Taxonomic authorities for free living protists and algae?

Taxonomy for protists is a mess, but especially so on iNat. We should elect some taxonomic authorities to give preference to in order to avoid having an eclectic bunch of conflicting schemes. Right now the only one we have is WoRMS, but that doesn't cover everything and a lot of it is just an outdated mirror of Algaebase.

The ideal situation would be to have a single global authority for each taxa that we rigidly adhere to, and then keep a list of every time we explicitly deviate from it. That's what iNat does with vascular plants using Plants of the World Online. That won't work for protists, but we could pick some of the best ones and try to stick to them as feasible. It is especially helpful to try to keep anything from Order and above stable since only iNat staff can make changes to such high level nodes.

So, what are some good ones to use? Are there any objections to my suggestions?

Algaebase seems like a good choice for what it covers. WoRMS is already accepted. I don't know what's good for other things like ciliates and ameoboids.

Also, if you would like to edit the taxonomy yourself, read the curator guide and then send an email to help@inaturalist.org.

@djpmapfer @sarka @roman_romanov @bdstaylor @karolina @daviswj @stephaniemartin @actinophrys @swampy

Anotado por zookanthos zookanthos, 05 de diciembre de 2019 a las 11:59 AM

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Algaebase is widely used by phycologists as the ultimate nomenclatural hub, and increasingly cited in publications as such (I have mixed feelings about the latter). It's not perfect but probably the best we have, and certainly very appropriate and accessible for citizen science projects.
I am pretty agnostic about non-algal protist taxonomic resources but I agree that having a consensus on iNat is important. I'm happy to help in any way I can.

Anotado por karolina hace mas de 2 años (Advertencia)

I don't know enough about either group to take part in this.

Anotado por daviswj hace mas de 2 años (Advertencia)

For ciliophora (a robustly monophyletic group), the best framework is the consensus classification published in Nature: https://www.nature.com/articles/srep24874 It's a ranked, phylogeny-based system, and agrees with the unranked classification scheme sponsored by the International Society of Protistologists (current version, Adl et al., 2019: https://onlinelibrary.wiley.com/doi/full/10.1111/jeu.12691).

The latter is one of two comprehensive, widely-accepted high-level schemes for protists. The other is Cavalier-Smith's framework, as incorporated into Ruggiero et al., 2015, which forms the taxonomic skeleton of Catalogue of Life, WoRMS etc. Like it or not, his system, with its paraphyletic kingdoms Chromista and Protozoa, is the one we're stuck with here. It has the virtue of broad agreement with phylogeny (if you can tolerate the paraphyly), and it offers reassuringly familiar--and pedagogically entrenched--formal ranks (phylum, subphylum, etc.). On the down side, because Cavalier-Smith's system makes a formal kingdom of that handy term of convenience "protozoa," we have a situation where slime moulds are in Protozoa, but ciliates (surely the most "protozoan" protists of all!) are not.

(Algaebase seems like a great database for phototrophs...if you like that sort of thing :-P It's of no use for the others, though...it has never heard of familiar non-green genera, such as Acanthocystis, Opalina, Colpoda, etc.)

Anotado por bdstaylor hace mas de 2 años (Advertencia)

BTW....I've found that the curators at WoRMS are very prompt about correcting taxonomic problems when you point them out.

Anotado por bdstaylor hace mas de 2 años (Advertencia)

iNat does not have to endorse one scheme. The technology exists to allow for the co-existence of many systems (see EOL or Global Names about this). Such a system must be aware of all alternative names for the same taxon, and must know where each taxon is located in all (reputable) hierarchies. Hence, if I submit a name under Cryptomonadida, the system will know that I have submitted a name of a member of Cryptista in WoRMS, and so if my name is not known in WoRMS, it can be added to it. The system should be aware of synonyms for the same taxonomic concepot, whether the synonyms are common names or are scientific names. Given that iNat covers all living organisms, it must be capable of disambiguating homonyms. And in this area, be aware that there can be more than one legitimate use of a name, and a taxon can have more than one legitimate name. But the solutions to all of these issues are known. It would be great to see the solutions incorporated within iNat, ideally via a service that would be available to other biodiversity projects. Two other major principles are clear. The first is that protistan taxonomy is still a mess and no single current system will be satisfactory. The second principle is that those schemes that use (and seek) monophyletic (and holophyletic) groups will eventually come out on top.

Anotado por djpmapfer hace mas de 2 años (Advertencia)

And. There is no single reliable system for 'protists' out there.

Anotado por djpmapfer hace mas de 2 años (Advertencia)

I appreciate you including me in this! I agree that multiple schemes should be accommodated to whatever extent possible, but I'm not sure what that extent actually is; most taxonomic sites seem to end up at least privileging one scheme. In any case, in many places it looks like having one applied consistently would at least be a step up.

What level of detail do you suppose is needed? For instance ciliates are one of the best classified groups of protists, and as @bdstaylor says Gao et al. (2016) can be taken as a reasonable standard. But you can see it only goes down to orders. For families and genera the last comprehensive review seems to be Lynn (2008), The Ciliated Protozoa, which would then have to be adjusted to the higher taxa; I don't know of anything trustworthy for species beyond particular monographs. I think this same kind of split plays out in many other groups, with reviews of lower ranks separate from more modern systems for higher ranks, but if the former are easier to curate maybe that's less of a concern.

Anotado por actinophrys hace mas de 2 años (Advertencia)

Yes, as @actinophrys says (hi Josh! :D), the ciliate resources I mentioned only cover higher ranks. That's been on my mind because the images posted here often permit identification only to very high levels. Since the software accepts overlapping concepts (Gymnostomatea/Litostomatea, Hypotrichea/Hypotrichia etc.) things have gotten fairly messy, and I do feel that using a single hierarchy would make it easier to assign plausible names to the (often murky) images posted here.

At the same time, I recognize the wisdom of the comments by @djpmapfer (who has vast experience in adapting taxonomy to biodiversity informatics). When a site hitches its fortunes to particular schemes--as many Wikipedians did in the mid-2000s, investing heavily in unsettled evolutionary hypotheses like Chromalveolata and Unikonta--the longterm result may be more "messiness," instead of less.

Anyway, I have been made aware of the fact that allowing users to curate higher taxa on iNat is problematic, and can even cripple the site, so those choices aren't really on the table.

For ciliate genus and species, the project that is best at keeping up with recent work is Catalogue of Life, I think. I'm not sure what pipes fill their database (Aescht's World Ciliate Catalog seems to be one of their sources: http://www.catalogueoflife.org/annual-checklist/2019/details/database/id/113 ). Lynn's book is a handy resource, as actinophrys says, but certainly not complete (family Colepidae has acquired half a dozen new members since 2008). And for particular groups, we just rely on the most recent revisions, when any exist, or if necessary, dig through the old Victorian middens on BHL. :D

Splitting of genera continues apace, and every year it gets a little harder to identify ciliates to genus without DIC, special stains or SEM.

In short...a real can of WoRMS. ;)

Anotado por bdstaylor hace mas de 2 años (Advertencia)

Nice one! (that can of WoRMS). It is disappointing that while the logic and technology is available, we are obliged to work with substandard solutions. Many projects need to be able to employ more than one classification, or call on different authorities for recognition of valid taxa. That creates the right context for a service that could be developed within one project or the load distributed across many. The service would then be available to any project that wishes to use it. Until then, iNat will use approaches that cannot satisfy all users.

Anotado por djpmapfer hace mas de 2 años (Advertencia)

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