fungee's Journal

Sometimes DNA sequenced specimens come back with names. No, not the names in quotations, AKA provisional names, but actual names. Usually, if they are included somewhere in the phylogeny of the broad umbrella of a placeholder identification, they will reflect in the identification of the mushroom. Often times there is disagreement. This is frustrating for many, including myself, who have many sequenced specimens matching accurately named species. The good news is anyone can help out.

First, click on over to the explore or identify pages and select the Fungi icon. There is this box that says Low under Rank where, if you hover over it, a menu pops up. You can select anything besides species and get a bunch of observations that aren't identified to species yet. The broader the phylogeny of the Low rank is, the fewer specimens there will be.

Then, navigate your cursor to the end of the resulting url on your browser and paste something like this on the end sans apostrophes: '&field:Provisional Species Name=' or '&field:DNA Barcode ITS='

Then you can start trying to make everything that is not identified to species the closest thing to what the DNA points to. This has either been entered in the Provisional Species Name field, been added in the text of one of the sequence validation crew's comments, or, often, the latest identification, contradicting previous identifications.

There is often not a lot of activity post DNA results, for whatever reasons, so they often will get overlooked and not confirmed. Usually the hard work has been done to make sure that the DNA has been attributed to the right specimen. This isn't always the case, so if you don't stay on top of your notifications, maybe this job is not for you. Also, DNA barcoding is still in its pre-adolescence, so you will have times where what seemed like the best name no longer applies. This problem will be addressed by paying attention to your notifications as well.

I think and hope that this is one of the most useful ways that anyone can jump in and help with the broad DNA barcoding project on here and also learn a couple of things along the way. If anyone runs into anything I should add or change to this, feel free to comment or contact me directly.

Have a Wonderful Year (not posting lots lately here),
Garrett

I have a presentation to give at a local library tomorrow, so I made a list of observations of things I would eat or serve to my friends, and then a list of what is acceptable to sell in many states (I believe this was initially a list made by some people in Pennsylvania but is now being used for certification courses).

Here is that list of what mostly eat when I do eat, some of which were just one-offs, but I would probably eat again. https://www.inaturalist.org/lists/4424352-Great-Edible-Fungi

Here is the list of what I would eat, in the eastern part of North America excluding Mexico. https://www.inaturalist.org/observations?place_id=19,37,18,36,12,44,13,7590,6883,13336,7587,6853,9116,17,41,2,47,49,8,48,51,42,4,5,39,33,7,31,29,20,32,35,24,38,28,25,36,19,26,45,30,43,23,21,27&per_page=200&list_id=4424352

Here is the list of things that are acceptable for a certified expert to sell for consumption by the public. https://www.inaturalist.org/lists/4424360-acceptable-edible-mushrooms

Here is that list put into the explore page for the eastern part of N. A. avoiding Mexico. https://www.inaturalist.org/observations?place_id=19,37,18,36,12,44,13,7590,6883,13336,7587,6853,9116,17,41,2,47,49,8,48,51,42,4,5,39,33,7,31,29,20,32,35,24,38,28,25,36,19,26,45,30,43,23,21,27&per_page=200&list_id=4424360

I tried to be mostly inclusive for species that maybe were intended to be included on the acceptable list of things to sell. It probably scooped up a couple of species that maybe shouldn't be sold, but working those out might be too difficult to bother with. I'm thinking of the excluded Cantherellus persicinus for one example.

I also made a list of fungi that were nice seafood replacements. Some of these I included on my list, some of them I didn't, for whatever reason. Here that list is: https://www.inaturalist.org/lists/4424350-Seafood-Fungi

And those which are found in Eastern North America. https://www.inaturalist.org/observations?place_id=19,37,18,36,12,44,13,7590,6883,13336,7587,6853,9116,17,41,2,47,49,8,48,51,42,4,5,39,33,7,31,29,20,32,35,24,38,28,25,36,19,26,45,30,43,23,21,27&per_page=200&list_id=4424350

Just to balance things, here is a list of some deadly poisonous mushrooms. It's a work in progress. I'm going to include some of the worldwide species here . https://www.inaturalist.org/lists/4424397-deadly-poisonous-mushrooms

Here they are, from around the world, not just here since some of them haven't been observed here, but might be here anyways. https://www.inaturalist.org/observations?place_id=any&per_page=200&list_id=4424397

Just for fun, really. I'm saying this was developed rather late in the day so I'm saying it is by no means well thought out, I just wanted to make it to have something to talk about for my presentation tomorrow.

Cheers,
Garrett

I've kind of hit the pause button on this project, but anyone is welcome to take up the mantle. I've been seeing other taxa I also want to add to this, but I always considered this tip-of-the-iceberg stuff. Here is the list of stuff that needs to get straightened out: https://www.inaturalist.org/lists/4305054-east_N--A-_trash_list. And here is the stuff that has been https://www.inaturalist.org/lists/4305060-east_N--A-_fixed_trash_list. You can look at what still is remaining out of the stuff we cleaned up by searching this: https://www.inaturalist.org/observations/identify?list_id=4305060&place_id=19,37,18,36,12,44,13,7590,6883,13336,7587,6853,9116,17,41,2,47,49,8,48,51,42,4,5,39,33,7,31,29,20,32,35,24,38,28,25,36,19,26,45,30,43,23,21,27&per_page=200. And you can check out the 18,000+ observations still remaining by looking at these pages here: https://www.inaturalist.org/observations/identify?list_id=4305054&place_id=19,37,18,36,12,44,13,7590,6883,13336,7587,6853,9116,17,41,2,47,49,8,48,51,42,4,5,39,33,7,31,29,20,32,35,24,38,28,25,36,19,26,45,30,43,23,21,27&per_page=200. I figure we probably fixed around 10,000. I only recieved two complaints really, the first was frustration at the AI for suggesting poor ID's and lack of help, and the second from people who think that maybe they should be left with the European names because it's close to that. Well it may be, but it's probably close to something from here too, in the case of Russula anyway. So I don't feel too bad. Most of my cut-and-pastes gave some kind of guidance where one could at least go and find it's named cousins if not the exact species, though in the case of a red Russula it would be likely be a gamble either way. I would love to continue it as there are a couple more low hanging fruit on there. Stereum versicolor, anyone? But I have some real work that needs to be attended to. And if you catch me doing this in the next couple weeks, feel free to tell me to quit it and to get back to work.

This is good news, it's always great to see things get better. You can learn about becoming a beta tester here. It will roll out later on for iPhone and the web.
One thing that would be great is to get the AI to stop suggesting things that don't really belong in our area. I did my part today as I added several species to this list-wiki of "stuff that needs curation" here. Since so many users are from eastern N. A., and that the expert user to casual ratio is so high for Fungi in a general sense and in particular for the East, it's like playing 'Whack-A-Mole' with these things. Hopefully, if we keep at it, next time I'll have to look a lot harder to find things that are clearly misidentified. I think Fungi is particularly challenging since our species concepts are so hazy. We don't even have pictures in all of the possible bins yet. Certainly not for any of the tough or large families. It is even harder to determine if something is in its range or not.
This is just another starting point for people who want to get involved. I tried to make it really easy to jump in and contribute by flagging all of my submissions. That way you can click on it and see my logic, see if anyone else has added their own, join in and add to the discussion or any combination of those things. Then just jump in and start taking things back to Genus or elsewhere if you don't feel confident with that. If you want to do yourself a huge favor have this up while you ID. When the little green shield icon is there in line with the species name that specifies that the ID was taken from an AI suggestion. That makes it even less likely that it will cause any arguments with the user or others who have chosen it. Use your judgment though, there is no reason to get upset or to upset anyone. Feel free to tag me if you run into issues or if you are having a discussion and are looking for help with an explanation. If you are local to N. A., ignore the ones without tags as they were unusual species or things I don't see as problems, here anyway. I think someone from Down Under must have added them.
Here is a search string to copy and paste to start in on this with for Russula sanguinea, then just go to the Russula sanguinea flags under curation and the copy and paste text is there in the comments. https://www.inaturalist.org/observations/identify?taxon_id=352308&&place_id=19,37,18,36,12,44,13,7590,6883,13336,7587,6853,9116,17,41,2,47,49,8,48,51,42,4,97454,39,33,7,31,29,20,32,35,24,38,28,25,36,19,26,45,30,43,23,21,27&per_page=200

A lot of good people on here would be reluctant to ID mushrooms because of the way we learn them, species by species. It can be very daunting to build the family architecture to understand them better. I'm a pretty good identifier, but still mostly average at the Family or Genus level. I was incorrigible about learning from picture matching when I started, and, like almost everyone else, I just wanted to learn if something was edible or if it could make you happy. Now, and thanks to people wanting to know how I know what something is, I've started asking myself why more. My first NAMA foray at Clarion, PA, near my home on the Allegheny Plateau, I was lucky enough to have befriended quite a few good mycologists who didn't hate me for those traits. They all told me what I knew to be true, that I needed to learn to use the keys more. Well, they told me that and that I'd probably never get really good at mushrooms unless I was hooked up with the big city clubs. I ignored the latter advice for a little while longer, but I did try to tackle the keys more. It wasn't until later, after learning many Generic concepts, and interacting with some of my new found now-cyber-friends that I decided to immerse myself in the phylogeny. A lot of water has passed under the bridge since then. While we may live in drier, hotter times, the knowledge is in the flood stages. There are just are so many new things out there. If you've been around mycologists, or botanists, you are familiar with lumpers and splitters. Well DNA has finally made splitters out of most of us. The only splitters that would have been embarrassed by DNA are way too long-dead to feel that way.

I think this is one of the blocks to getting more good people into making identifications on here. We get on a roll identifying, but we get curious by some new-to-us name or something else that's on our mind we've been trying to know better, and then get sucked down the science rabbit hole. I try to separate the two, but it is impossible. That is a huge issue as there aren't that many identifiers for Fungi compared to other organisms. With nearly 8 million observations, there is a little bit more than twice the amount of observations of birds than there are of mushrooms on here. You can look at the other stats here

Expore Page-Fungi Identifiers

. This shows that while the amount of identifiers is fairly similar, that the number one identifier of Fungi would be in the top five of bird identifiers, the number 2 would be number 17, and the number 3 would be 46. The 250th and the 500th birder has seven times the amount of identifications as their counterpart in mushroom land.

Identifying mushrooms should be always couched by the fact that there is so much unknown and only so much that humans are capable of (even sitting behind these wonder machines). I don't think we should hesitate to give a species' names out if we might have heard from someone that the thing we are trying to identify has been separated by DNA into multiple species. It might be years to publishing if it is even being worked on. I will often give the best currently available information. Like with Hygrophoropsis, it might be more than one species here and we really don't know. The false chanterelle could just be one of the false chanterelles, well it always was one of the false chanterelles, but I digress. The same thing could be said for a number of common things we find. I favor a top-down approach is favored for this. Just call it Hygrophoropsis, but I will sometimes agree with the other. This doesn't work sometimes though. Like when the genera have been split as well.

As an identifier, one of the things that endear me to people (and I really try hard to not play favorites) is trying to identify Fungi on here, for others. It may not feel like a lot, but start out by learning the classes and their traits. Move things from Unknown, Life, or Fungi, into a Class or even a Phyllum eliminates thousands of possibilities for the users. Even the most casual of new users get a boost from this interaction. They have a Wikipedia page to look up the thing they didn't know anything about, or they may have some validation for being on the right track. Sure they could go to Facebook and have a bunch of people they don't know give them five different names and maybe three different PM's. Here you might get an average ID out of the AI and have to wait and see if someone comes along to put it right or verify it, but the AI is better than many of those identifiers already, and the identifiers here have stats at least to tell you who they are (to some extent). Like their awful Facebook cousin, who shouts out a garbage species ID and hopes they aren't chastised for it, the identifier now has a stake in the process and can see it unfold. Identifying shows me, a more seasoned identifier, that this person is hungry for the information I may have for them, and it is more likely they will learn from it and pass it on, plus it gives me a sense of purpose other than beating the site statistics. It makes me happy to see it. Try to identify, it might be for you. Most importantly, don't forget, don't be afraid to get things wrong.

There are some other things that can be done from the identification standpoint, like cleaning up some of the AI's prolific mistakes. I mean really AI, you can suggest species for things all the time just by picture matching, but I'm supposed to be looking through a microscope at things and reading all the pre-prints to know mushrooms before I'm allowed to even put a Family to something? Really?

What do you all think about just binning everything to Fungi that isn't a plant or an animal? It would make it easier for the folks who have to deal with unknowns like @peakaytea. Most of us Fungi people know what slime molds are. Insect galls, virus-plant things would be an obvious problem for me, but really, what percentages would we be talking? 0.1%, 0.01%? It would create some openings for anyone looking to specialize in Fungi or slime molds by getting into binning things from Fungi down. It's the proper way to learn, and you will get loads of help from anyone serious. Really, I don't know anyone who is into identifying slime molds who isn't curious about mushrooms, and vice versa. The lookalikes for one are generally the other. We NEED to know lookalikes!
Also, if people are serious about helping identifying mushrooms, curating the mushrooms as they come in without undersides shots and without close-ups would be pretty helpful. I saw,"Provide Cropped Photo
It's helpful if you can crop the photo more closely to the subject. iNaturalist resizes images, so while we can zoom in to try to see it closer, the image does lose some resolution. Cropping usually makes it easier to get an identification too." Here: https://www.inaturalist.org/pages/responses This would be great for people to tag blurry or far away mushroom pics with. Maybe not so much this time of year. In places like California or Australia, this probably isn't a problem as they have active groups of people identifying things. I've been looking through thousands of observations in my area that just don't have enough information for me to help out on. Some pretty cool things too! They will just sit there in my area of the world. For the purpose of this discussion, I extrapolate "my part of the world" to everywhere other than California, Australia, and Europe. Here, I am often the only one who identifies something. I typically don't bother when the mushrooms are active. I would make more of a point of doing it if people were helping curate things at least. I will anyway. Maybe it's my fault for waiting so long to identify things? I don't know about that though, there are plenty of easy things still sitting there from Summer and beyond waiting to be identified.

I spent most of the day yesterday researching Trichaptum and trying to distill them down to salient characteristics. Here is what I have so far: Trichaptum "Key" Now I need to try to use it! I just copied down what one of the good European people said on someone's iNat post (in Europe) just to see if it holds up over there. It's at the bottom of this document.

For us in North America, I don't think it will be very easy to do anything but "field" ID the Trichaptum without micro or exact tree ID. Maybe, we can figure out abietinum, fuscoviolaceum, and laricinum on conifers. T. secor and trichomallum seem fairly easy down south, though there are two other names being used down Texas way (Jared McRae, and Aidan Campos) that I have not included. I'm am interested in the couple Alan has from Mexico too as he's listed Ricardo Valenzuela (no, not Richie Valens) as having confirmed them, but I didn't include them either. Danny Newman has a cool one from S. A. So far I haven't seen any pics of T. trichomallum. Micro seems so close for so many of them. A good thing to start doing for collections on Maple would be to check for a gel layer between the context and the pores (would require microscopy, I think), that way we could separate any T. abietinum that may be on them. That's also supposed to blacken with age (pore surface?).

For me, the three best things about the internet for Fungi are Mycoquebec, MO and iNat. Facebook is as harmful as it is helpful, in my opinion. You feel me? Otherwise, why would we need SO Many mushroom pages?

iNat gets made fun of a lot in certain circles. The one I'm familiar with would say something like this: "iNat, you say? Really? Every time I go on there it's a shit show of bad ID's and top down pics?!? No provisonal names, slow taxonomic curation. Hahaha, this guy! Am I right?! Hi-five! Damn, it's not even close to MO, he's way off his rocker."

To those people I would say, I'm not going to say it's not these things. In some ways it is. For example, what if I told you that there are almost as many observations in the last three months as there are on all of MO? That surely would explain the quality issues.

"But there are no good people on there!" What if I tell you that 6 out of the top ten mushrooom ID'ers who I know are my better have identified more mushrooms than are on all of MO?

"But MO?!!" Yeah, I hear you, it needs help, as much or more than we've been giving it. I'm not here to tell you to pick sides. I want MO to keep going and growing as much as anyone. I would switch back if it were easier, or upload my iNat stuff there if it were possible.

Facebook was cool, at one time, I am told, and they're still are pockets of good. I am hopeful still, but it is a microcosm of the world we live in.

So my point is this: take some of the time you would spend on there, and put it into MO or iNat. iNat needs the ID help, and MO is probably good with ID help but, $ or programmers, I don't know, I'm neither of those things right now.

OK, I'm a nerd about mushrooms. I've been a lot of other things, but this one seems to be winning lately. One thing I know now: if I were a more particular of a nerd, like about a certain type of mushrooms, maybe my keenness would be more greatly honed. I've been that in the past too, and I don't regret it, but when I do I give so much slack to the other areas of mushrooms that much I have learned gets lost. I guess suffering happens no matter what what path one chooses.

So I guess my call to action for myself is to be better. To do more.

For the rest of you who consider yourselves identifiers, I suggest looking at common taxa in your area. The stuff you know you know, or the stuff you think you know that cannot be known, especially from a photograph with no info attached, and spend a few minutes a day sorting them out. Sorry for making anyone conjure thoughts of the other Donald, Rumsfeld. I have periods where I skip out on the online mentoring, and am fairly selective with what I identify or comment on (not naming names here, and there is nothing wrong with any of it). I know that things are defaulted here in a way that stuff disappears when it obtains "research grade", and the AI ever so convincing. These are challenges. I am beginning to feel strongly that I shouldn't be identifying things wrongly, even if that means withholding information I might have regarding what I think it could be. Perhaps that is born out of laziness, perhaps out of not wanting to cause confusion.

For those of you posting your finds. Do some reading. Look at the suggestions the AI makes, are they in the same Families, or the same Classes, or even the same Phyllum? Try to look for more similarities and do a little reading about your ultimate choice. It might surprise you what you learn. If the suggestions are all over the place, consider the AI to be just wildly guessing. I'm sure it work best with things like birds or butterflies which are in a more similar range of morphology and mostly known. Mushrooms often can't get named to species when many aren't even named yet.

Anyone can be an identifier of anything, and certainly they can identify what clearly is not something.

I'd be happy to discuss. I'm just thinking out loud mostly, trying to refine something. Maybe it can't be?

I go back to visit and collect one observation to collect it finally after over a year of observing it. It's a cordyceps fungi attacking a spider. What I haven't noticed is that it's perched on a dead maple branch. How do I know what dead wood it is, you ask? Well that's not because I am some tree guru, I am not, but rather it's because there is a very familar (to me) mushroom associated with the tree. It's anamorphic spikes stud the entire branch. I am sure it's in my observations somewhere. It's telemorph is Durandiella, and I'm not sure what species despite having gained access to the paper with the key. Somebody contacted me from the Farlow and wanted a sample of it, but they put me off until after Christmas break and apparently forgot, so they still don't have it, and I sort have shelved it both figuratively in my brain and literally. So anyway, I take a 4 stacks with my fancy Panasonic Lumix DMC G85 and Olympus 60mm Macro lens and they have all turned out nicely. I collect the specimen. I was rushing so I tried to collect the bark underneath, but didn't cut it out nicely and the spider falls off it cleanly into my hand.

So when I get home to stack the pics I notice a tiny brown cup that is growing on a few of the shriveled cup clusters of the Durandiella at the hind leg region of the spider. I now am forced to wonder all week if it is elsewhere on the bark as I am afraid that bark hit the forest floor and can never be found again. Or maybe I wait longer: as it's not on my regular route, and the woods has been recently logged so it's unattractive otherwise, except for that recently logged woods fungi ;) The whole branch is covered with the stuff, but the anamorph outnumbered the cups as I saw it. Plus, there was also only one tick crawling on my when I got out of there! Definitely need to bring in the dissecting scope for some nicer pictures to put on here if I do indeed find it.