Taxon Framework for Fungi

[dav...@umich.edu]

In a recent blog post (https://www.inaturalist.org/posts/19977-introducing-taxon-frameworks), @loarie unveiled some new tools for taxonomy on iNat. Included in the blog was the following passage:

"For Fungi, it would be great if Fungi leaders in the iNaturalist community could come together and provide some guidance. In the past we used Index Fungorum but there were too many instances where the community wanted to deviate from this reference so Fungi are currently a bit of a free for all. If we could use taxon frameworks and deviations to rein Fungus taxonomy in to something that would have broad buy in by the community that would be fantastic."

Although I rank as #79 on the leaders board, this is something I feel strongly about and so want to help. I asked @loarie about where such a discussion could take place, and he mentioned the Google groups. (I didn't know iNat had this!) So, I figured I'd open a thread (or hijack an existing on) to get the ball rolling.

First, I think Index Fungorum is a reasonable resource for iNat to draw from. My main problem with it is that, with its link to e-publishing, some areas became a mess after one or more individuals took advantage of the system. Though, those seem to have been resolved with the latest update of the site. Otherwise, EOL appears to be a reasonable second choice.

Second, I honestly don't know much about the "higher" fungi (e.g., Dikarya). My expertise is limited to Chytridiomycota, Blastocladiomycota, and Zoopagales.

Third, although I am firmly of the mind that taxonomy should reflect phylogeny, @loarie and others reminded me that stability and usability are important criteria to consider too. Thus, I would be in favor of keeping "Zygomycota" as a taxonomic grouping here on iNat rather than trying to decide among the myriad of names currently being floated around for the groups (e.g., Mucoromycota, Zoopagomycota, Entomophthoromycota, etc.).

For those of you who also use Mushroom Observer, what taxonomic scheme/database do they use?

~William

[ja_c...@hotmail.com]

I'm probably the key cause of concern over the fungal taxonomic hierarchy within iNat because I made some fundamental changes recently. It’s been 4-5 years since I last tried to bring it all up to date. Recently there have been a growing  number of flags about the ascomycete taxonomy, so it is time for a re-visit. I agree it would be good to have a wider discussion.

 

First some lengthy background, which might be relevant but also might be clouding my judgement about what’s best for iNat.  

People often mention IndexFungorum as an authoritative source, and it is for nomenclatural data. I created the IndexFungorum (IF) & SpeciesFungorum (SF) websites and databases, but that was many years ago now (25 years!), and there has been little subsequent technical support for them. Originally IF was managed by the International Mycological Institute (IMI) which provided significant resource to support content management, especially the taxonomic hierarchy, which was the backbone for our key book publication at the time:  'The Dictionary of The Fungi'. But times change, and IMI is no longer exists, I moved on to New Zealand, and the IF systems moved to Kew. The key driver of IF information content is now retired but still manages IF out of Kew (although nominally my current organisation still has co-ownership, along with CAS, Beijing). But the IF classification is falling behind the accepted literature. The key role of IF, and the related Mycobank resource (managed by the International Mycological Association), is nomenclatural name registration rather than tracking synonymy or higher classification. That is a significant task since the ICN code now requires registration. IF does not currently have enough resource to adequately fulfil the role of tracking global taxonomic consensus (in my opinion). Neither is the Catalogue of Life (CoL), EoL or GBIF appropriate for taxonomic opinion, as they all derive their fungal content ultimately from IF/SF. So, what to do? I, and a few other taxonomic mycologists, have often suggested the professional mycological community should adopt the WoRMS model (World Registry of Marine Species), where data on nomenclature and taxonomy is maintained by the broader expert community in a system designed for that purpose (although a bit squeaky in parts). That has never happened. The taxonomy/nomenclature part of iNat also isn't up to that task, and there aren’t enough professional mycologists involved in iNat who have the necessary time anyway. I wish iNat could be used as the management tool by taxonomic mycologists, but I accept it wasn't designed to do that.

I don't have a simple solution to the problem of maintaining a consensus taxonomy within iNat for fungi. Certainly, there is no single external resource that provides adequate data across the various groups of fungi in my view. So, it seems to me we, the iNat mycological curators, will have to take on that role within iNat as best we can, and making judgments on the accepted literature. For many groups of fungi that isn't so difficult because of an activity over recent years (since 2011) called 'One Fungus One Name' (1F1N). It has catalyzed a lot of collaborative effort. 1F1N came about because, until recently, fungi could have multiple names applied to different states of the same organism. Imagine if larvae had a different name to the adult insect! ICBN was the only code of nomenclature which allowed that.  Very many fungi have only been known from their asexual forms. They were named as 'form species' assigned to 'form genera'. I.e. assignment according to the relatively few morphological characters of the asexual states available for classification (and applying mainly to the ascomycetes). All that changed with the molecular revolution. Over the last two decades it has now been possible to recognise linkages between states through sequencing and pull together the sexual and asexual forms into a single phylogenetic framework. The provision for multiple names for fungi was therefore dropped from the International Code for Botanical Nomenclature in 2011 (now called ICN) as agreed by consensus among mycologists in general. The price of progress was potential nomenclatural instability, because old, well-known names for many genera could potentially be usurped by long forgotten names, according to the principle of priority. For that reason, the mycological community (ascomycete mycologists mainly) organised themselves into specialist groups to make recommendations about appropriate names within their group and apply name-conservation under ICN if necessary, to preserve stability. That activity has paralleled significant progress in establishing a robust phylogenetic framework for the groups. I should add at this point that I, like most of my colleagues, strongly prefer a phylogenetic framework over a ‘natural’ one where they differ. It is why most mycologists adopted 1F1N in the first place. The results of the work by those groups appears in peer-reviewed publications at regular intervals. Certainly, there are times when decision-making has proved premature, where insufficient taxa have been sampled, significant geographical bias in sampling, type species of genera not considered properly, or insufficient genes sequenced to deliver adequate support, especially towards the root of the fungal tree of life. In addition, the process has required many new genera to be recognised. The impact on the fungal hierarchy has also been significant, with many more ranks necessary to reflect the genuine phylogenetic differences and distances between taxa which is quite apparent in the data. The pace of change has been rapid in the last five years, hence the need for updates in iNat.

In the absence of a global reference system the New Zealand taxonomic mycologists (there aren’t many of us) track the subset of global literature and maintain the hierarchy (and species taxonomy) relevant to New Zealand taxa. We use it to manage the national fungal data (available via the NZFUNGI2 and NZOR websites).  What we need is the same process within iNat at the global level. But, as I said, we don’t have enough experts involved to do that. In the absence of that effort it seems to me the best compromise is to follow the reasonably regular published summaries of state-of-play synthesised across the major groups. Some mycologists will disagree with parts of those these summaries, so it can be problematic. Within New Zealand we prefer to track at a finer taxonomic scale according to our own preferences about reliability of various contributions. iNat cannot afford that luxury in my view so following these large syntheses probably provides the most pragmatic way forward. But that is up for discussion.

 

Here are some examples of those global level syntheses…

Within the ascomycetes the latest such compilation is this ….

https://link.springer.com/article/10.1007%2Fs13225-018-0394-8

I stress, it is a compromise. Not everyone would agree with all the changes in this synthesis.

For the basal groups across many other fungal groups, including the zygomcyota, then a key publication is this …

https://link.springer.com/article/10.1007%2Fs13225-018-0409-5

This I think has probably created more of an issue than the asco hierarchy because of the adoption of an inflation in the number of taxa in the basal clades (which curators can no longer edit within iNat). Again, the synthesis is debatable, and contains some significant changes to these basal fungal groups. The authors discuss the issues. Personally, I’d say the evidence compiled from recent publications and brought together within this synthesis is sufficient for its wide-scale adoption, but I’m open to being convinced otherwise by those with more detailed expertise.

For the basidiomycetes – mushrooms, brackets etc - there are no collaborative specialist working groups, which is a pity.  In general, this group hasn’t had the 1F1N issue to spur activity. Consequently, a consensus basidio hierarchy is problematic, even within the literature, and especially within IF. NZFUNGI2 is better than IF in that respect, but then I would say that because I maintain it.

And, finally, as I said earlier, some of this (but perhaps not as much as you might think) will remain in flux for some time to come, especially as we move rapidly into the new era of affordable full genome sequencing and phylogenomics which will better resolve (or not!) the major ranks of the kingdom fungi. I hope we can find a way for the iNat community can support that effort. Certainly, within NZ I have come to rely on some iNat observers who see important material I am never likely to see, and who provide really important collections and subsequent phylogenetic data.

Within iNat I hope all this continuing change by mycologists doesn’t mean we should ignore changes to our classification for another 20 years (or even 5 years) because it appears too radical or difficult to keep up with. I don't believe we would be helping anybody by ignoring the problem. But I’m a professional taxonomic mycologist and iNat is designed for a different audience so it’s not really my call. Suggestions for a way forward are welcome.

Jerry Cooper

[dav...@umich.edu]

Oh boy, that is a lot!

I just want to state that, aside from a couple of the authors on the paper, the experts of the "lower" fungi (at least the ones I know) do NOT accept many of the phyla listed in https://link.springer.com/article/10.1007%2Fs13225-018-0409-5. For example, accepting Caulochytriomycota makes Chytridiomycota polyphyletic. Accepting Olpidiomycota potentially makes Zoopagomycota polyphyletic. So, I'm not sure it is a good guide for levels higher than order.

~William

[Christian Schwarz]

Hi all,

Christian Schwarz here (Santa Cruz, California). 
I am a field biologist and public interpreter/natural history educator, with my taxonomic work primarily focused on Agaricales.

Thus my interests and concerns in establishing and stabilizing taxonomic/systematic congruence are biased towards the 'leaves' of the tree.
(from about the Family level downwards).

It strikes me that the birding community has a good system in place (although with the expected factions, disagreements, etc.).
A panel of experts ranging from research academics to public-focused interpretive naturalists convenes annually to review primary literature and
the consequent proposals for changes, and then provides public, reasoned votes recommending the adoption (or not) of new systematic and taxonomic changes
for use by the academic and amateur communities under their area of coverage.

An example of their public documentation can be seen here:
http://checklist.aou.org/assets/proposals/PDF/2018-C.pdf

It would clearly take some heavy lifting to establish such a community and procedure for fungi, but at least at the level of "North American Macrofungi"
I feel like it could work. Some geographic and taxonomic bounds will speed up the process, but would also benefit from the various committees agreeing

on fundamental protocols and criteria.

Looking forward to seeing folks' responses and working on this important task.

C

[ja_c...@hotmail.com]

Good to know. I know one of the authors quite well, but not the rest. It was my belief they were summarizing the findings in the literature, but it seems they were going beyond that.

[ja_c...@hotmail.com]

Hi Christian,

I totally agree. It would be good to see such a group, although it would definitely need to be broader than North America. Like you I am an agaricologist (mainly) and quite envious of the self-organisation within the ascomycete community.

Jerry

[vog...@gmail.com]

As a bit of a hobby, I've been updating the taxonomy of Fungi in Wikispecies. I've almost finished down to the genus level for all groups (that is every genus placed in its proper family/ incertae sedis), only the Xylariales left to go. I also have to deal with shifting a lot of "Coelomycetes" to ascomycota incertae sedis. I've been doing this mostly manually by cross referencing index fungorum to mycobank and checking incongruencies with original publications. As a general rule I just go by most recent published taxonomy, and have an alert set up so I can change and add new taxons when they're published. Currently, new wikspecies entries get copied into wikidata. Wikidata will in theory become the backend for all data in wikipedia, so having the data there should make it available to everyone. So far I'm mostly working alone on wikispecies, except for a couple lichenologist that curate those groups fairly well. I've never heard of iNaturalist before and got pointed to this group by another wikispecies editor. I'm very interested in getting the fungal community to work together to keep a curated database and would be happy to help out. 

Aaron

[dav...@umich.edu]

We seem to be moving in the direction of building a curated database for fungi from scratch. While probably needed, that is not the goal here. As Jerry Cooper pointed out below, iNat isn't designed for this nor are there sufficient numbers of fungal curators to keep up with that task.

Even if imperfect, using already existing system would probably be preferable, whether that means adopting IndexFungorum (clearly not in favor here) or adopting the scheme laid out in the two publications Jerry Cooper mentioned. (Though, as he and others pointed out, that leaves out Basidiomycota.)

~William

On Friday, November 23, 2018 at 6:05:41 PM UTC-5, dav...@umich.edu wrote

[Fun...@aol.com]

I am glad to see this being brought up here.  One of the things I have been struggling with is with what to do about provisional names.  If we see a mushroom on here that we are using a European name for ever though it does not occur in our region.  Should we use the European name still?  Should we use a provisional non published name if one is available or should we use just the genus name? 

[Christian Schwarz]

Hi Fungi01

That's been a long-standing question.
iNat explicitly tries not to incorporate provisional names into their taxonomy, so the best way to include them is using Tags and the Provisional Name field (ideally only in cases where there is some well-documented, publicly visible, stable-ish concept attached to that name).

As for the Euro/American borrowed name problem, I use the commonly applied name in CA (even when it is known to be incorrect) until there is some better way to refer to the organism. You can include your hesitance, or other details in the notes if you want to acknowledge that genetics have indicated a phylogenetic gap between things.

C

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