollusca Infoon GitHub
                &lt;p&gt;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. <a href="http://comenius.susqu.edu/biol/202/animals/protostomes/spiralia/trochozoa/mollusca/mollusca-description.html">http://comenius.susqu.edu/biol/202/animals/protostomes/spiralia/trochozoa/mollusca/mollusca-description.html</a>&lt;/p&gt;
                • Vascular Plant phylogenyon GitHub
                  &lt;p&gt;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. <a href="https://www.researchgate.net/figure/Cladogram-of-extant-lineages-of-vascular-plants-based-on-Pryer-et-al-2001-2004_fig1_266864861">https://www.researchgate.net/figure/Cladogram-of-extant-lineages-of-vascular-plants-based-on-Pryer-et-al-2001-2004_fig1_266864861</a>&lt;/p&gt;
                  • Unikont/bikont now into questionon GitHub
                    &lt;p&gt;I found a study finding Escavates at the root and SARP and AMR being the next brannches&lt;/p&gt;
                    • New study I found about systematic errors in molecular phylogenies and how people minimize those errorson GitHub
                      &lt;p&gt;<a href="https://www.sciencedirect.com/science/article/pii/S0960982215009288">https://www.sciencedirect.com/science/article/pii/S0960982215009288</a>&lt;/p&gt;
                      • Here is a study comparing similarities and differences in possible Molluca phylogenyon GitHub
                        &lt;p&gt;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&lt;/p&gt; &lt;p&gt;<a href="https://academic.oup.com/sysbio/article/64/3/384/1630492">https://academic.oup.com/sysbio/article/64/3/384/1630492</a>&lt;/p&gt;
                        • Careful with understudied phyla: The case of chaetognathon GitHub
                          &lt;p&gt;I found a study about Chaetognath that places them as the sister group to the rest of Prodtostomes&lt;/p&gt;
                          • Monoplacophora is polyphyleticon GitHub
                            &lt;p&gt;perhaps it would be a good idea to make the tree monophyletic&lt;/p&gt;
                            • &lt;p&gt;Edit: paraphyletic&lt;/p&gt;
                            • &lt;p&gt;Hi Danielle, Thank you for your comments! Have you seen how to upload trees into the curator? More information is here: <a href="https://github.com/OpenTreeOfLife/opentree/wiki/Submitting-phylogenies-to-Open-Tree-of-Life">https://github.com/OpenTreeOfLife/opentree/wiki/Submitting-phylogenies-to-Open-Tree-of-Life</a> 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! ejmctavish@ucmerced.edu &lt;/p&gt;
                            • &lt;p&gt;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&lt;/p&gt;
                            • &lt;p&gt;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&lt;/p&gt;
                          • Pancrustacea studyon GitHub
                            &lt;p&gt;I've been searching for info about isopods and found this study&lt;/p&gt;
                            • Pelmatozoa no longer a cladeon GitHub
                              &lt;p&gt;Pelmatozoa is no longer a clade. The members do not share common ancestry&lt;/p&gt;
                              • Servers down?on GitHub
                                &lt;p&gt;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&lt;/p&gt;
                                • &lt;p&gt;Thanks for reporting this. The server is being <em>very</em> slow for me too. I'll try to diagnose the issue. I can <code>ssh</code> into the front-end and the back-end. But something is definitely not working as intended...&lt;/p&gt;
                                • &lt;p&gt;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).&lt;/p&gt;
                              • Eukaryota and Archea more closely related to each other than to bacteriaon GitHub
                                &lt;p&gt;I’ve been reading about how Archaea and Eukaryota might be closely related to each other more than to bacteria&lt;/p&gt;
                                • &lt;p&gt;and <a href="https://courses.lumenlearning.com/boundless-microbiology/chapter/archaeal-genetics/">https://courses.lumenlearning.com/boundless-microbiology/chapter/archaeal-genetics/</a>&lt;/p&gt;
                                • &lt;p&gt;I think you should take a look at this&lt;/p&gt;
                              • Dotted lines?on GitHub
                                &lt;p&gt;What do the dotted lines mean? What do the solid lines mean?&lt;/p&gt;
                                • &lt;p&gt;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.&lt;/p&gt;
                              • Insectivora Wastebasket Taxonon GitHub
                                &lt;p&gt;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?&lt;/p&gt;
                                • &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;Understanding the situation is more work than I can do now, so any help would be welcome.&lt;/p&gt;
                                • &lt;p&gt;note that we have the Afrotherian mammals with common names including "shrews" and "moles" in Afrotheria (see <a href="https://tree.opentreeoflife.org/taxonomy/browse?id=746703">https://tree.opentreeoflife.org/taxonomy/browse?id=746703</a>) not in Insectivora (see <a href="https://tree.opentreeoflife.org/taxonomy/browse?id=796664">https://tree.opentreeoflife.org/taxonomy/browse?id=796664</a> ). 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.&lt;/p&gt; &lt;p&gt;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".&lt;/p&gt;
                              • Species Concept?on GitHub
                                &lt;p&gt;Which species concept is used in the synthetic tree for which groups?&lt;/p&gt;
                                • &lt;p&gt;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 <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515096/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515096/</a>&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt;
                                • &lt;p&gt;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?&lt;/p&gt;
                                • &lt;p&gt;Not for any feasible level of programming effort.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;What is your use case, out of curiosity?&lt;/p&gt;
                              • Annelidaon GitHub
                                &lt;p&gt;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&lt;/p&gt;
                                • &lt;p&gt;I tried to link to opentree.org because a website was required and it showed an error message&lt;/p&gt;
                                • &lt;p&gt;Here is the link I was trying to get to&lt;/p&gt; &lt;p&gt;<a href="https://tree.opentreeoflife.org/opentree/opentree9.1@ott155737/Lophotrochozoa">https://tree.opentreeoflife.org/opentree/opentree9.1@ott155737/Lophotrochozoa</a>&lt;/p&gt;
                                • &lt;p&gt;Hi Danielle, thanks for reporting the issue. Annelids are not flagged as extinct in our taxonomy. The taxonomy page for them is <a href="https://tree.opentreeoflife.org/taxonomy/browse?name=Annelida">https://tree.opentreeoflife.org/taxonomy/browse?name=Annelida</a> (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.&lt;/p&gt; &lt;p&gt;I think you can find most of them from navigating around: <a href="https://tree.opentreeoflife.org/opentree/opentree9.1@mrcaott24ott102965/Myzostomida--Clitellata">https://tree.opentreeoflife.org/opentree/opentree9.1@mrcaott24ott102965/Myzostomida--Clitellata</a>&lt;/p&gt; &lt;p&gt;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: <a href="https://github.com/OpenTreeOfLife/germinator/pull/112">https://github.com/OpenTreeOfLife/germinator/pull/112</a> and <a href="https://github.com/OpenTreeOfLife/reference-taxonomy/issues/238">https://github.com/OpenTreeOfLife/reference-taxonomy/issues/238</a>&lt;/p&gt; &lt;p&gt;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 <a href="https://github.com/OpenTreeOfLife/germinator/issues/85">https://github.com/OpenTreeOfLife/germinator/issues/85</a> ). 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.&lt;/p&gt;
                                • &lt;p&gt;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.&lt;/p&gt;
                                • &lt;p&gt;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.&lt;/p&gt;
                              • Is this project still active?on GitHub
                                &lt;p&gt;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?&lt;/p&gt;
                                • &lt;p&gt;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. &lt;/p&gt; &lt;p&gt;The software developers use an open chat at <a href="https://gitter.im/OpenTreeOfLife/public">https://gitter.im/OpenTreeOfLife/public</a> 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: <a href="https://tree.opentreeoflife.org/contact">https://tree.opentreeoflife.org/contact</a>&lt;/p&gt; &lt;p&gt;all the best, Mark&lt;/p&gt;
                              • Allow the search for known familiar animalson GitHub
                                &lt;p&gt;Like chicken, dog, horse, etc.&lt;/p&gt;
                                • &lt;p&gt;related: <a href="https://github.com/OpenTreeOfLife/reference-taxonomy/issues/160">https://github.com/OpenTreeOfLife/reference-taxonomy/issues/160</a>&lt;/p&gt;
                              • New synthesis for Thecostraca?on GitHub
                                &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;Thank you, Christine&lt;/p&gt;
                                • Myomorpha incorrectly synonymised with Sciurognathion GitHub
                                  &lt;p&gt;If you type in "myomorpha" to the search box, it thinks you are looking for squirrels (Sciurognathi), not the same at all &lt;/p&gt;
                                  • &lt;p&gt;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 <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=33553">https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=33553</a> which is why OTT treats these as synonyms). I'm not sure that we have an easy fix for this. &lt;br&gt; 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.&lt;/p&gt;
                                  • &lt;p&gt;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."&lt;/p&gt; &lt;p&gt;So it may be that NCBI is not using a monophyletic taxon, which will (presumably) vanish if a correct phylogeny is incorporated. &lt;/p&gt;
                                  • &lt;p&gt;@mtholder in fact, myomorphs <em>does</em> exist on the OpenTree, it is simply not named. It is at <a href="https://tree.opentreeoflife.org/opentree/opentree8.0@mrcaott42ott55949/Dipodidae--Muroidea">https://tree.opentreeoflife.org/opentree/opentree8.0@mrcaott42ott55949/Dipodidae--Muroidea</a>. What happens in this case?&lt;/p&gt;
                                  • &lt;p&gt;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.&lt;/p&gt;
                                  • &lt;p&gt;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 <a href="https://tree.opentreeoflife.org/curator/study/view/pg_2688">https://tree.opentreeoflife.org/curator/study/view/pg_2688</a> or one of those other trees? Or do you not take clade names from phylogenetic studies?&lt;/p&gt;
                                  • &lt;p&gt;No. Currently the taxonomy creation is quite separate from the phylogenetic study curation. But thanks for pointing out that study. We have one <em>ad hoc</em> 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.&lt;/p&gt;
                                  • &lt;p&gt;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 <a href="https://github.com/OpenTreeOfLife/reference-taxonomy/issues/316">https://github.com/OpenTreeOfLife/reference-taxonomy/issues/316</a> to track it.&lt;/p&gt;
                                  • &lt;p&gt;@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?&lt;/p&gt;
                                • Is Life only 3.5 billion years old, or older?on GitHub
                                  &lt;p&gt;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: <a href="https://en.wikipedia.org/wiki/Evolutionary_history_of_life">https://en.wikipedia.org/wiki/Evolutionary_history_of_life</a> 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.&lt;/p&gt;
                                  • &lt;p&gt;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 <a href="https://www.scientificamerican.com/article/all-2-3-million-species-are-mapped-into-a-single-circle-of-life/">https://www.scientificamerican.com/article/all-2-3-million-species-are-mapped-into-a-single-circle-of-life/</a> 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.&lt;/p&gt;