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Danny’s DNA Discoveries – Mycenaceae of the PNW
by Danny Miller


abundant common uncommon rare - colour codes match my Pictorial Key and are my opinions and probably reflect my bias of living in W WA. Rare species may be locally common in certain places at certain times.

Click here to download the FASTA data of all my DNA sequences

I had not really studied the bleach Mycenas much yet, so it took some time to wrap my head around them. It seemed this was as good a time as any for me to deep dive into them, so here goes.

DNA studies are more and more bearing out what ecologists have long known instinctively… habitat is one of the best indicators of relationships and genetics. So my gut told me we have at least two good species, too, separated by habitat.

Mycena alcalina was so poorly understood that Maas gave up on it and described 2 species to take its place… Mycena stipata and Mycena sylvae-nigrae. Both EU species.

Mycena leptocephala is in common use. Also an old Persoon EU species.

So although I expected to have 2 distinct species in the PNW, they may not be the same as the 2 common EU species.

UNITE can be useful to play with, as well as Genbank, as it shows you a map where all similar sequences are from.



If you search UNITE for Mycena leptocephala, with 0.5% tolerance for a species, you get 7 genetic species. One of them has been sequenced 541 times, surely a record (you usually see single digits or occasionally a couple dozen). This is clearly a very, very common species. Click on it and the map shows it was found 539 times in the EU, once in BC and once in AK. It was only identified as Mycena leptocephala before sequencing four times. About a half dozen times it was just identified to genus before sequencing. The other 530 times it was just a soil sample DNA blast (no mushrooms). So that is not overwhelming evidence that this is the real M. leptocephala.

If we look at the other 6 genetic species, only one of them is found in the EU, so it’s the only other possibility. Found, identified and sequenced twice in Estonia. (The other 5 species are not found in the EU so they can’t be the real thing, no matter what they looked like, if the genetics don’t match any genetics found in the EU).

I’m going to assume the first species is the real thing, since it’s so common, even though I could be wrong. We don’t have a type sequence, and the first species was only identified as M. leptocephala 4 times vs. the second species identified twice, so it’s not quite as overwhelming as 541 sequences versus 2 sequences sounds at first, but still, let’s assume we now know what M. leptocephala is.


UNITE has 3 genetic species at 0.5% threshold. The third one is locked, so we can’t see it. Of the other two, if you go to 1% threshold, there’s only 1 species. So all 5 sequences are pretty close to each other, so we kind of know what Mycena stipata probably is, within 1%.

This shows another advantage of UNITE. It’s a second, separate database. Nobody ever submitted any sequences of M. stipata to GenBank, but they DID put sequences in UNITE, which is curated and considered somewhat more reliable than Genbank (although you can’t really trust IDs in either of them).



UNITE has 5 species concepts at 0.5%. If you go to 1.5%, they are all 1 species except for one outlier. So we kind of know (within 1.5%) what Mycena sylvae-nigrae is. 

Then I collected all the PNW sequences I could get my hands on, all yours, some of my own, and everything I could find in Genbank.

Unfortunately, there’s no easy way to find PNW sequences in GenBank. Here is what I search on, using common prefixes for herbariums found in our states and provinces.

“Mycena (its* or spacer) (british or ubc* or washington or wtu* or oregon or osc* or jlf* or idaho)”

Then I took all hundred plus results and hand picked the ones in a tree that come close to the bleach mycenas.

Then I made my tree using Mega, because the BLAST website has a very poor algorithm for aligning sequences, so the trees are poor quality. Mind you, a tree that takes 10 seconds to make in BLAST can take 6 hours to make in MEGA, so you get what you pay for.

My tree is attached. So is my FASTA file of all the sequences in it.



Mycena stipata and Mycena sylvae-nigrae are about 4% different from each other. Three WA sequences match M. sylvae-nigrae within 2%, better than they do M. stipata. Some match some EU sequences very closely, so I am assuming we have the real M. sylvae-nigrae here, but it’s possible the complex could be split into several species.

Our 7 local sequences of M. leptocephala match very well with our assumed real EU sequences we found above! Mostly within 1% or even within 0.5%, although a pre-ITS region has a bunch of differences in one sequence, but I’m not going to make too big a deal out of that.

SO… OUR LOCAL SPECIES (SO FAR) ARE MYCENA SILVAE-NIGRAE (not stipata) and LEPTOCEPHALA. And we have evidence that they could be the same species as in the EU, not needing new names.



We don’t know what this is. There are some Korean sequences purporting to be this, but no California sequences, the type area. The reason people are thinking this might be our common species instead of M. stipata is probably only because it is a CAL species and M. stipata is from the EU, so odds usually favour using a local name over an EU name. But in this case, we seem to have the EU species, we are not in search of a new, local name for our collections. Also, it is described as under oak on the ground, not on conifer wood, so the habitat is all wrong to be our PNW common species. I say we ignore it for now.



One collection with this name sequenced in the same section, so the bleach odor may indicate a close relationship. One collection is just a rumour, so it’s just a theory for now.



Buck found a great micro match to this species, and it smelled bleachy, and it sequences in a different section, not closely related. I don’t know if that’s really what it is or not, but it shows that not all of the bleach species are related.



They sequenced 3 old Smith collections, and they were three different species, but one of them sequenced to be a close match to M. leptocephala. You’ll see it in the tree. Just an interesting tidbit.



Some BC GenBank sequences of M. leptocephala are labeled M. polygramma because they matched a mis-identified collection with that name. This is wrong, UNITE shows a few possibilities of what M. polygramma is, and none of the plausible possibilities are those BC mushrooms.



My best guess is that we have MYCENA SILVAE-NIGRAE and MYCENA LEPTOCEPALA in the PNW. That’s a small sample size of 10 local sequences, so let’s keep sequencing more of them and see if we have other species as well.

Now let’s look at the actual collections that sequenced one way or the other and see if they do indeed separate on habitat. Not all have photos and info, but these do:


Mycena sylvae-nigrae




Mycena leptocephala


(Buck 981 attached photo)

https://www.inaturalist.org/observations/32114681 (uh oh, this was Fred’s ID’d as M. stipata)


Do the observations of habitat seem to support how you would split these species? What do you think about the one you ID’d as M. stipata that turned out to be M. leptocephala?


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