sergbolshakov
commented
1 year ago Hello, everyone.
In the classification of Fungi (https://www.checklistbank.org/dataset/2073/), there are several taxa that do not exist. For a mycologist familiar with the modern classification of fungi, these look like unfortunate typos that have no place on such a reputable source of knowledge. I have not yet written directly to Paul Kirk, perhaps it should be passed on from you so that this can be corrected as soon as possible.
When preparing Index Fungorum data for export to CoL, one would have to include checks to see if the taxon name used in the classification at any rank is present among all existing names in IF db.
According to the results of the check (I do it in R with a snapshot of the full IF database, obtained by the API in 2023-01-22), these names are not exist:
- phylum Agaricomycota — should be Basidiomycota
- phylum Cladochytriomycota — should be Chytridiomycota
- order Allotrechisporales — should be Trechisporales
- family Allotrechisporaceae — should be Hydnodontaceae
And two more orthographic variants, for which there are accepted variants:
- order Asterotexiales — orthographic variant of Asterotexales
- family Nannizziopsiaceae — orthographic variant of Nannizziopsidaceae
They probably arose when the authors of the new taxa filled in the corresponding fields of the classification. It is desirable to ensure validation of the data entered to prevent such cases.
Also, in the current classification there are cases when the same taxon appears in different parent taxa:
rank name parent
<chr> <chr> <chr>
1 class Agaricomycetes Basidiomycota
2 class Agaricomycetes Agaricomycota
3 class Kickxellomycetes Mucoromycota
4 class Kickxellomycetes Kickxellomycota
5 order Chaetothyriales Eurotiomycetes
6 order Chaetothyriales Chaetothyriomycetes
7 order Cladochytriales Chytridiomycetes
8 order Cladochytriales Cladochytriomycetes
9 order Helotiales Leotiomycetes
10 order Helotiales Dothideomycetes
11 family Apiosporaceae Incertae sedis
12 family Apiosporaceae Xylariales
13 family Clypeosphaeriaceae Amphisphaeriales
14 family Clypeosphaeriaceae Xylariales
15 family Dissoconiaceae Capnodiales
16 family Dissoconiaceae Mycosphaerellales
17 family Kirschsteiniotheliaceae Pleosporales
18 family Kirschsteiniotheliaceae Kirschsteiniotheliales
19 family Septochytriaceae Cladochytriales
20 family Septochytriaceae ChytridialesAccording to the current accepted classification of Fungi*, the parental taxa should be:
- Agaricomycetes — Basidiomycota
- Kickxellomycetes — Kickxellomycota
- Chaetothyriales — Eurotiomycetes
- Cladochytriales — Cladochytriomycetes
- Helotiales — Leotiomycetes
- Apiosporaceae— Amphisphaeriales
- Clypeosphaeriaceae — Xylariales
- Dissoconiaceae — Mycosphaerellales
- Kirschsteiniotheliaceae — Kirschsteiniotheliales
- Septochytriaceae — Cladochytriales
And still missing all the intraspecific tautonyms of accepted names — see example below. To solve this problem, it is obviously necessary to assign the same acceptedNameID to all taxa with the same basionymID. However, in some cases for infraspecific tautonyms there are different basionymIDs for some reason.
sqlite> SELECT
...> name_of_fungus
...> , infraspecific_epithet
...> , basionym_record_number
...> , current_name_record_number
...> FROM if_raw
...> WHERE (name_of_fungus != 'UNPUBLISHED NAME')
...> AND (accessrights IS NULL)
...> AND (name_of_fungus LIKE 'Agaricus bisporus%')
...> ORDER BY
...> basionym_record_number
...> ;
name_of_fungus infraspecific_epithet basionym_record_number current_name_record_number
-------------------------------------- --------------------- ---------------------- --------------------------
Agaricus bisporus var. perrubescens perrubescens 117700 531546
Agaricus bisporus f. microspora microspora 124277 531546
Agaricus bisporus 267375 531546
Agaricus bisporus 267375 531546
Agaricus bisporus 267375 531546
Agaricus bisporus f. bisporus bisporus 267375
Agaricus bisporus var. bisporus bisporus 267375
Agaricus bisporus var. albidus albidus 348995 531546
Agaricus bisporus var. avellaneus avellaneus 348996 531546
Agaricus bisporus f. conicopodus conicopodus 348997 531546
Agaricus bisporus f. depressus depressus 348998 531546
Agaricus bisporus f. langei langei 353243 531546
Agaricus bisporus var. burnettii burnettii 357921 531546
Agaricus bisporus var. eurotetrasporus eurotetrasporus 466019 531546*Wijayawardene N. N., Hyde K. D., Dai D. Q., Sánchez-García M., Goto B. T., Saxena R. K., Erdoğdu M., Selçuk F., Rajeshkumar K. C., Aptroot A., Błaszkowski J., Boonyuen N., da Silva G. A., de Souza F. A., Dong W., Ertz D., Haelewaters D., Jones E. B. G., Karunarathna S. C., Kirk P. M., Kukwa M., Kumla J., Leontyev D. V., Lumbsch H. T., Maharachchikumbura S. S. N., Marguno F., Martínez-Rodríguez P., Mešić A., Monteiro J. S., Oehl F., Pawłowska J., Pem D., Pfliegler W. P., Phillips A. J. L., Pošta A., He M. Q., Li J. X., Raza M., Sruthi O. P., Suetrong S., Suwannarach N., Tedersoo L., Thiyagaraja V., Tibpromma S., Tkalčec Z., Tokarev Y. S., Wanasinghe D. N., Wijesundara D. S. A., Wimalaseana S. D. M. K., Madrid H., Zhang G. Q., Gao Y., Sánchez-Castro I., Tang L. Z., Stadler M., Yurkov A., Thines M. 2022. Outline of Fungi and fungus-like taxa – 2021 // Mycosphere 13(1): 53–453. https://doi.org/10.5943/mycosphere/13/1/2
redewalt
yroskov
[x] WoRMS of 2023-03-01; imported 2023-03-06; synced 2023-03-06
[x] ITIS of 2023-03-01; imported 2023-03-07 (incl. new global checklists for Anomura crab superfamilies Hippoidea, Lithodoidea, Lomisoidea and Paguroidea); synced 2023-03-07
[x] Scarabs of 2023-03-06; imported 2023-03-06; synced 2023-03-06
[x] 3i Auchenorrhyncha of Mar 2023; imported 2023-03-07; synced 2023-03-08
[x] SF Isoptera of 2023-03-06; imported 2023-03-07; synced 2023-03-08
[x] WCO (Opiliones) of 2023-03-06; imported 2023-03-07; synced 2023-03-08
[x] WOL (Odonata) of 2023-03-06; imported 2023-03-07; synced 2023-03-08
[x] World Plants ver. 15.0 of 2023-03-06; imported 2023-03-07; new corrected version received 2023-03-07; imported 2023-03-08; synced 2023-03-09
[x] World Ferns ver. 15.0 of 2023-03-06; imported 2023-03-06; new corrected version received 2023-03-07; imported 2023-03-08; synced 2023-03-08
[x] Tortricid.net - a new dataset; imported 2023-02-15; synced 2023-03-06 @dhobern, 2023-02-14: _Hi Yury. Following coordination with the editors of https://tortricidae.com/, review/decision in the Taxonomy Group, and a lot of polishing, this dataset can now be used to replace the family Tortricidae in the Lepidoptera: https://www.checklistbank.org/dataset/219318/about It is current up to 2018 and we plan now to fill in the last few years. Very best wishes, Donald_
Other 7 of 11 GSDs for updates: https://docs.google.com/spreadsheets/d/1WRxfYQF8h2Xiu3gNUvQ3de-zRH-BSq3wYWIAbHHBrhY/edit?usp=sharing