Hi everyone,
I am working on a project with a dataset containing all research-grade fungal observations from a specific country. My goal is to filter this dataset to retain only the species that form visible fruiting bodies (e.g., caps and stalks, puffballs, coral fungi, polypores, etc.), which are typically referred to as mushrooms. I want to exclude microscopic fungi (e.g., molds, yeasts) and all lichens.
I have a few questions to guide my filtering process:
Lichens: I’m not entirely sure if fungi that form lichens can also produce visible fruiting bodies like caps, stalks, or puffballs. Should I exclude all fungi capable of forming lichen symbioses, or are there exceptions? And how can I find them in the iNaturalist datasets?
Taxonomic Filtering: Ideally, I would like to exclude lichens and non-mushroom-forming fungi based on taxonomic information (e.g., genus, family, or order) rather than relying on observation tags or metadata. Are there specific taxonomic groups that I should entirely exclude or retain for this purpose? If so can someone help me with which those are?
Families of Mushroom-Forming Fungi: On the flip side, are there specific taxonomic families or groups that include most of the mushroom-forming fungi commonly encountered in forests, parks, and other environments? If so, what types of fungi might I miss by relying solely on these groups or incorrectly retain?
Accuracy and Coverage: I’m okay with some errors in the filtering process (e.g., a few lichens slipping in or missing a few mushroom species), but I’d like to get a sense of what I might miss or include incorrectly. Are there any commonly available references or taxonomic resources that could help me verify my results?
To clarify, my dataset includes fields like species names and taxonomy (genus, family, etc.), but it does not contain specific details about fruiting body morphology. My ultimate goal is to reduce the dataset to focus only on mushroom-forming fungi, so I don’t need to retain any species that are not mushrooms but are closely related.
Please feel free to ask follow-up questions or suggest approaches—I’m not very well-versed in fungal taxonomy and would appreciate any guidance!
Lichens are polyphyletic with many different taxa having evolved in such a way. Most of them fall in the Ascomycota and have Apothecia as fruiting bodies (though a bunch of species very rarely or never actually have them and reproduce via soredia or isidia)
Here is Xanthoria parietina with a lot of Apothecia.
The lichens closest to actual fruiting-body-structures I’m aware of are the trumpet-shaped Cladonia spp. But they are still quite different. Additionally, the few lichens in the Basidiomycota do produce more pronounced fruiting bodies, but at least where I’m at, these are very rare and I don’t know a lot about them.
Due to their polyphyly, lichens are difficult to exclude completely, but if you exclude Lecanoromycetes and Lichinomycetes from your search, you should filter out most lichen-observations.
It will be a difficult task. And you did not mention whether you plan to include larger ascomycetes, such as morels. If you use only Agaricomycetes, you should cover all agarics, boletes, polyposes, etc. But you will still be out of a number of large-fruiting fungi which belong to Pezizales, Geoglossales, Tremellales, etc.
Hi there,
The taxonomy of fungi is quite confusing, and what is a mushroom is not necessarily set in stone.
As mentioned before lichens are quite polyphyletic with many species in various different groups of ascomycete. Some lichens do form mushroom like fruiting bodies such as basidiolichens like Lichenomphalia. Many lichens also contain apothica as mentioned in the above comment, which are fruiting bodies, but perhaps not particularly mushrooms.
Most ascomycetes are not “mushrooms” in the sense that they don’t have a cap and stem. However, many people would consider some fungi in the genus Helvella or Morchella mushrooms which are ascomycetes! I think in this project you would have to very specifically define what you are considering a mushroom in the scope of the project, in which case you could more easily filter out fungi based on taxonomy. If you are including ascomycetes this makes your job much harder as there are scores of ascomycetes that are tiny in the same taxa where there are large fungi!
As for fungi I would take away all together, anything in the Puccinales (rusts), Erysiphales (powdery mildews), and perhaps genera such a Typhula and the cyphalloid fungi (these are cup forming basidiomycetes). There are many ascomycetes and therefore I think it would be more prudent to exclude all ascomycetes and then add only a few genera or species, e.g. Helvella etc…
As for some fungi to always include, Agaricomycetes is a good shout, this will include the large majority of mushroom forming fungi, but you would still have to remove a couple odd taxa which are microscopic, microfungi, or yeasts.
I am sure that there are people more well versed than me in this but it will require a bit of trial and error.
Also perhaps prudent to note that a lot of the yeasts and microfungi are extremely under-recorded, and certainly yeasts are. So for some orders e.g. tremellales which contain tramella but also some weird basidio-yeasts almost no one actually records the yeasts, which means that in all likely hood this will not be a problem, so the lack of fungi expertese actually helps you in this case!
I would like to include all larger mushrooms (including morels, Helvellaceae, Tuberaceae, Pezizaceae and probably more I am not yet familiar with) so I will have to filter those in but I need assistance in where all of them belong :)
I would love it if you guys would help me with a list of what to include and what to exclude, perhaps with a short comment as to why an inclusion or exclusion is recommended so I understand this a bit more deeply and can research it further, if an explanation seems necessary.
It could be that a larger taxonomic group is suggested in include list but some subgroup of those are in the exclude list. This tips I’ve already got from you guys are awesome. I am deeply thankful for your expertise :)
I am taking a course in Computer Vision and will attempt to train a (rather simple) Neural Network for classification. As I have a big interest in fungi, specifically in edible mushrooms when being out for hikes and tracks and such, this seemed like a fun project.
