Open damianooldoni opened 4 years ago
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?
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?
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.
... 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.
@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
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 |
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.
@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:
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) andnubKey
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?