Taxonomy, Cladistics, and iNaturalist

someone up above somewhere said birds weren’t as complex as plants (taxonomically). if there are some parts of the structure that are less difficult, that’d be where to start imho… only map Aves to a new structure and see how many species can’t fit into the new structure and how the new structure is inherently more (or less) adaptive when trying to accommodate the more difficult cases.

Could you explain this more please? What do you have in mind? I’m not quite sure what you mean with relational structures. :sweat_smile:

existing data structure is parent/child. in a purely relational model there would be no parent/child relationships. there would just be relationships between living things (objects in a database). like I said, it’s a stretch goal. :) doesn’t mean that no one should be thinking about it.

btw… the data presentment is inherently disassociated from the underlying data structure in a relational model. it can still be presented hierarchically when the taxa object and its inherited traits call for it.

So what would be relational for iNat? Similarity of appearance among not-necessarily-related organisms rather than phylogenetic relatedness and taxonomic hierarchy?

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I think right now is a good time for people doing taxonomic revisions to step back and look at the posts today on this forum. A huge proportion of the problems happening on the site and forum are linked to the demand by some to keep up with taxonomic revisionism. While i recognize some feel strongly about it, please do step back and think about the broader community. There are major impacts being caused to the site every day, which make it inaccessible to a lot of users who aren’t served by other pathways to access nature. Remeber the core mission of iNat is to connect people with nature, not to make the site perfect match unpublished papers and non-peer reviewed taxonomic revisions. Please think about whether a ‘splitter’ mindset really serves the community. If you really think about how it does, please think about how you can use subgeneric divisions to help smooth out the impact. If it bothers you that they aren’t monophyletic or something, remind yourself that no one is making you personally use them, and they can’t hurt you if you don’t use them. Just because it isn’t useful to you doesn’t mean it isn’t really helpful to others. Thank you!

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I don’t see this at all. I see posts on birding, games, lifers, statistics, perennial IDing and DQA topics, iNat in the news, and experiences with the Next app.

There is one post on taxonomy today in “General” and a couple in “Curators”, where it is to be expected that a lot of the discussion revolves around things like updating the taxonomy because this is one of the main functions of curation.

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a large proportion of the problems noted here are linked to taxonomic splitting, but i wouldn’t consider posts about birding, games, etc, to be problems. It’s true there are plenty of posts which aren’t about problems.

I think we are currently in the phase where a lot of these changes are happening. Genome sequencing and fingerprinting have started getting affordable and are now relatively quick. Sequencing has allowed better insights into the relatedness of organisms, so now the entire phylogeny is essentially being double-checked which is a good thing. It may be annoying for those having to adapt to these changes (in that way it is a bit like the German railway network at the moment) but it will ultimately lead to a better and more stable taxonomy.

I think the real issue is that botanists, zoologists, mycologists, etc. haven’t yet managed to sit down together at one large table and design a more universal system with clearer rules for which rank to use when (to prevent hyper-splitting, merging, or just weird inconsistencies like zoologists not allowing sub-subspecies-ranks). I realise it is not possible to have a one-size-fits-all system that is also usable and at least somewhat accurate, but I think that it can be a lot more “organised” than it is now.

As a citizen-science site, I think iNat should use a reasonably up to date version of the system scientists actually use—so no paraphyly or polyphyly. It is not iNat’s responsibility to create its own taxonomy. But I agree that taxonomic changes on this site shouldn’t be made immediately after (or while) a study has come out of peer review, but wait a few months.

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I think it’s ‘annoying’ to you and it’s site-breaking to others, and furthermore there’s no urgency to do it since a lot of this stuff will bounce back and forth over the next decade or two anyway.

Agree with this being an issue too!

I think firstly we have a different defintion of reasonable (the current status of the site’s taxonomy isn’t reasonable to me!) and also of scientist (field ecologists are scientists! Most of the ones i know don’t do hyper-revisionism or they wouldn’t have time for anything else).

Or a few years. There’s plenty of other work to do in the mean time. Again this is meant to be a community science site, not an up to date representation of the back-and forth of taxonomic research.

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I mean, I agree with you that immediately realising taxon swaps right after the scientist has even just thought about writing the paper isn’t reasonable (see the point below about waiting a few months after peer review). It was just meant to rule out deliberate poly- or paraphyly, or very outdated taxonomy.
I agree with there being no urgency behind taxon swaps though.

I never said they weren’t scientists, nor that there aren’t other important areas of studies biologists need to spend some time on. I don’t expect everyone to only do revisions of the taxonomic tree. But it is my impression, judging from the papers I’ve read, that in most of them, an up-to-date taxonomy is used (which has been created by others who do spend the time on doing revisions).

Maybe, but tbf I cannot see how it would make iNat actually unusable (or a broken site) for anyone. Even with taxa most affected by taxon swaps. It’s not like the entire tree of life is reimagined. The issues taxon swaps cause don’t seem to me to be that big (I’m not talking about hyper-splitting, which is an issue, IMO, but I see it as somewhat separate from simple revisions)… Could you please explain this to me (or link to a reply or topic about this I may have missed), so I can better understand the problem? The taxa I deal with haven’t had that many revisions lately, so perhaps I’m just blissfully ignorant about what it’s actually like. Haha

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I agree we shouldn’t intentionally create polyphyletic species, but for species groups, complexes, etc, it certainly seems like allowing them is a better solution than “sorry the current system doesn’t work for a bunch of people, but too bad for you all, because semantics.” Because some people are so intent on pushing constant and immediate change, i am trying to find middle ground, and it’s discouraging when the people doing it aren’t willing to budge a bit, even if it doesn’t harm them or their data at all.

I guess my point is, what i am proposing is not in any way contrary to ‘scientists’ and many scientists already do it. it’s just contrary to one sort of taxonomy.

Okay, but you don’t have to understand, you can just listen to people saying it’s the case. Just because it isn’t an issue for you doesn’t mean it isn’t an issue to others. Please pause and consider a bit of empathy for those struggling with this.

https://www.inaturalist.org/journal/charlie/68030-my-take-on-taxonomy

https://www.inaturalist.org/journal/charlie/99272-hypersplitting-taxonomic-revisionism-and-taxonomic-inflation-will-not-help-conserve-more-biodiversity

and if you’re thinking that it’s ‘only weird user Charlie’ who cares about this issue, please read the comments of that first one as well. a LOT of people have issues with this, but if you look how i am treated when i insist on bringing this up, you will see why others see this and just don’t try at all. They just stop using iNat or use it less. I’ve also gotten multiple private messages from people who agree with me but don’t want to post at all because they will get harassed.

Thanks for your interest!

I agree this seems like the big issue; once the taxonomy system ball gets rolling it takes a lot of effort to stop it and point it in a different direction. I assume most taxonomists are going to have their head down in their field working away at whatever group they focus on in a way that aligns with how their colleagues also do work in that group. Not many are going to be reading meta-taxonomic literature, and I’m not sure to what extent it even makes sense for individuals to change and go against the grain if everyone else is doing things in a certain way (even if that way isn’t ideal), since it at least keeps things consistent.

It doesn’t take a lot of effort to find that there are people making meta-taxonomic critiques, but I’m not sure what the pathway would be for those to spread though academia up to the larger influential organizations etc.

Those papers aren’t exactly new (2004 and 2013) and are cited in hundreds of other papers. I looked through a handful of those and there are lots discussing issues affecting particular taxa, or exploring how to redefine species concepts in general, or discussing how this all creates issues for conservation. But there aren’t any clear answers or lines to draw so I don’t know how you’d tell if any progress is being made.

(Edit: I’m curious what conclusions this paper made but can’t find a full text - ‘A bare-bones scheme to choose between the species, subspecies, and ‘evolutionarily significant unit’ categories in taxonomy and conservation’)

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Hopefully it does lead to a stable taxonomy… New technologies keep being introduced giving taxonomists new ways to explore the phylogeny and I don’t know how much instability each new technology introduces. It’s also going to take a long time to work through every taxon with each method.

Now introducing Species delimitation 4.0: integrative taxonomy meets artificial intelligence. Fun times haha.

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This I agree with. I don’t think hyper-splitting will aid conservation. And I think species shouldn’t be defined purely genetically (at least in eukaryotic macro-organisms). The best way to aid conservation is by public interest which will not be achieved by some ridiculous level of inaccessibility.

I like the proposal to apply taxon swaps “in bulk” only every couple of years, though I do not know whether that would necessarily be easier to deal with than a gradual change.
It seems to me, though, that we have been talking past each other a bit. I was never really against the notion of limiting the rate/speed at which they happen on iNat or limiting the power single curators (or groups of them) have over potentially disruptive changes. Again, I was mainly arguing for the need for monophyly as a guiding principle in taxonomy. Basing taxonomy on evolution was the decision, so it is only right to stick with it and apply it to everything, IMO. You can disagree with this choice, but I don’t know which system would be better.

I don’t agree with the portrayal that there is some small minority of cladists in charge of creating taxonomy who force whatever changes they come up with on the unwilling majority. It’s not so much “sorry, the current system doesn’t work for a bunch of people”, instead it is “sorry, according to new observation, the current classification needs to be adjusted for the system to be in itself consistent”. I think a consistent system is far better than whatever the status quo is because people are used to it and do not want to readjust.
Again, I have no issue with iNat being more conservative with changes and not applying everything everywhere all at once, and I actually agree with you that it would be better if it was, but I still think iNat should generally follow the system.

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I do think so (perhaps naively). I think we will continue to find exceptions, statistical improbabilities, and will have to do small refinements, but I think as DNA is the basis of inheritance, it will make for a pretty good system in conjunction with existing taxonomy. Many placements have a very high certainty already.

As it is impossible to look into the past and actually witness evolutionary history, I don’t think there is (or will be) any technology that would allow a better/safer placement of species than DNA analysis

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Yeah. Sorry. I will try to be a better listener. I hear a lot of people are very set on monophyly even in informal sub-generic groupings. I’m not sure where that gets us as ecologists though because there are cryptic and semi-cryptic polyphylletic groups and there needs to be a way to deal with them in an applied sense, which includes inaturalist observations. So i guess i just don’t know where strict monophyly leads. Especially since evolution is so complex, at least within plants and fungi, that things don’t form strict cladograms that readily - so much backcrossing and such.

Well… i think the status quo mostly works and what is being proposed and pushed by a few people doesn’t work. Certainly you can’t argue that the majority of people on iNat are taxonomists working on revising taxonomy. Nor can you argue that ‘new observation’ is always straightforward. Nor that any taxonomy can be perfectly monophylletic and still viable in the field. Right?

That’s certainly at least a workable starting place. Thanks for recognizing the issue from this end.

Perhaps so, but until everyone gets a free genetic sequencer, how do we reconcile that with what you see when you’re out in an ecosystem, given many of these entities are not visibly possible to distinguish?

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I’m not arguing DNA should be used to define species (I think I said so somewhere above, but I don’t remember) IMO, there needs to be some morphological difference, but I think it is an amazing tool for determining the placements and relatedness.

I will answer to the rest of your post later. My family is watching TV and talking and I’m a bit overwhelmed by trying to do everything at once and cannot think that well with all of that going on haha :sweat_smile:

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understandable!

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No need to apologise, this isn’t just on you, I’m probably not the best at that either ^^

Correct me if I’m wrong, but it was my impression that the categorisation based on ecological function is separate from taxonomy anyway?
Taxonomy seemed to me to be mainly a tool for the identification of organisms without any application in mind (basically, just a common vocabulary so that everyone can understand what’s talked about), I don’t think it needs to be useful beyond that.
Also, since it is central to all organismic biology, it would make sense to base it of evolution as that is the central theory of organismic biology. That’s why I defend that approach (including monophyly) so much.

Why not? You identify a species in the field, taxonomy gives it a certain name, then you can research that to find out its placement.
For the rest use non taxonomic groupings. What do you want from taxonomy beyond that?

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