ITIS, Bacillariophyceae: missing parent binomials

[yroskov]

@DaveNicolson

Dealing with import crash for ITIS, Geoff spotted that some accepted trinomials have no parent binomials (neither autonyms): https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=3649#null

See genus Navicula and forms/varieties as direct children to the genus at the top of children list.

@mdoering, Can it be a barrier for the clearinghouse software? https://github.com/CatalogueOfLife/backend/issues/954

@DaveNicolson What is a reason for missing parent species?

How we can manage such cases in the CoL?

[gdower]

The importer is supposed to just flag it with the PARENT_SPECIES_MISSING issue, which was introduced as a feature 2 weeks ago. So in the future it would show up on the ITIS dataset issues page without crashing the importer.

Here's the list of 130 infraspecies that are missing a parent binomial:

tsn	scientificName	authorship	parent	parent_rank
193750	Melosira distans var. perglabra	(Ostrup) Jorgensen, 1948	Melosira	genus
2300	Melosira granulata var. curvata		Melosira	genus
2302	Melosira granulata var. procera	(Ehrenberg) Grunow	Melosira	genus
2305	Melosira granulata f. spiralis	Grunow	Melosira	genus
2307	Melosira islandica var. helvetica		Melosira	genus
2308	Melosira islandica var. vanernsis	(Cleve-euler) Cleve-euler	Melosira	genus
2322	Melosira distans var. africana	O. Müll.	Melosira	genus
2324	Melosira distans var. laevissima	Grunow	Melosira	genus
2443	Cyclotella kuetzingiana var. planetophora	Fricke	Cyclotella	genus
2444	Cyclotella kuetzingiana var. radiosa		Cyclotella	genus
2687	Biddulphia longicruris var. hyalina	(Schröder, 1906) Cupp, 1943	Biddulphia	genus
2883	Rhizosolenia alata var. gracillima		Rhizosolenia	genus
2884	Rhizosolenia alata f. indica	(H. Peragallo, 1892) Hustedt, 1929	Rhizosolenia	genus
2917	Rhizosolenia eriensis var. morsa	West and West	Rhizosolenia	genus
591667	Rhizosolenia eriensis var. zachariasi	(Brun) Playf.	Rhizosolenia	genus
591670	Rhizosolenia eriensis var. pusilla	Wolosz. in Schröd.	Rhizosolenia	genus
2951	Fragilaria leptostauron var. fossilis		Fragilaria	genus
2952	Fragilaria leptostauron var. rhomboides		Fragilaria	genus
2959	Fragilaria construens var. binodis	(Ehrenb.) Grunow	Fragilaria	genus
2961	Fragilaria construens var. minuta		Fragilaria	genus
2962	Fragilaria construens var. pumila		Fragilaria	genus
2970	Fragilaria virescens var. mesolepta	(Rabenh.) Schönfeld	Fragilaria	genus
2971	Fragilaria virescens var. oblongella	Grunow	Fragilaria	genus
3051	Synedra affinis var. intermidia	Kuetzing	Synedra	genus
3052	Synedra affinis var. gracilis	Mereschkowsky, 1902	Synedra	genus
3053	Synedra affinis var. obtusa	Arnott Ex Van Heurck, 1881	Synedra	genus
3054	Synedra affinis var. parva	Kuetzing, 1944	Synedra	genus
3228	Diatoma anceps var. linearis		Diatoma	genus
3231	Diatoma elongatum var. pachycephala		Diatoma	genus
3391	Eunotia lunaris var. subarcuata	(Nägeli) Grunow	Eunotia	genus
3432	Achnanthes peragalli var. parvula	(Patrick) Reimer	Achnanthes	genus
3438	Achnanthes clevei var. constricta		Achnanthes	genus
3439	Achnanthes clevei var. rostrata	Hust.	Achnanthes	genus
3450	Achnanthes exigua var. constricta	(Grunow) Hust.	Achnanthes	genus
3452	Achnanthes exigua var. semiaperta		Achnanthes	genus
3468	Achnanthes sublaevis var. crassa	Reimer, 1966	Achnanthes	genus
3476	Achnanthes elliptica var. elongata	A.Cleve	Achnanthes	genus
3483	Achnanthes hauckiana var. rostrata		Achnanthes	genus
3487	Achnanthes kryophila var. africana		Achnanthes	genus
3490	Achnanthes lanceolata var. apiculata	Patrick	Achnanthes	genus
3491	Achnanthes lanceolata var. bimaculata	Hustedt	Achnanthes	genus
3492	Achnanthes lanceolata var. capitata	Mull.	Achnanthes	genus
3497	Achnanthes lanceolata var. lanceolatoides	(Sovereign) Reimer	Achnanthes	genus
3499	Achnanthes lanceolata var. oestrupii	Patr.	Achnanthes	genus
3501	Achnanthes lanceolata var. robusta		Achnanthes	genus
3502	Achnanthes lanceolata var. rostrata	Hustedt	Achnanthes	genus
3503	Achnanthes lanceolata var. ventricosa	Hustedt	Achnanthes	genus
3505	Achnanthes lanceolata var. minor	Schultz	Achnanthes	genus
3517	Achnanthes linearis var. curta		Achnanthes	genus
3522	Achnanthes minutissima var. cryptocephala		Achnanthes	genus
3523	Achnanthes minutissima var. robusta		Achnanthes	genus
3524	Achnanthes minutissima var. macrocephalus	Hustedt, 1937	Achnanthes	genus
3526	Achnanthes minutissima var. microcephala	Grunow	Achnanthes	genus
3532	Achnanthes peragalli var. fossilis		Achnanthes	genus
1021203	Navicula anglica var. minuta	Cleve	Navicula	genus
1021237	Navicula ruttneri var. capitata	Hustedt	Navicula	genus
1021242	Navicula anglica var. lapponica	Cleve-Euler	Navicula	genus
1021246	Navicula creuzburgensis var. multistriata	Patrick	Navicula	genus
1021249	Navicula incompta var. incurva	Reimer	Navicula	genus
1021250	Navicula lagerheimii var. intermedia	Hustedt	Navicula	genus
1021256	Navicula major var. dilatata	M. Peragallo	Navicula	genus
1021257	Navicula major var. maxima	Tempère and M. Peragallo	Navicula	genus
1021258	Navicula mediocris var. intermedia	Reimer	Navicula	genus
1021259	Navicula mesogongyla var. interrupta	Cleve	Navicula	genus
1021260	Navicula nyassensis var. capitata	O. Miller	Navicula	genus
1021261	Navicula oblongum var. subcapitata	Pantocsek	Navicula	genus
1021263	Navicula paramutica var. binodis	Bock	Navicula	genus
1021265	Navicula perpusilla var. distans	Cleve-Euler	Navicula	genus
1021267	Navicula placentula var. maculata	Hustedt	Navicula	genus
1021270	Navicula scutelloides var. minutissima	Cleve	Navicula	genus
1021271	Navicula scutelloides var. mocarensis	Grunow	Navicula	genus
1021272	Navicula terrestris var. relicta	(McCall) Lund	Navicula	genus
1021296	Navicula glacialis var. hudsonii	Poulin and Cardinal	Navicula	genus
1021326	Navicula approximata f. elongata	Hustedt	Navicula	genus
1021330	Navicula gastrum f. maxima	Tempère and M. Peragallo	Navicula	genus
1021332	Navicula gracilis f. minor	Guermeur	Navicula	genus
1021338	Navicula paludosa f. rhomboidea	Reimer	Navicula	genus
1021339	Navicula ventraloconfusa f. simplex	Lange-Bertalot	Navicula	genus
3660	Navicula clementis var. quadristigmata	Manguin ex Kociolek and Reviers	Navicula	genus
3708	Navicula lyra var. dilatata	Schmidt	Navicula	genus
3758	Navicula amphibola var. perrieri	M. Peragallo and Héribaud in Héribaud	Navicula	genus
3760	Navicula amphibola var. polymorpha	Fusey	Navicula	genus
3811	Navicula anglica var. subsalsa	(Grunow) Cleve	Navicula	genus
3843	Navicula exigua var. capitata	Patrick	Navicula	genus
3976	Navicula seminulum var. hustedtii	Patrick	Navicula	genus
4004	Navicula tuscula var. obtusa	Hustedt	Navicula	genus
4027	Navicula subhamulata var. undulata	Hustedt	Navicula	genus
4396	Caloneis silicula var. minuta		Caloneis	genus
4497	Pinnularia leptosoma var. elangensis		Pinnularia	genus
4517	Pinnularia undulata var. subundulata		Pinnularia	genus
4626	Gyrosigma spencerii var. curvula	(Grunow) C. W. Reimer	Gyrosigma	genus
4686	Amphiprora paludosa var. hyperborea		Amphiprora	genus
4839	Cymbella minuta var. latens	(Krasske, 1937) Reimer, 1975	Cymbella	genus
4851	Cymbella muelleri var. javanica	(Hustedt) Hustedt	Cymbella	genus
4868	Cymbella sinuata var. ovata		Cymbella	genus
4877	Cymbella ventricosa var. girodii	(Her.) Kob.	Cymbella	genus
4878	Cymbella ventricosa var. ovata	Prescott, 1976	Cymbella	genus
4879	Cymbella ventricosa var. silesiaca	(Bleish) Cleve	Cymbella	genus
4880	Cymbella ventricosa var. ventricosa	C. A. Agardh, 1830	Cymbella	genus
4939	Gomphonema constrictum var. subcapitatum	Van Heurck	Gomphonema	genus
4958	Gomphonema lanceolatum var. insigne		Gomphonema	genus
5267	Nitzschia angustata var. antiqua		Nitzschia	genus
202440	Surirella ovata var. crumera		Surirella	genus
5363	Surirella ovata var. pinnata		Surirella	genus
822690	Abies concolor X Abies grandis		Abies	genus
182493	Agrostis idahoensis var. idahoensis	Nash	Agrostis	genus
182512	Agrostis vinealis ssp. vinealis	Schreb.	Agrostis	genus
526995	Bromus sitchensis var. sitchensis	Trin.	Bromus	genus
529358	Panicum bulbosum var. bulbosum	Kunth	Panicum	genus
531429	Puccinellia vaginata var. elegans	T.J. Sørensen	Puccinellia	genus
41327	Beckmannia eruciformis var. eruciformis	(L.) Host	Beckmannia	genus
185318	Aristida ramosissima var. ramosissima	Engelm. ex A. Gray	Aristida	genus
185336	Arundo donax var. donax	L.	Arundo	genus
193429	Avena sterilis ssp. sterilis	L.	Avena	genus
798260	Avena byzantina var. biaristata	(Hack. ex Trab.) Parodi	Avena	genus
798261	Avena byzantina var. hipomelanathera	(Thell.) Parodi	Avena	genus
529239	Muhlenbergia filiformis var. filiformis	(Thurb. ex S. Watson) Rydb.	Muhlenbergia	genus
525028	Stipa caucasica ssp. glareosa	(P.A. Smirn.) Tzvelev	Stipa	genus
154707	Golfingia rugosa mauritaniensis	(Hérubel, 1925)	Golfingia	genus
969364	Actinomyces neuii anitratus	Funke et al., 1994	Actinomyces	genus
969365	Actinomyces neuii neuii	Funke et al., 1994	Actinomyces	genus
1021196	Navicula hustedtii var. obtusa	Hustedt	Sellaphora	genus
3977	Navicula seminulum var. intermedia	Hustedt	Sellaphora	genus
591593	Achnanthidium brevipes var. intermedia	(Kütz.) Cleve	Achnanthidium	genus
1053181	Nysson basalis taiwanus	Tsuneki, 1968	Nysson	genus
969619	Sporolactobacillus nakayamae nakayamae	Yanagida et al., 1997	Sporolactobacillus	genus
969620	Sporolactobacillus nakayamae racemicus	Yanagida et al., 1997	Sporolactobacillus	genus
3891	Navicula minima var. okamurae	Skvortzov	Eolimna	genus
3892	Navicula minima var. atomoides	(Grunow) Cleve	Eolimna	genus
981147	Pheretima (Pheretima) americana bidentata	Cernosvitov, 1942	Pheretima	subgenus

[DaveNicolson]

My first thought is you could omit them. Many, but not all, of them have comments explaining an issue with their placement. One issue that is involved is the unfortunate cases where someone placed a species in synonymy or transferred it to another genus, but didn't address the status or placement of trinomials linked under it, or give new combinations even. Some specialists instructed us to leave the trinomials behind since there was no publication that resolved their status! We do not have the luxury of deleting them, of course.

[DaveNicolson]

E.g.: from Animalia : Bilateria : Protostomia : Ecdysozoa : Arthropoda : Hexapoda : Insecta : Pterygota : Neoptera : Holometabola : Hymenoptera : Apocrita : Aculeata : Apoidea : Crabronidae : Bembicinae : Nyssonini : Nyssonina : Nysson

TSN 1053181, Nysson basalis taiwanus, comment: "Nysson basalis taiwanus Tsuneki, 1968 is treated by Pulawski (website, 2017) as a subspecies of Nysson 'basalis auctorum nec F. Smith, 1856' (meaning a subspecies of a species mis-named Nysson basalis by various authors), which is there treated as a valid species. If the species is to be recognized, it is apparently in need of a name, as Nysson basalis F. Smith, 1856 is accepted in Brachystegus. The current species & subspecific status of Tsuneki's 1968 subspecies epithet taiwanus are unclear at the moment. Any new species name would be junior to taiwanus, so the species should apparently be called taiwanus, and any other subspecific taxonomic group would then need a subspecies name within N. taiwanus"

[yroskov]

We have the same situation with absence of valid trinomial combinations in Species Fungorum and some other checklists under botanical Code.

OK. CoL will block those names from assembly.

Geoff is trying to jump over technical barrier with import and secure the process.

[mdoering]

During a sync any missing species or genera in the hierarchy are created as "implicit" taxa, so I don't think that harms the software or COL results. You can block them if you think it is too ambiguous, but if the sync encounters Nysson basalis taiwanus Tsuneki, 1968 linked to the genus only, the missing species Nysson basalis will be created without any authorship

[DaveNicolson]

I think it would be inappropriate to create an "implicit" Nysson basalis in this case, as that name is now valid as Brachystegus basalis (F. Smith, 1856). And there was yet another use of that name, a junior primary homonym, Nysson basalis F. Smith, 1869, which is now included in Acanthostethus mysticus (Gerstäcker, 1867). So adding an authorless "Nysson basalis" would just add to the confusion, in my view.

[yroskov]

Agree. Better to remove these trinomials from the import.