Flag for Taxon: Carex Hirta Clade (Complex Carex hirta)
| Flagger | Content Author | Content | Reason | Flag Created | Resolved by | Resolution |
|---|---|---|---|---|---|---|
| charlie | rynxs | Carex Hirta Clade (Complex Carex hirta) |
at least some of my Vesicariae group sedges lumped into this clade erroneously |
Jun. 21, 2023 21:24:38 +0000 | loarie |
Comments
The current infrageneric classification of Carex follows the most recent treatment published by Roalson et al. (2021), which lumps Vesicariae into a broadly defined Carex hirta clade.
that's your current classification, but it isn't what everyone else uses. Please reverse this, it's absurd. you taxonomic revisionists are literally making the site unusable for anyone who isn't a taxonomic revisionist. Leave the group alone, it isn't even a species, it's a group.
this flag should not be resolved, as the issue stands.
I unresolved the flag. I have no dog in this fight, but this does seem like an extraordinarily large change to have pushed with no prior warning flag for discussion anywhere (unless the title is very weird? I just skimmed the titles of every carex flag ever, but I didn't read the bodies). Especially because this is changing a deviation from the taxon framework in a way that does not align it with the framework either. And this is a better place to have the discussion than the forum or ID comments.
Ok I did find the flag, sort of: https://www.inaturalist.org/flags/534167
But it is true that there was no discussion of the implementation details at all until after it was already done.
@wildskyflower this change was not pushed with no prior warning, I'm not sure how you came to this conclusion so fast. People interested in Carex taxonomy have known about the changes since the paper came out, and a flag addressing it (https://www.inaturalist.org/flags/534167) was made two years ago following the publishing of the paper, which, like most things involving Carex taxonomy, attracted little attention. A google doc was made to help curators with organizing group efforts to restructure the genus Carex, but the progress on that was incredibly slow, as, again, no one seemingly had any interest in it. I decided to take up the reins and push out all the necessary changes myself over the course of several days, years after people involved in the restructuring had started the process, through which I resolved an enormous number of enduring issues with the genus on iNat created by the inconsistent updates.
Have you read the paper? It's authored by the same people who wrote the prior versions people have been using.
"Phylogenetic studies of Carex L. (Cyperaceae) have consistently demonstrated that most subgenera and sections are para- or polyphyletic. Yet, taxonomists continue to use subgenera and sections in Carex classification. Why?"
"Rather than leaving Carex classification in its current state, which is misleading and confusing, we here take the intermediate steps of implementing the recently revised subgeneric classification and using a combination of informally named clades and formally named sections to reflect the current state of our knowledge. This hybrid classification framework is presented in an order corresponding to a linear arrangement of the clades on a ladderized phylogeny, largely based on the recent phylogenies published by the GCG."
i have no problem with a carex hirta clade being created that includes vesicariae, but the removal of vesicariae and lumping into this clade based apparently on some primary research favored by one users is wildly inappropriate here.
yeah one paper tears up all the carex groups we all use to idnetify carex and makes new ones. I hardly think that's justification for this all, certainly we should at least have a choice
No I didn't read the paper like I said I have no dog in this fight. Because it just calls it a 'clade' anyway without giving it a named rank, and because it doesn't assign any subsections, could a workable solution be to move the clade up to subsection and reconstitute vesicareae as a complex? From what @charlie is saying it sounds like for his use case it is more important for the classification to exist than what rank it is called?
Yeah that would work for me. Vesicariae is a group i use a lot to keep track of a small group of sedges that can be hard to ID. I have no idea what carex hirta clade exactly entails but it looks much broader than vesicariae and also breaks all of my vesicariae observations. I don'tw ant to use hirta clade and i saw several others commenting the same. it should never have been forced on us. apparently there is some group of curators who have decided to take it upon themselves to revise Carex, and statements like ". People interested in Carex taxonomy have known about the changes since the paper came out," are completely false. Many many people are interested in identifying Carex and most don't want the groups constantly being changed especially without any say in the matter.
i mean, i was literally the person who created vesicariae group and sorted all the sedges into it, so one would think someone would ask me before doing this. But no, because i am not in said 'in group', no one told me, i just had a bunch of my observations rendered useless.
I don't even know where to begin here, so I'm going to keep it as short and to-the-point as possible.
"One paper." Yes, a comprehensive restructuring of the genus written by some of the most prominent names in the field, including co-authorship by Reznicek & Ford, the taxonomists who probably wrote the circumscription for Vesicariae you want to use. If you have an issue with this treatment, reach out to the authors directly now, because this is probably going to be the way the genus is handled going forward.
@wildskyflower the reason reading the paper is important is because it makes clear Vesicariae is not a natural group and should not be maintained. We do not permit these taxa on iNat. The higher infrageneric ranks are reserved for named taxa, an informal clade cannot be represented by anything other than a complex.
Charlie, self admittedly, is opposed to every taxonomic change (at least in the short term), and wants them at most to be postponed for 5-10 years before being acted upon all at once. This is to say that Charlie is not seriously criticizing the ideas presented in the paper, but opposed to any proposition of taxonomic change, considering any change a form of "ruining" their observations. For this reason, the only discussion of relevance is whether or not changes should happen in the short term, to which the answer will, overwhelmingly, be an emphatic "yes" from a community dedicated to a scientific study of the natural world.
Right, as you say species complexes are allowed to be paraphyletic groups because they are not a formal rank, thats why I suggested it could work to elevate Versicariae to one.
I know theoretically the named ranks are supposed to just be the named ranks, but in part because inaturalist doesn't even have all the named formal ranks, like species group and series (see, e.g., https://forum.inaturalist.org/t/create-a-new-taxon-rank-for-inaturalist-the-species-group/14543) there have been other cases on inat where the inaturalist rank of subsection has been appropriated to handle such missing ranks, as @tonyrebelo mentions partway down.
I also want to be clear that I do think it is great that you put so much effort into improving the infrageneric classification. I recognize that with such a large project it isn't possible to create flags for every taxa you have to create, and doing so would have been hugely tedious and annoying to people watching the feed of flags anyway. But it is good to have at least some documentation of the discussion in flags because we cannot see what was discussed in outside google groups, the discord, the forum, etc.
@bouteloua @jdmore @frousseu @sedgequeen @elacroix-carignan @natemartineau @chrise @sedge @sedgehead @birds_bugs_botany @wildlandblogger
I did not say complexes are allowed to be paraphyletic groups. They are not allowed to be paraphyletic. Please re-read my comment.
There was essentially no discussion outside of iNat. The Google doc was created by someone else to manage Carex changes, but I never saw anyone use it.
@rynxs why do you feel you have the right to totally redo carex based on a paper you found, without consulting with the broader community? You disagree with my taxonomic opinions, but i also created the vesicariae group on inat, which you removed without consulting me, that seems kind of important. Clearly you are of the opinion of 'the more change the better' and maybe you find my views extreme but i find yours extreme and damaging as well. I have no interest in reaching out to taxomists you view as 'important', i am only interested in documenting biodiversity, and the relevent forum for that here is inaturalist, and your damaging of data and i take issue with your dismissiveness toward others who don't want their data damaged.
844 people have observed Carex in your purported clade, i am curious how many of them you talked to before making this change? 10%? 1%? 0.1%? Just your friends? You have to understand that literally millions of people use this site, and 3,949 people have observed sedges on iNat. Only a small fraction of these people are interested in reading your preferred papers and constantly changing the groups and taxa of their data to match those changes. Most of the people want to use the site to track and monitor biodiversity, which your deletion of the vesecariae group is deleterious to.
if you have to resort to questioning my credentials or trying to get me to read your favored papers, you're not actually defending your choice, just obfuscating. The question isn't even whether or not you should be allowed to create this clade. The deletion of Vesecariae is the issue here, and i think it was a huge overstep to delete it and an even bigger one to react the way you did after being called out for doing so.
" the only discussion of relevance is whether or not changes should happen in the short term, to which the answer will, overwhelmingly, be an emphatic "yes" from a community dedicated to a scientific study of the natural world."
What paper do you get that from? i strongly suspect it's very much false. I interact with dozens if not hundreds of field ecologists and naturalist and only a tiny fraction support what taxonomists are doing now.
Thanks for the tag. I basically have nothing to add here but in my opinion this restructuring of the genus is the correct thing to do. Sections are incredibly helpful for quickly narrowing a sedge down to species, but they have no taxonomic standing and therefore unfortunately do not have a place in iNat’s framework. I wish it was not so, but it is so. I don’t even know what to do with charlie’s comments. “A tiny fraction of field ecologists support what taxonomists are doing now” . . . you mean testing hypotheses and putting forward changes based on results? I don’t know what field ecologists you are talking to, but most of the ones I know are reasonable and understand that this is how science works.
@natemartineau how can you say they don't have a place on iNat, just because they don't have taxonomic standing in your own definition as such. We've been moving towards more section level entities not less, and they are incredibly powerful tools.
The iNat community (or more specifically the mods) choose what has a place in iNat's framework. As they've repeatedly stated iNat is intended to connect people with nature, and a usable taxonomy is essential in being able to do that.
"I don’t know what field ecologists you are talking to, but most of the ones I know are reasonable and understand that this is how science works."
This is just ad hominem and intentional misunderstanding of what i am saying. Taxonomy isn't like chemistry, where you combine 1 mol of element X and 1 mol of element Y and always get the same result (more or less). Removing vesicariae isn't based on testing a hypothesis and getting a result. It's based on someone's opinion on how to sort the planet's biodiversity. And deleting the existing section to force people into a different clade witn their observations, doesn't seem like science at all, rather power and control. There's nothing inherently unscientific about sorting a bunch of sedge species with similar traits into vesicariae. Nothing at all. And i don't know what field ecologists you are talking to (if any) but most people i know understand that taxonomy is a human construct and as such needs to be usable by humans. I stand by my claim that nearly everyone i talk to in the field is highly critical of what taxonomy has turned into. It's true that some people of high social status have bought wholesale into it, but that's not science at all, it's politics.
just reactivate the removed sections and restore the IDs you forced into this other taxonomic entity, and you can resolve the flag and i'll let it be.
No, removing Vesicariae is not based on merely opinion, it is based on phylogenetic work showing it to be polyphyletic. I’m not arguing with you beyond this as you have shown from the beginning that you will not have a productive conversation. I look forward to other opinions on this if other people decide to speak up.
I don't think i am the one not having a productive conversation. There is no way to actually prove whether a group is polyphylletic unless you have a time machine. and even if it is polyphylletic, it is a tool we need and are using for the important work of conserving the planet's biodiversity. Why are you breaking tools used by field ecologists? Is this what you want your legacy to be? an obstruction to those of us doing applied conservation? Are you really totally unable (or unwilling) to see the issues you are causing?
Imagine being a chemist when some other outside group decides to keep changing the periodic table. The symbol of Hydrogen has been changed from 'H' to 'T%E!)QQQQZ'. Iron is now a noble gas because a Really Important Chemical Taxonomist has declared it such. Gold has been split into three 'microelements' all that have the same number of protons, neutrons, and electrons. If you question it your credentials will be attacked or you will be labeled as 'out of hand'. Only extreme adherence to the status quo and social norms is permitted in the New Chemistry. If you use the code H for that really light gas, you will be told you are stupid and unable to read a scientific paper (which by the way you also don't have access to because it's behind a paywall). But of course if you're a Chemical Taxonomist you can always call your friends in to back you up, and since the harassment to those who disagree is constant, most people don't bother to stand up against it any more. But slowly chemistry breaks and doesn't work any more.
it might be worthwhile to actually listen to what i am saying instead of dismissing me, because it's pretty heavy hubris to assume you are certainly right about the arbitrary entities you are forcing down our throats.
Thanks for keeping the conversation civil. Our reference, POWO gives us guidance on Genus Carex and the Species contained within it.
Curators have added Subgenera, Section, and Complex internodes for which POWO provides no guidance. Please work together collaboratively to discuss whether we need these internodes and what their membership should be. If the structure of these internodes is controversial, and a compromise can't be civily reached, I recommend we remove them and just stick with Genus and species for Carex
@loarie hi, thanks. The Carex sections are incredibly powerful in being able to sort this large and difficult genus into smaller coherent groups. Vesicariae is one of the most important, at least in my area, and removing it can really disrupt myself and others' ability to identify, track, and monitor sedges, which are one of our most important species for discerning wetland health (among other things). Vesicariae as a group is widely used and well known. I don't have an issue with this other Hirta Clade existing, but i am asking for Vesicariae and others like it to please be restored, because they are really important. I spent a lot of time with several other curators setting up and adding the Vesicariae section and others, and it's really frustrating to have someone come and just wipe them off the map. I'm not even able to get my observations back to Vesicariae by rejecting community ID! Restoring it doesn't harm anyone, and helps a lot. Thanks.
Vesicariae may be useful, but it is no longer supported by the literature. We have moved past maintaining Vesicariae, as it is now known to be polyphyletic, and to re-add it would be to break iNaturalist's suggestions for taxa being monophyletic. As it stands, we are in complete alignment with the best and most accurate circumscription of Carex infrageneric taxonomy. There are tenable workarounds to most of what the existence of Vesicariae would have helped with, and the expanded Carex hirta clade catches all of the species that were in Vesicariae prior. I cannot see any way it would impede sedge tracking and monitoring, but I can see how an expanded clade might pose somewhat of an issue for identification. There's not a way around that, though.
Charlie is also asking for every other previously accepted infrageneric group to be restored, which would take days of work (if you focus exclusively on it like I did) and create an enormous mess of polyphyletic groups that were already straightened out. I don't see why Charlie values their curation work on one section above my curation work with the entire genus, but that's irrelevant to whether it should be maintained, anyway.
Point being, restoring Vesicariae and the other groups that have been shown to be polyphyletic is harmful because it would be an enormous amount of effort thrown into creating polyphyletic groups, which is entirely unreasonable.
I made this spreadsheet which includes 2 sheets:
whats currently on iNat
and all the accepted Carex species in POWO
if folks could work together to determine what they want in this spreadsheet before making any changes to iNat that would be ideal, everytime we change this clade it triggers a tone of reindexing and other processes on the site. ideally lets work it out in the spreadsheet and then jointly curate in that direction
Most everything (with Carex) on iNat is as it should be right now, or close to the best it can be at the moment. I was as thorough as I could conceivably be in making sure everything was as it should be during the change. I'm sure I made some mistakes, and I want others to check my work, but I don't think we have any outstanding errors at the moment. I think we may be missing a few species here and there that weren't in the paper, and a lot of hybrids are missing, but everything from the Appendix of the Roalson et al. (2021) paper should be on the site in its proper station (https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fjse.12722&file=jse12722-sup-0001-Roalsonetal_appendix_20920.pdf).
If you do add a hybrid, please add it in its appropriate station and add the combinatorial name as a synonym, as I have been doing. It makes it much easier to find them in the future.
If anyone wants to contest the placements in the Roalson et al. (2021) paper (which includes the Global Carex Group), they would have to find a source delineating prior placements that includes the polyphyletic groupings, which would probably also be from the Global Carex Group, but older and out-of-date.
So I actually looked at the paper and this is basically the extent of what I can see that it says re: the status of vesicariae:
"The majority of the currently accepted sections more or less correspond to largely monophyletic subclades when using additional markers (Waterway et al., unpubl. data; Gebauer S et al., unpubl. data). However, the current state of knowledge prevents a reclassification at this point."
So that sounds like they just say that based on some unpublished data they think Vesicariae is probably ok-ish, but not perfect. Which does not seem like a specific argument that it is bad or even paraphyletic, just that we don't know. In which case I don't think my 'subsection/complex' compromise proposal is particular radical.
Also, it is worth noting that the curator guide places a lot more emphasis on its preference for secondary sources over primary literature than its preference for certainly monophyletic intermediate taxa. And the FNA, the best available secondary source that covers this matter, does still have Vesicariae. Also, FNA uses Vesicariae as a major step in its key, so there could be an argument that it may make it harder for IDers to learn the taxa if there is no adequate public secondary source providing a good key.
I dont agree with rynxs or his analysis of this issue and i don't agree that the proportedly polyphylletic groups should be removed for that reason. I'm sorry you had wasted effort, but you changed all the groups without talking to the people who created the previous ones, causing a bunch of problems. I am not asking you to remove the new groups, just to restore the old ones within them, or in the very least, restore vesicariae.
@tiwane i recall several years ago having another spreadsheet and already sorting all the sedges that belong in vesiariae. That information is still within the iNat database in the 'invalid' group, is it not? I can go through the process of doing that all over again but given rynxs us dead set on refusing use of these established sections, i'd rather if we just got the info from the existing group via re-validating it under the clade section. is that not possible? I'm also not sure how to jointly work with two people who keep insulting me. It doesn't feel good faith.
Also in your spreadsheet you have sections listed, but i think it should read clade and have another section column to the right, correct?
@wildskyflower Good points and thanks for doing that digging! I had missed that statement. I mean… if we can agree on a good reason to keep these long-established sections in iNat’s taxonomy, I think we should. There is no denying how useful they are. They’re basically essential to anyone who identifies Carex species - including me, to be clear.
So can we be clear then that what i am concerned about and asking for is restoring these groups that nearly everyone here sees as highly essential, and that doesn't make me a bad scientist or malicious or lazy? I really feel like a lot of personal insults get directed towards me because my view on taxonomy is supposedly weird, and i don't think that's cool. I literally just want a continuation of the very well established Carex sections that are used widely throughout the field. Yes, i am frustrated that the groups myself and other spent a great deal of time setting up were wiped off the map without asking me at all, based on one paper that isnt reflected in any secondary sources and also doesn't even seem to clearly indicate Vesicariae is polyphylletic, never mind that a polyphylletic section isn;t even a problem as they are identification based groupings. I find the compromise of retaining the new clade and keeping the existing sections acceptable, though i'd prefer to have the new clades removed. Iet's just go with this and in the future not make dramatic changes without a broader discussion beyond the one group of taxonomist revisionists on here?
@rynxs you say in your profile "Don't take my number of IDs as evidence. Check for yourself. Feel free to ask questions or correct me if you believe I have made a mistake. I make mistakes."
certainly i make mistakes too. i think deleting the sections was a mistake you made, though. I think it's appropriate for you to un-delete them. I'm sorry it creates a lot of work. but i also spent a lot of work creating them the first time, which got erased. And please refrain from ad hominem stuff, thanks.
With apologies to everyone for sharing my opinion too early, I’m going to have to give this paper another read, because I am getting confused. Matthew found the verbiage he shared, but the very first sentence of the abstract is: “Phylogenetic studies of Carex L. (Cyperaceae) have consistently demonstrated that most subgenera and sections are para- or polyphyletic. Yet, taxonomists continue to use subgenera and sections in Carex classification.” . . . and this is repeated a number of times throughout the paper. Beyond this, I don’t suppose “more or less correspond to largely monophyletic subclades” is actually all that compelling.
This work is extensive but also explicitly supposed to be an intermediate step between what we have/had and a future framework for Carex, so I guess it probably does make sense to erect new clades while retaining the widely useful sections. If that’s even possible.
@wildskyflower that is the paper stating that the sections are at least somewhat polyphyletic, in my opinion (I don't think paraphyly is relevant here at all). Any amount of polyphyly would require the section to be swapped into a higher taxon and re-created, anyway. Again, you need names for anything other than complexes, which don't currently exist. Also, the FNA treatment is out of date, which is why Vesicariae being listed as a synonym of the Carex hirta clade is useful for people wanting to ID as Vesicariae but unaware of recent taxonomic developments.
If you can come up with a scheme for somehow making Vesicariae a group below the Carex hirta clade, that would work, although I don't think that's possible with what we currently have access to.
@charlie, I don't care that much about my wasted effort, I just don't want the updated and accurate infrageneric taxonomy to be destroyed for no good reason. My point about effort being put in was to illustrate that your effort put into organizing Vesicariae isn't an argument, and isn't relevant. I don't need to ask people to correct their outdated/incorrect taxa.
@charlie, I have not insulted you, I've only recapped statements you made yourself (because they are relevant to your perspective on taxonomy), and made factual statements about the taxa involved here. I don't know about being a "bad scientist," but your complete refusal to read the relevant paper and your opinions on taxonomy not being scientific are concerning. I invite you to read the paper we are discussing here if you have not done so already. The ad hominem point you made earlier was directed at Nate, not me.
@natemartineau Yes the sentence I quoted is specifically just talking about the sections that are lumped into clade hirta so that isn't incompatible with what the abstract says.
For the record, I also don't think my proposal about reconstituting the section as a lower clade is that much work because the appendix is basically a spreadsheet that maps proposed sections to old sections so it can essentially be copy pasted into @loarie's spreadsheet, if that is what we decide to do. I think most of the time investment is usually making the list of what to do, not executing it.
Also, what to call the clade if elevated to a subsection is not ambiguous because the paper actually specificially says what it should be called if it is elevated to a formal rank: "If the Hirta Clade is to be regarded as a section in the future, the sectional name “Carex” would have priority."
my 'scheme' is just remove the 'invalid' tag from the section(s). I can't do that any more as i am not a curator any more, largely because i was tired of getting insulted by other taxonomists. I don't want to read a taxonomic paper, as i am highly skeptical of the current state of that field and also i need to go to bed. If i get a chance i'll read it tomorrow, but i can't imagine any paper on taxonomy is going to make me want all of the widely used, crucial Carex sections deleted from inaturalist. I don't feel like we can be sure if a group is polyphylletic based on the sort of evidence available to us at all, and i also think trying to make every taxonomic entity (including sections) strictly monophylletic is a horrible idea that is going to damage the ability to classify organisms even more.
Is the issue that inat wont allow both a clade and a section to exist at the same time? What if you just re-activate the sections?
I certainly thing it was out of line for you to seek out my observation and try to force your clade on it, when i was trying to get it back to vesicariae, going so far as to explicitly disagree with a 'vesicariae' ID from an observation that clearly was indeed in that group. I guess that isn't exactly an ad hominem but i think it's a pretty big violation of the good will treatise of inat.
@charlie the clade is a complex, which are beneath sections. Reactivating Vesicariae would result in an empty section (without any species) adjacent to the Carex hirta clade. As @wildskyflower and I have been discussing, it would not be possible to place a section under a clade without elevating the clade to a level for which it does not have a name. Thus, it is currently not possible. If you don't want to read the paper then there's nothing I can do, but I'm going to take your objections to its content with a grain of salt.
Making all taxa strictly monophyletic is the entire point of classification. There is absolutely no point in applying scientific names without ensuring that the name only applies to one lineage. If you hold the opinion that taxa don't have to be monophyletic, then I one could apply the name Actinopterygii to your Carex observation and they would not be wrong, in your opinion at least, because their interpretation of Actinopterygii could be inclusive of Carex. This is obviously an extreme example, but I think you should understand my point here.
This is a minor correction, but the taxa were not "deleted," they were swapped and inactivated, which is why you're able to restore IDs of Vesicariae (no one can find those without a URL search for Vesicariae using its taxon ID, by the way. Not sure how much that matters to you).
I didn't seek the observation out out, you linked it in the flag. I IDed it with the name that is currently in use so that it shows up in content searches. The disagreement is because the two are mutually exclusive, there's no way to ID Carex hirta clade without disagreeing with Vesicariae. Strictly speaking, to ID something as Vesicariae, in the current moment of iNat, is to say that it is in subg. Carex but is not any particular species, as Vesicariae is empty.
I am of the firm and unshakeable opinion that there cannot ever be anything wrong or bad will with adding a factually correct ID, and I will never withdraw an ID I believe to be correct.
Yes, the parents of the species that were in Vesicariae are now the clade so simply re-activating the old section with no other action is not possible; it would have to be reconstituted. As I said, as long as there is a specific list of agreed upon instructions the actual act of reconstituting would not be especially difficult technically.
I can't access the unpublished data so I have no idea whether they think the old section is paraphyletic, polyphyletic by one disputed species, probably monophyletic but they aren't yet willing to commit to that definitively, or whatever. This is part of why inat's stated general preference for secondary sources exists, because everyone with an internet connection has access to those. On the other hand, I'm well aware that the FNA treatments can be outdated or not ideal (see, me, @aspidoscelis, and others trying to make sense of west coast alliums), and that it can be useful to deviate or expand on the FNA et al in some cases.
This isn't really the place to get into the philosophy of taxonomy and exactly what the role of inat is or should be in relation to cladistics vs ecological considerations. Inat has chosen to adopt formal ranks instead of a purely clade-based hierarchy with no set depth. A fixed depth hierarchy is essentially necessary from a practical point of view, but because the formal ranks are purely an artificial human construct it is more or less inevitable means that certain parts of the tree will slightly displease almost everybody in some way. Which is why I think it is great that, in this particular case, there does exist a pretty good candidate compromise solution which would probably be slightly mutually annoying taxonomically but basically preserve all interested parties practical identifying, mapping, and exporting workflows undisturbed.
"Thus, it is currently not possible. If you don't want to read the paper then there's nothing I can do, but I'm going to take your objections to its content with a grain of salt."
I don't think that is fair. It doesn't matter what the paper says, that's kind of my point. You should not just be able to delete a whole existing classification framework based on a paper you found. without more oversight and consideration of how it affects others using the site. So i don't want to engage with you about the contents of the paper because i don't see it as relevant. It doesn't matter if Linnaeus and Darwin co wrote it, one paper doesn't give you the imperative to totally delete stretches of iNat taxonomy.
that being said the paper clearly indicates it is 'working towards a new system' of Carex groupings, not that it is a finalized list. So, that verifies what i am saying anyway. Maybe some day another well established Carex grouping will achieve wide use and be important enough that we delete the old one. But this paper isn't it. It's some ideas to build towards that. it was very premature to remove the existing classification. So if anything, the paper backs up what i am saying anyway.
" it would not be possible to place a section under a clade without elevating the clade to a level for which it does not have a name. Thus, it is currently not possible."
You just literally state how to do it, and then say it is not possible. If you want to keep the clade, do what you said there. If not, delete the clade and restore the subsection. Problem solved.
"I am of the firm and unshakeable opinion that there cannot ever be anything wrong or bad will with adding a factually correct ID, and I will never withdraw an ID I believe to be correct."
"Vesicariae" isn't actually wrong, so disagreeing knowing that is a violation of iNat rules. I was going to flag the ID but was hoping it would get resolved here. Just delete it, please, until things are straightened out so i can reject that 'community' ID ie your breaking of my observation to make a point...
"I can't access the unpublished data "
Then it shouldn't be referred to here.
" Inat has chosen to adopt formal ranks instead of a purely clade-based hierarchy with no set depth."
I don't think that is actually true. I think that is something a few curators decided and started pushing, and admin is too buried in the day to day of keeping iNat afloat to go and stop it all. iNat is about 'connecting people with nature' not chasing a technically correct but practicably unusable taxonomic framework. It alarms me that people are pushing this claim. If you can link to a section of iNat guidance that says that new taxonomic papers including unpublished ones must be followed at all times, including deleting of old sections, i'd love to see it. Otherwise, we need to go back to secondary sources. I mean really POWO doesn't really work either and i think we should go back further to an older policy, but i'm willing to accept the compromise. But i don't think rynxs is open to anything except 100% getting their way, which isn't reasonable...
Oh my... y'all are at it again I see. I'm not going to dig into every single specific point raised because at a certain point it becomes tedious, so I'll just state my overall thoughts.
I would like to go back to the sections for now... if certain species have to be switched between sections or put in a new section, so be it.
I don't think we need to pile on @rynxs for trying to adopt the most taxonomically-accurate scheme possible, but it would've been good for there to be more consultation before rolling out a complete revision. I mean, we're working with a taxonomy that splits dicots and monocots out as two groups. That's widely known to be wrong but we do it for simplicity's sake.
Also y'all need to chill in your interactions with each other. Snipping at each other is unprofessional.
i found some really old document once with lumpers and splitters going at it and man, were they mean to each other. This stuff has been going on forever. That being said, i am not presenting that as an excuse. I apologize for getting so riled up. I really care a lot about this place and have vey strong feelings about this issue, I'll try to be less toxic.
Understandable- you both care very deeply. I would suggest we need to figure out how to get back to the sections for now and we'll deal with the clades once more research has been done down the road.
To copy Tony Rebelo's comment in a flag referencing this:
"Since I cannot comment on the above flag because charlie has blocked me -
We need to decide if the best taxonomy to follow is one that is evolutionary correct and state of the art (but not necessarily tested science), or one that helps with identifications.
Personally, given a choice, the most useful taxonomy to follow is that which aids with identification, even if it is out of date or even incorrectly polyphyletic. If we know a specimen/observation is one of a handful of species, that is far more useful, than if those species are split up into n monophyletic clades.
Let us be pragmatic: let the cladists fight in the literature, and keep the iNat taxonomy most useful for identification.
Obviously not for silly concepts such as fish-dolphins-ichthyosaurs - those can readily be distinguished, but for real cases where further ID is not possible at present, but ID to group or complex level is relatively easy and useful.
How bad would it really be to have a few unrelated species in the "wrong" group if they look like the others and cannot be told apart? Surely having to ID them as Genus or Section "unidentifiable further" is silly under these circumstances?
I presume that no one has yet annotated Scott's spreadsheet as it merely contains the current iNat classification. Can the original/alternative please be illustrated?
Sorry that I cannot contribute on the page, hence this comment. Can someone please resolve it - it does not need to remain open."
well, there is a reason i blocked them and don't want to engage with them, but i mostly agree with them in this case.
@rynxs @natemartineau
Something was bothering me last night so I thought I'd check; where in the paper does it say the Hirta clade is in Section Paludosae, as it currently is on inat?
As far as I can tell, they have the Hirta clade, VI.H.1, as a sister clade to Praelongae, VI.H.2 which is currently a section. Paludosae, VI.M.2, is in their Molliculae-Castanea clade, which is sister to the Praelongae-Hirta clade. So if we're being monophyletic the Hirta clade can't be in Paludosae if Praelongae is not, right? That makes more sense with the statement I quoted above that suggests the Hirta clade might just be the nominate section for the subgenus. And if its sister clade is assigned sectional rank then it should also be grafted as a section for self-consistency. So, what if we take that approach; just elevate the Hirta Clade to the nominate section of subgenus Carex, and reconstitute Vesicariae as a subsection? I think that fixes the nomenclatural concern with my subsection/complex compromise proposal.
That seems reasonable at least for this part of the issue.... maybe we can also recreate Lupulinae? If Hirta Clade is a proposed sugbenus... i don't really feel great about having it in iNat at all since it isn't even a fully established entity under this paper, but it's an acceptable compromise.
The Hirta clade is not nested in the Paludosae. The type species of sect. Paludosae is not closely related to the Hirta clade. This is a mistake that should be easy to correct on INat in placing the Hirta clade directly under subgenus Carex.
I discussed the Hirta Clade taxon swap with some curators in another thread. Maybe some of the tools proposed there should appease you @charlie. I agree the situation at the moment is far from ideal, and using species complexes instead of sections could be a workable workaround to recognize polyphyletic entities as belonging to the same morpho-group: https://www.inaturalist.org/taxon_swaps/124952#activity_comment_e1e9b3f3-2f00-4a35-95ce-7f2c88669dd7
I could share my opinion on the best way to split apart the Hirta Clade, but this would be based on unpublished data and would be premature. I will refrain from doing so. That is one of the goals of my PhD. Hopefully in the next 5 years this should be resolved.
Everything that was in Lupulinae is still in the Hirta clade, so it can also be reconstituted as a subsection exactly the same way as Vesicariae can. Some of the miscellaneous other stuff in the Hirta clade will have to be left ungrafted at subsection though.
Is calling the elevated Hirta clade Section Carex acceptable? Obviously it is a preliminary name, but because the whole description is based on a preliminary classification I think it is the best we can do.
@elacroix-carignan So to be clear, it is ok with you to reconstitute Vesicariae and Lupulinae in some subordinate rank, cited to the FNA, for IDer purposes for the time being?
I guess i am not even sure polyphyly vs monophyly is as well defined as people make it out to be. Evolution is so messy, taxonomy will never perfectly represent the family tree of all life on earth. So if sections are incredibly valuable in identifying sedges, i am not bothered at all by the fact they aren't 'perfect'. Especially given they are sections, not species. I think it may be impossible to distinguish polyphylletic groups in some species as well but that's another issue. And i don't want to join into that other thread because i've spread enough chaos and people already know where i stand. Being able to filter by species is helpful for sedges we already know the species of, but the main thing i use the sections for is tracking ones where i don't (yet) know the species but do know the section. That won't work as they were forced into this other clade and even are being pushed into the clade by rx when ive asked them not to.
That all being said i don't care if you call Vesicariae a species complex rather than a section either. I'm really trying to be flexible here, but it's ahrd when people are insistent on only one course, which i view as really extreme, and use their 'curator' rank to impose it on all users.
How many other sections were impacted by this action? I noticed cyperoideae (ovales) is still there (whew) so it doesn't look like all the sections were deleted, just some.
Hmm. One more I can see is that I believe it would also be possible to reconstitute the old section carex as another subsection of the Hirta clade. No one has mentioned needing that for ID so I don't know if it is desirable or not?
No other sections subordinate to the clade can be reconstituted, so the rest of the species would have to be left grafted to the clade directly. If we reconstituted Vesicariae, Lupulinae, and Carex as subsections, then the clade would be broken down:
Section Carex (Hirta Clade): 105 species, 13 hybrids
-> Subsection Vesicariae: 48 species, 7 internal hybrids
-> Subsection Lupulinae: 6 species, 0 internal hybrids
-> Subsection Carex: 16 species, 1 internal hybrid
-> Ungrafted: 35 species, 5 inter-subsectional hybrids
I personally don't use subsection Carex much as I just don't see those very often in areas I am using iNat. But that isn't a good reason not to recreate the subsection of course.
Cyperaceae molecular systematist here (and also co-author on Roalson et al. 2021, although my input was limited).
I believe that it was too early to push the changes to a website like iNaturalist, which is mostly used by amateurs and field biologists.
Those that pushed the changes clearly did it with good intentions, but good intentions do not necessarily result in good outcomes. The classification proposed in Roalson et al. (2021) is still highly preliminary in some parts of the phylogeny, and I fail to see how pushing it in its raw form to iNaturalist is of help to users of the platform, including me and my students.
The informally named Hirta Clade is a good example. It is not a section and likely never will be. My lab is currently planning phylogenetic and systematic work on this clade which is most probably going to end up splitting it in several smaller sections. These newly-circumscribed sections are likely going to be very similar to traditional ones (sects. Vesicariae, Lupulinae, Carex, etc.) with a small number of important changes.
As part of this work, my student @elacroix-carignan was using iNaturalist to locate observations of interest, but the implemented taxonomic changes make his work more difficult by blurring the division between morphologically distinct groups of species.
The fact that the Hirta Clade had to be implemented in iNat as a "species complex" is additional evidence that this change was pushed too quickly. If iNat is not constructed in a way that it can properly implement informal clades at any level of the hierarchy, then why was this change pushed anyway? The Hirta Clade is not a species complex by any means. I understand, from the discussion, that this decision leaves no space for subgroups to be recognized within the Hirta Clade, which is making things even less satisfying for users like us, who would very much like to be able to assign observations to groups of closely related taxa.
Putting the whole Hirta Clade in a "sect. Carex" is not better. It is still trying to go too fast, but doing it in a way that is even more confusing (how will people know that we are talking about the Hirta Clade, rather than the traditionally-circumscribed sect. Carex?).
I am far from advocating the recognition of paraphyletic or polyphyletic groups, as I am a convinced cladist, but one has to understand that taxonomic stability is important as well. Pushing changes only for the sake of being "up to date" with the latest scientific results is dangerous. Being patient, moving slowly and thoughfully, is the better way to proceed in taxonomy. In this particular instance, the classification proposed by the Global Carex Group is supposed to serve as a framework for future revisionary work, not as a framework for organizing specimens in a museum collection or a photo database.
I am advocating for a complete reversal of this change. Having access to traditional sections Vesicariae, Carex, Paludosae, etc. is actually more helpful to us than the informal clades.
Eventually, we will propose a formal Linnean classification with newly circumscribed sections and perhaps subsections. When that time comes, I will be all for implementing the changes and letting the whiners whine.
After sleeping on this, re-reading the paper, and thinking about it today I find myself agreeing with the above. @elbourret I’m glad someone much more qualified than me jumped in and commented all of what I wanted to say and much more. The paper is so explicit in being an intermediate step, preliminary even, that pushing changes broadly to a citizen science site was probably not the ideal solution, although I have no doubt it was done with good intentions.
So, some numbers for consideration in discussing the undo everything proposal:
Across all of the new 'complex clades', there are currently 3,387 observations at 'complex' exactly, in 26 different clades. 2500 of those are in the Hirta clade, probably mostly bumped back due to the elimination of the previous sections. If the clades were eliminated we need to decide what to do with those.
There are current 5,011 observations at 'section' exactly, split across 47 sections. Many of those might be fine, but a lot of the sections had their species rearranged extensively, so we would need to think about what to do with those.
There are currently 5,572 observations at subgenus exactly. We can't necessarily do anything with those directly, although some were probably old IDs to Sections that were dumped into the subgenus level, and I'm not sure if those can be reactivated.
There are currently 291,210 observations ID'd to species or better across 1,192 species. Those can just be moved, but the composite re-indexing load is large enough to require staff approval before committing (even though every individual move would not necessarily be blocked by the size limits). However, even making a list of destinations for 1,192 species is daunting, so we should really be sure of what we want to do before we do it if we go the route of moving a bunch of stuff again. Especially if a lot of those groups would basically just get put back together in a couple years. Are there any groups that almost definitely will get elevated to sections more-or-less as is?
It sounds like most of the groups will NOT get elevated to sections, the paper was a work in progress with some ideas but was never meant to be pushed onto citizen scientist/field ecology sites. Is there not a way to just re-activate the sections? Or can iNat staff do some kind of rollback to get rid of these changes?
I recognize the initial action wasn't malicious at all, but this has caused a huge issue. I really hope there's a broader conversation about curators doing things like this without broader community consultation (i mean the INAT community not other taxonomists). Because 'this issue certainly isn't limited to Carex.
I have no idea what the staff are capable of, but it certainly isn't possible to do it that way with regular curator powers. I guess a narrower version of the question is, are the things that have moved from one named section to another named section going to stay moved? In those cases, it seems like they have committed to a definitive answer. There are currently 771 species in these 'clade complexes' things and 1,289 that are assigned to a section, so not moving around the things that are currently in a section could more than halve the work now and also in the future if they were just going to get moved back again.
yeah i am not sure. I know they rolled back a taxonomy change error i made back when i was a curator but it was less complex than this. @loarie ?
I don't think things will just get moved back again, it sounds like the actual new sections that these authors want to propose (should we choose to accept them - it shouldn't just be blindly changed) - are going to be similar to the old sections, i think they just want to move a few taxa that they feel are polyphylletic or don't fit, which sounds a lot less dramatic than what happened here.
we can imperfectly revert taxon changes but not moving taxa or other changes and if theres alot of moving pieces reverting tends to just add one more to the pile
Been away from iNat for a bit but happy to see I missed the main part of this discussion. Also, happy to see that it appears folks have come to the conclusion that sections should be reinstated, at least for now. Not doing that is potentially damaging to researchers that are actually doing the important work to settle some of these taxonomic matters. The Global Carex Group is clearly an authoritative reference on this subject and the paper cited is an important step but obviously, as others have stated, it is an intermediate step that partially intended to highlight future research needs. Hopefully this example illustrates the importance of not immediately making taxonomic changes as soon as a new paper is released. I believe iNats use of secondary literature is intended to avoid these very issues and allows us to wait for some consensus to develop.
Thanks especially to @elbourret for his input and being a voice of reason and for providing the guidance that was needed here and to @wildskyflower for being a mediator between two opposite opinions.
Ok, so just to get an idea of the number of IDs directly lost with change of observation taxon, I used this tool https://jumear.github.io/stirfry/iNatAPIv1_identifications to run through most of the Section merges that directly affected just subgenus Carex (I didn't get to the rest). This should be a rough proxy for the amount of ID specificity that will be lost if the sections are reconstituted without reverting the mergers. If I understand correctly, I think in total about 8500 observations in subgenus Carex would directly have their observation taxon slip backwards with no reversals. I could have missed some or made mistakes, it is not the easiest thing to search for.
Lingering results of https://www.inaturalist.org/taxon_changes/124956:
There are approximately 900 former direct Vesicariae IDs that were transferred to 'Hirta Clade' IDs that are still controlling the observation taxon.
There are no former direct Physocarpae IDs now at 'Hirta Clade'
Lingering results of https://www.inaturalist.org/taxon_changes/124952
There are about 400 former direct Lupulinae IDs now at 'Hirta Clade'
https://www.inaturalist.org/taxon_changes/125092
There are no former Anomalae IDs now at 'Subgenus Carex'
There are no former Aulocystis IDs now at 'Subgenus Carex'
There are about 100 former Section Carex IDs now at 'Subgenus Carex'
There are about 10 former Clandestinae IDs now at 'Subgenus Carex'
There are no former Debiles IDs now at 'Subgenus Carex'
There are about 250 former Hymenochlaenae IDs now at 'Subgenus Carex'
There are no former Lageniformes IDs now at 'Subgenus Carex'
There is one former Lamprochlaenae ID now at 'Subgenus Carex'
There is one former Mitratae ID now at 'Subgenus Carex'
There are about 1800 former Phacocystis IDs now at 'Subgenus Carex'
https://www.inaturalist.org/taxon_changes/125090
There are no former Molliculae IDs now at 'Subgenus Carex'
There are no former Mundae IDs now at 'Subgenus Carex'
There are no former Decorae IDs now at 'Subgenus Carex'
There are about 600 direct Acrocystis IDs now at 'Subgenus Carex'
There are no former Depauperatae IDs now at 'Subgenus Carex'
There are about 100 former Careyanae IDs now at 'Subgenus Carex'
There are about 150 former Paludosae IDs now at 'Subgenus Carex'
There are about 50 former Paniceae IDs now at 'Subgenus Carex'
There are about 250 former Squarrosae IDs now at 'Subgenus Carex'
There is 1 former Scitae ID now at 'Subgenus Carex'
There are 17 former Limosae IDs now at 'Subgenus Carex'
There are no former Hallerianae IDs now at 'Subgenus Carex'
https://www.inaturalist.org/taxon_changes/124960
There are no former Thuringiaca IDs now at 'Subgenus Carex'
There are no former Hispidae IDs now at 'Subgenus Carex'
https://www.inaturalist.org/taxon_changes/124935
There are no former Scabrellae IDs now at 'Subgenus Carex'
There are about 1000 former Indicae IDs now at 'Subgenus Carex'
https://www.inaturalist.org/taxon_changes/125022
There are no former Hirtifolieae IDs now at 'Carex Castanea Clade'
There are no former Longicaules IDs now at 'Carex Castanea Clade'
There are about 100 direct Porocystis IDs now at 'Carex Castanea Clade'
https://www.inaturalist.org/taxon_changes/125021
There are no former Confertiflorae IDs now at 'Section Paludosae'
https://www.inaturalist.org/taxon_changes/125002
There are no former Shortianae IDs now at 'Section Squarrosae'
https://www.inaturalist.org/taxon_changes/125000
There are no former Podogynae IDs now at 'Section Phacocystis'
There are no former Forficulae IDs now at 'Section Phacocystis'
There are about 500 former Phacocystis IDs now at 'Section Phacosystis'
https://www.inaturalist.org/taxon_changes/124999
There are no former Tuminenses IDs now at 'Section Phacocystis'
https://www.inaturalist.org/taxon_changes/124959
There are no former Pellucidae IDs now at 'Carex Flacca Clade'
https://www.inaturalist.org/taxon_changes/124958
There is 1 former Obtusatae now at 'Carex Capitata Clade'
https://www.inaturalist.org/taxon_changes/124957
There are 2 former Abditispicae IDs now at 'Carex Flacca Clade'
https://www.inaturalist.org/taxon_changes/124950
There are 10 former Bicolores IDs now at 'Section Paniceae'
There are about 650 former Laxiflorae IDs now at 'Section Paniceae'
There are about 850 former Paniceae IDs now at 'Section Paniceae'
ttps://www.inaturalist.org/taxon_changes/124934
There are no former Euprepes IDs now at 'Carex Indica Clade'
https://www.inaturalist.org/taxon_changes/125030
There is 1 former Polystacheae ID now at 'Carex Setigera Clade'
https://www.inaturalist.org/taxon_changes/125029
There are no former Echinochlaenae IDs now at 'Section Spirostachyae'
https://www.inaturalist.org/taxon_changes/125024
19 former Granulares IDs now at 'Section Griseae'
650 former Griseae IDs now at 'Section Griseae'
Thank you for doing that digging @wildskyflower. I did not fully realize how many moving pieces there are here, though with such a complex genus it obviously makes sense. It seems that the consensus from both informed users and experts on the genus is to move back toward using sections on iNat, which I am fully in agreement with after digesting the GCG paper. Again, sorry I came in swinging with a strong opinion only because I thought I understood the contents of the paper.
So is there any feasible way to reinstitute sections without observations that were formerly at section level slipping back to subgenus or genus level? I'm getting a sense that there isn't, which kind of sadly makes sense. I've not been successful in becoming a curator yet, but if I can do so I'll offer my help with getting this issue sorted out.
Ok, I fully filled out @loarie's spreadsheet (https://docs.google.com/spreadsheets/d/1DONzP2kCHpMidqZZdNw-39mR4MVj22C30t-qxsNUmKg/edit#gid=852947787%0A) with the previous sections for all 2090 species, as best as I can determine. A bit over half of the species need to move to reverse the changes. If anyone wants to check or suggest any changes that would be great; I know @elacroix-carignan has proposed some more limited tweaks in other flags and it may or not be a good idea to combine those.
So, if possible, I think the order of operations to do a reversal would be something like
1.) Reverse all the Genus Carex swaps and merges from ~March that targeted a subgenus, section, or complex (but not the ones directly affecting just species or subspecies, which are fine). I think the taxa were all or nearly all empty of species at the time the merges happened, so if I understand correctly (it is very possible I don't) the only effect would be to reactivate the O(10,000) old IDs to Section. I'm not sure if this is practical; is that how it works @loarie?
2.) Graft all the species back where they belong (mostly to Section, but a few to Subgenus or Genus)
3.) Merge any lingering direct IDs from the empty clades back to the section where they belong, or subgenus/common ancestors, and inactivate the clades. I don't think it makes sense to kick back all the potential unintended disagreement IDs to rearranged sections back to the common ancestor, as I expect the number of unintended disagreements in the last couple months will be very small compared to the number of intentional Section IDs that could be disrupted by doing that.
In any event I think we should wait at least a week before changing anything to give people chances to comment, discuss, and check things.
I would like to figure out if there is a way to have a broader conversation about this type of curation action on iNat. I recognize my views differ from those of most taxonomists, but in this case it was clearly a broader issue where many people including even some of the people involved with the paper, felt that this was way too premature a move. I am also not trying to specifically attack the person who made this change, because indeed this sort of thing is prolific across all of iNat. Changes are made based on obscure flags and 99% of the people who use iNat have no way to weigh in on these things. I recognize most curators will not agree with my 'step back to 2011 and make no more changes until 2030' proposal, but i think it is clear we went too far in the other direction here and we need a more clear sense of balance and pragmatism than what is occurring across iNat right now. This is a community science site, not an experimental place to test out new possible taxonomic schemes using everyone else's data as a guinea pig. Really the taxonomy on inaturalist.org, a community science space for connecting people with nature, should match the most available field guides most people have access to, not the current unpublished concept papers.
lets keep this flag focused on the Carex clade. There are other venues such as the forum for discussing iNat's taxonomic policies more broadly. For Vascular plants, we follow POWO which makes our job easier. But I agree we need better decision making policies on internodes (e.g. subgenera, sections, etc.) for whether to include them and if so what to reference
The more my ID skills have improved the more I like internodes generally in many cases and I have comments I could add about that but I'll take your advice and try not to sidetrack the conversation on the flag.
What I realized yesterday is that the issue here is that the use of the preliminary complex-clades guarantees that all of the direct IDs to those clades will eventually have to be bumped back to subgenus at some point in the future when Linnaean ranks are available, unless the entire clade as a whole is elevated to Section as-is (could be mitigated in some cases with some kind of weird atlased split hacks but we should obviously avoid that if possible). So I think as of yesterday I have decided that at least all of the complex-clades need to be undone until they have at least proposed formal ranks. This argument doesn't apply to things that moved from one named Section to another named Section (or, in a handful of cases, subgenus), and I'm personally still open to arguments that some of those should stay.
My main concern with only a partial reversal of Section to Section moves is it might break self-consistency and some keys, though I think people with more Carex expertise are better equipped to say how big of an issue that is, especially for the large chunk of species with few or 0 observations anyway.
@loarie If/when we decide to begin some kind of reversal, are you able to somehow execute the Section moves in the spreadsheet in some automated or semi-automated fashion or would they have to be done manually?
As long as they don't surpass 200,000 observations, taxa can be renamed/reranked by whoever made them without a swap or split, which was the plan for when these groups were named.
Some of the complexes should remain, such as the Carex rosea clade.
It does look like the Carex rosea clade is a species complex in the strict sense of the curator guide, and has a long history of being referred to as a species complex in the literature, as is typically required (see e.g. https://www.jstor.org/stable/40211915). So I guess I don't see any serious objection to keeping it as a rank, the question for that one would just be if it should be placed back as a child of Section Phaestoglochin to avoid breaking keys.
Are there other similar situations?
Yes, if you are expanding the concept of Phaestoglochin in a roll-back, then all of the species that were in Phaestoglochin prior should end up subordinate to it again.
Yes, there are similar situations for other complexes. Many of the smaller clades are useful. I would recommend keeping as many of them as possible.
Ok @rynxs, here are the complexes other than carex roses that I can see (I could have missed some) that can be kept with no modifications to their current concept (some others could be kept with only one species removed), and I tried to quickly google whether they have specifically commonly been called a complex:
Carex flava complex (description as a 'species complex' is also well attested in the literature, see e.g. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1756-1051.1994.tb00583.x)
Carex concinna complex (unsure if commonly called a complex)
Carex curvicollis complex (unsure if commonly called a complex)
Carex fuliginosa complex (unsure if commonly called a complex)
Carex liparocarpos complex (unsure if commonly called a complex)
Carex luzulina complex (unsure if commonly called a complex)
Carex nebrascensis complex (unsure if commonly called a complex)
Carex sartwelliana complex (unsure if commonly called a complex)
Carex vanheurckii complex (unsure if commonly called a complex)
Carex curticeps complex (unsure if commonly called a complex)
Carex myosuroides complex (I found references to a 'Kobresia complex', which might be the same thing, but I'm not sure)
Carex lepida complex (unsure if commonly called a complex)
Carex stenophylla complex (the FNA refers to these two species as a 'difficult complex', though doesn't specifically call it the 'Carex stenophylla complex' that I can see http://www.efloras.org/florataxon.aspx?flora_id=1&taxon_id=200026560)
Also, @elacroix-carignan has suggested in other flags that we should create three additional complexes and I think we should decide on them at the same time:
'Carex crinita Complex': https://www.inaturalist.org/flags/623205
'Carex lupulina Complex': https://www.inaturalist.org/flags/623185
'Carex frankii Complex': https://www.inaturalist.org/flags/623170
Thoughts? Did I miss any?
I don't think you missed any.
The final three complexes all definitely make sense, as well.
Oops I did an excel trick and discovered that I missed that 'Carex ericetorum complex' also does not have its concept modified so could be kept.
My feeling is that at this point we now have consensus on what to do here. I'll tag everyone who has commented on this flag to give a chance to disagree with that assessment.
@rynxs @natemartineau @charlie @sedge @sedgequeen @elbourret @elacroix-carignan @wildlander
After giving a bit of time for any last comments or tweaks, we can move on to planning the execution of the moves as described in the spreadsheet. My feeling is that after performing this re-arrangement, we should agree to treat the general concept of Carex infrageneric taxonomy on inat as basically frozen until a formal Linnaean reclassification with adequate descriptions to enable ID has been either 1.) available from an open access peer-reviewed literature source for at least several years to give time for any follow-up or commentary in the literature and inat flags or 2.) accepted by a commonly publicly available/reputable secondary literature source.
I fully agree.
This looks like a good treatment to me. Specifically on the "accepted by a commonly publicly availible/reputable secondary source" that should be Plants of the World Online.
I've known about the major paper re-organizing Carex for some time. Parts of it have been incorporated in my work. The changes didn't just come out of nowhere.
Many of the traditional sections in Carex are clades, but many others are arbitrary groupings. I'm OK with making these changes, though I am sure I won't like all of them. Some of them will be helpful.
I agree with the changes proposed and thanks to the people putting in the work here!
Yes, thank you all!
Any movement on this? It's been a month of peak field season and this is still broken. I hope this will actually get fixed and not left broken.
happy to help if someone could very concisely explain the changed that need to be made - but maybe better left to a curator who already understands these changes
@loarie I apologize I myself don't have time to do it all manually right now. We have consensus and agreement to embargo future infra generic changes for a specified time frame. The moves needed are exactly mapped in the spreadsheet you made. Is there any chance the spreadsheet moves can be executed in some kind of semi-automated fashion on the backend?
Can someone at least please recreate Vesicariae so we can use that?
wildskyflower and charlie - I recommend trying to convince a curator who has time to curate in the direction of the spreadsheet.
with all due respect, shouldn't the person who broke it fix it? there are so many things constantly being split to the point it's hard to even use iNat, so curators have plenty of time to spend on taxonomy, is it really true no curator can be spared to revalidate Vesicariae? I'm frustrated here. Splitting this out too early was a priority, but fixing the mistake hasn't happened for months. @rynxs ?
The group consensus here is that there's a rather large problem, so it would be nice to have more conversations about when it could possibly be fixed. Rushing it won't fix anything, though.
Pulling something down here that @rynxs said farther up the thread - "taxa can be renamed/reranked by whoever made them without a swap or split, which was the plan for when these groups were named." What's the possibility that this could start happening fairly soon?
@charlie I can't undo taxon swaps, and I have had no involvement in the planning of the reversal of these changes. If you want the changes reversed, I am not a person to ask for this to happen. As you are aware, only staff can reverse taxon changes. I'm also not unsatisfied with the current state of Carex taxonomy, regardless of what you choose to call it.
@natemartineau see comment above. If you send me the list of name/rank changes to make to minimize stress on iNat's system and user confusion, I can do that, but that will be the extent of my involvement.
In this case I don’t recommend reverting any taxon changes- too much complexity and liable to add layers of more mess. The curation work I recommend is to create new taxa and move taxa following the spreadsheet .
If we don’t have the curation capacity to maintain subgenera sections and subsections nodes not in POWO I recommend removing them and grafting species to genus Carex
In that case, I would propose keeping the GCG/Roalson paper as the framework for infrageneric classification of Carex, and "deviating," so to speak, underneath it. From talking with a number of people on iNat, apparently many fewer people are concerned with accurate taxon rank labels than was my original impression, so elevating the Hirta Clade to section becomes plausible, with staff consent. Reconstituting the former groups that happen to be placed in their entirety within a parent clade also becomes possible, as do the smaller complexes under the Hirta Clade.
Is it possible to lock Carex once this is done? The move of the Carex Hirta clade to sect. Paludosae was not done by me, but another curator. No reason was given for why, but I suspect there are many inexplicable changes of this nature that would need to be investigated to be brought back into a conformity with GCG/Roalson. The 2021 paper by far and away presents the best model for a global infrageneric treatment of Carex, so I think using it as a baseline (much in the same way POWO is used) is probably the best model going forward. Once this is done, locking the genus and only opening it following community discussion would prevent similar incidents from happening.
I've moved the Hirta Clade back to subg. Carex. I'm going to be leaving for a trip soon, so don't expect any timely replies, although if I have internet I may be able to at least read what's being said. Please try to limit the bloat on this thread, it's incredibly difficult to keep up with this flag as for some reason it's always most active when I'm about to leave/on a trip.
Can you please just recreate the vesicariae clade then? I get that you don't want to, but it's causing problems to have it continue to be broken. I'll stop posting here when the problem is fixed, i promise.
"Rushing it won't fix anything, though."
Fixing it will fix it though. By restoring the Carex sections.
"If we don’t have the curation capacity to maintain subgenera sections and subsections nodes not in POWO I recommend removing them and grafting species to genus Carex"
This just feels unnecessarily punitive. We had an agreed upon scheme, breaking it further won't help. Some people like this not fully peer reviewed (?) paper from 2021, but it's not appropriate to use it for iNat's taxonomy at this time. Hopefully it's never used, but that's another issue.
"Once this is done, locking the genus and only opening it following community discussion would prevent similar incidents from happening."
I'm OK with it being locked as long as the entire community is able to be involved not just the splitter faction.
I will see if I can find time to fix the Hirta clade/Vesicariae specifically this weekend as there are only a few dozen taxa affected and I think that set of changes is basically self-contained. I'm not sure that I'll be able to get to everything else in the whole genus. Maybe splitting it up into manageable chunks like that is better for server load anyway. Its mostly just that if each regraft takes even 10 seconds that adds up when doing over 1000.
Yeah, i know it is a pain, it took a long time to do the first time i created it when i was still a curator, too. It's a lot easier to undo stuff like that than do it, and i am surprised it can't just be restored, but i guess staff isn't able or willing to do it that way. Sorry and thanks.
Well the advantage of the way it is now is that @rynxs did a good job of getting everything in the whole genus to an exact match, which is what makes it possible to just have a spreadsheet with an exact one-to-one mapping of the way it is to the way we want it to be. Even if it could be done wholesale, on the level of the whole genus just reverting the changes could risk creating more work, because then we'd have to go back through and figure out what matched the desired state and what still needed more work. That would require more cognitive effort, whereas executing the changes in the spreadsheet directly is tedious but easy; I usually find that most of the effort of making a change is deciding what to do in the first place.
The way the database is currently designed changes are probably not really fully invertible in a simple way anyway, and a partial inversion could be the worst of both worlds. I know there are some forum posts by e.g. @aspidoscelis that advocate database changes to make it easier to invert complex changes but I'm not sure it is an entirely simple thing to do at the sites current scale and resources.
I mean clearly there needs to be better communication, in the least people who created a taxonomic unit should be notified if there is a proposal to change it this dramatically. I agree it was a lot of work for something that has to be undone, which is unfortunate, and should have been avoided. It's a broad problem here, curators are rushing to put in the newest taxonomy that often isn't finalized or peer reviewed, POWO isn't great but at least using it was consistent but people have gone even beyond that. I know this thread has gotten huge but I am not sure where else to address it, any time i post about it on the forum i get told to move the discussion to taxa threads, and here i am being told to not have the discussion in taxa threads.
We made Section Vesicariae and followed the spreadsheet to move species to that Section https://www.inaturalist.org/taxa/1500945-Vesicariae
If other curators are inclined to follow the spreadsheet to move other species around following that spreadsheet that would be great. But that should be done by curators, not staff, so please set expectations accordingly when persuading volunteer curators to make changes
thanks all
@loarie if you and whomever else have committed to dissolving part of the Carex hirta clade, then the entire thing needs to be dissolved and a new deviation created for that group. I wouldn't consider this resolved until that's done, as the current state leaves Carex hirta clade IDs as disagreeing with anything in Vesicarieae.
Staff only committed to following the spreadsheet to recreate the Vesicariae clade when we were asked to intervene there. We're not getting further involved but thank you to all volunteer curators for making any additional needed changes or discussions.
Speaking for myself - I'd strongly prefer a policy of strictly adhering to POWO including the absence of internodes (e.g. eliminating nodes between genus and species) to reduce taxonomic decision-making burden/expectations of iNat but I know thats not widely shared
(alternatively if someone set up and maintained a taxonomy for Genus Carex or Family Cyperaceae with different taxa/nodes on http://taxonworks.org/, iNat could link into that as a reference or a taxon framework anchored to the Genus or Family that we could link in to and we wouldn't have to decide on and keep track of internodes here).
Thanks for fixing that Scott. It would be a real loss to lose clades like that especially given the state taxonomy is in right now, so I hope that never happens. It would really create challenges in this group, but so does this free for all with unpublished primary sources that caused this flagged edit and all the problems here.
This tool by @pisum https://jumear.github.io/stirfry/iNatAPIv1_identifications.html?taxon_id=1460536&rank=complex&user_id=frousseu might be helpful to spot and clean the Complex Carex hirta IDs that are now blocking IDs.
I am communicating with @wildskyflower and The Hirta Clade complex will soon be dissolved, so don't worry too much about the conflicting Ids at the moment.
Sorry I was unable to finish this last summer. Thanks to the staff for recreating Section Vesicariae in my absence.
The Hirta clade is now empty of taxa, but not observations. Lupulinae is reconstituted, as is Squarrosae with the new Carex frankii complex, and Section Carex. In total, as of this writing, I have made about 300 changes, but there are still over 900 to go to reach agreement with the spreadsheet. I will update the taxon framework relationship for the Sections later but it adds time to edit it as I go so I have not yet.
So far, I have finished Section Anomalae, Section Chlorostachyae, Section Confertiflorae, Section Euprepes, Section Graciles, Section Ischnostachyae, Section Molliculae, Section Paludosae, Section Setigerae, and Section Shortianae. Section Spirostachyae has been edited to the sense of Section Echinochlaenae listed in the spreadsheet, but I have not swapped the name to Section Echinochlaenae because I realized the name has always been Section Spirostachyae even before the rearrangement, and there appear to have been some kind of previous discussion outside this flag about that, so I am holding off on changing the name.
I will have to swap the remaining IDs in the Hirta clade back to to subgenus Carex, but I will leave it for a few days to allow people to change their direct carex hirta IDs so the sense of them does not change. Waiting is preferable because it is very difficult to search for the old IDs after the swap and there are something like 1000 observations affected and I would hate to lose those IDs.
This search should give all observations where the sense of the display taxa will be relaxed to Subgenus carex if they are not altered before the war after the swap (as of this writing there are 485, but @elacroix-carignan has been working through them):
This search will give all observations with an active Carex Hirta clade ID. It isn't fully working yet because the re-indexer hasn't finished processing the species moves (which is another reason to wait to swap the clade). I expect it will work by the ~morning. I will tag IDers with direct IDs to the taxa once the search works. Fixing these IDs may affect the community taxa after the swap, but will not affect the display taxon, and will only affect RG status if 'cannot be improved' is voted for:
Thank you for all the work!
@wildskyflower I went through pretty much all of the observations under the Hirta Clade complex and added revised identifications. I think it is time to go forward and dissolve the Hirta Clade complex on INaturalist!
Thanks so much for moving so many observations in such a short time!
I will swap it back to subgenus, but I am about 100 moves from finishing subgenus Carex and am focusing on finishing some more of the Sections first; I'm trying to spread out the moves that affect >~ 1000 observations over several days at least to make it easier on the servers and dissolving the hirta clade will be one of those. No individual move is huge so far, but in aggregate I worry it is kind of a lot to be queueing all at once right now. At the moment I'm breaking up the Castanea clade.
The city nature challenge taxonomy change freeze is officially starting tonight so I don't think I should make any more changes because they might not finish running by the start of the freeze. Most of the sections in subgenus Carex are either finished completely or not really started.
@frousseu @birds_bugs_botany @wdvanhem @alexgraeff @bickel @seanblaney @sedgehead @jakes26 @elbourret @charlie @ericpo1 @benandkerstyn @michael_oldham @choess @wildlander @radbackedsalamander @elacroix-carignan You each have at least 10 IDs on observations that will be affected by the removal of the carex hirta clade. Any IDs left in the clade when it is removed will revert to subgenus carex, but many of your IDs could potentially be refined to a Section, e.g. Vesicariae, Lupulinae, Carex, or Paludosae. @elacroix-carignan has corrected over 1,000 of the observations that would have been most affected. If you would like to review your IDs that may be affected, this search should give them to you:
There are currently only 70 or so observations that will have their display taxon changed by the move that elacroix-carnigan has not been able to refine. More will likely have their community taxon change, but it is very difficult for me to estimate exactly how many. If anyone I tagged (or anyone else in the thread already) would like to review the 70 or so observations that will have their display taxon reverted to subgenus carex by the move, they are here:
Also if anyone wants to review the similar set of observations that will be affected by the removal of the Carex castanea clade, it is here:
Thanks! This was helpful.
Thanks for all your work on this!
Fixed mine :^)
Any sedgeheads want to get www.sedgehead.com? I'm considering closing my website. As for the above discussion, I'm not involved. I'm to the point in life, age 72, the next generation will have to worry with it. I spend my time playing on inat, studying Chinese, or exercise.
Does anyone have an objection if I leave Section Praelongae intact instead of lumping it with Phacocystis? Praelongae already existed on inat before these changes, and none of the changes affected the concept of it at all. Therefore it was and is monophyletic (and the Phacocystis concept will be polyphyletic with or without it). It is also a tiny amount of observations that would be lost in the much larger Section Phacocystis. I suppose I could also demote it to a complex, but that seems kind of unnecessary because it really is a Section.
Also, Carex Flacca Clade is empty now, if @elacroix-carignan anyone wants to check the IDs in it you can find them here: https://www.inaturalist.org/observations/identify?reviewed=any&quality_grade=needs_id%2Cresearch%2Ccasual&place_id=any&exact_taxon_id=1460522&photos=true there are less than two pages of observations to review so it shouldn't be much work compared to the other complexes.
I'd vote to leave section Praelongae at this time.
https://www.inaturalist.org/observations/13434027#activity_comment_5897d6ea-acfd-4103-a674-c350a7498818
"vesicariae" is still being used as a section, do not delete this