Taxon swap removes disagreements

The sedge genus Carex has had a number of high level taxon swaps recently, changing the various groupings below genus. With the swaps, I have noticed that many former disagreeing higher level IDs (orange option) have been replaced with different higher level non-disagreeing (green option) taxons. The effect of this is that many former IDs have been effectively nullified. Here is an example: https://www.inaturalist.org/observations/2824397. It appears that there may have been a large number of observations affected in this way. Is there any way these can be corrected so that the replacement IDs are also disagreeing?

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Unfortunately, this is the current reality of taxon swaps, and the highly volatile concepts of infrageneric classification (which are constantly changing, especially for groups like Carex). The “options,” as you call them, weren’t changed, but a new, non-disagreeing ID was generated automatically. The reduced concept of the sections required that they be swapped into the subgenus in order to preserve ID accuracy. The example you linked includes an ID of sect. Phaestoglochin, which had many pieces split from it, necessitating that it be swapped into the higher subgenus Vignea and a new sect. Phaestoglochin be created. I’m pretty sure that if the old ID is restored by the user who made it, it should once again disagree with Carex austrina.

This link should provide you with a list of all of your withdrawn IDs that have been affected by taxon changes (if anyone else wants to use it, change out @dan_johnson’s name with your own in the URL, same with the other links below): https://jumear.github.io/stirfry/iNatAPIv1_identifications.html?current=true&is_change=true&per_page=200&user_id=dan_johnson

This link should provide you with all of your IDs on your content that have been affected by taxon changes: https://jumear.github.io/stirfry/iNatAPIv1_identifications.html?current=true&is_change=true&own_observation=true&per_page=200&user_id=dan_johnson

This link should provide a list of all of the withdrawn IDs of taxa subordinate to genus Carex, if someone is brave enough to take up the task of going through them (there are over 16,000 of them, not all of them being IDs affected by my recent reorganization of Carex): https://jumear.github.io/stirfry/iNatAPIv1_identifications?taxon_id=48571&taxon_active=false&current=false&per_page=200

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This sort of thing is a major problem with taxon swaps and changes in iNat.

There really needs to be a better way of dealing with them as these changes often wind up wiping out thousands of IDs, often ones that never get properly re-identified back to species again.

An example of this is while back the Siberian Stonechat, Saxicola maurus, was split into the Siberian Stonechat and the Amur Stonechat, Saxicola stejnegeri. It’s finally starting to sort itself out, but this is not an isolated example, just the one that first came to mind.

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Yes, I agree. The problem can occur as a result of the simplest taxon change, such as a name change. There’s a workaround that can be used to restore the disagreeing IDs after the fact.

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See also
https://forum.inaturalist.org/t/disagreeing-higher-ids-changed-to-agreeing-due-to-taxon-swap/39096

And other threads with similar opposite problems.

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I honestly don’t perceive this as a problem. I much prefer to see disagreements nullified in this way than artificially created by a split. As in, one user identifies to genus, then another identifies to species in that genus. They agree at genus level and it moves closer to RG. Then that species is moved into another genus. Suddenly, the two users disagree at genus level without either of them changing their minds, and it moves further from RG.

If a disgreement disappears because of taxonomic change, that’s a change I can get on board with.

The problem is that this is what’s happening. See the link to my post in the comment above: the CV generated a lot of incorrect species level IDs, I put in disagreeing higher-level IDs, and then when the higher-level taxon was changed they all were made non-disagreeing and the incorrect species IDs came back.

yeah, it needs to stop. taxon changes need to stop, full stop. Every 10 years you can do a big update with all the changes of the last decade, doing it piecemeal is breaking inaturalist. The current system has the whole site all but unusable to anyone except hardcore taxonomists. But since curators on the site are selected from hardcore taxonomists there’s a massive bias that excludes everyone else using the site. Yes i get that genetics changes our view of how the species concept works, but right now, it doesn’t ‘work’ at all for 99% of the users of the site. Remember, iNat is to ‘connect people with nature’ and this is doing the opposite.

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I wouldn’t stop them, but I would very much like to see a lot more structure and regularity in how they’re addressed and applied. Applying them en-mass periodically rather than whenever someone gets new information would probably be a good idea (kind of like how the CV is updated periodically rather than just slowly upgrading in the background - different systems, but the point stands).

When taxon changes are made it would also be nice if the new species name on the observation had a note under it reading something like, “Formerly Common name (Binomial),” to help reduce confusion.

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Then we could have a blog post.
With a list.
And could see where we are.

well i wouldn’t stop them either, just a decade seems like a small ask in response to how messed up taxonomy has gotten, it’ll take at least that long to try to fix it :D

but, taxonomists rule iNat and botany in general and in my experience the ones making the decisions aren’t interested in the needs of the people who actually use the names. I love a lot of the science they do, and and think it’s incredibly valuable work contributing to the body of science, but they can do that without the constant microspecies splitting to species level and changes. It’s time for the majority of people who use taxonomy to have a say, not just the exclusionary few,

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seems like it could be done, but it would be a potentially inefficient process. instead if just adding new identifications that would automatically withdraw previous ids, you would probably have to withdraw existing ids, then add the replacement ids, keeping the disagreement if the interim community taxon was the same as the taxon that was disagreed to in the original id.

i’m sure that this kind of process would not cover all cases, and i expect there would be some additional manual cleanup still needed at least some of the time. so i’m not sure how much of an improvement this might be.

probably the problem described in this thread could be addressed if the proposal in another thread was implemented: https://forum.inaturalist.org/t/eliminate-the-observation-level-can-the-community-taxon-be-improved-dqa-item-in-favor-of-an-id-level-cannot-be-improved-flag/26945.

The problem is that information is being lost. IDing at genus level without disagreement is a different ID from IDing at genus level with disagreement. I.e. it’s the difference between “I’m sure it is in this genus, but not making any claims of whether or not it is a particular species.” and “I’m sure it is in this genus, but I am also sure it is not this particular species.”

So changing to a general ID is not “wrong” in the sense that it’s not creating false information. But it is deleting useful and relevant information that a user provided.

In many cases, the disagreement is essential, i.e. because it is obvious that the organism in question belongs to the higher taxon, but it is not necessarily obvious whether or not it belongs to the more specific taxon. The debate centers around the specific taxon and the disagreement might be the only relevant input that one or more users might be giving to the ID discussion.

In this case, deleting this information is a serious loss. It is undoing or erasing the work that people have put into the ID process.

I absolutely think this is a serious problem and it puzzles me why this problem hasn’t been fixed. A flag was set to communicate disagreement before, so why can a new flag not be set?

In many (an overwhelming majority of?) cases there was no merging or splitting happening, it was just a question of a renamed taxon, or merging of duplicate records referring to the same taxon, so there is absolutely no reason to delete or lose this information.

In some cases, such as where there is a merge or split, there may or may not be a need to update the information, but these could be handled on a case-by-case basis, perhaps by prompting the user to re-examine whether or not they disagree.

An easy way to handle this would be to just add a third option for the field, so instead of just having “disagree” / “not disagree”, also have a third option “disagree before reclassification” or something. This would show that the user disagreed but that there has been a taxon swap and so the user may or may not disagree, and then allow the user to come in and manually flag whether or not they disagree.

This seems the only way to do it that would make sense, because it’s the only way to do it without information loss.

Information loss in a system like iNaturalist is dangerous, with the creep of change after change, a lot of information could be lost in the long-run, and it’s entirely unnecessary. Just handle it in the only way that makes logical sense.

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