Species Fungorum Plus - possible missing species

[ManonGros]

Describe the problem:

This is a message we originally received on the GBIF Helpdesk. It seems that those fungi species are missing from the GBIF backbone and the CoL:

Acarospora jenisejensis H. Magn., Svensk bot. Tidskr. 30: 248 (1936) Caloplaca subpyracea (Nyl.) Zahlbr., Cat. Lich. Univers. 7: 185 (1931) Cladonia terrae-novae f. cinerascens Ahti, Ann. bot. Soc. Zool.-Bot. fenn. Vanamo 32(no. 1): 82 (1961) Fissurina leuconephela Nyl., Flora, Regensburg 52: 73 (1869) Flavopunctelia darrowii (J.W. Thomson) Hale [as 'darrowi'], Mycotaxon 20(2): 682 (1984) Graphis virginalis Tuck., in Eckfeldt, Bull. Torrey bot. Club 17: 256 (1890) Heterodermia linearis Moberg & T.H. Nash [as 'lineare'], Bryologist 102(1): 7 (1999) Paulia Fée, Linnaea 10: 471 (1836) Pertusaria moreliensis B. de Lesd., Lich. Mexique: 18 (1914) Pyrenula herrei Fink ex J. Hedrick, Mycologia 25(4): 309 (1933) Usnea pallida Motyka, Usnea 2(1): 435 (1937)

Link to effected CoL webpages: https://www.catalogueoflife.org/data/taxon/F

Literature references: (see above)

[yroskov]

All these names present in Species Fungorum Plus @ CLB souce, but flagged as "bare names", and didn't pass to the Catalogue of Life. Paul Kirk notified about the comment.

Acarospora jenisejensis H. Magn., Svensk bot. Tidskr. 30: 248 (1936) = BARE NAME Caloplaca subpyracea (Nyl.) Zahlbr., Cat. Lich. Univers. 7: 185 (1931) = BARE NAME Cladonia terrae-novae f. cinerascens Ahti, Ann. bot. Soc. Zool.-Bot. fenn. Vanamo 32(no. 1): 82 (1961) = BARE NAME Fissurina leuconephela Nyl., Flora, Regensburg 52: 73 (1869) = BARE NAME Flavopunctelia darrowii (J.W. Thomson) Hale [as 'darrowi'], Mycotaxon 20(2): 682 (1984) = BARE NAME Graphis virginalis Tuck., in Eckfeldt, Bull. Torrey bot. Club 17: 256 (1890) = BARE NAME Heterodermia linearis Moberg & T.H. Nash [as 'lineare'], Bryologist 102(1): 7 (1999) = BARE NAME Paulia Fée, Linnaea 10: 471 (1836) = Paulia [no author] present https://preview.catalogueoflife.org/?taxonKey=6JN5 Pertusaria moreliensis B. de Lesd., Lich. Mexique: 18 (1914) = BARE NAME Pyrenula herrei Fink ex J. Hedrick, Mycologia 25(4): 309 (1933) = BARE NAME Usnea pallida Motyka, Usnea 2(1): 435 (1937) = BARE NAME

[yroskov]

Paul commented: "These are just ‘good names’ w.r.t. Index Fungorum".

So, these names dropped in the category "names", not "taxa". It's still unclear to me, whether checklistbank software applied “bare name” status or Paul chosen it for taxonomically unvetted names

[yroskov]

It's still unclear to me, whether checklistbank software applied “bare name” status or Paul chosen it for taxonomically unvetted names

CLB software done this: names which have no relationship with taxa.

[mdoering]

Nearly 200.000 names in IF+ are bare names that don't get into COL !!!

[mdoering]

The last ColDP file uploaded by @gdower had these verbatim records given:

wc -l Name.tsv 508026 Name.tsv wc -l Taxon.tsv 154571 Taxon.tsv wc -l Synonym.tsv 158405 Synonym.tsv

That is 195.050 more names than taxa and synonyms together!

[mdoering]

A bare name is a lone name record without being referred to by a synonym or taxon. It is useful for listing names that are not placed taxonomically anywhere.

But this simply looks like an error in generating the archive

[mdoering]

How is the coldp archive generated?

[yroskov]

That is 195.050 more names than taxa and synonyms together!

Correct. Because Species Fungorum Plus includes both taxonomic checklist and also a set of taxonomically unvetted names from Index Fungorum.

How is the coldp archive generated?

Species Fungorum Plus CoLDP generated by Paul.

[mdoering]

It's still unclear to me, whether checklistbank software applied “bare name” status or Paul chosen it for taxonomically unvetted names

CLB software done this: names which have no relationship with taxa.

Well, CLB did what was given. There is nothing wrongly interpreted. It was given pure, "bare" names and they are stored as such. I do wonder if that amount of names are really unvetted and not to be included in COL

[yroskov]

Paul supplied names which have no relationship with taxa in CoLDP export. CLB software flagged them as "bare names" (there is no such status in Paul's ColDP).

It's not a mistake. Behavior, as expected.

[ManonGros]

The user who reported the original issue wrote to us to ask if the names could be integrated in the Catalogue of Life. I am not sure I fully understand the issue but is there a way to attach these names to taxa?

[mdoering]

We cannot integrate bare names that have no placement at all and no status assigned. But there has been work started by @thomasstjerne to extract IF data through its API and that had more placed names if I understand. My hope would be to switch to this source as soon as possible to a) cover more names and b) have regular, monthly updates.

@thomasstjerne any idea what is needed to finish the work? A call with Paul?

[yroskov]

is there a way to attach these names to taxa?

Taxonomically unresolved names ("bare names" according Markus) from Index Fungorum cannot be placed in taxa without expert knowledge/research. Mycologists should join their efforts in building global taxonomic checklists.

Just in case, I did not hear yet from Paul about his plans to update Species Fungorum in CoL via Index Fungorum API. I'll be happy to do it as soon as Paul approve this move.

I had a look through Index Fungorum of 2022-10-15 (id 129659) on DEV & production CLB. Looks like, it has no classification:
https://www.dev.checklistbank.org/dataset/129659/classification https://www.checklistbank.org/dataset/129659/classification

@thomasstjerne, is it a latest iteration of API crawling? (Perhaps, id 129659 is a wrong dataset. It is associated with Roderic Page as contact person. Another move?).

[thomasstjerne]

Seems the API crawler catches these names (links below). I think we should have a call with Paul soon.

Acarospora jenisejensis H. Magn., Svensk bot. Tidskr. 30: 248 (1936) Caloplaca subpyracea (Nyl.) Zahlbr., Cat. Lich. Univers. 7: 185 (1931) Cladonia terrae-novae f. cinerascens Ahti, Ann. bot. Soc. Zool.-Bot. fenn. Vanamo 32(no. 1): 82 (1961) (Api crawl has the species, but not the form) Fissurina leuconephela Nyl., Flora, Regensburg 52: 73 (1869) Flavopunctelia darrowii (J.W. Thomson) Hale [as 'darrowi'], Mycotaxon 20(2): 682 (1984) Graphis virginalis Tuck., in Eckfeldt, Bull. Torrey bot. Club 17: 256 (1890) Heterodermia linearis Moberg & T.H. Nash [as 'lineare'], Bryologist 102(1): 7 (1999) Paulia Fée, Linnaea 10: 471 (1836) Pertusaria moreliensis B. de Lesd., Lich. Mexique: 18 (1914) Pyrenula herrei Fink ex J. Hedrick, Mycologia 25(4): 309 (1933) Usnea pallida Motyka, Usnea 2(1): 435 (1937)

[collema]

Hello, I am the person who originally sent the question of this thread to GBIF. I wonder if the problem can be fixed? There are many valid fungal (lichen) taxa that are marked as "taxon match none" in GBIF.

[yroskov]

I only can say that CoL is expecting a new update for Species Fungorum from Paul Kirk in this month (i.e. March. Keep fingers crossed). If Paul recognizes these names as valid species, they will appear in the global CoL in next 1-2 months after we receive update.

Dear @collema, you may contact Paul directly and discuss validity of the species you are interested in.

[collema]

@yroskov Thank you for the reply and information!

[collema]

Actually, I think I expressed myself unclearly. It is not about the validity of the species. What I meant is that there are many taxon names that are included in Species Fungorum, but are missing (="taxon match none") from GBIF (and thus from COL?). I wonder why they are missing and if those can be added to COL? I do not understand your discussion above. I do not know what "bare names" are.

[yroskov]

"Bare name" is a term used in the Checklistbank. This status is applied to the names which are not recognized as valid taxa or synonyms by taxonomists (or, at least by the editors of Species Fungorum). These names are present in the Index Fungorum (= nomenclator, a flat list of ever published scientific names), but absent in the Species Fungorum (= taxonomic checklist of species recognized by taxonomists as valid taxa with synonyms). Bare names must not be included in CoL. They are present only in the nomenclator.