Gentianella anglica deleted in UK Master List

[JimBacon]

As an outcome of https://github.com/BiologicalRecordsCentre/BSBI-Card-and-PlantPortal/issues/55 it has been noticed that the taxon Gentianella anglica, an endangered species endemic to the UK, is deleted from the UK Master List. It was further observed that hundreds of other taxa were deleted at the same time. This could be associated with an UKSI import and many of the deletions may be valid.

To investigate, the , following query was run.

SELECT DISTINCT 
  t.id, t.taxon, tg.title, t.created_on, t.updated_on, 
  t2.id, t2.created_on, t2.updated_on, t2.deleted 
FROM taxa t
LEFT JOIN taxa_taxon_lists ttl ON ttl.taxon_id = t.id
LEFT JOIN taxon_groups tg ON tg.id = t.taxon_group_id
LEFT JOIN taxa t2 ON t2.taxon = t.taxon AND t2.id <> t.id
LEFT JOIN taxa_taxon_lists ttl2 ON ttl2.taxon_id = t2.id AND ttl2.taxon_list_id = 15 AND ttl2.preferred = true
WHERE 
t.updated_on > '2015-04-03' AND t.updated_on < '2015-04-04' AND t.deleted = true
AND  ttl.preferred = true AND  ttl.taxon_list_id = 15 AND t.taxon_rank_id = 26 
ORDER BY t2.updated_on

This selects all preferred species taxa in the UK Master List that were deleted on 3/4/2015 and joins them to any other preferred taxa in the UK Master List with the same name. It shows that, of the deleted taxa,

• some had duplicates which were are not deleted so are still present in the list.,
• some were recreated on 8/6/2016,
• more were recreated on 13/10/2016
• some had duplicates that had already been deleted, like Gentianella anglica so are not currently available,
• others were unique so are not currently available,

Of those no longer available, many are butterflies, non-UK species from a sample, so let us look for other plants e.g. _Ophrys oestrifera, Armeria pseudoarmeria, Primula spectabilis, Bromus grossus_

These appear to be endangered non-UK species based on some very inexpert internet searching. This suggests that, though these species can all be found in UKSI, this is through the incorporation of a European endangered species list and they are not relevant to UK recording and were intentionally removed. Gentianella anglica may be the baby thrown out with the bathwater. Only a thorough check would determine if there are others. The full list, excluding butterflies contains 35 species.

+--------+--------------------------------+-----------------------------+------------------+
| 52640  | Lithophyllum lichenoides       | alga                        | NBNSYS0000163285 |
+--------+--------------------------------+-----------------------------+------------------+
| 323017 | Laminaria ochroleuca           | chromist                    | NHMSYS0021058678 |
+--------+--------------------------------+-----------------------------+------------------+
| 139905 | Ceriodaphnia rotunda           | crustacean                  | NHMSYS0001593326 |
+--------+--------------------------------+-----------------------------+------------------+
| 177220 | Daphnia (Ctenodaphnia) similis | crustacean                  | NHMSYS0001593478 |
+--------+--------------------------------+-----------------------------+------------------+
| 88726  | Daphnia (Daphnia) cristata     | crustacean                  | NHMSYS0001593481 |
+--------+--------------------------------+-----------------------------+------------------+
| 141683 | Woodwardia radicans            | fern                        | NHMSYS0000465080 |
+--------+--------------------------------+-----------------------------+------------------+
| 17452  | Armeria pseudoarmeria          | flowering plant             | NBNSYS0200001817 |
+--------+--------------------------------+-----------------------------+------------------+
| 75454  | Armoracia macrocarpa           | flowering plant             | NBNSYS0000163531 |
+--------+--------------------------------+-----------------------------+------------------+
| 45828  | Bromus grossus                 | flowering plant             | NBNSYS0000163594 |
+--------+--------------------------------+-----------------------------+------------------+
| 174706 | Caldesia parnassiifolia        | flowering plant             | NBNSYS0000173039 |
+--------+--------------------------------+-----------------------------+------------------+
| 304762 | Caropsis verticillatoinundata  | flowering plant             | NHMSYS0020823738 |
+--------+--------------------------------+-----------------------------+------------------+
| 302617 | Cochlearia acaulis             | flowering plant             | NHMSYS0020823740 |
+--------+--------------------------------+-----------------------------+------------------+
| 181617 | Dendranthema zawadskii         | flowering plant             | NBNSYS0200003757 |
+--------+--------------------------------+-----------------------------+------------------+
| 293655 | Dioscorea chouardii            | flowering plant             | NHMSYS0020823746 |
+--------+--------------------------------+-----------------------------+------------------+
| 161833 | Genista linifolia              | flowering plant             | NBNSYS0200002222 |
+--------+--------------------------------+-----------------------------+------------------+
| 75308  | Gentianella anglica            | flowering plant             | NHMSYS0000459021 |
+--------+--------------------------------+-----------------------------+------------------+
| 307788 | Helictotrichon hackelii        | flowering plant             | NHMSYS0020823141 |
+--------+--------------------------------+-----------------------------+------------------+
| 301555 | Himantoglossum comperianum     | flowering plant             | NHMSYS0020823751 |
+--------+--------------------------------+-----------------------------+------------------+
| 301639 | Himantoglossum metlesicsianum  | flowering plant             | NHMSYS0020823752 |
+--------+--------------------------------+-----------------------------+------------------+
| 309412 | Hypochaeris oligocephala       | flowering plant             | NHMSYS0020823159 |
+--------+--------------------------------+-----------------------------+------------------+
| 304067 | Lepidium navasii               | flowering plant             | NHMSYS0020823762 |
+--------+--------------------------------+-----------------------------+------------------+
| 210853 | Narcissus angustifolius        | flowering plant             | NBNSYS0000163318 |
+--------+--------------------------------+-----------------------------+------------------+
| 241758 | Ophrys oestrifera              | flowering plant             | NHMSYS0020704593 |
+--------+--------------------------------+-----------------------------+------------------+
| 41508  | Primula spectabilis            | flowering plant             | NBNSYS0000163814 |
+--------+--------------------------------+-----------------------------+------------------+
| 301718 | Scilla lochiae                 | flowering plant             | NHMSYS0020823773 |
+--------+--------------------------------+-----------------------------+------------------+
| 146104 | Silene holzmannii              | flowering plant             | NBNSYS0000163391 |
+--------+--------------------------------+-----------------------------+------------------+
| 300195 | Silene laxipruinosa            | flowering plant             | NHMSYS0020823780 |
+--------+--------------------------------+-----------------------------+------------------+
| 309969 | Silene pardoi                  | flowering plant             | NHMSYS0020823781 |
+--------+--------------------------------+-----------------------------+------------------+
| 291484 | Sonchus bupleuroides           | flowering plant             | NHMSYS0020823784 |
+--------+--------------------------------+-----------------------------+------------------+
| 77409  | Trachysiphonella carinfacies   | insect - true fly (Diptera) | NHMSYS0020706104 |
+--------+--------------------------------+-----------------------------+------------------+
| 32177  | Lecidea sanguineoatra          | lichen                      | NHMSYS0020987782 |
+--------+--------------------------------+-----------------------------+------------------+
| 11002  | Marsupella profunda            | liverwort                   | NBNSYS0000035904 |
+--------+--------------------------------+-----------------------------+------------------+
| 199240 | Bruchia vogesiaca              | moss                        | NBNSYS0000163957 |
+--------+--------------------------------+-----------------------------+------------------+
| 34929  | Buxbaumia viridis              | moss                        | NHMSYS0000309525 |
+--------+--------------------------------+-----------------------------+------------------+
| 113452 | Hamatocaulis vernicosus        | moss                        | NHMSYS0000310012 |
+--------+--------------------------------+-----------------------------+------------------+

[sacrevert]

From the plants, the following (including G. anglica) should be reinstated, as they definitely occur in the British Isles:

| 11002 | Marsupella profunda | liverwort | NBNSYS0000035904 | +--------+--------------------------------+-----------------------------+------------------+ | 199240 | Bruchia vogesiaca | moss | NBNSYS0000163957 | +--------+--------------------------------+-----------------------------+------------------+ | 34929 | Buxbaumia viridis | moss | NHMSYS0000309525 | +--------+--------------------------------+-----------------------------+------------------+ | 113452 | Hamatocaulis vernicosus | moss | NHMSYS0000310012 .

I do not have the expertise to assess the crustaceans, alga, or chromist

[johnvanbreda]

• G. anglica will indeed be reinstated at the next UKSI update. I am waiting on a fix to the lichen names in the current UKSI data before doing the update.
• The other names on the list in the post immediately above are marked as redundant and non-native so they will not appear. I suspect Chris believed these sp did not occur in the British Isles.

[sacrevert]

Presumably the bryophytes i listed will be reinstated too?

[johnvanbreda]

No, the 4 bryophytes (Marsupella profunda, Bruchia vogesiaca, Buxbaumia viridis, Hamatocaulis vernicosus) are all marked as redundant in the UKSI database so will not appear, nor will most of the species in Jim's original post. Jim is correct in his assumption that this appears to be deliberate. Therefore you will need to get UKSI corrected before they can appear in the Indicia species lists.

[johnvanbreda]

No, the 4 bryophytes (Marsupella profunda, Bruchia vogesiaca, Buxbaumia viridis, Hamatocaulis vernicosus) are all marked as redundant in the UKSI database so will not appear, nor will most of the species in Jim's original post. Jim is correct in his assumption that this appears to be deliberate. Therefore you will need to get UKSI corrected before they can appear in the Indicia species lists.

You can search the latest import from UKSI into Indicia at http://test.brc.ac.uk/irecord_dev/enter-casual-record. Note that this version of UKSI is not live yet because there were problems in the lichen names which Richard Shotbolt is resolving.

[sacrevert]

G. anglica and the four bryos reinstated by Chris Raper 14/03/2018

[sacrevert]

@JimBacon do you want to close this now?

[JimBacon]

I would be inclined to wait until they have all made it in to the Indicia warehouse copy of the list and can actually be recorded.

[sacrevert]

OK, I hope that I remember that this issue exists/can find it when it comes to it then. :)

[johnvanbreda]

If there is any urgency let me know and I can force them back in.

[sacrevert]

It would actually be worth doing that for Buxbaumia viridis at least, there was a project in Scotland that was targeting this species, and there are a few records that are at genus level as result (I only realised this recently, and was surprised that David Genney (SNH) hadn't told me about the loss of the species!)