Taxonomic Swap 130650 (Guardado el 20/09/2023)

Agaricus umbellifer is now the name of what was formerly known as Marasmius epiphyllus. It would be too difficult to manually re-identify all records under this name so this misapplied name is treated here as a synonymy.

Añadido por nschwab el septiembre 20, 2023 09:54 TARDE | Comprometido por nschwab el 20 de septiembre de 2023
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"Agaricus umbellifer is now the name of what was formerly known as Marasmius epiphyllus" doesn't make much sense to me as my record is for Lichenomphalia umbellifera not Marasmius epiphyllus. The British Lichen Society, the official taxonomic body for the UK Lichens says the current name of species BLS Number 931 is Lichenomphalia umbellifera, and previous synonyms were Omphalina ericetorum and Botrydina vulgaris. Agaricus umbellifer is a fungus, Lichenomphalia umbellifera is a lichenised fungus.

Publicado por sim_elliott hace 5 meses

@sim_elliott Please read the detail of the cited source.

Publicado por nschwab hace 5 meses

Moreover, I specified that this change was made in accordance of the IDs of the previous observation to avoid having to re-identify all of them as it is a misapplied name.

Publicado por nschwab hace 5 meses

I genuinely don't understand what you are saying. It is not a misapplied name. I have uploaded photos of what I think is Lichenomphalia umbellifera which is listed in the join British Mycology Society and British Lichen Society UK official database for fungi (lichenized and non-lichenised) with that name, Lichenomphalia umbellifera, as a lichenised fungus, A05683 see: https://fungi.myspecies.info/file/17917 Neither Agaricus umbellifer nor Marasmius epiphyllus exist as taxa on the UK official taxonomic listing of fungi and lichens. In the UK Lichenomphalia umbellifera which was previously called Omphalina ericetorum.

Moreover in your own country, Switzerland, Lichenomphalia umbellifera is a taxon recognised by the Swiss National Lichens Databank https://www.gbif.org/fr/species/5244016

I

Publicado por sim_elliott hace 5 meses
Publicado por nschwab hace 5 meses

That it an interesting paper. But that does not mean that the taxon Lichenomphalia umbellifera is not used any more; taxa names change when the appropriate taxonomic authorities change them. In UK and Switzerland the taxon Lichenomphalia umbellifera has not been changed by the bodies given responsibility for the naming of lichen taxa. Therefore Lichenomphalia umbellifera should be the taxon used on iNaturalist until the taxonomic authorities given the responsibility for lichen taxonomy choose to change this species name. If names are changed on iNaturalist every time a paper is published, iNaturalist will become chaotic.

Publicado por sim_elliott hace 5 meses

We don't follow authorities for fungi as no taxonomic frameworks exist. We, as curators, use our expertise to find the best suitable taxonomic and nomenclatural concepts. We don't follow every paper blindly, as you seem to imply. It's only logical that this hasn't been published yet in the different checklist as they're way out-of-date for most taxa. Also, most databases are never complete, poorly maintained and there are many clashes between concepts in different database.

Publicado por nschwab hace 5 meses

But taxonomic frameworks for lichens do exists and the national databases of lichen taxa follow them. The databases for lichen taxa are published by the the Swiss National Lichens Databank and the Fungi of Great Britain and Ireland (a collaboration of the British Lichen Society, the British Mycological Society, and the Royal Botanic Society Kew). Both in Switzerland and the UK Lichenomphalia umbellifera is the current taxon names for this species, and is used by all lichenologist in the UK. iNaturalist should be following the agreed taxonomy of taxonomic databases; otherwise iNaturalist will become chaotic.

Publicado por sim_elliott hace 5 meses

National databases aren't suited for the use on iNaturalist. It can help getting information in some cases but it's very limited for the reasons I previously mentioned. As far as I know, no reliable global taxonomic framework exist and iNaturalist doesn't suggest the use of any framework (except for North American lichens). This means that all other groups need to be curated according to the state of literature and our personal expertise. If it became chaos, mycologists (professionals and amateurs) wouldn't praise the curation I've done in the past few years. However, I prefer to discuss the change.

This nomenclatural change hasn't been updated in most databases as it's very recent. However, we don't lose the history of the name as it's still listed as a synonym. Lichenomphalia umbellifera is a misapplied name and as the current name of Marasmius epiphyllus is now Owingsia umbellifera, we can't have to homotypic synonyms listed in iNaturalist in two completely different families. As Owingsia is a relevant name in family Physalacriaceae, it was necessary to commit this swap.

Publicado por nschwab hace 5 meses

Attempts to resolve the issue of L. umbellifera versus L. ericetorum has a long history in the literature. Voitk et al's recent arguments are compelling, and I would accept the conclusion that the name L. umbellifera has systematically been misapplied. The shear volume of pages written on the matter indicates Linnaeus' Agaricus umbellifer is a name of uncertain application. Whether you accept that Linnaeus was really describing the marasmioid Owingsia umbellifera is a secondary issue.

I also support the view that iNat must follow the literature in most cases. Sometimes I believe there are debateable cases where some time should be allowed for consensus to appear within the mycological community (usually due to inadequate phylogenetic sampling and analysis, or superfluous splitting). I don't think this is not one of those cases.

I believe we have no choice but to follow the primary literature in the absence of well researched and continuously maintained global taxonomic resource for fungi. Certainly, any particular national list should not be accepted as having global authority, without global coverage. Indeed, it is the case in my own country that our national plant taxonomy does not always agree with the iNat accepted POWO. That's fine. POWO may eventually catch up, or we will concede. We don't have a fungal version of POWO so the primary literature wins. In this case I think there is no doubt that national lists will eventually catch up. Although I wouldn't hold my breath concerning national lichen lists and Lichenomphalia names. Basidiomycete lichens are often treated as the poor relatives by the lichen community. Their taxonomy is currently better served by the agaricologists working on these groups, and people like Voitk, Redhead and Kuyper are those experts.

For the larger basidiomycete fungi I think the iNat taxonomy is probably the best there is. i.e. it IS the global checklist, or at least the nearest thing we have. National checklists probably need to take notice of changes in iNat, not the other way around.

Publicado por cooperj hace 5 meses

I don't disagree with anything you say @cooperj ; but as currently all lichenologists I know in the UK follow the British Lichen Society's taxonomy; there may be fewer records from British naturists of L. ericetorum on INaturalist, as unless they use iNaturalist AI picture recognition and it recognized L. ericetorum correctly, which most knowledgeable lichenologists wouldn't use, as it's very unreliable for lichens at species level, they may not recognize what they thought was L. umbellifera as L. ericetorum.. I tested re-uploading my last observation of L. ericetorum/L. umbellifera (and then deleted them as the would have been a duplicate record; (and they are probably reliable records of L ericetorum/L. umbellifera as I had them checked by an expert lichenologist from the BLS): iNaturalist identified then through AI picture recognition as Lichenomphalia sp, with L. ericetorum listed as one of the possibilities without the synonym L. umbellifera listed in the options. With the lack of use of the taxon L. ericetorum in the UK it is possible that records will now remain just as Lichenomphalia sp., so previous identification of Lichenomphalia at species level may be lost. There may be fewer observations of this rare lichen on iNaturalist from British lichenologists.: exact taxonomy can be changed at any time, but you have to have records for their taxonomy to be changed. Very few people check lichen records made by INaturalist users; so nobody might ever notice that something listed as Lichenomphalia sp. is L. ericetorum. If the synonym L. umbellifera was listed as a synonym L. ericetorum in the iNaturalist generated suggestions (as it is if you manually type in Lichenomphalia umbellifera), it would help.

Publicado por sim_elliott hace 5 meses

I don't quite follow the argument, so maybe I am missing something.

Currently in iNat if you use the name Lichenomphlia umbellifera you are redirected to L. ericetorum. If you try and find taxon detail for L. umbellifera- such as the map, and photos - then you are redirected to L. ericetorum, and you can see L. umbellifera listed as a synonym. iNat is now treating the name as though it were a synonym (although it is really a misapplication and not a synonym). We have lots of these similar 'pseudosynonyms' in iNat and they point people in the right direction. So when you say 'You have to have records' then there are records and they are easy to find.

In this scenario I don't see why this would result in fewer records by those wanting to record what they think is L. umbellifera? It's the same as any other taxonomic change for fungi, which we are all well used to seeing.

The iNat CV is generally rather pathetic for fungi because it is trained on too many erroneous Research Grade observations and many species are macromorphologically cryptic (even within Lichenomphalia). I spend most of my iNat time re-identifying observations incorrectly recorded using the CV suggestion by those not familiar with fungi. There is no escaping that issue at the moment. Although in this case it may perhaps take some time for the iNat taxonomic changes to be reflected in the CV suggestions. Maybe when the next model is loaded.

Although I sense from your text you think the usual workflow is to use the CV to list the names you are expecting to see? i.e. you expect to see L. umbellifera in the list generated by the CV so you can select it? If so then that is an odd workflow. If you think something is L. umbellifera then you should type that name in - and get redirected. Never rely on the CV to prompt you with the correct name. Not for fungi anyway.

If UK lichenologists are not checking iNat data then yes, sure, it is likely that observations at genus level will be left without good species level identifications, and that misidentification will also occur. That's true of any group where the local experts don't engage in iNat.

Publicado por cooperj hace 5 meses

Thanks for the clarification @cooperj. And thank for for spending the time to engage with me about this. I agree with what you say above and I don't think I explained myself well in my last comment. I think iNat is an extremely useful project that encourages citizen scientists (amateur naturalists) to engage in useful biological recording. I make a monthly donation to iNat to fund its useful work. I agree with what you say about identification and I try not to rely of iNat suggestions but suggest IDs based on my (limited) knowledge; but in reality many amateur naturalists do rely on the lists generated. I actively encourage people to use iNat and I shall continue to do so but few lichenologists (academic or amateur) use it in the UK. It is useful to have these conversations. I think most amateur lichenologists assume that their national taxonomy for lichens is correct; why wouldn't they? Amateur naturalists don't have the time to read or ability to access papers that challenge nationally accepted taxonomies. When an iNat curator changes the taxon name to something that doesn't correspond to what is typically accepted in the country in which you live, it is confusing. I suppose what I am saying is it would be useful to have clearer explanations of why taxonomic changes are made when taxonomic changes are made by iNat curators - and thanks for providing that. Lichens are underreported in all data recording schemes because amateur naturalists are put off identifying lichens by the difficulty of lichen ID and the taxonomic complexity of lichens. I am not sure that there is an easy way of resolving this. I think the most important thing is to encourage people to record lichens on INat even if their IDs are not necessarily always correct, as I hope, one day, more people interested in lichens, especially those with expert knowledge, will verify amateurs' records; but they don't at the moment. In a world of massive loss of biodiversity due, in the UK, mainly to habitat loss, it strikes me as really important to encourage amateur naturalists to contribute to widening the knowledge of the general public that lichens exist, so that their habitats can be conserved, and to conserve something something has to have a name. I think iNat is useful for this; that's why I use it. I think sometimes some academic taxonomic debates are like rearranging the deckchairs on the Titanic; my priority is to try to engage the general public in lichens (and every other species in their home environment) so that they know that lichens (and other things) exist around them and are interested in conserving them, because much of nature is disappearing at a rate of knots because of habitat loss and climate change; most of the general public have no names at all for most lichens let alone the correct names for them. Good to have this conversation - thanks.

Publicado por sim_elliott hace 5 meses

I don't really have anything to add to what @cooperj said but if your concern is that the CV is not currently including this species, it won't last more than a month (CV model is updated monthly and a new geomodel will be released soon which is more powerful than ever). We can't update iNaturalist according to all national checklists. It's impossible. There are mismatches between all of them and we need to select the best fitting name for the taxa. Currently, it's done with primary literature as no global checklist exists. That's generally how we work as curators on iNaturalist but it's not always possible. For example, when we have to add forgotten taxa to the database.

Publicado por nschwab hace 5 meses

Thanks for explaining.

Publicado por sim_elliott hace 5 meses

@nschwab I've now read a good chunk of that paper, you linked to, explaining its reason that "Lichenomphalina umbellifera" (as well as “Marasmius epiphyllus”) may have been misnamed, but would like a short summary of the conclusion. Does the paper suggest that when Linnaeus named a fungus "Agaricus umbellifer" in 1753, a name which later became the oldest synonym of “Lichenomphalina umbellifera”, that Linnaeus was actually referring to a fungus in an illustration that doesn't look like the fungus that has long been referred to as "Lichenomphalina umbellifera", but that he was referring to a fungus in an illustration of a species that has an umbrella shaped cap, and has a very long stipe, compared to the cap width, looking more like what has been called “Marasmius epiphyllus” (Pers.) Fr. 1838? The paper has since renamed “Marasmius epiphyllus” “umbellifera” to match the name the authors indicated Linneaus must have intended to give to the fungus in the illustration that looked like it, and a genus other than “Marasmius” due to an excessive DNA deviation of what was called “Marasmius” epiphyllus from the DNA of other members of Marasmius, making the name “Marasmius” inappropriate for it, and thus needing a more appropriate genus name for it, with "Owingsia" chosen to recognize the scientist that had shown that the section epiphylli, that Marasmius epiphyllus was in, didn't belong in Marasmius.

Publicado por stewartwechsler hace 5 meses

Your conclusion seems rather correct, even though it's difficult to read due to punctuation :)

Publicado por nschwab hace 5 meses

Apparently, the authors overlooked the sanctioned status of Agaricus umbellifer which has some consequences which will be dealt with in a follow-up paper. I don't think it alters anything though.

Publicado por cooperj hace 5 meses

@cooperj Can you briefly explain the "sanctioned status of Agaricus umbillifer" you are referring to?

Publicado por stewartwechsler hace 5 meses

@nschwab Thank you for confirming that my summary above is an accurate summary of the conclusion of that Mycotaxon paper you linked to as the source for your committing these 2 fungus name changes for iNaturalist.

(During my school years, rather than doing my writing assignments, I spent my time learning about butterflies, birds, and other biota, so I'm proud to have the strong naturalist skills I have, even if came a bit at the cost of not being a better at punctuation.)

Publicado por stewartwechsler hace 5 meses

Yes, I understand. I rarely note these thing but as the paragraph was quite technical as well I had a hard time reading it :)

Publicado por nschwab hace 5 meses

@nschwab If you would like to edit a copy of my summary of the Mycotaxon paper conclusions to make it easier to read, and send it to me, I might use those edits to edit my comment above, making it easier for everyone to read.

Publicado por stewartwechsler hace 5 meses

"We don't follow authorities for fungi as no taxonomic frameworks exist. We, as curators, use our expertise to find the best suitable taxonomic and nomenclatural concepts. "

This is definitely not how iNat is supposed to work, and definitely a problem. I can't speak much to any particular fungi taxonomy issue as i'm a botanist, but we really should not be changing taxonomy based on primary sources. One can argue that it is justified for documenting totally new species,but otherwise it's really problematic to 99% of the users on the site.

I recognize excitement over new taxonomic research and the desire to describe life as fully and thoroughly as possible. But pushing to have microsplitting and constant revisions on a website meant primarily to connect people with nature does a lot of harm. It's a boon to the faction of taxonomists who love constant changes i suppose, but most of the users here are either amateur nature observers, low-administrative-level land managers, or field ecologists, neither of whom benefit from constant taxonomic revisionism.

See also https://www.inaturalist.org/journal/charlie/68030-my-take-on-taxonomy

And to clarify this is not a personal attack on anyone, so please don't take it as such.

Publicado por charlie hace 5 meses

Charlie,
the fact is that fungi do not have a global authority, and the few regional lists are generally poorly managed and inconsistent. We have no choice but to appeal to the primary literature, and in fact the iNat species checklist is rapidly becoming the global authority. I cannot agree that a locked taxonomy is the best approach for fungi - but then I am a taxonomist. I agree that sometimes iNat curators move a bit too fast and do not wait for consensus to emerge. This is not one of those cases.

Just for background ... Fungal taxonomy differs from plants in many respects. There is at least an order of magnitude more of them, most fungal species have not been described, and at least an order of magnitude fewer mycologists relative to botanists. Fungal species often display few stable morphological characters and many of them are microscopic. Phylogenetics usually tells us that traditional morphological species concepts and classifications were often wildly wrong. On top of that mycology for many years ran dual-nomenclature with different names for different life-stages. For that reason, mycologists for over 20 years have been led by phylogenetic species concepts and insights on evolutionary classification. Those changes to the way taxonomic mycology is carried out were revolutionary. The new paradigm continues to have significant impacts, and that results in on-going significant changes, as the fewer available mycologists work on clarifying past work and chipping away at the vast numbers of undescribed fungal species. New fungal species are described at the rate of about 50-100 per week and each new species often results in wholesale revision of what we thought we knew before.

Of course, that has led to the tendency by some workers to shift every variety to species, and to name every clade as another new genus. I dislike that approach unless it adds value. I also sympathize strongly with the fact that this approach to the way we now do taxonomic mycology can disconnect the public. It is however the reality and we as mycologists cannot ignore what the data is telling us. Objectively definable species concepts are the essential bedrock for biodiversity conservation, and for biosecurity management. Fungal ecologists tend to work with higher ranks and with functional traits, and not so concerned with species concepts. Personally, I'd like to see some form of stable 'folk taxonomy' in place that is not linked one-to-on to the Linnean classification, as well as the ability to support multiple Linnean-based taxon concepts (without confusing the hell out of people).

Here is my take on the curation issues.
https://inaturalist.org/journal/cooperj/63059-a-note-on-curating-fungal-names-on-inat-and-my-personal-policies

Publicado por cooperj hace 5 meses

@cooperj I see that in your linked journal post on curation issues that you think if a name is in IndexFungorum or MycoBank it can be added, but the name Lichenomphalina ericetorum is in neither.
https://www.indexfungorum.org/names/NamesRecord.asp?RecordID=199492
Google Search for Lichenomphalina ericetorum + Mycobank

Publicado por stewartwechsler hace 5 meses

" I agree that sometimes iNat curators move a bit too fast and do not wait for consensus to emerge. This is not one of those cases."

Yeah, i guess that is my broad concern, among a few other things. I know i can't be that authoritative on this particular taxon change, so sorry if i am overreaching with that one.

In terms of mycology for sure it is more complex than botany. But even with botany the taxonomists have really devastated the site in a lot of ways over the last two or three years. I know that sounds dramatic but it really is my observation. It isn't malicious at all, but that doesn't change the impact. I want to find a way to understand species diversity without totally breaking the ability to collect a species list at a field site, much less maintain a relational database or communicate with people without professional info. My hope in the least would be some sort of counter to excessive splitting, as well as some sort of limit on rate of change so people can at least adapt. It's truly gotten to the point where the rate of change alone makes things unusable and i don't believe when the taxonomists say it will settle out at some point.

But yeah, 'folk taxonomy' would be great but i can imagine cranky taxonomists ans major government entities, conservation organizations, and all of the general public will need to use that, not the neo-linnaean pantheon of turbocharged name shuffling :D

Publicado por charlie hace 5 meses

@ stewartwechsler
Lichenomphalina isn't a published name. The correct spelling is Lichenomphalia ...
http://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=845595
I don't say if a name is in IndexFungorum or Mycobank then it can be added. I say you should check Indexfungorum or Mycobank to ensure the name is nomenclaturally correct, and spelt correctly.

Publicado por cooperj hace 5 meses

Thank you @cooperj For some reason I have long had the name "Lichenomphalina" in my head for that species, but I usually end up finding the listings for Lichenomphalia.

Publicado por stewartwechsler hace 5 meses

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