Flag for Taxon: vascular plants (Phylum Tracheophyta)
| Flagger | Content Author | Content | Reason | Flag Created | Resolved by | Resolution |
|---|---|---|---|---|---|---|
| loarie | vascular plants (Phylum Tracheophyta) |
proposal for adopting POWO as a taxonomic reference |
Aug. 12, 2018 09:27:34 +0000 | loarie |
made transition official |
Comments
I antecipate a few weeks of curating hell, but I like the proposal and the fact that you took the time to explain the curating procedure.
I had a look at the families I'm most familiar with (seagrasses), and generally I like what I see. There's a lot of controversy in some genera but I think they did a good job. I do see a bit of a British bias in recognising Zostera angustifolia as an accepted species (no phylogenetic support but still used in the UK due to tradition), but I can live with it.
I guess you were talking about fossil species when you mention extinct taxa, but POWO does seem to include recently extinct species. Personally I don't see the point of having fossils on iNat, but it's good to keep recently extinct species to account for possible Lazarus taxa.
I'm also looking forward to finally having a clear, global authority and settle the Sedum/Petrosedum wars here on iNat and prevent stuff like this:
https://www.inaturalist.org/observations/406466
Ok with me to proceed. Thank you for building a productive collaboration with colleagues at Kew, and for all the thoughtful effort that you put into this detailed proposal. Nicely done.
Both TPL and POWO still have some taxonomic discrepancies. For example neither authority considers Dichanthelium to be distinct from Panicum. This seems like a major discrepancy considering the multitude of morphological and molecular studies demonstrating that these should be treated as separate genera. There seem to be some other discrepancies in Poaceae that would be a mistake to adopt on iNat (in my opinion).
@loarie creating an up to date, global vascular plant database is a massive challenge and I like where POWO is going. I just wonder if there are some taxa, like Poaceae, that need more review before we adopt POWO's taxonomy on iNat.
Edit: to expand on the Dichanthelium issue - POWO uses a 2000 reference to support lumping Dichanthelium with Panicum. Surely there are more recent and more authoritative references that would support splitting the two genera based on recent molecular evidence.
As noted in the Google Group post, discrepancies are bound to arise with so many species under one global authority, but I think adopting Plants of the World Online is an overwhelmingly positive decision, and one I have been hoping for. I checked out Solanaceae, the plant family I am most familiar with, and it seems to have been greatly expanded since I last looked at the site. I think we should proceed with POWO.
Maybe we should start a Google spreadsheet for the requested changes or possible explicit deviations? Dichanthelium is also one I feel pretty strongly about :)
Do you have available a list of spp. on iNat not accepted by POWO? I would like to compare to our regional flora.
I'm in favor of this, especially if it helps to get rid of those annoying duplicates, like Mimulus breweri and Erythranthe breweri. It'll definitely take some getting used to, but I think it will lead to a more workable system in the end.
Better now then later
I do a lot of observations to collect data
And have noticed a few issues here and there
I support moving forward on this
The Mimulus case study is a perfect example of why I'm for stitching to POWO and the sooner the better as I'm sure there are more re-orgs coming that will make the regional lists more and more complicated to join.
hmm, at a glance it looks ok with me, though there's probably something in there that I don't like. At least it doesn't mutilate Cornus. The mimulus ----> erythranthe swap seems like something a lot of people are looking for and hoping for soon, so this would get us that.
Among the ferns, POWO seems to be inconsistent in whether it follows PPG 1 or not (e.g., it follows the segregation of Blechnum s.l., but not of Botrychium s.l.).
(POWO cites the Checklist of Ferns which in turn seems to largely go back to PPG 1.)
While I have reservations about PPG at the genus level, it seems confusing for POWO to follow some but not all of it, without explanation.
I support using POWO to standardise the family level tree for plants on iNat, and perhaps genus-level too. It makes a lot of sense to follow Kew's lead on that, as long as they're invested in keeping POWO up-to-date and do so in a consensus-driven way.
However, I'm wary of making iNat constrained to POWO at a species level in cases where regional databases are being kept more up-to-date.
I asked some NZ plant taxonomists and they see POWO as an improvement over TPL but, with a quick look, found missing NZ taxa.
For example Pittosporum serpentinum was described as a subspecies in 1998 and elevated to a species in 2003 but is still missing from POWO. It's on iNaturalist here, with observations, and sourced to the NZ Plant Names Database.
Also missing is Anemonastrum tenuicaule (on iNat) and Oxybasis ambigua (on iNat). These were described earlier this year but are already accepted and available on the NZ Plant Names Database and observations of them are on iNat.
I imagine there are plenty more cases like these.
Admittedly New Zealand is a simpler situation than most as we're a large isolated archipelago with high species-level endemicity. Adopting changes from our regional names database doesn't tend to complicate things for others on iNat.
I expect a regional-POWO hybrid model is still the best for iNat, at least at the species level and lower.
It's frustrating trying to make an observation of a species locally accepted but not on iNat. We already have enough grief keeping track of taxa that are widely accepted as different by NZ botanists but nobody's found the time yet to update them in print. For example, a 1997 revision regarded Ozothamnus vauvilliersii as synonymous with Ozothamnus leptophyllus but most botanists are skeptical of this and continue to use Ozothamnus vauvilliersii. Because NZ Plant Names follows the 1997 publication, people are begrudgingly identifying their Ozothamnus vauvilliersii as Ozothamnus leptophyllus, with comments. If there's a many months to years lag in regionally accepted species showing up in POWO, I worry that this will make this kind headache much bigger.
FWIW, I would still use FNA as the primary authority for North American plants before POWO. For all of the reasons just described by @jon_sullivan.
I agree with @wdvanhem on North American flora but for all others I think POWO is a good model to have. I don't think there is any database without its flaws
Thanks for all the feedback on this.
@bouteloua the potential explicit deviation doc sounds like a good idea.
@wdvanhem and @jon_sullivan, I just wanted to double check that your case-by-case concerns with POWO (e.g. that its missing Pittosporum serpentinum) can be interpreted as lobbying for explicit deviations from POWO and not maintaining the regional flora-first approach we've been having so many problems with (e.g. my Mimulus example)
@leonperrie my understanding from Kew is that they're not ready to stand behind the POWO ferns yet, e.g. from Rafaël Govaerts: 'The fern families are very messy (the species of some genera are in 7 different families!) they are to be cleaned up over the next months so you should not rely on those for now.' Could we just go with PPG for now (which just goes to genus) as a global authority and hope we can shoehorn the species into that?
We haven't heard from everybody (eg @tsn @sambiology @choess @tonyrebelo @whiteoak @stevejones) But sounds like folks are generally on board with this idea? Pending any new red flags, how about giving the green light Wednesday of this week? If so I'll kick it off with a short blog post to let the broader community know.
I'm all for it. Whatever authority we go with, I will start to link to it with all taxonomic questions. No authority is flawless, and of course there will be discrepancies, but I do think that choosing one and running with it is the best way to go.
My plant taxonomy professor told me, "If you're comfortable with the names of plants, then you're not up-to-date." :) It's eternally changing, and that's ok with me! :)
SANBI through BODATSA supports POWO. Although southern Africa was not in the core initial region, there is sufficient overlap that most of our taxa are well covered.
This is a significant improvement on previous (and most other) sites.
There were significant ambiguities introduced in the loading of the southern African BODATSA dictionary into iNaturalist, and at last we have an up-to-date external reference in POWO to defer to (versus TPL - over 5 years out of date).
Any discrepancies between BODATSA and POWO should be referred to both authorities for attention, but our community can take care of that.
I do suggest though that iNat offers POWO the use of its photographs: ours are far more variable and superior in many cases.
An issue for us is extinct species. We have significant of these (see
https://www.inaturalist.org/projects/extinct-in-the-wild/journal/archives/2018/03 ) - and like the https://www.inaturalist.org/projects/the-search-for-lost-species we would like to focus on these. However, I presume by extinct above that "long extinct" or fossil is implied.
I fully support the move to POWO, and that any valid discrepancies be first addressed by bringing these to their attention.
Yep, sorry, didn't have too much to add. I do support the move, though with the same reservations concerning regional floras expressed by @jon_sullivan, @wdvanhem and @bugman1388. I like the idea of lobbying for explicit deviations where taxa are completely missing from POWO, not simply synonyms listed under another name (I repeat my frequent refrain: thank goodness for synonymy). However, it appears POWO will be adopting, adapting and improving more or less continuously. Proceed with my blessings.
There seems some suggestion that where iNaturalist differs from POWO, iNaturalist will ask POWO to make a change. Sometimes they will do that, but there will also be plenty of instances where there are genuinely competing taxonomic schemes, especially given that most genera (and ranks above them) are international.
I appreciate the usefulness of having one international framework like POWO underpinning iNaturalist. And while I note that people are appealing to their regional authorities, I'm assuming that the point of the proposal is that POWO takes precedence wherever there is conflict, even for those who'd prefer FNA.
So @loarie, my main question is how does iNaturalist deal with situations where regional representative taxonomic authorities differ from POWO? There is a nice existing solution for regional differences among common names, but I'm not aware of one for scientific names.
The Australians, for instance, have their Australian Plant Census, which involves a representative from each state herbarium determining the name to be used nationally (with voting if need be). There are good reason why APC's determination might differ from POWO, and where it does, knowledgeable iNaturalist users in Australia are going to be perplexed as to why "their" taxonomy is not being followed. If all of a country's authoritative resources follow one taxonomy, but iNaturalist uses a different 'international' taxonomy, it's arguably not good for iNaturalist or naturalists in that country.
Is there an elegant solution that covers such regional differences to taxonomic schemes even if iNaturalist is using a single underpinning framework? Or do we just have to suck-it-up and all treat POWO as the one world authority? (even though that's not their stated intention.)
Separately, I'd be wary about making exceptions to POWO; that would seem to be asking for work and trouble - who will make the call as to whether iNaturalist deviates from POWO? Isn't the point of using POWO for it to be the ultimate reference in all cases of (regional) conflict? If not, why use it at all?
I did actually respond earlier. See my (brief) comments above.
whoops sorry tsn!
leonperrie, iNaturalist shares a single taxonomy so there's no solution if different people on the site want to use different taxonomies. If regional representative taxonomic authorities differ from POWO our options are to go with POWO, or make an explicit deviation from POWO in such a way that matches the regional authority. Re: who will make the call as to whether iNaturalist deviates from POWO, it would be a community decision. If there's a issue with POWO that someone in the community feels strongly about they should raise it with the community by flagging the taxon. Then the community would discuss and if people feel like its an improvement over POWO (and I realize this is often arbitrary/subjective) we should run it by Kew and see if they'll update POWO. If they won't/can't in a timely matter then we can decide to deviate from POWO. I agree with you that deviating from POWO creates lots of work/trouble. But a shared taxonomy will only work if it has enough buy in from the community.
There is precedence for the 'explicit deviations' approach. We've been managing deviations from Reptile Database for Reptiles, from Amphibian Species of the world for Amphibians, from the IUCN Global Mammal Assessment for Mammals, and from Fishbase for Fish (see more here). Fishbase is probably the best example where we have a really engaged community of Fish experts (a good thing) and as a result lots of explicit deviation requests to manage (a bad thing). You're right that its a lot of work, but if you can think of a better way for reach rough consensus around a shared taxonomy that has broad community buy in please propose it!
I just want to clarify something: is the proposal to go through and update iNat's vascular plant taxonomy on a species by species basis? While I appreciate that it may be beneficial for some taxa (e.g. Phrymaceae), such an "update" would be a step backwards in many cases.
How do we know that POWO's treatment reflects the most up-to-date treatment for all taxa? Clearly there are issues in Poaceae. Another example I've just found is the genus Lithospermum. The plant formerly known as Onosmodium molle was recently split into several taxa, all of which have been lumped into Lithospermum. Plants called O. molle in Ontario and the northern US are now generally accepted as L. parviflorum, but POWO shows L. parviflorum as a synonym of L. carolinianum...a taxon which USDA calls a synonym of L. caroliniense, a completely different species. If we apply POWO as the primary authority, northern plants formerly called Onosmodium molle will now be called L. carolinianum, a name that regional authorities associate with a completely different species (L. caroliniense).
Another concern is that we don't "undo" taxonomic changes on iNat which already deviate from TPL and other global authorities but which are well-researched and supported by experts in those taxa. Much hard work has gone into curating some of these taxa.
I support having some global authority as a final arbiter for taxa over which there is major disagreement. I am fairly indifferent to what resource we use for this...POWO, TPL, or something completely different. I just want to make sure that we don't dive into a total overhaul of vascular plant taxonomy that will then have to be re-curated...
Onosmodium/Lithospermum is a good case to examine on iNat because it also has multiple duplicate taxa that have been active for a while, since TPL is an unsatisfactory arbiter (e.g. treats several varieties as synonyms of their parent while regional authorities actually call them separate species). As I commented on the taxon swap yesterday, there would be several taxa which should be ironed out before committing anything (brought up to POWO as incorrect, added to the database, or treated as explicit differences) https://www.inaturalist.org/taxon_changes/36633
That said I'm not sure what or how "rough consensus" happens in this online format when there is just a small number of voices out of the whole community being put forth as well as a limited amount of taxonomic expertise to recognize/understand the above situations.
I'm continuing off bouteloua's and wdvanhem's Boraginaceae/Lithospermum example. Remember Kew treats Boraginaceae sensu lato, ie they include Hydrophllaceae etc. I did a quick analysis of the Boraginaceae species currently in iNat that are not valid names in POWO to explore this further more concretely.
There were 325 names that were found in POWO as synonyms and there were 184 names weren't found in POWO as synonyms. Here's the complete table https://docs.google.com/spreadsheets/d/19UKCVW5OeCcrnAMFA5XXXuAKX0i7PwW-6Iqj_vaQCz8/edit?usp=sharing
Lets define 2 types of issues:
1) where a name was found in POWO as a synonym and we think it is a legit species
e.g. in bouteloua's Lithospermum example, POWO thinks:
Lithospermum bejariense -> Lithospermum caroliniense
Lithospermum parviflorum -> Lithospermum carolinianum
it seems there's support that Lithospermum bejariense & Lithospermum parviflorum should be valid species. So we'd be proposing to deviate from POWO as follows:
{inat: ["Lithospermum caroliniense", "Lithospermum bejariense"], powo: ["Lithospermum caroliniense"]},
{inat: ["Lithospermum parviflorum", "Lithospermum carolinianum"], powo: ["Lithospermum carolinianum"]}
2) where a name wasn't found in POWO at all and we think it is a legit species
e.g. Phacelia californica has nearly 500 iNat obs https://www.inaturalist.org/taxa/53170-Phacelia-californica and here in CA is definitely considered a legit species. I suspect its commission from POWO is an error. We'd propose deviating as follows:
{inat: ["Phacelia californica"], powo: []}
As tonyrebelo mentioned, ideally we'd first get buy in from any proposed deviations from the community, then we'd bring these to the attention of Kew and see if they can make updates. If they can/will/do that would probably make using POWO much more palatable. If they can't / won't then we would have to decide whether we'd want to / be able to make and maintain these deviations.
It might be nice to try gauging Kew's response to some deviation proposals that we feel strongly about. It doesn't look like my analysis of Phrymaceae surfaced any of these, so maybe lets work on Boraginaceae and see if we can agree on a set of proposed deviations to bring to Kew. We can use this doc:
https://docs.google.com/spreadsheets/d/19UKCVW5OeCcrnAMFA5XXXuAKX0i7PwW-6Iqj_vaQCz8/edit?usp=sharing
Step 1: try to find POWO destinations for the names not found in POWO as synonyms
Step 2: highlight any names that we think are valid without POWO destinations (e.g. Phacelia californica) as a proposed deviations
Step 3: highlight any names that we think are valid with POWO destinations (e.g. Lithospermum parviflorum distinct from Lithospermum carolinianum) as proposed deviations
Step 4: present these to Kew and see what they say
Thoughts?
I fully support switching the main reference to POWO from TPL as long as we treat it similarly to the way we treated TPL. It does reflect a huge improvement but still has many of the same problems of the previous reference (and really any plant database). As long as we all understand that, keep it in mind when making taxon changes, and check to make sure that there isn't aren't legitimate reasons why our taxonomy differs from the source, I feel like the switch should go off seamlessly.
FYI, I found a few situations where POWO definitely differs from current taxonomy, but I can live with the examples I have found so far that haven't already been brought up. Probably just means I need to do more digging.
Hi nathan - to be clear, the proposal is to (a) switch from TPL to POWO, but also (b) switch from regional flora first with TPL/POWO as a tiebreaker to TPL/POWO first with case-by-case deviations to resolve high priority regional issues. Are you on board with both (a) & (b)?
I definitely agree with (a). (b) is a much more complicated question. What are you including in the category "regional flora"? Are primary literature sources included in that category or otherwise? What about monographs? If so, I'm not really on board with (b). Monographs and most taxonomy-based primary literature sources are by far the most reliable unless they are quite old. Floras, on the other hand, address a wide diversity of plant groups making it easier to overlook certain recent taxonomy changes. Flora of North America is in some ways more like a collection of monographs (if a rushed one that has led to a few mistakes here and there), which is why I trust it, in general, more than some other floras. Ideally, I would want recent (maybe defined as 5-10 years old?) monographs and taxonomy based primary literature sources as first priority and consider POWO second (since most people are not going to check or perhaps even have access to the sources, you may essentially have the same effect except in the better-researched taxa). You could then have the regional floras last I suppose (though my preference would be to compare and consider recent ones if there are recent floras).
The exception for expert opinions may essentially be expressing this acceptance of the monograph/taxonomy articles above the database, but it isn't really articulated. Anyway, that's my two cents from a plant taxonomist point of view.
if you're not on board with b, nathan, whats your proposed solution to the Mimulus/Diplacus problem, the Lithospermum/Onosmodium problm etc.?
I have to agree with @nathantaylor7583 on this one. The current vascular plant taxonomy on iNat reflects years of curation by experts and most of this has followed literature and expert opinion which are far more reliable than any existing global database. I am fine with switching from TPL to POWO but I see no reason to universally adjust our taxonomy to match POWO. It's clear that POWO's taxonomy will help to clean up some taxa (like Mimulus) and in these cases I say we use it. But it will also further muddle other taxa (like Lithospermum) and I see no reason to adopt its taxonomy there. The most concerning situation is where POWO's taxonomy is clearly outdated (e.g. Panicum vs Dichanthelium) and would set iNat's taxonomy back to a position where major curation is needed to reflect taxon-specific literature and regional checklists.
Is the solution not simply to update POWO?
There will always be lags, and iNat has slightly more curators than POWO, so iNat can always be expected to be more up to date for charismatic groups.
I dont know for other regions, but I am often beleaguered by users with preprints demanding to know why we have not updated our southern African part of the dictionary, when the publication date is still weeks away. In other groups no one notices the same species on twice under different genera.
Can we not negotiate with POWO that updates to plants on iNat (suitably referenced) will be automatically forwarded to them for consideration?
The question is what to do if they reject the update? But how often will that happen?
Meantime, can we not merely document any such discrepancies, as being done for mammals?
((I still find it amusing that iNat gives so much credit to experts on the taxonomy side vs global databases (also maintained by experts), but none on the ID-reputation side where an expert is rated the same as a novice. Hopefully the proposed reputation system is maturing ... :: sorry: this aside is not for discussion here))
I feel like some users here are under the impression that iNaturalist's plant taxonomy is all a well-curated, community-driven system that would only be compromised by POWO. This may be true for some charismatic groups, but in my experience on this site, most plant genera and species are missing. Subfamilies are empty. Other parts of our tree are just neglected. I feel like this is a problem that arises from being overly reliant on regional databases over international ones. We may have all of our plants from North America, New Zealand, Australia, Southern Africa, and Europe, but what about everywhere else? We can't find a regional plant database for every location on Earth. How else are we to convert some plant groups into complete nodes, with an active list of how many exist and still need to be observed on the site? I think we need POWO. There is a precedent for deviations from global authorities for other complete taxa (mammals, reptiles, cephalopods). There is no reason to think that the curatorial work that pushed deviations from The Plant List will be undone. All it takes is a working list of intentional discrepancies from POWO.
"I still find it amusing that iNat gives so much credit to experts on the taxonomy side vs global databases ..." - i don't understand this statement, because the opposite is true. Only secondary references are used for taxonomy, per the guidelines.
I'm starting to wonder if the 'regional' side of the argument might be misunderstanding iNat's current policies.
We do have some branches of the tree of life like Fungi which represent 'careful direct curation by the community of the primary literature' (or 'free-for-all anarchy' however you want to look at it). But thats not the current case with plants. Is this primary-literature approach actually what the 'regional' side is arguing for?
Or is the argument truly for maintaining the current policy: with plants we're supposed to be comparing 6 regional floras and using TPL as a tie breaker.
Because the current regional flora first policy has some has some weird side effects. For example, some people consider the Saxifrage family Mitella sensu lato and others consider it to be Mitella sensu stricto with Mitellastra, Mitella, Pectiantia and Ozomelis split off.
Of the 6 floras Ozomelis diversifolia/Mitella diversifolia only occurs in Calflora which uses Ozomelis diversifolia so the policy would say we need the genus Ozomelis and species Ozomelis diversifolia to be included
But similarly Pectiantia breweri/Mitella breweri occurs in both VASCAN (as Mitella breweri) and Calflora (as Pectiantia breweri) so the policy would be to use the global reference (POWO or TPL) as the tie breaker. POWO goes with Mitella breweri. So we'd also have bits of Mitella sensu lato lingering around.
From my perspective the major 3 bad side effects of the regional first approach are:
1) confusion about which name is the valid name - its really tough to look through all these floras and find out where a species is represented in order to tally the votes. Plus there's requests to add new floras all the time which impacts all of these decisions (e.g. say we added a hypothetical Oregon flora that had Mitella diversifolia, we'd have to swap Ozomelis diversifolia -> Mitella diversifolia). If we went with the 'global reference with explicit deviations' policy we'd instead just need to refer to POWO and a single shared table of explicit deviations.
2) confusion about what genera 'mean' - while its clear that POWO is aware of the Mitella split but are choosing to go with Mitella sensu lato for now (presumably because the paper that made the split didn't examine asian Mitella)
http://www.plantsoftheworldonline.org/?q=Ozomelis+diversifolia
iNat's definition of Mitella currently means mostly Mitella sensu lato except for excluding Mitella diversifolia as Ozomelis diversifolia and maybe a few other things like that. This makes it very hard to quickly get on the same page about what Mitella refers to.
3) the current 'regional flora first' policy actually prevents curators from doing things like curating consistently towards Mitella (sensu lato) or Mitella (sensu stricto) by tying our hands with these weird rules. Both the 'free-for-all primary literature' approach and the 'global reference with explicit deviations' approach would allow us to do. If folks are 'free-for-all' curating plants at the moment, while that might be helpful its technically against the current policies.
I'm happy to discuss the pros/cons of the 'free-for-all primary literature' approach vs the 'global reference with explicit deviations' approach if thats what is actually being debated here. But I first wanted to get clarity on whether the 'regional' side of the argument here is really advocating for the current 'regional flora first' policy or actually a 'free-for-all primary literature' alternative.
@loarie, to answer your question, I would probably follow POWO or some other trusted database (I admit to liking ITIS, though I know others don't) for the groups you mentioned until someone looked into the primary literature to find what the best nomenclature would be (or until I found the time to do so). The thing I'm worried about is that someone puts the time into finding and changing the taxonomy to reflect the most recent literature and someone changes it back to reflect a database like POWO. If there is a way to safeguard against that, I'm not quite so worried about what the primary reference is.
Also, I'm not really arguing for the regional flora side. I'm fine with POWO taking higher priority. My main point about Flora of North America was that it is more like a collection of monographs which gives it a bit greater nomenclatural weight in scientific circles. That said, some parts of FNA are becoming out of date as long as it has taken to produce (the introduction was published in 1993 and they're still not done with the project).
As for free-for-all literature vs. global reference with deviations, I do prefer the former but see the appeal of the later. Global references work better in general and act as a standard that less knowledgeable curators can refer to, but will create mistakes. The primary literature approach allows more flexibility, makes it much easier to correct mistakes when they are made, and generally provides the best nomenclature if a member of the community is knowledgeable enough to provide it. But, there are certainly going to be times when we are not on the same page and could potentially lead to more conflict. But with this approach, I don't see any reason why we can't use POWO in cases of poorly curated taxonomy. I would tend to prefer the flexibility over the potential for conflict.
Are there any plans to add comments sections to taxa? If there were a way to tell other curators on the taxon pages the nomenclatural method that is being followed and room for us to discuss it on a case-by-case basis, it might prevent future conflict if the primary literature free-for-all is chosen. A curator could discuss directly why they differ with the global reference of choice and cite new literature. It might not even have to be visible to the public and could be another tab under curation.
well, i myself don't support chasing primary literature for plants. Things are changing so fast, it would create a nightmare of constantly changing names and sometimes even swapping back and forth. The nice thing about secondary literature is it doesn't change as fast. iNat is a place for people to share and record biodiversity data, and that doesn't work well if we are constantly trying to chase the latest paper, which even the 'pro' policymakers and botanists generally don't do, at least not consistently. To say nothing for all the plant newbies who wll probably find it really frustrating and confusing. Let's please not try to do it here.
Regional floras like Jepson, Flora of Nova Anglicae etc... those i am not opposed to continuing with
Many thanks to those who helped go through the Boraginaceae spreadsheet. I just emailed our collaborators at Kew with the subset of Boraginaceae names we're brining to their attention. Of the 325 iNat names that were found in POWO as synonyms, we're bringing these 3 to there attention because we think they should be valid names:
Lithospermum bejariense
Lithospermum parviflorum
Onosmodium bejariense
Of 184 iNat names weren't found in POWO as valid names or synonyms, we're brining these to there attention as potentially valid names (or if not, help figuring out what valid names Kew thinks they are synonyms of).
Amsinckia furcata
Anchusa ovata
Cryptantha traskiae
Echium coincyanum
Echium portosanctensis
Echium pustulatum
Heliotropium socotranum
Myosotis bryonoma
Myosotis caespitosa
Myosotis persoonii
Myosotis retrorsa
Myosotis retusifolia
Myosotis subvernicosa
Myosotis umbrosa
Nama constancei
Nama jamaicense
Nonea daghestanica
Phacelia adspersa
Phacelia ambigua
Phacelia anelsonii
Phacelia argentea
Phacelia argillacea
Phacelia argylensis
Phacelia austromontana
Phacelia barnebyana
Phacelia beatleyae
Phacelia bicolor
Phacelia bolanderi
Phacelia breweri
Phacelia buell-vivariensis
Phacelia californica
Phacelia calthifolia
Phacelia capitata
Phacelia coerulea
Phacelia congdonii
Phacelia cookei
Phacelia corymbosa
Phacelia cottamii
Phacelia covillei
Phacelia cronquistiana
Phacelia curvipes
Phacelia davidsonii
Phacelia egena
Phacelia eisenii
Phacelia exilis
Phacelia filiae
Phacelia filiformis
Phacelia geraniifolia
Phacelia glabra
Phacelia glandulifera
Phacelia glechomifolia
Phacelia greenei
Phacelia grisea
Phacelia gymnoclada
Phacelia hirsuta
Phacelia howelliana
Phacelia hubbyi
Phacelia humilis
Phacelia hydrophylloides
Phacelia idahoensis
Phacelia inconspicua
Phacelia indecora
Phacelia keckii
Phacelia laxa
Phacelia laxiflora
Phacelia leibergii
Phacelia lemmonii
Phacelia leonis
Phacelia leptosepala
Phacelia longipes
Phacelia lyonii
Phacelia magellanica
Phacelia mammillarensis
Phacelia marcescens
Phacelia minutissima
Phacelia mohavensis
Phacelia monoensis
Phacelia mustelina
Phacelia mutabilis
Phacelia nashiana
Phacelia nemoralis
Phacelia novenmillensis
Phacelia orogenes
Phacelia palmeri
Phacelia parishii
Phacelia peckii
Phacelia pediculoides
Phacelia peirsoniana
Phacelia perityloides
Phacelia petiolata
Phacelia petrosa
Phacelia platyloba
Phacelia pringlei
Phacelia procera
Phacelia pulchella
Phacelia quickii
Phacelia rafaelensis
Phacelia rattanii
Phacelia rotundifolia
Phacelia saxicola
Phacelia stebbinsii
Phacelia suaveolens
Phacelia thermalis
Phacelia utahensis
Phacelia vallicola
Phacelia vallis-mortae
Phacelia verna
Phacelia welshii
Plagiobothrys austiniae
Plagiobothrys glomeratus
Plagiobothrys hispidus
Plagiobothrys infectivus
Plagiobothrys shastensis
Plagiobothrys uncinatus
Pulmonaria australis
Pulmonaria carnica
Pulmonaria collina
Pulmonaria filarszkyana
Pulmonaria helvetica
Symphytum podcumicum
Tournefortia odorata
Trigonotis peduncularis
Ideally Kew will respond with feedback and by updating POWO. If they do, I think that would go along way towards helping convince folks that they'll be a good taxonomic collaborator for iNat.
Re: Onosmodium bejariense --
Taxon splits aren't treated clearly on POWO (or any other website I've found beside iNat). By adding "yes" in the "proposed deviation?" -- now "followup with Kew?" -- column, I meant that it should not be treated as a 1:1 synonym of Lithospermum occidentale, but rather split into several different Lithospermum spp., as in this iNat taxon split draft, though also see comments.
I try to limit the work on plants that I do, but one area I dont really see addressed in the discussion above is how to handle cases where a genus crosses geographic areas.
For example the Knotweeds disputed between Koenigia and Aconogonon. POTWO lists all the 35 or so species as being in Koenigia. 90 percent or so are Asian species. 3 or 4 members are found in North America.
I'm not aware of a regional authority for Northeast Asian plants, so it would seem to make sense to use Koenigia per POTWO ? But Calflora still keeps the small number found in NA in Aconogonon.
I don't think (maybe others disagree) that the ideal outcome is having the members split between the 2 genera ?
@camilojotage I see you resolved this flag, I unresolved it since we're still discussing these issues in this thread
Hi folks, Kew to my Thursday email re: Boraginaceae the next day (apologies for my tardiness relaying here) - which is a great. Here's some general comments from Rafaël Govaerts at Kew:
"The first principle of POWO is to offer TAXONOMIC STABILITY.
So this means:
That controversial or incomplete taxonomic changes are not made until a global complete solution is agreed and published. For that reason e.g. we are still using a broad Panicum and Stipa as nobody has yet delivered a finished globally agreed solution. So Dichanthelium is probably a good genus but it is not fully settled and the last thing we want to do is change Panicums to Dichanthelium and then to another genus or an enlarged Panicum again as that is exactly what users don't want.
The aim is to have all families reviewed by experts when they are completed. The reviewed families are listed here:
http://wcsp.science.kew.org/incfamilies.do
Many others are in review (like Fabaceae & Malvaceae). The quality of the data is of course much improved by a family review.
We would not include partial/inconclusive/incomplete results. So if Phylogenetic papers have indicated that Zostera angustifolia is the same as Z. marina but nobody seems to have written a formal taxonomic part synonymising the 2 then POWO will wait for someone to do this before changing the taxonomy.
I know that the first thing anyone checks is to see if the new species they just published is in POWO and, no, it is not. That is because there is a lag time of 1-2 years from publication to displaying on POWO. This is partly intentional and partly technical & physical restraints. A name is published in a book on 17 August 2016. The book is brought to the attention of the Kew Library and they order one on 11 November 2016. It arrives on 22 December 2018. It then goes to IPNI where the names are added to the IPNI database on 15 January 2017. The names are then imported into WCSP on 1 January 2018 and edited (this is why we don't want it online immediately as about many names are synonymised within 1 year of publication and we also often ask expert advice on some groups) so that the fully edited name is online on 11 April 2018. POWO is updated every 3-5 Months so the name finally is online on POWO today. This is a long example and most names make it within 1 year.
The aim is to reduce this to 1 week, but this will need the support of the community and funding. The way that would work is:
Names are registered in IPNI on 1 January 2018. The name is published and released on IPNI on 11 April 2018. On that day, the name is then also flagged as new in WCSP. The name is then edited (which is mostly quick but may need expert advise) and released to POWO on 18 April 2018. This does however require acceptance of name registration at the next nomenclatural conference and the creation of a new database system for IPNI/WCSP/POWO.
I am very happy to receive any correction (preferably with a literature reference), though we would be very reluctant to include any unpublished data (to avoid taking away the credit from others).
The first point to mention is that the data are only 96% complete. The biggest gaps are
Genera starting with letter P
Fern taxonomy
Rosaceae synonyms
They are being worked on and our goal is completion by 2020.
On some of the other thing mentioned in the discussion.
Fl. N. America is incorporated into POWO so if there is any deviance then that means that that was changed after the publication of the Fl. N. America part, the first one of which was published 25 years ago.
And Finally, remember there are 1,345,175 names in the database so if only 1% is incorrect that is still 134,517 so I think it is important to focus on the 1,210,658 that are correct and give feedback on the tiny 1% that are not."
In the same exchange, Rafaël checked several of the names I sent helping find valid POWO names for some to be swapped into, agreeing that Lithospermum parviflorum should be valid and asking for more information about the status of Lithospermum bejariense. I think we can take all of this as good evidence that Kew is willing to work with us.
I made this spreadsheet to track deviations and populated it for Boraginaceae. Notice there are
"New species", "Can't match", and "Pending Deviation" issues which match this decision tree for what to do about names in iNat but not in POWO:
All names on the spreadsheet should reference flags where we can have more in depth discussion about these. If these discussions involve getting feedback from Kew make it clear that they've been contacted leave the flags open until we hear back. If Kew agrees that a name should be valid (as in the case of Lithospermum parviflorum then we should note this on the flag, resolve the flag, and add 'Accepted Deviation' to the spreadsheet.
If Kew doesn't consider a name as valid the discussion on the flag should continue until folks decide to follow POWO or deviate from POWO anyway.
If Kew updates POWO (e.g. if they add Lithospermum parviflorum) then we should remove the corresponding deviation from the list.
Notice in the decision tree I say "Do any issues jump out?". One problem that will happen is that issues won't surface until after a curator makes a change. For example, @bouteloua realized that Lithospermum parviflorum should perhaps be considered valid (event though POWO lists it as a synonym of Lithospermum carolinianum) before making the swap. After bringing it to the attention of Kew they agree so we will add it to the deviation list and not make the swap. But what if bouteloua hadn't noticed this and went ahead and made the swap. Even if we do our homework before making swaps, this kind of thing is bound to happen. Unfortunately, in these cases we'll have incur a bit more disruption by having the conversation about deviating from POWO after (rather than before) the swap was made. If you care strongly about a taxon and want to try to catch situations where we should deviate from POWO before a curator makes a taxonomic change, please start comparing with Kew now and get the conversation going proactively (similar to how I did with Boraginaceae). I'm happy to help folks do a comparison of iNat vs. what's in POWO (similar to how I did with Boraginaceae) for your taxon of choice if you ping me.
I know there are some voices on this thread that are lobbying for the 'primary literature' approach. But there don't seem to be any lobbying for the 'regional tie breaker' approach. So lets officially move forward with the original proposal to switch to the 'POWO as global authority with deviations' approach now. These deviations let us grade into the primary literature approach as needed. And if folks continue to have issues with this approach, lets revisit soon.
Does this sound good? I'll update the Curator guide now to reflect this decision
oh I'm so sorry, my intention was not to solve the problem I was just trying to put a comment and I was looking at this case to solve another problem of a local species in my area
I touched something I should not, but I did not intend to. The problem is that with the flags the whole Taxon is blocked for, for example, adding the establishment means and the state of occurrence of said taxon downwards. I tried cycads because I needed to put Cycas revoluta and Cycas rumphi as introduced to my country
Ok folks, its official. I updated the curator guide policies, I made a shiny new iNaturalist Vascular Plant Working Group project and an initial journal post describing the transition. Please let me know if you'd like to be a member of this working group. All it really means is that I'll add you as an admin to the project which will give you permissions to post to the journal. But it will also help identify yourself as someone who cares about vascular plant taxonomy curation on iNaturalist and would like to definitely be included on discussions moving forward.
Closing this issue for now. Thanks everyone for helping work through this process.
i care about vascular plant taxonomy and do want to be informed and in the loop, but also probably won't delve too deep into taxonomic curation and also recognize my lumper-y opinions often don't match with others so i won't impose them (though having clear policy will help with that). So, not sure if it makes sense to put me on there or not
I'm a zoologist at heart, but I care a great deal about plants. I have a particular fondness for Solanaceae after being assigned the family in my college botany class. I am one of the most active curators on iNat, am experienced with its policies, have taxonomic curatorial experience through the work we have done on mammals and cephalopods, and would like to help manage our plant taxonomy. If it's not too much trouble, I would like to be a member of the Vascular Plant Working Group, @loarie.
I care very much and I'd like to be involved in the project. Unfortunately I have limited time to do much curation but I will try to flag any inconsistencies I notice.
Thanks.
One thing that would be very helpful is some kind of indicator or comment section on taxa pages that are being retained under the explicit deviations. Just an icon or little note similar to the inactive taxon notifier on those that have had explicit deviations applied.
Keeping track of all the different projects / spreadsheets across all the taxa groups that this is being done for is tough, and the indicator may prevent issues from cropping up.
So this morning I noticed a Taxon swap affecting some of my observations, is that no longer being done automatically ???
I've added everyone who requested as an admin of the working group project. @cmcheatle I agree that would be a good feature. @ck2az I'm not sure I understand your question, can you clarify?
@loarie Please add me to the project as an interested plant taxonomist.
Please keep the changes in check. Too often.... is a nightmare.
As for specific California plants the Jepson is the guideline.
I see we are deviating from the on-line Jepson a lot, the last few days.
You can add me too!
I ran into one problem
Mimulus aurantiacus var. aridus
Mimulus aurantiacus var. pubescens
are two recognized variations by the Jepson and now seem to be:
Diplacus aurantiacus
@loarie can you add me.
efmer and dgreenberger I added you to the project
re:
Mimulus aurantiacus var. aurantiacus
Mimulus aurantiacus var. pubescens
Mimulus aurantiacus var. aridus
POWO actually has Diplacus aurantiacus with no infraspecies
And they imply (as does Calflora) that Mimulus aurantiacus var. aridus is a synonym of the accepted species Diplacus aridus (although they annoyingly don't list Mimulus aurantiacus var. aridus as a synonym) which is how I swapped it https://www.inaturalist.org/taxon_changes/37654
It does seem that POWO is missing alot of infraspecies (both as accepted species and as synonyms). I'll write an update to make this clearer now, but there are three 'states':
1) when POWO recognizes an iNat taxon as an infraspecies as a synonym (or implies this as in the case of Mimulus aurantiacus var. aridus)
2) when POWO doesn't recognizes an iNat taxon an infraspecies (as accepted or synonym) but the parent binomial is unchanged (e.g. 'Genus1 species1' is accepted in iNat and POWO but POWO doesn't include iNat taxon 'Genus1 species1 var. variety1' as a valid name or synonym)
3) when POWO doesn't recognizes an iNat taxon an infraspecies (as accepted or synonym) and the parent binomial is changed (e.g. 'Genus1 species1' is in iNat but POWO has 'Genus2 species1' and POWO doesn't include iNat taxon 'Genus1 species1 var. variety1' as a valid name or synonym)
In case (1) the best practice is to make the swap since POWO is clearly aware of the infraspecies
In case (2) the best practice is to just leave the infraspecies in iNat since there seem to be so many infraspecies still missing from POWO
In case (3) its important that the infraspecies matches the parent species. I was swapping the infraspecies into the POWO parent (e.g. 'Genus1 species1 var. variety1' into 'Genus2 species1') but the practice could rather be to make 'Genus2 species1 var. variety1' even though its not in POWO and then swap 'Genus1 species1 var. variety1' into 'Genus2 species1 variety1' if folks would prefer that.
I reverted
Mimulus aurantiacus var. aurantiacus -> Diplacus aurantiacus
and replaced it with
Mimulus aurantiacus var. aurantiacus -> Diplacus aurantiacus var. aurantiacus
https://www.inaturalist.org/taxon_changes/37680
and
Mimulus aurantiacus var. pubescens -> Diplacus aurantiacus
and replaced it with
Mimulus aurantiacus var. pubescens -> Diplacus aurantiacus var. pubescens
https://www.inaturalist.org/taxon_changes/37653
is this preferable?
In case 3 I think that since infraspecies are so fraught at POWO it makes sense to try and hang onto our existing granularity as much as possible. I'd especially like to avoid lumping over taxa with conservation implications (consider in the current example if Diplacus aurantiacus var. pubescens were a CNPS 1B.2 plant). So while it's a Frankenstein of a name, I think it's better than the alternatives.
@loarie and all, I would like to advocate for curatorial caution in one specific situation: (1) a taxon is endemic to a continent (or other large region) with a well-established modern floristic literature, and (2) the POWO name for that taxon is not used by ANY of the current floristic literature for that region (whether or not previously adopted by iNat).
Before making wholesale changes that agree with NONE of the applicable floras (references likely to be used by many iNat users), let's flag them, and work with POWO first to see why they are supporting a name clearly not accepted where the taxon is native. In some (hopefully most) of these cases POWO may just not yet have caught up to the regional usage. (Again, I'm only talking about endemics for a region with a good current floristic literature.)
@loarie, I think this is already implied if not explicit in your current policy on this transition, but I also think it bears emphasis. I don't think we want curators biting off chunks of POWO and implementing them uncritically in iNat taxonomy, without first understanding the context of the changes. Otherwise a number of changes could end up being very disruptive and annoying to the iNat community.
I will soon be proactively flagging several examples of the above in my area of expertise (certain North American Asteraceae), but as a quick example, Micropus amphibolus is a California endemic that POWO still treats as Stylocline amphibola. In both Jepson Manual editions, and in FNANM -- the current applicable floristic literature for this taxon -- Micropus amphibolus is the recognized name, with Stylocline amphibola in synonymy. (Full disclosure, I am the author of those treatments.)
I am not concerned about the changes like the ones you have been working on in Phrymaceae and Boraginaceae, for example, since those are clearly in process of being accepted in the Jepson eFlora and upcoming FNANM volumes. But those are important things for curators to know or find out first, before deciding to implement a POWO update.
Thanks for listening
@loarie
For now that seems to be OK until we find a better solution.
Mimulus aurantiacus var. aurantiacus -> Diplacus aurantiacus var. aurantiacus
Mimulus aurantiacus var. pubescens -> Diplacus aurantiacus var. pubescens
Mimulus has been reordered a lot in the past and I wouldn't be surprised if they did it again.
You don't make us happy by choosing a name that isn't generally used.
A simple Google search of Diplacus mostly ends up in Mimulus.
An additional problem is that is you search for a key that separates the species, there isn't any on-line.
So rule number one: If there isn't a clear key, leave it as it is. ONLY if there is a recognized paper that separates/names things differently there may be a reason to switch.
Second rule: No changes within e.g. 4 years of a previous change, to keep everyone sane.
So again (for California) my urgent request, stick to the Jepson unless there is a very very good reason not to do so.
Don't know many who use the POWO, so using names in POWO instead of the Jepson will be very confusing and prone to errors.
In the on-line Jepson, it recognizes 6 variations of Mimulus aurantiacus.
For instance: Jepson mentions Mimulus aurantiacus var. pubescens Synonyms:
Diplacus arachnoideus Greene; Diplacus calycinus Eastw.; Diplacus speciosus Burtt Davy; Mimulus glutinosus J.C. Wendl. var. brachypus A. Gray; Mimulus longiflorus (Nutt.) A.L. Grant; Mimulus longiflorus var. rutilus A.L. Grant; Diplacus rutilus (A.L. Grant) McMinn; Mimulus longiflorus (Nutt.) A.L. Grant subsp. calycinus (Eastw.) Munz
@efmer please give
https://docs.google.com/document/d/1gNwJRDUJQ8sqTz_oJrMiABqFVXkLRkOd2_4Y2LH6Uic/edit a read where I tried to articulate some of the exacerbating-with-scale problems iNaturalist has been having with the regional-first policy (I used the mimulus split as an example). Interestingly, most but not all of iNat's previous regional sources are post-mimulus split (e.g. Vascan, Calflora etc.), but the Global Tie Breaker (the Plant List) is still pre-mimulus split.
Many of you have mentioned how The Plant List (TPL) is out of date and we should consider instead using Plants of The World Online (POWO). Since POWO now finally includes all families (see discussion here) I think its time to consider this more seriously. Here's a proposal I wrote up and just emailed to the google group: https://docs.google.com/document/d/1gNwJRDUJQ8sqTz_oJrMiABqFVXkLRkOd2_4Y2LH6Uic/edit?usp=sharing
curious to hear your thoughts.
FYI mentioning top vascular plants iders and observers and top curators:
@tsn @sambiology @grnleaf @jrebman @graysquirrel @alexiz @glmory @charlie @tiggrx @mcaple @catchang @wdvanhem @ajwright @pioleon @bugman1388 @stevejones @srall @alisonnorthup @aztekium @jasonrgrant @choess @tonyrebelo @whiteoak @bouteloua @aguilita @nathantaylor7583 @ck2az @erikamitchell @silversea_starsong @jaykeller @nicky @francisco100 @cedric_lee @finatic @reallifeecology @thunefeld @kueda @jon_sullivan @damontighe @owenclarkin @gonzalezii @terrydad2 @aaroncarlson @ripleyrm @tiwane @treichard @stephen_thorpe @borisb @hkmoths @maxkirsch @duarte @berkshirenaturalist @jakob @kokhuitan @jonathan142 @coreyjlange @sea-kangaroo @eol_education @cmcheatle @bobby23 @kai_schablewski @wongun @cooperj @tony_wills @d_kluza