Analysis of the infraspecific taxa

[damianooldoni]

@timadriaens found strange that there was no analysis of Trachemys scripta, although this species is in the Union list of concern species. The answer was simple: in the unified there are three subspecies of it, but not the species itself (see www.gbif.org/species/163636890), although it is an alien species.

Why are there infraspecific taxa in unified and source checklists? There are two possible reasons, so we can divide such taxa in two groups:

1. there are both alien and native subspecies present in Belgium
2. their native ranges, pathways, habitats, distributions or year of introduction are different

Subspecies of Trachemys scripta belong to second group as the 3 subspecies have different date of first observed in ad-hoc checklist (see raw dump). But the species itself is alien...
So, how to distinguish infraspecific taxa of group 1 from those of group 2? An idea could be to add the species to taxon core without extensions, so no informations about pathways, native range, distribution etc. are present as they are specified at infraspecific level.

This solution will not affect checklist indicators at all as they are based on the information in the extensions. For occurrence indicators we should add a step in the pipeline for making the cube to avoid doubling the number of occurrences, but it is feasible.

In this file, infraspecific_alien_taxa_source_info.txt, you can find a list with all infraspecific taxa in the unified with their source checklist where key is the key of the taxon in the unified (e.g. 152543132) and nubKey is the key of the corresponding taxon in the GBIF backbone (e.g. 6157050).
@timadriaens and I think it is worth to find them. They should not be so many.

@peterdesmet, @qgroom & co.: what do you think about it? Is it something to add at unified level? Or at source checklist level?

[qgroom]

My gut feeling is that each line in the file should be independent. Therefore, if there are alien and native subspecies present in Belgium, then only the alien subspecies should be in the list. Whereas, when all the subspecies are present you a row for the species could be added without creating exceptions.
However, I suppose you then have the possibility of double counting in the indicators, but couldn't this be resolved by defining the indicator by the number of species, not the number of taxa?

[peterdesmet]

My thoughts:

when all the subspecies are present ...

I'm not sure how we can easily assess that: how do we know we have all?

An idea could be to add the species to taxon core without extensions

Not really sure what the benefit of that is. We wouldn't even be able to express that something is non-native.

So, I would say it's up to the analysis (e.g. occurrence indicators) if infraspecific taxa should be lumped.

One thing we could try to tackle is being smarter about lumping infraspecific taxa and species when both are present in source lists. So if one source checklist has Trachemys scripta and another only 3 subspecies of Trachemys scripta, then we currently get 4 taxa in the unified list. Maybe we trust the source checklist enough to only list the species then?

[damianooldoni]

Thanks @qgroom and @peterdesmet for your insights.

@peterdesmet: I have just checked: there are no infraspecific taxa and their related species in unified. But it's good you put the question for the future. Listing only the species could be dangerous as we risk to lose a lot of information. In case of Trachemys scripta subspecies, they have different date of introduction. What if we trust a source checklist where Trachemys scripta appears without no date of introduction? Don't we risk then to lose information?

@timadriaens : can you check in the file I made which infraspecific taxa belong to group 2? I don't think they are many... In this case then we can lump at indicators level as proposed by @peterdesmet.

[peterdesmet]

... appears without no date of introduction? Don't we risk then to lose information?

I would merge those just like we merge same taxa across checklists. So if date info is available for just one, it will be included. And in case of 2008-2012 + 2006-2014, it will become 2008-2014.

[timadriaens]

@damianooldoni I have checked the list to see if the taxon is alien/native at specieskey level but only the ones I knew. There are indeed quite a few subspecies of native species that are alien, will have different information on dates etc. and I feel the unified should definitely keep those.

Trachemys scripta, Ludwigia peploides and Ludwigia grandiflora are Union List species so the information on them in the indicators (e.g. for the pathways) will not be ok presumably (as for the pathways, we do not have the subspecies taxonkey in the list of union list species). That is presumably why they were lacking from the protected areas analysis. For the "number of introductions" indicator, I would also keep it at taxon level as this indicator is trying to visualize the number of introduction events more than the number of species.

In brief: I would NOT start to lump intraspecific taxa. But for the Union List species, I pragmatically propose to

• either include an extra line in the checklists at SpeciesKey level (this way they are all. right for the indicators and both the species and subspecies will be there).
• or, alternatively, add the subspecies of the Union List species that we know occur in Belgium in the Union List species file so that the indicators can link on those taxonkeys as well.

What do you think @qgroom @peterdesmet ?

key	nubKey	scientificName	kingdom	dataset	Species Alien
152543132	6157050	Graptemys pseudogeographica kohnii (Baur, 1890)	Animalia	Ad hoc checklist of alien species in Belgium	yes
152543136	7190901	Graptemys pseudogeographica pseudogeographica	Animalia	Ad hoc checklist of alien species in Belgium	yes
152543139	6157035	Trachemys scripta troostii (Holbrook, 1836)	Animalia	Ad hoc checklist of alien species in Belgium	yes
152543140	6157026	Trachemys scripta elegans (Wied, 1838)	Animalia	Ad hoc checklist of alien species in Belgium	yes
152543141	7062200	Trachemys scripta scripta	Animalia	Ad hoc checklist of alien species in Belgium	yes
152543370	4925890	Acer tataricum subsp. ginnala (Maxim.) Wesmael	Plantae	Manual of the Alien Plants of Belgium	yes
152543427	5545159	Ludwigia peploides subsp. montevidensis (Spreng.) P.H.Raven	Plantae	Manual of the Alien Plants of Belgium	yes
152543836	6304873	Cicerbita macrophylla subsp. macrophylla	Plantae	Manual of the Alien Plants of Belgium	yes
152543838	4227439	Cicerbita macrophylla subsp. uralensis (Rouy) P.D.Sell	Plantae	Manual of the Alien Plants of Belgium	yes
152544024	6077549	Artemisia campestris subsp. maritima (DC.) Arcang.	Plantae	Manual of the Alien Plants of Belgium	subsp. campestris is native
152544576	4271356	Heracleum sphondylium subsp. sibiricum (L.) Simonk.	Plantae	Manual of the Alien Plants of Belgium	no
152544749	4048052	Hippophae rhamnoides subsp. caucasica Rousi	Plantae	Manual of the Alien Plants of Belgium	no
152544786	7271631	Pyrus communis subsp. communis	Plantae	Manual of the Alien Plants of Belgium	no
152545105	5352372	Anthyllis vulneraria subsp. polyphylla (DC.) Nyman	Plantae	Manual of the Alien Plants of Belgium	no
152545106	5352425	Anthyllis vulneraria subsp. carpatica (Pant.) Nyman	Plantae	Manual of the Alien Plants of Belgium	no
152545165	7225471	Vicia villosa subsp. villosa	Plantae	Manual of the Alien Plants of Belgium	yes
152545174	2974936	Vicia villosa subsp. eriocarpa (Hausskn.) P.W.Ball	Plantae	Manual of the Alien Plants of Belgium	yes
152545179	2974921	Vicia villosa subsp. varia (Host) Corb.	Plantae	Manual of the Alien Plants of Belgium	yes
152545264	2914404	Galium verum subsp. wirtgenii (F.W.Schultz) Oborny	Plantae	Manual of the Alien Plants of Belgium	only subsp. Verum is native
152545471	7853188	Reseda lutea subsp. vivantii (P.Monts.) Rovira	Plantae	Manual of the Alien Plants of Belgium	no
152545641	7331861	Cymbalaria muralis subsp. muralis	Plantae	Manual of the Alien Plants of Belgium	yes
152545642	5559841	Cymbalaria muralis subsp. pubescens (J.Presl & C.Presl) D.A.Webb	Plantae	Manual of the Alien Plants of Belgium	yes
152545691	9508942	Origanum vulgare subsp. hirtum (Link) A.Terracc.	Plantae	Manual of the Alien Plants of Belgium	no
152545739	6411098	Lamium galeobdolon subsp. argentatum (Smejkal) J.Duvign.	Plantae	Manual of the Alien Plants of Belgium	no
152545891	4090836	Armeria maritima subsp. elongata (Hoffm.) Bonnier	Plantae	Manual of the Alien Plants of Belgium	no
152546440	3065244	Euphorbia amygdaloides subsp. robbiae (Turrill) Stace	Plantae	Manual of the Alien Plants of Belgium	no
152546507	5825913	Pinus nigra subsp. laricio (Poir.) Maire	Plantae	Manual of the Alien Plants of Belgium	yes
152546508	7230699	Pinus nigra subsp. nigra	Plantae	Manual of the Alien Plants of Belgium	yes
152547184	6387033	Equisetum hyemale subsp. affine (Engelm.) Calder & Roy L.Taylor	Plantae	Manual of the Alien Plants of Belgium	no
159747611	5679819	Spartina townsendii var. anglica C.E.Hubbard	Plantae	WRiMS: World Register of Introduced Marine Species	yes
159748038	8309092	Ludwigia grandiflora var. hexapetala (Hook. & Arn.) D.B.Ward	Plantae	Manual of the Alien Plants of Belgium	yes

[damianooldoni]

Reference file added in indicators repo: https://github.com/trias-project/indicators/blob/master/reference/assessment_alien_status_species_with_alien_infraspecific_taxa.tsv.

@qgroom: as most of the species/infraspecific taxa are plants, feel free to fill the field species_is_alien where not done by @timadriaens. You can do it by branch and pull request. I will take care to merge check it and merge it to master. Thanks.