Content Author Object Flagger Flag Created Reason Resolved by Resolution
needlegrasses and allies (Tribe Stipeae) jdmore Sun, 28 Feb 2021 05:34:52 +0000

Time to curate toward POWO genera?

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[PREFACE: I have erred on the side of @ tagging a lot of people here - feel free to ignore if this topic isn't of interest to you.]

The generic classification of Poaceae Tribe Stipeae in POWO appears to be fairly mature at this point, although there could still be a few pending changes in the larger genera.

Meanwhile, iNat taxonomy for the needlegrasses remains a mess.

-- 41 species are currently duplicated in multiple iNat genera.
-- 136 of the 370 iNat species taxa (37%) currently deviate from POWO.

This spreadsheet shows the current (as of 2021-02-26) crosswalk between iNat species and POWO species. There are two sheets, one sorted by POWO name, and one sorted by iNat name. I did not drill down to subspecies and varieties, since the main purpose here is to decide whether we are going to curate toward the classification of genera reflected in POWO. Any eventual taxon changes will need to deal with any subspecies also.

I would like to start curating toward the genera now accepted in POWO (see spreadsheet), mainly so that we have a guidepost for consolidating the duplicated species in iNat, and just to get everything on a consistent footing for now. While recognizing that this will likely not be a final "stable" classification, I don't think that the current mess should have to wait for that magical day.

If we do this, however, I know that us North American users would have to get used to unfamiliar names for most of our needlegrasses (Peterson et al. 2019). This may be true on other continents too, so let's have some discussion first. If anyone knows of a different world-wide classification of Stipeae that would be better for iNat to follow, please provide a link or other access information so that we can evaluate.

I have already added draft taxon changes for the current "easy" scenarios, where curating toward POWO would not affect any observations (at least at the species level) and the POWO name is already available in iNat. These are in a change group named "Stipeae2021" along with three pre-existing but uncommitted changes, and are also reflected on the spreadsheet.

Please @ tag additional interested users that I might have missed below.

Authors and commenters on open Stipeae flags:
@abedggood @aspidoscelis @bouteloua @charlie @cmcheatle @coreyjlange @jdjohnson @kitty12 @kokhuitan @loarie @marigoldjoy @melodi_96 @mftasp @oscargsol @yargeritaville

More authors of past Stipeae taxon changes:
@choess @faerthen @hanly @jaykeller @kastani @najera_tutor @pjd1 @rfoster @sanguinaria33 @silversea_starsong @stephen_thorpe @stevejones @tonyrebelo @wdvanhem @xpda @zroskoph

More key identifiers and observers of Stipeae by continent:

Oceania: @david_lyttle @jon_sullivan @knicolson @knicolson @lloyd_esler @mark_smale @mattintas @meurkc

South America: @aira_chilensis @alfredo_f_fuentes @anibalakd @david1531 @mateohernandezschmidt @preli

Africa: @abounabat @daverichardson

Europe & Asia: @aleksandrebel @alexanderdubynin @allaverkhozina @alzov @apseregin @ariel-shamir @davydovbotany @fragmansapir @igor_olshanskyi @pavel_golyakov @vadim_prokhorov @yanghooncho @yury_kopylov-guskov

North America: @cwbarrows @efmer @glmory @grnleaf @jrebman @lysandra @prairie_rambler @rickwilliams @rojosmojo @sambiology @sedgequeen @sheriff_woody_pct

Posted by jdmore 9 months ago (Flag)

No issues with proposals from southern Africa.
BUT: note that POWO is very poor on subspecific taxa (subsp. and vars) and I would recommend that we deviate from POWO on these. Apparently POWO acknowledges this, but it is not a high priority: so many valid subspecies are listed under their species on POWO, without implying true synonymy. (the only priority subspecies for POWO are when they have been moved between species or elevated to full species status, otherwise subspecies on POWO should be disregarded.

From our flora (http://newposa.sanbi.org/sanbi/Explore), currently:
Stipa capensis (but not so on POWO which has Stipellula capensis): both on iNat.
Stipa dregeana has two vars - as on iNat: dregeana & elongata (no vars mentioned in POWO)
[[these comprise our sum indigenous species, the following two deviations being among the aliens, and probably out of date:]]
Amelichlora clandestina still recognized (Stipa clandestina in POWO & iNat)
Jarava plumosa still recognized (Stipa papposa in POWO & iNat).
Other species are no issues.

Posted by tonyrebelo 9 months ago (Flag)

POWO still doesn't accept Hesperostipa for some reason, so I followed up on some old flags and entered deviations. There are a few pending taxon changes for Hesperostipa/Stipa duplicates.

I also agree on treating each infrataxon as individual cases, POWO frequently just lumps them with the species willy nilly.

Posted by bouteloua 9 months ago (Flag)

i think i'm always just going to say 'the less changes the better' but with less volume as time goes on since it seems a lost cause. At least iNat tracks the synonomies

Posted by charlie 9 months ago (Flag)

Apparently infraspecies are not willy nilly: they are the ones that have changed status in some way (changed rank, or changed parent or have been synonymized). Otherwise they are not included, although there are plans to include infraspecifics in the future.

Posted by tonyrebelo 9 months ago (Flag)

OK Jim. I just validated 2 drafts for species that I know very well :
https://www.inaturalist.org/taxon_swaps/67091
https://www.inaturalist.org/taxon_swaps/89324
Errol.

Posted by abounabat 9 months ago (Flag)

@abounabat ok.... but the idea was that we were going to wait to be sure there is community agreement first to follow the genera used by POWO. Hopefully that will be the case...

Posted by jdmore 9 months ago (Flag)

OK, sorry. But from my own opinion, deviating from POWO when taxonomy is equivalent (same species number and species names, only genus change) is useless.
Furthermore, I agree with @tonyrebelo when he said that POWO does not contain a lot of infraspecific taxa (subsp. and var.). Nevertheless, I would not use the term "deviation" when we want to add subsp. or var. not considered (or considered by default as included) by POWO, but only when we want to consider these subspecies or variety as full species or infraspecific taxa of another species...
Errol.

Posted by abounabat 9 months ago (Flag)

So I'm trying to wrap my head around the issue with infraspecific taxa that several of you have brought up.

1-- In my experience, there are a lot of infraspecific taxa in POWO, old and new, most of which are in synonymy under other taxa. Are you saying that there are a lot in current use elsewhere, but that are missing entirely from POWO, even as synonyms? (I do see that's the case for Stipa dregeana varieties.) Maybe my experience is biased because North American infraspecific taxa were incorporated disproportionately to other parts of the world (from the old Gray Herbarium Index)?

2-- in many cases when POWO accepts infraspecific taxa, they have not (yet) created a taxon for the autonym (=nominate infraspecific taxon). In such cases, the synonyms that would be assigned to the autonym are instead just listed under the main species, for lack of another place to put them.

3-- in many cases when species with infraspecific taxa are moved to new genera in POWO, the combinations for the infraspecific taxa have not (yet) been published under the new genus, so POWO can't list the infraspecific taxa as accepted in the new genus.

When POWO lists infraspecific taxa as synonyms under any of the three cases above, it would be hard to say whether or not that is a conscious taxonomic decision on their part, without asking about each individual case.

In cases like #3 above, when we still want to recognize the infraspecific taxa, that would be a good argument for deviating from POWO and not moving a species to its accepted genus.

Am I missing any other issues?

@abounabat I hear you about the term "deviation." I have slowly learned that "deviation" has a very specific meaning in iNaturalist, which is any difference whatsoever between iNat taxonomy and the names listed (or not listed) in POWO (or other taxonomic authority). That includes, as I've been told, autonyms that are implied by other accepted infraspecific taxa, but are not actually listed in POWO, and also names that are just completely missing from POWO.

Posted by jdmore 9 months ago (Flag)

POWO is a taxonomical database. So autonyms are simply that: automatic. Including them would be redundant. They are thus not listed, even when other varieties and subspecies are accepted :: so on iNat all autonyms would strictly be "deviations".
e.g.
Leucospermum hypophyllocarpodendron: http://www.plantsoftheworldonline.org/taxon/urn:lsid:ipni.org:names:705026-1
accepted infraspecifics lists only sub. canaliculatum not the autonym
Leucadendron spissifolium: http://www.plantsoftheworldonline.org/taxon/urn:lsid:ipni.org:names:704952-1
four subspecies recognized: but autonym not listed.

Posted by tonyrebelo 9 months ago (Flag)

I can explain the issue with infraspecific names and POWO: the POWO Poaceae dataset was originally a copy of GrassBase. Derek Clayton did not have time to treat infraspecific names globally for GrassBase, and he did not consider them to be important. So they are not rejected, they are just not dealt with properly.

Thank you for updating the grass classification on Inat @jdmore, let me know if I can help. If there are big errors on POWO I might be able to get those updates made. The POWO compilation deliberately chose not to follow to recent publications in the Stipeae which I disagree with, you are right to update these.

Some history is explained in my paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408733/

Posted by vorontsovams 9 months ago (Flag)

As @bouteloua mentions, POWO doesn't recognize Hesperostipa, putting them at odds with both researchers on the tribe and regional floras. Following Peterson et al. is probably the best bet.

Personally, of course, I would ignore POWO entirely. :-)

Posted by aspidoscelis 9 months ago (Flag)

@vorontosovams - Your papers prompted me to check GrassBase and GrassWorld to see how they treat Stipeae. In a quick look, it seems GrassBase is following the "traditional" (pre-molecular phylogenetic) treatment, with a big Stipa that includes the various segregates, while GrassWorld is following what looks like the "modern" (molecular phylogenetic) treatment as it was generally accepted prior to the Peterson et al. 2019 paper. By accepting Eriocoma but not Hesperostipa, POWO has probably found an arrangement of genera that has not been used in any previous work or database...

Posted by aspidoscelis 9 months ago (Flag)

@tonyrebelo this is not the case, POWO lists autonyms for very many taxa, and is missing a lot of others. I don't think they choose explicitly to exclude them at all. In my experience when linking our taxa to POWO, it's about 50/50.

I do not think POWO prioritises infraspecies to the same degree as species. @jdmore, in my experience: POWO has not captured many infraspecies altogether that are in current usage in the taxon's range. In other cases POWO explicitly treats separate infraspecies as synonyms of the parent species, even though the infraspecies are in current usage throughout the taxon's range. It can be difficult to find the reason why.

Deviations are any taxon that is in iNaturalist and is either not in POWO at all, or we have decided to treat differently to how iNaturalist treats the taxon. This means that yes, all autonyms missing from POWO are by necessity deviations.

Finally, in my experience, names from non-English-language literature are less likely to have been captured by POWO that those in well-known English-language publications.

Posted by mftasp 9 months ago (Flag)

@aspidoscelis @bouteloua and all, I am totally open to following the genera recognized in Peterson et al. 2019, if that seems like a more stable way to go. That is, if we think POWO will eventually be converging toward that classification. Including Hesperostipa, the differences with POWO look like this:

Peterson et al. 2019 => POWO
× Achnella => unplaced name
Amelichloa => Stipa
Anatherostipa => Nassella except A. brevis (unplaced)
Hesperostipa => Stipa
Jarava => Stipa
Lorenzochloa => Ortachne
Timouria => Achnatherum
Trikeraia => Stipa

One downside to this is that, until POWO catches up, it may be more difficult to determine which species belong in some of these genera. For example, Peterson et al. (2019) note that their (then) current circumscription of Jarava was polyphyletic, but didn't provide any species-level details.

What do others think?

Posted by jdmore 9 months ago (Flag)

@mftasp - POWO has changed its policy about infraspecies, but it will be many years before it approaches completeness, and in the meantime it cannot be regarded as comprehensive or definitive regarding infraspecies.

Another issue with POWO as a database, its its use of IPNI. We have had three cases in the last year where species were rejected because of code issues, but these rejections are not explained, documented or communicated. One that was rejected three years ago was because of a proofing error, where a line was omitted in publication that included the word "Type" and therefore rendered the name typeless. It was only detected during posting deviations on iNaturalist, and the authors of the name were totally unaware of any issues with the name. POWO only accepted the name after an erratum was published, but the real issue is the lack of transparency, referencing and feedback on these decisions. In another case a name in use for over 200 years in the Cape Flora has been designated invalid in the last three years, without any documentation, explanation or notes. The reason turns out to probably be valid, but no one using the name would even now be aware of the issue where it not for an Australian MS that misused it (and thus cited a wrong locality for this extinct species, otherwise it would not have been detected).

@jdmore : I dont think hopping from publication to publication is "stable" - if POWO is not acceptable then rather revert to Grassbase or Grassworld, and if they are equally problematic, then we may as well stick to POWO.

Personally I dont think that these generic reshufflings are that important: the species are not affected, and the synonomies on iNaturalist work very well at coping with alternative names. However, that assumes only one instance of any species in the dictionary, and not duplicates under the different genera.

In my experience POWO is reasonably fast (less than a week turnaround) with all issues I have raised. This includes local journals - it is not just non-English language publications that POWO is slow to harvest.

Posted by tonyrebelo 9 months ago (Flag)

To Everyone -

Research on the Poaceae evolutionary history shows deep and widespread incongruences between the newest phylogenetic trees and any extant classification. The rearrangement of the grass classification to reflect monophyletic clades is by no means complete and will continue for many years. POWO does aim to keep up and will do so, but it is technically tricky when some new combinations have been published but not others.

In my opinion the best option for the iNat community is to continue working closely with POWO - as long as we realise and accept that it will not deal with infraspecific taxa. Most likely GrassBase and GrassWorld taxonomies will not be updated again, but POWO is responsive and backed by long-term investment.

Posted by vorontsovams 9 months ago (Flag)

I agree with Maria Vorontsova"s "In my opinion the best option for the iNat community is to continue working closely with POWO "

on grasses and everything else. I think if we accept (and enjoy!) that we are in the midst of a time of rapid discovery, and go with it, accepting the changing taxonomy that goes with increasing understanding, that will be our best forward path.

Posted by marigoldjoy 9 months ago (Flag)

Personally, I'm not at all averse to changing taxonomy that is based on increased understanding. That's not the issue with POWO. For Stipeae in particular, the issue is that they seem to be arbitrarily accepting some genera and not others, and it's completely opaque as to why that is or if it's even intentional. My bet is that rejecting Hesperostipa is not a deliberate and informed decision made by someone who is familiar with the taxonomy of Stipeae, but a goof made by someone getting paid a crappy hourly wage to run a bunch of updates on plants they've never heard of.

In my experience, this is pretty typical of POWO, and most big aggregate databases. As the number of species covered by a database goes up, the involvement of people who know the taxa goes down, the arbitrariness & opacity of any particular taxonomic decision goes up.

Posted by aspidoscelis 9 months ago (Flag)

@aspidoscelis the difficulty is that rearrangements have been published using a limited subset of regionally common species that were available for sequencing/study. But in order to make full changes POWO needs to make a decision and implement it for a ALL species within e.g. Stipa sensu lato. But many species from inaccessible places have not been included in the new combinations and published rearrangements, so there is no clear place and name for them in the new system. This is why large groups with a global distribution always lag behind

Inevitably these compilations do rely on specialists to email in and ask for the changes to be made, backed up by papers

Posted by vorontsovams 9 months ago (Flag)

For cases of the kind you mention, "incertae sedis" or a similar marker of uncertainty would be appropriate. POWO gives the appearance of scientific authority but is opaque and arbitrary in practice.

The status of, e.g., Hesperostipa neomexicana as "not accepted, synonym of Stipa neomexicana" tends to give the impression that the proposed split of Hesperostipa from Stipa was reviewed for its scientific merit by Official Kew Scientists and rejected, an impression that I'm certain is incorrect. I'm betting the real explanation is mere inattention or error, but an explanation like yours (Hesperostipa neomexicana is unambiguous, but perhaps someone didn't want to move them all until there was a certain placement for them all) is entirely plausible. The problem is that we don't know. We just have a list that presents itself as authoritative, and which iNaturalist has decided to treat as authoritative, but which provides no explanation or justification for its decisions.

Posted by aspidoscelis 9 months ago (Flag)

This tendency to treat or present scientific questions as matters of institutional fiat really rubs me the wrong way. Frankly, I think it's anti-scientific.

Posted by aspidoscelis 9 months ago (Flag)

Thank you everyone for the informative and spirited discussion so far, and please do continue as needed. I just wanted to summarize that, as of now, the only specific objection I am hearing to the current POWO classification would be to maintain Hesperostipa as a deviation from POWO for the time being.

Are there any other genera that anyone feels strongly should be treated differently from POWO?

Posted by jdmore 9 months ago (Flag)

You had a purpose in mind other than general expression of disgruntlement?!

Hesperostipa (specifically, Hesperostipa comata, Hesperostipa neomexicana, and Hesperostipa spartea, all placed by POWO in Stipa) is the only anomaly I see for the New Mexico Stipeae in POWO.

Posted by aspidoscelis 9 months ago (Flag)

I reached out to POWO to look into updating their Hesperostipa taxonomy.

Posted by bouteloua 9 months ago (Flag)

Speedy Rafaël already responded - essentially it's on their near-term to-do list. He cited all the things Maria listed above and said it should be updated sometime this year.

Posted by bouteloua 9 months ago (Flag)

@bouteloua great to hear, thanks for doing that! Did anything in Rafaël's response suggest to you that we ought to hold off on curating toward the existing POWO classification (except Hesperostipa)? Or does it seem reasonable to move ahead now?

Posted by jdmore 9 months ago (Flag)

I have this on my to do list and am in regular contact with Rob Soreng from the Smithsonian who manages the Catalogue of New World Grasses. We did over the past year try and sort Panicum as much as possible even though many species still are not in the right place as names have not been published. We hope to do this with Stipa this year as much of the New World has now been sorted and much has been published on this recently though uncertainties remain and numerous species lack a name in a correct genus [...] I will check with Rob and Maria Vorontsova with whom I consult on generic circumscriptions in grasses to see where we are and if changes can now be made with confidence.

Posted by bouteloua 9 months ago (Flag)

Ok, so it sounds like the North American genera for which species combinations were validated in Peterson et al. (2019) (or already exist and are endemic) would be good to go, but maybe not the others yet?

I hate to only do a partial job now, but I also hate to let all of those duplicated North American species hang much longer...

Posted by jdmore 9 months ago (Flag)

? Perhaps prioritize the duplicates?

Posted by tonyrebelo 9 months ago (Flag)

@tonyrebelo that would definitely be my preference! And maybe we are good to go on the South American, South African, and Australian-Oceanian taxa too. Seems like most of the remaining unpublished names may be for Eurasian taxa.

All - would be interested in your thoughts on this forum post https://forum.inaturalist.org/t/taxon-changes-for-change-in-hybrid-status-not-needed/20899 which applies to some of the current Stipeae deviations.

Posted by jdmore 9 months ago (Flag)

Hi all, just a heads-up that I will be committing all of the changes for the New World and Southern Hemisphere genera in about 24 hours, unless there are any last-minute concerns. This will bring iNat species into alignment with POWO for the genera Anemanthele, Austrostipa, Barkworthia, Eriocoma, Nassella, Pappostipa, Piptatheropsis, Piptochaetium, Pseudoeriocoma, Ptilagrostiella, Stipellula, and Thorneochloa; maintain a deviation for the genus Hesperostipa; and clean up a few inconsequential deviations in other genera.

There are fewer changes needed for the remaining species of genera centered in Eurasia (Achnatherum, Chionochloa, Macrochloa, Neotrinia, Patis, Piptatherum, Ptilagrostis, Stipa), but am holding these for a second batch of changes, since it seems like these genera may have more revisions pending for POWO. If you all think it's better to go ahead with them now, though, I'll set up the changes. These would be the ones with yellow highlighting on the updated spreadsheet.

Posted by jdmore 9 months ago (Flag)

Thank you for getting these updated @jdmore good job

Posted by vorontsovams 8 months ago (Flag)

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