Duplicates in scientific name

[LienReyserhove]

It appears that some taxa in the checklist appear twice :unamused: (see table bellow for a summary of all duplicated taxa). This is because:

• most duplicated species have contrasting presence information for one country (e.g. Anchusa arvensis). For some of these species, one record has the note "data based solely on DAISIE portal", while the other records lacks this note. In the main article, I found this:

data based solely on DAISIE portal - taxon listed as present by the DAISIE portal but not by any of the other databases consulted; no additional portal was consulted regarding geographical distribution (also see Methods section)

So, does this mean that, in the one case, only the DAISIE portal was consulted, and in the others, all portals were consulted? Which distribution information do we use then? I see that this also affects species presence for Belgium.

• Some duplicated species are assigned to two kingdoms, i.e. Elachista and Acrophyllum dentatum. I can find information that verifies both cases...So if this is information is in fact true, then we will get the same taxonID for both species, which is problematic.

In case of the first problem, I think it is best to contact the authors for advice. In the second problem, I'm not sure what to do. I can generate a taxonID based on the combination of phylum and scientifc name in this case?

phylum_division	class	genus	species	great_britain	france	belgium	netherlands	environment	notes	scientificName
Angiospermae	Eudicotyledoneae	Acrophyllum	dentatum	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Acrophyllum dentatum
Angiospermae	Eudicotyledoneae	Anchusa	arvensis	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Anchusa arvensis
Angiospermae	Eudicotyledoneae	Anchusa	arvensis	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Anchusa arvensis
Angiospermae	Monocotyledoneae	Avena	sterilis	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Avena sterilis
Angiospermae	Monocotyledoneae	Avena	sterilis	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Avena sterilis
Angiospermae	Monocotyledoneae	Avena	strigosa	present	present	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Avena strigosa
Angiospermae	Monocotyledoneae	Avena	strigosa	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Avena strigosa
Angiospermae	NA	Beta	vulgaris	not confirmed	present	not confirmed	not confirmed	terrestrial	NA	Beta vulgaris
Angiospermae	NA	Beta	vulgaris	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Beta vulgaris
Angiospermae	NA	Brassica	elongata	present	present	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Brassica elongata
Angiospermae	NA	Brassica	elongata	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Brassica elongata
Angiospermae	NA	Chenopodium	berlandieri	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Chenopodium berlandieri
Angiospermae	NA	Chenopodium	berlandieri	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Chenopodium berlandieri
Angiospermae	NA	Chenopodium	strictum	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Chenopodium strictum
Angiospermae	NA	Chenopodium	strictum	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Chenopodium strictum
Angiospermae	Monocotyledoneae	Cynodon	incompletus	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Cynodon incompletus
Angiospermae	Monocotyledoneae	Cynodon	incompletus	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Cynodon incompletus
Angiospermae	Eudicotyledoneae	Epilobium	x novae-civitatis	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Epilobium x novae-civitatis
Angiospermae	Eudicotyledoneae	Epilobium	x novae-civitatis	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Epilobium x novae-civitatis
Angiospermae	NA	Hypericum	hircinum	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Hypericum hircinum
Angiospermae	NA	Hypericum	hircinum	not confirmed	present	not confirmed	not confirmed	terrestrial	NA	Hypericum hircinum
Angiospermae	NA	Lythrum	junceum	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Lythrum junceum
Angiospermae	NA	Lythrum	junceum	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Lythrum junceum
Angiospermae	NA	Mentha	x piperita	present	not confirmed	present	not confirmed	terrestrial	data based solely on DAISIE portal	Mentha x piperita
Angiospermae	NA	Mentha	x piperita	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Mentha x piperita
Angiospermae	Monocotyledoneae	Papaver	atlanticum	present	not confirmed	present	not confirmed	terrestrial	data based solely on DAISIE portal	Papaver atlanticum
Angiospermae	Monocotyledoneae	Papaver	atlanticum	present	not confirmed	present	present	terrestrial	NA	Papaver atlanticum
Angiospermae	NA	Populus	nigra	present	not confirmed	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Populus nigra
Angiospermae	NA	Populus	nigra	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Populus nigra
Angiospermae	NA	Salix	x sepulcralis	present	present	not confirmed	not confirmed	terrestrial	data based solely on DAISIE portal	Salix x sepulcralis
Angiospermae	NA	Salix	x sepulcralis	not confirmed	not confirmed	present	not confirmed	terrestrial	NA	Salix x sepulcralis
Arthropoda	Insecta	Cinara	pini	present	present	not confirmed	present	terrestrial	NA	Cinara pini
Arthropoda	Insecta	Cinara	pini	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Cinara pini
Arthropoda	Insecta	Elachista	sp.	present	present	present	present	marine	NA	Elachista sp.
Bryophyta	Eudicotyledoneae	Acrophyllum	dentatum	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Acrophyllum dentatum
Heterokontophyta	Phaeophyceae	Elachista	sp.	not confirmed	not confirmed	not confirmed	present	marine	NA	Elachista sp.
Nematoda	Adenophorea	Xiphinema	rivesi	not confirmed	present	not confirmed	not confirmed	terrestrial	NA	Xiphinema rivesi
Nematoda	Adenophorea	Xiphinema	rivesi	not confirmed	present	not confirmed	not confirmed	terrestrial	NA	Xiphinema rivesi
Pteridophyta	Pteridopsida	Dicksonia	antarctica	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Dicksonia antarctica
Pteridophyta	Pteridopsida	Dicksonia	antarctica	present	not confirmed	not confirmed	not confirmed	terrestrial	NA	Dicksonia antarctica

[qgroom]

Regarding the kingdoms:

Elachista seems to be a hemihomonym problem, one is an algae (http://www.algaebase.org/search/genus/detail/?genus_id=c94298cee5ba4e03f&sk=0) one is a moth (https://en.wikipedia.org/wiki/Elachista).

This paper has a useful list http://mapress.com/j/bn/article/viewFile/bionomina.4.1.3/29

Acrophyllum also has the same problem. https://species.wikimedia.org/wiki/List_of_valid_homonyms

However, in this case it the homonym is not the problem it seems to be a spelling mistake. Achrophyllum dentatum is a Bryophyte in the class Bryopsida. Acrophyllum is a dicot, but there is no such thing as Achrophyllum dentatum.

[qgroom]

Regarding the "data based solely on DAISIE portal"

The provenance information is very poor on DAISIE so I don't like to use it, if I can help it. However, it seems from the data in this table that the provenance information is even worse in RINSE.

Could we just ignore the rows that say "data based solely on DAISIE portal"? If you output a list of the species we might miss by doing this we could potential add them to the ad hoc list.

[timadriaens]

good idea to confront those lists and use this as inspiration for the ad hoc list but as those records are part of the RINSE register I would leave them in even if we know they are probably a copy paste from a website with little information behind. I believe these kind of decisions (which sources from which autoritative checklists) are typically something for the pipeline to build the unified checklist, no?

[peterdesmet]

+1 to leave them in. The register is referenced as having 6661 taxa (see here). Would indicate source literally as data based solely on DAISIE portal, which would allow to filter them out.

Regarding the duplicates, I would:

• Allow minor corrections (as suggested by @qgroom)
• Check for duplicate taxonIDs and append :1, :2 for those

[qgroom]

OK 4 Me 2