I know for fungi at least there is an absurd rule that species names can’t be updated to reflect genera name changes except in official taxonomic publications, so when a species is left with an outdated name, curators here seem to deal with this in one of four ways:
Listing the species under the new genus name even though the binomial doesn’t match.
Listing the species directly under family with no genus in the ancestry.
Retaining both genera names as separate taxa until all the species are published with the new genus name.
Renaming the species even though its name hasn’t been officially updated.
I would like to get curators opinions on which of these four approaches is the best. Personally, I’m fine with any option except #2 since it causes all sorts of havoc with tools that use iNaturalist’s taxonomy. How do other platforms handle this problem?
@alan_rockefeller@cooperj@pulk@lothlin - Pinging some fungi curators. Please forgive me if I don’t properly understand this issue, which I will readily admit (I’m much more familiar with the rules for animal taxonomy). I just want to get rid of cases using option #2 since it breaks things, but I don’t know which alternative is best.
Option 4 is not an acceptable solution, as it creates nomina inedita that don’t actually exist; this is the only one explicitly against iNaturalist rules.
However, for the case I believe you’re describing where genera have been synonymised, species should be grafted under the genus where they nomenclaturally and taxonomically belong even if the correct combination has not been made yet — if they would otherwise only be part of an unaccepted genus. This is not exclusive to fungi and is seen in some plant and other taxa as well.
But that means using combinations that have not been published yet. Someone should validly publish the combination (and get their name in the citation). I recall this situation with Noccae erratica a year or two back when valid combinations were I think only for Thlaspi and Microthlaspi so it was not possible to add the species by automatic addition from external sources by us ordinary users.
No, regrafting a species under a different genus name doesn’t automatically change its name in iNaturalist. There is no new combination generated. For example, look at Mycosphaerella fraxinicola, which is grafted directly to Ramularia.
Just to define the issue more precisely …
A generic name (says Genus #1) is typfied by a particular type species. If that type species becomes a synonym of a species name in a different genus (Genus #2) then Genus #1 becomes a synonym of Genus #2. In iNat Genus #1 must be ‘taxon swapped’ into Genus #2 and can no longer remain as an active/independent name (which is a problem with the iNat design unfortunately). However, there may remain species named in Genus #1 that do not have valid/legitimate combinations in Genus #2. Unlike animal names these new recombinations cannot simply be declared. Recombinations must be registered and validly/legitimately published. That is the issue here.
Under those circumstances I think all the orphaned species in Genus #1 should be grafted under Genus #2. From a nomenclatural perspective that is the correct course of action. I know sometimes there may be additional information to suggest a particular species belongs in Genus #3 and not Genus #2 or Genus #1, and then there is a strong taxonomic inclination to move the name under Genus #3. From a nomenclatural perspective that is incorrect. The orphaned name should follow the type of the genus of the accepted binomial.
Even without generic synonymy I have seen cases in iNat where species names have been re-grafted under a different genus because of additional information. That is also nomenclatarally incorrect and may lead to significant confusion as many species are then likely to get moved without published justification.
A good example, I think, is the genus Collybiopsis - https://www.inaturalist.org/taxa/374622-Collybiopsis. There are still a number of binomials where the genus is Marasmiellus that are grafted under Collybiopsis
So it sounds like the consensus is for option #1: List the orphaned species under the new genus name even though the binomial doesn’t match.
My follow-up question, which is admittedly off-topic is: Why does this rule exist?? What purpose could it serve that justifies the chaos it causes? How many orphaned species are out there? And why doesn’t someone just publish a monthly article called “Orphaned species clean-up” where they officially register and publish the new names of all the orphaned species? If this rule existed for animals, the taxonomy of beetles (where genera are renamed on a daily basis and sometimes contain thousands of species) would probably devolve into total chaos. Is this rule controversial or do mycologists like it? I’m so curious.
And it looks like the family Campanellaceae has 4 Marasmiellus species grafted under it directly with no genus. Can I move these 4 to Collybiopsis or will someone yell at me?
The vast majority of the “trouble”, if it can really be called that (no one in the field objects that much to ir), results from the change to follow the “One Fungus, One Name” rule. Most of what you’re seeing are not just average taxonomic synonymies playing out, but (at least in the ascomycetes) the old anamorphic or asexual name clashing with the teleomorphic or sexual name. People didn’t used to know how to even connect the two very different life phases of a single organism, but with genetics, the synonymies at species level became apparent, and the change became necessary. I don’t think beetle larva are nearly as difficult to rear into adults as many Pezizomycotina anamorphs are to coax into forming their sexual phase, for example. This is only one part of it, but it’s such a large part that it needs said.
“One Fungus One Name” is one factor, but perhaps the largest factor is the universal shift in mycology from morphological concepts to those underpinned by phylogenetics. Unlike most plants and animals the relatively few morphological characters available for fungi, and historically used to classify them, have not been supported by modern phylogenetics. The result has been a massive and on-going shift both in the higher classification and species level concepts.
There are currently around 600,000 published binomial names of fungi representing about 150,000 species (with 25,000 currently used on iNat). That is a small subset of the estimated 5 million fungal species. So the task of sorting out where existing names belong, in a phylogenetic-based classification, is a substantial task and there are relatively few professional systematics mycologists to do that. It has been helped, to some extent, by the ability to rapidly introduce new names/re-combinations through e-published journals like the IndexFungorum journal. These allow the nomenclatural boxes to be ticked. However, rapid publication journals frequently by-pass peer review and so the quality varies. Nomenclaturally the new names pass the tests, but sometimes the hidden taxonomic evidence is poor. The push-back against rapid e-publication in the mycological community has been significant.
Sometimes the quality is poor because there has been a tendency to move things around based on inadequate phylogenetics. The shortfalls have been inadequate and biased taxon sampling, poor choice of out/in groups, and especially a lack of gene sampling. Basing phylogentic concepts purely on the common barcode loci like ITS and LSU alone is usually not enough, and certainly not enough for deciding where to place genus/family/order boundaries. Even with adequate phylogenetic data deciding boundaries remains an issue, especially where morphological characters do not help at all.
The current situation is rather unstable with lots of splitting by some camps, and a more conservative approach supported by others. I sit somewhere in the middle.
The flux in mycological classification is substantial and shows no sign of stabilising. I think large-scale, un-reviewed recombination to provides homes for orphaned names is not a good approach.
Although it seems there is consensus here, @pulk and @komille277 are advocating for approach #2 (listing orphaned species directly under family) at https://www.inaturalist.org/flags/767137. I have invited them to join the discussion here. It would also be good to get the opinion of @nschwab, who does a lot of fungi curation.
I see this “rule” as avoiding chaos, not causing it. Chaos to me is
If any curator on iNaturalist could do things like that on their own whim, there would truly be chaos, and iNat’s taxonomic backbone would rapidly approach zero credibility with consumers of its information. It would also become increasingly hard to match iNaturalist names to GBIF names, and therefore to incorporate iNat records into GBIF.