Plant taxonomy for iNat

[Charlie Hohn]

Hi all, i thought we were following Jepson manual for plant taxonomy on iNat when relevalt... but someone went in and started messing with Mimulus. My belief (and hope) were that we were going to leave this be until a new jepson came out... if we just chase every little taxonomy paper that comes out we will be running all over the place and no one will be able to classify anything (already feels that way to me in the taxonomy world anyway)

So yeah... if others feel differently I could be overruled of course but let's not go nuts on the Mimulus.

[Scott Loarie]

I believe it's the New Zealanders who did that - I'd comment on any taxon changes

Sent from my iPhone

On Jul 29, 2015, at 4:40 AM, Charlie Hohn <naturalis...@gmail.com> wrote:

Hi all, i thought we were following Jepson manual for plant taxonomy on iNat when relevalt... but someone went in and started messing with Mimulus. My belief (and hope) were that we were going to leave this be until a new jepson came out... if we just chase every little taxonomy paper that comes out we will be running all over the place and no one will be able to classify anything (already feels that way to me in the taxonomy world anyway)

So yeah... if others feel differently I could be overruled of course but let's not go nuts on the Mimulus.

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[Charlie Hohn]

Yeah... I did leave a comment. But is there a way to stop them from changing all the mimuli? Or is it too late?

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[Sam Kieschnick]

Ugh... Mimulus...

I hear that this genus is about to be massacred into a whole slew of genera.  

http://www.phytoneuron.net/PhytoN-Phrymaceae.pdf

But I have no real emotions about it.  :)  Outside of the Californian plants, I have been using The Plant List as the ultimate guide to taxonomy.  Always right?  Nah -- but it at least gives me something to point at.  I would hope that most of the plants on iNat would follow The Plant List's accepted taxonomy.

[Ken-ichi]

I think our rules are pretty clear, especially for North American
plants: Calflora and GoBotany are our references, with The Plant List
as a tie-breaker. In NZ we're following Ngā Tipu Aotearoa. If you see
some examples of people not abiding by the policies, please provide
URLs.

[James Bailey]

So in a situation where multiple but not all members of a genus are distributed over different countries and said countries treat that genus differently, what happens then? I assume theplantlist would take priority in this situation theorized below?

For instance let's say we have these theoretical species:

Mimulus speciesA

Mimulus speciesB

Mimulus speciesC

Mimulus speciesD

Mimulus speciesE

Mimulus speciesF

Three species, A, B and C occur in New Zealand. In New Zealand they are treated under genus Neomimulus. New Zealand changes those species on iNaturalist, then we get this:

Neomimulus speciesA

Neomimulus speciesB

Neomimulus species C

Mimulus species D

Mimulus species E

Mimulus species F

Then say Mimulus species D, the only species in Antarctica, is treated there as Mesomimulus species D and they make that change on iNat:

Neomimulus speciesA

Neomimulus speciesB

Neomimulus species C

Mesomimulus species D

Mimulus species E

Mimulus species F

This is a mess because each country is only treating specific members of the genus, and the coverage is incomplete. Thus we get a "jigsaw" taxonomy on iNaturalist and taxon are all over.

I assume the solution would be to go for the "universal" classification on theplantlist, and add the country specific names as synonyms? I wonder if adding location for scientific names could become a reality for those in countries which don't follow the "universal" standard? I assume place name functionality is not set for scientific names, only "common" names?

[Eric Hunt]

Ken-ichi,

Here is Mimulus guttatus:

http://www.inaturalist.org/taxa/470643-Erythranthe-guttata

Calflora has not reclassified using the 2012 Phytoneuron paper from Barker, Nesom, Beardsley, Fraga.

See: http://www.calflora.org/cgi-bin/species_query.cgi?where-calrecnum=5519

-Eric

[lelliott]

I hate to jump in on this (probably an over-discussed topic), but where might one find the "rules".

On Friday, July 31, 2015 at 6:34:24 PM UTC-5, Ken-ichi Ueda wrote:

[Sam Kieschnick]

http://www.inaturalist.org/pages/curator+guide#policies

[Charlie Hohn]

Oh wow, I just found that long discussion posted there.

At risk of causing more fuss (sorry) I want to reiterate that we REALLY shouldn't use primary literature for name changes, for all the names Ken-Ichi posted. I guess for obscure taxa only experts can ID it doesn't matter that much but... for plants, it would create a huge nightmare that would all but remove the usability of the site for everyone but a couple of experts. FWIW I am not really an amateur, I am an ecologist, and I even see field eperts struggle with what to do about all the new names, to say nothing for amateurs.  I don't understand how the site is being used over there across the world but it must be something very differetn than what we are doing here.
Here's Mimulus guttatus on The Plant List. http://www.theplantlist.org/tpl1.1/record/kew-2506223 . Jepson: http://ucjeps.berkeley.edu/cgi-bin/get_IJM.pl?key=11384 AND flora of nova anglicae: https://gobotany.newenglandwild.org/species/mimulus/guttatus/ .  Sometimes it's hard to decide how to best follow the iNat guidelines but here it's very straightforward. I'd change it back myself but don't want to act unilaterally (and plus I am a bit afraid of the iNat taxonomy database, still don't fully understand it). I should message the person who did the name change so they can see this post too.

Just to be clear I am not trying to 'scold' anyone.. this stuff is tricky as all heck. I just want to prevent a taxonomy nightmare.

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============================
Charlie Hohn
Montpelier, Vermont

[Charlie Hohn]

names = reasons

[Rowan Hindmarsh-Walls]

The reasons why I made the change for this species are not going against i-nat rules. It was done using the New Zealand Plant Authority- Ngā Tipu Aotearoa,  which in this case happens to disagree with the north American ones. James Bailey's description above explains this quite well. In New Zealand we have been using the names in Barker et. al. for some time, but I now understand that this paper has not been universally accepted. Two solutions I can see are either a universal source, which wouldn't work as it would not be updated fast enough for most countries, or we have a page for each entity with country specific synonyms, which in my view would be a good solution, otherwise we end up going round in circles.

Rowan

[Rowan Hindmarsh-Walls]

Hello all.

I was 'The New Zealander' who made this change.
Before people start critiquing taxomomists or counties I think they need to check the facts and maybe ask why, rather than passing blame.
When I made this taxon change, it was because people on NatureWatch New Zealand (one of the taxon schemes under inaturalist) asked me to, as Erythranthe guttata is the preferred name recognised by the New Zealand Plant Authority- Nga Tipu Aotearoa. This plant authority also happens to be the authority recognised and used by NatureWatch New Zealand (inaturalist) in New Zealand, so I have not broken the rules as some of you have suggested (see the comments section on this taxon change).

I was unaware that other countries have not followed this taxonomic revision, and if I had known this I would not have made the change, as I understand that it is disruptive.
I think James Bailey sums this situation up very well in his comment.
It seems a solution does need to be reached as this is a reoccurring problem. I don't think using a universal source would be the answer as it would not be updated regularly enough for most countries.
I think having one taxon page for an entity, but with country specific synonyms which are associated with different taxon schemes would be the way to go, if that is possible?

If someone wishes to put this entity back into Mimulus for consistency I would not raise a complaint, but this would not solve the root issue stated above.

Thanks,
Rowan

[Charlie Hohn]

Hi Rowan! I want to be very clear that I am not 'blaming' you for anything and I would have done the same in your situation. I rather just want to call attention to the issue so we can figure out what to do with these sorts of issues. 

So far we have used 'the plant list' for 'tiebreakers' like this and that still uses Mimulus. So, my understanding of the guidelines (which could be wrong) would be to stick with Mimulus. In this case, I *think* this species is much more abundant in North America. We have many dozens of mimulus species here that do not occur in New Zealand.  Changing some but not all causes a lot of confusion, whereas changing all is contrary to our floral authorities. This is a common and widespread species, at least in California, not an obscure little one that only a few experts will map.

I think the research Fraga et. al. are doing is really neat and my concern isn't that the taxonomy is wrong. My main concern here is that constant rushing to change things on iNat based on new papers will cause problems. While I think this particular excellent taxonomic work will stand, in many other cases name changes do not stand, and are changed back, merged, split, etc. which could cause real problems to our database.  This creates a lot of confusion and trouble for iNat, especially the more casual users. I guess what I'd like to ask is what are you hoping to gain from changing the taxonomy so fast. Is there a pressing reason for you to do so? If so we should add that to the discussion and if not, I propose we not change things before the taxonomy is in line across the sources.  If that doesn't sound good, my second proposal would be to go with the resource published where the plant is native (IE a plant native to California but introduced to New Zealand would use Jepson while a plant native to New Zealand but introduced to California would use New Zealand Plant Authority). Not sure if that makes sense but it would at least be a start since very few plants are native to both (Bracken fern?).  

Personally, I'd keep the names forever set in stone from where they were when iNat started.  I'm not kidding... but I know no one will agree with that so no reason to ask for it.  I'd just ask that we make sure to be consistent with the methodology.  I'm not going to change it back to Mimulus because I feel like I am being unilateral here... I don't want to override everyone else. But I think it should be considered.

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[Ken-ichi]

Thanks for the discussion, all. Given the policies at
http://www.inaturalist.org/pages/curator+guide I think this should be
moved back to M. guttatus. I've described the reasoning in this taxon
swap which will revert the change:

http://www.inaturalist.org/taxon_changes/12231

Please have a look, and if it seems ok I'll commit it.

More generally, these issues are just going to pop up from time to
time, and in the absence of a decent global taxonomic *authority* (not
just a name index like IPNI), I think our current solution to the root
problem is the best of a bunch of bad options: respect regional
authorities when possible, follow The Plant List when there's
controversy. Yes, The Plant List is out of date, but it is both global
and synoptic for vascular plants, and it makes clear, static opinions
about what is and isn't current. I don't know of another plant
authority like that. If our policy results in a "jigsaw" taxonomy, so
be it. I think that's an accurate representation of the conflict and
lack of global coordination among systematists and taxonomists.

[James Bailey]

Just a note that even if your preferred name is not the prominent name on iNaturalist, there should be no problems if the synonym is added.

Even if we put that species as Mimulus guttatus, entering Erythranthe guttata will still come up as that same taxon.

I figured this was worth noting even if you all know this already.

Cheers,

James

[Jon Sullivan]

Hi all,

I'm another New Zealander chiming in. One of the botanists at our government's Department of Conservation alerted to me to this yesterday. He was puzzled by why Ken-ichi had reversed the update. I explained how iNat wants to remain a step behind taxonomic changes to provide some stability to our names and avoid getting mired in taxonomic disputes. He thought this was an odd policy to take for an undisputed global monograph from 2012. It's quite a different case from Charlie's "if we just chase every little taxonomy paper."

Some secondary databases have already incorporated the changes, like NZ, and others haven't yet, like CalFlora. The Plant List hasn't got it yet because it's still at version 1.1 which is based on plant taxonomy up to May 2012. They don't give a timeline on their website for when to expect version 1.2. This is not like the <a href="http://www.birds.cornell.edu/clementschecklist/">Clements global bird list</a> which is updated annually. Outside of birds, these secondary databases often struggle to find the funding to keep themselves current.

As Ken-ichi explained, according to the iNat curator rules, in the case of contradictions in the regional databases we follow (like CalFlora ≠ NZ), the Plant List is what we default to. That rule is serving us reasonably well.

But brace yourselves. Whenever the Plant List gets updated to 1.2, expect these <em>Mimulus</em> changes to come to iNat. Or sooner, if CalFlora catches up first.

:-)

Cheers,

Jon

[Scott Loarie]

Hi all,

According to Mimulus scientist David Lowry, the Mimulus changes are disputed, see http://www.inaturalist.org/taxon_swaps/12231. But I care more about consistency than which names we all use.

I saw this a few months ago about Google helping create a global checklist:

http://www.ibtimes.com/googles-support-plant-biologists-build-first-online-database-all-worlds-plant-species-1964872#.VXsoouVmmPc.facebook

here's hoping that will be the list we can all get behind...

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[Charlie Hohn]

Nothing is a step backwards. It's a different name for the same plant species. 

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[Belinda Lo]

I'm perfectly fine with it staying Mimulus guttatus for now.

But I just wanted to point out that Erythranthe guttata is more narrowly defined than M. guttatus. In fact, M. guttatus was inflated into more than 10 extra taxa in Guy Nesom's paper: http://www.phytoneuron.net/PhytoN-sectSimiola.pdf

And as far as the current taxonomic status in North America, the new taxonomy has been submitted to Flora of North America: http://floranorthamerica.org/Review/under-prod-17

Hopefully it will be reviewed and published soon.

[Charlie Hohn]

Well, that brings up a whole bag of other issues. Skimming the paper it doesn't appear that these 10 species are all that distinct in their form and appearance. If the species can't be distinguished reasonably by anyone except 10 experts or genetic sequencing we would need to either keep them lumped here or create a unit between species and genus to put them in. 

In short this type of research is fascinating and essential in understanding evolution and it's wonderful. Really. But when plants get classified as species that can't be distinguished in the field it creates a host of other problems for field ecology, conservation, etc. I'm not sure what the answer is. I wish for things like these apparently heavily inter grading groups the subspecies unit were used - in fact I don't understand why it isn't. I thought that was by definition what these intergrading  entities were. If they freely intergrade and aren't distinguishable... That's basically the definition of a subspecies. Or it eas. If they are in fact to be species for whatever reason and if taxonomy as a whole is moving towards numerous cryptic species I think the creation of use of a possible unit between species and genus needs a closer consideration. 

Sorry to add another element to this whole thing. I don't know the answer. I just don't want to lose the M. guttatus entity and other such "species". I truly fear for the future of field ecology and botany. Maybe that's silly and maybe it is precisely things like inat we need to navigate these new taxonomies. But if we lose the ability to identify many plants beyond genus the impacts will be profound and will echo far beyond the taxonomic field into conservation, ecology, and our very relationship with nature. Remember... Species are and have always been a human created unit we use to understand the living world around us. 

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[Ken-ichi]

Folks, we follow taxonomic authorities to *avoid* discussions like
this for every single species. No individual's opinion on the Nesom
paper is relevant to our taxonomy. The only opinion we need to
consider is that of the relevant secondary authorities, which for us
are Calflora, GoBotany, Ngā Tipu Aotearoa – New Zealand Plants, and
The Plant List. Not FNA and not Jepson. If you want to discuss the
definition of a species and what is and isn't good taxonomy, please
take it up with those secondary authorities.

[Charlie Hohn]

OK, sorry. you can delete the post if you want.

[Sam Kieschnick]

Just a personal response -- I was there with Guy as he was requesting all of these Mimulus (sensu lato) specimens from herbaria around the world (he had many shipped to the herbarium I used to work, BRIT).  My eyes are sore from rolling them so much!  ;)  He is a really great botanist and taxonomist -- I was quite fortunate to go out into the field with him a few times: http://www.inaturalist.org/observations/1142590  Definitely one that likes to separate taxa though!  As Charlies is mentioning, it does become quite the pickle to ecologists and species delimitation...

"If you're comfortable with the names of plants.. you're not up-to-date."  ~my plant taxonomy professor

:)