1 (edited by RobLarge 07-09-2012 15:28:33)

Topic: Not for the first time

This one has been pointed out before here http://forums.nbn.org.uk/viewtopic.php?id=3678

I have just had the same problem. In the wizard doing a report on Lesser Butterfly Orchid - Platanthera bifolia, with expand taxonomic groups ticked, it returns Greater Butterfly Orchid (P. chlorantha) as well.

As Craig pointed out, in the Recorder 3.3 list the hybrid between the two species is displayed as a child taxon (subspecies level) of P. bifolia, which is wrong as it should occur at the same taxonomic level as the two parent species. This hybrid has Platanthera chlorantha listed as a synonym as well, which it is not.

Is this something you can fix Chris, or should I be hassling the Recorder team?

Rob Large
Wildlife Sites Officer
Wiltshire & Swindon Biological Records Centre

2 (edited by ChrisR 07-09-2012 15:52:26)

Re: Not for the first time

Hi Rob

I think it will be a bit of both ... could you tell me what 'expand taxonomic groups' should do? That might help be deduce what it is doing with the underlying tables.

The 'parent' problem sounds very similar to the one we had on ferrets a few weeks back. This I think should be fixed by modifying the parent on the Recorder 3.3 checklist row for the hybrid. I will investigate and report back.

Best wishes,
Chris R.

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

3

Re: Not for the first time

The expand taxonomic groups option appears in the report wizard of Recorder. When creating a taxon report (querying the database for taxon occurrences) it is possible to select one or more taxa from any of the lists. In this instance we have selected Platanthera bifolia. The expand option should then include all other taxa which are listed as hierarchical children of the selected taxon. In the normal run of things that would mean subspecies and/or varieties, if the taxon is a species as in this case, but would also include species & monogeneric hybrids if a genus is selected (and so on).

Clearly a hybrid of two species in Platanthera is in one sense a child of the two parent species, but in terms of the dictionary hierarchy it should occupy the same level as the parents, i.e. a child of Platanthera.

I suspect that this and ferret will be far from the only examples in the Rec 3.3 list. I have encountered others and would not be at all surprised if it is the norm for dealing with hybrids in this list. Might be a big job for someone to pick them all out and correct them. I do consider this to be a vital task though. I imagine it would be easy enough to run a query to select all taxa marked as hybrids in the list which are recorded as children of species-level taxa. Where the genus of both parents is the same as that of the hybrid, it should be possible to do a batch update changing the parent to the genus. It would be necessary to check for transgeneric hybrids though, which would become children of the family, sub-family etc.

I do recall another instance in the Recorder3.3 list though, reported a long time ago, but as yet uncorrected. In the genus Tilia (vascular plant - Lime trees) there are three true species listed, but each of these has a hybrid as a child. This is an important example as Tilia platyphyllos (Broad-leaved Lime) is Nationally Scarce, while the hybrid marked as its child Tilia x europaea is one of the most commonly planted trees in UK parks and gardens. It is really not good enough that a query for T. platyphyllos should return records of the hybrid.

Sure I could find a dozen other examples but that really isn't my job.

Thanks

Rob Large
Wildlife Sites Officer
Wiltshire & Swindon Biological Records Centre

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Re: Not for the first time

Hi Rob

I see the problem - I will relink the Platanthera hybrids in the Recorder 3.3 checklist to the genus and that should sort the problem out. As you say, there are likely to be more ... I think I should be able to do a query that might bring them out. Something like, all rows in TAXON_LIST_ITEM where the TAXON_TYPE is "Hybrid" and the PARENT's type is not "Genus". :)

Many thanks
Chris R.

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

5

Re: Not for the first time

Thanks Chris

Rob Large
Wildlife Sites Officer
Wiltshire & Swindon Biological Records Centre

6 (edited by ChrisR 12-09-2012 17:28:46)

Re: Not for the first time

Just done a quick query on the Recorder 3.3 checklist and it looks like it must have been the policy, at the time the list was created, that hybrids were to be linked to one of the parents, rather like a sub-species ... not the current prevailing view that the genus should be their parent.

My query showed that only 4 hybrids are linked to a genus (including one that I fixed earlier), while 844 hybrids are linked to a species. This poses a conundrum because it would take a lot of time to go through the database "fixing" all of these instances (which are not mistakes - just a different way of doing it) and it would be a questionable use of time, considering how old the Recorder 3.3 list is.

I will raise the issue with the NBN & Recorder teams at our meeting later this month and report back :)

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

7 (edited by RobLarge 13-09-2012 08:36:49)

Re: Not for the first time

While I agree that they are not actually mistakes, they are the result of a way of doing things which conflicts with the design of Recorder in its current form and cause reports to return erroneous, or at least unexpected results.

For what it is worth, my position is that if left uncorrected they will continue to cause errors in the outputs produced by Recorder users and the knowledge of their existence means that many users will have to continue expending time and resources checking for such errors. The few examples I and others have reported will only be the obvious ones.

If a decision can be made that the Rec3.3 way is the wrong way, then a fairly simple update query could be designed to do most of the fixing in one go. However it would still need someone to go through and pick out those where the hybrid should not have a genus-level parent.

As examples I would draw your attention to Frog Orchid (Coeloglossum viride) in the Rec3.3 dictionary, which has three hybrid offspring, all of which are also children of species in the genus Dactylorhiza. On the face of it these hybrids should not be the 'children' of either Coeloglossum or Dactylorhiza. Yet some authors now call Frog Orchid Dactylorhiza viridis.

Interestingly I note that the preferred Vascular Plants list has the three Coeloglossum X Dactylorhiza hybrids as children of Orchidaceae, but it also lists a number of hybrid genuses, including X Dactyloglossum, which is the correct parent of all three (but has no child taxa at present).

An alternative approach to checking through all 844 examples in the Rec 3.3 dictionary might be to modify recorder so that the 'expand taxonomic groups' option is restricted only to preferred lists (or optionally so restricted).

I guess the question is what is the best way of dealing with the legacy of the Rec3.3 list?

Rob Large
Wildlife Sites Officer
Wiltshire & Swindon Biological Records Centre

8

Re: Not for the first time

ChrisR wrote:

and it would be a questionable use of time

Just to say I would be incredibly grateful for this! Despite the age of the Recorder 3 list, we have a lot of records that were/are input against it - my top 3 would be:

* Hyacinthoides hispanica x non-scripta
* Tilia x vulgaris
* the poplars

Of course, the other option is to ditch the Recorder 3 list completely and transfer all the determinations to another list?

Charlie Barnes
Information Officer
Greater Lincolnshire Nature Partnership

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Re: Not for the first time

RobLarge wrote:

I guess the question is what is the best way of dealing with the legacy of the Rec3.3 list?

Hi Rob, I absolutely agree with what you say and this last question is really the nub of the problem for me. The Recorder 3.3 list has always had its problems but it is the largest pan-group checklist so it has been the list of choice for many Recorder users who just want to log mixed batches of observations. Just over a year ago Charles started constructing his own master checklist, called the ORGANISM table, and he completed it earlier this year before his retirement. Later this month we will be meeting the developers and stakeholders to explore future uses of this table in Recorder and other recording applications. An obvious use would be to help with this 'master checklist' issue. I will just postpone any decision on the Recorder 3.3 list until we have discussed where the other stakeholders think the best direction is. :)

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

10 (edited by ChrisR 13-09-2012 11:10:21)

Re: Not for the first time

charliebarnes wrote:

Of course, the other option is to ditch the Recorder 3 list completely and transfer all the determinations to another list?

Hi Charlie, I suspect that the Recorder 3.3 list's days might be numbered and it could be better to transfer future development to a better, more complete list that is designed in a way that would allow it to be used in other projects too. But I am sure that backward compatibility with the Recorder 3.3 list would be retained because checklists have always formed the basis to the Recorder recordset. If we do decide to keep it going it isn't a huge job to re-point the hybrids ... just a big, boring one ... it might even be that we just fix the hybrids that cause people the most problems.  Rob's example of intergeneric hybrids do pose some interesting conundrums though - which genus should we attach the hybrid to? Plenty to think about and discuss in the coming weeks :)

Over the years recorders have commented to me that what they basically need is a flat database of names and a system where they can just enter general locality/survey details and then list the names (with an option of using those 5-character codes), like Recorder 3.3 used to do, and that recording against (and often swapping) checklists just slows them down. The advantage of using checklists is that they fix a taxon concept in time and can be useful when entering reams of paper records such as transects or recording-cards. But I am sure that a mixture of this should be possible :)

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

11

Re: Not for the first time

ChrisR wrote:

Rob's example of intergeneric hybrids do pose some interesting conundrums though - which genus should we attach the hybrid to?

That's an easy one Chris. The solution (partially) adopted by the vascular plants list as described above is the one. Within (eg) Orchidaceae there should be, in addition to the true genera, a number of pseudogenera such as x Dactyloglossum which should contain the intergeneric hybrids.

If you want to consider a genuinely difficult problem then what should we do with back-crosses between hybrids and one or more of the parents? Fortunately there aren't many people recording simple hybrids, let alone the more complex ones.

One thing that the Rec3.3 list has been especially useful for is recording aggregates and difficult to determine species. It is easy, in the highly technical discussions we tend to have regarding taxonomy, to forget that we are all encouraging public participation in recording and that records of poorly determined  taxa are going to become increasingly common.

Rob Large
Wildlife Sites Officer
Wiltshire & Swindon Biological Records Centre

12

Re: Not for the first time

RobLarge wrote:

That's an easy one Chris. The solution (partially) adopted by the vascular plants list as described above is the one. Within (eg) Orchidaceae there should be, in addition to the true genera, a number of pseudogenera such as x Dactyloglossum which should contain the intergeneric hybrids.

If you want to consider a genuinely difficult problem then what should we do with back-crosses between hybrids and one or more of the parents? Fortunately there aren't many people recording simple hybrids, let alone the more complex ones.

One thing that the Rec3.3 list has been especially useful for is recording aggregates and difficult to determine species. It is easy, in the highly technical discussions we tend to have regarding taxonomy, to forget that we are all encouraging public participation in recording and that records of poorly determined  taxa are going to become increasingly common.

Yes, we're a victim of our own success - it's marvelous that more people are recording the poorly-studied groups but then we have to provide the means to do so and that's when we find unresolved problems :)   I was having a similar chat with a taxonomist the other day and he made the distinction between taxonomic-concepts and recording-concepts. We make taxonomic lists but for recording purposes we also have to allow for unusual hybrids and aggregates that don't fit snugly into the classic tree diagrams ... I can see this one will run and run ;)

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

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Re: Not for the first time

It's already been running for quite a few years to my knowledge.

Rob Large
Wildlife Sites Officer
Wiltshire & Swindon Biological Records Centre

14

Re: Not for the first time

Any chance that this will get Fixed? I have Platanthera chlorantha coming out as S41 species. So am I to send out data without having any idea of correctness for the status? Several years is a long time to wait!

Data Manger
Somerset Environmental Records Centre

15

Re: Not for the first time

OK, I have sorted out the incorrect linkage between Platanthera chlorantha and Platanthera x hybrida. I think the other links should be OK too. I haven't tried sorting through the other hybrids in other genera but if anyone spots them do let me know. :)

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

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Re: Not for the first time

Brilliant

Data Manger
Somerset Environmental Records Centre