Danny’s DNA Discoveries – Physalacriaceae of the PNW (Marasmiineae)
Click here for my Pictorial Key to the non-pleurotoid white spored wood inhabitors, where Armillaria and Flammulina are found.
The Physalacriaceae family of the Marasmiinae sub-order contains both large and small white spored species that often grow on wood or pine cones, but rarely pleurotoid (oyster-like) as most have central stems. Armillaria (large) as well as Flammulina and Strobilurus (small) make up most collections, but recently resurrected genera Gloiocephala and Rhizomarasmius are now discovered to belong here as well, although sequences of Rhizomarasmius appear to be inside Gloiocephala, which may be polyphyletic, so many more sequences are going to be needed of both of them and other related genera to sort out the proper names of those species. The family also contains the very rare (in our area) rooting-stemmed Paraxerula as well as the eponymous southern hemisphere tropical genus Physalacria (which doesn't occur here). Many other genera in many other families meet this family's identification criteria as well. Unfortunately, there's not much rhyme nor reason to identifying the vast multitude of miscellaneous white spored mushrooms to family, as many mushrooms in different families and even sub-orders lack distinctive traits, so they have to be learned individually.
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
Summary of Interesting Results
Here are some of the newest, most interesting results of the study:
Armillaria - click to expand
Not much else this large (5-10 cm or more) with white spores and a ring grows on wood (but harder to identify when found on the ground from buried wood). Often scaly to boot, and always with a cottony pith inside the stem. Parasitic. They are called honey mushrooms for their typical warm brown uniform colouration. Decades ago, when we used to think our half-dozen species was all one species, it got the nickname "mushroom of a thousand faces" and people were confused why sometimes they could eat it and sometimes it caused them distress (perhaps they are allergic to some species and not others or some are "more edible" than others). Many species have glow in the dark mycelium (bioluminescence).
Species mentioned: Armillaria altimontana, cepistipes, gallica, mella, nabsnona, osoyae, solidipes, sinapina.
DNA group 1 - This large clade has ITS DNA that varies by up to 4% and the following species are found inside it, indistinguishable even by ITS, LSU and IGS-1 multi-gene analysis. I'm sure that other genes will be discovered in the future that can differentiate them, as mating studies have shown that not only are there morphological differences between them, but none can interbreed, so they really are distinct species. Flammulina also shows intra-species ITS variation that is a little high, but at least the species are better differentiated by ITS.
Armillaria sinapina PQ - commonly thought to be the species with golden universal veil remnants all over when fresh. Conifers and hardwoods.
Armillaria gallica EU (=A. lutea EU) -a supposedly non-descript hardwood species if you ask the PNW locals, except that in Europe it is synonymized with or even called Armallaria lutea, where it is said to be covered in yellow scales just like A. sinapina. Since several regions of DNA are indistinguishable for the two species, we should study the spores of a number of yellow hardwood collections to try and solve this mystery (A. gallica spores are smaller than A. sinapina spores).
Armillaria cepistipes EU -a somewhat nondescript large species on hardwoods, resembling A. gallica if that does not show much yellowing, and also resembling the much more common conifer species A. solidipes in the next section, but perhaps with darker marginate gill edges.
(Armillaria calvescens PQ is also in this clade but does not seem to occur here so it won't be confused).
Armillaria sinapina (or could it be A. gallica?) © Drew Parker, possible A. gallica © Michael Beug, possible A. cepistipes © Tom Volk
DNA group 1A - The IGS-1 gene can separate these 2 species from each other and from group 1, but Kim's study says that ITS and LSU cannot, so since my study is an ITS study, all 5 species will be difficult to ID using DNA. However, I believe I can distinguish Armillaria nabsnona by ITS.
Armillaria nabsnona WA - slender, bright orange-brown when fresh, few scales on alder. Spring and fall. There are 10 biological species of Armillaria known from North America. They were finally running out of good names, and ended up calling North American Biological species #9 "nabsnona" which stands for "North American Biological Species Number Nine". I believe I can separate this by ITS.
Armillaria altimontana ID - high elevation Rocky Mountain species. This was #10, NABSX, and is the most recently named. Thankfully they didn't call it "Armillaria nabsdeca".
Armillaria nabsnona © Steve Trudell
Armillaria solidipes CO/Armillaria ostoyae EU - a large, scaly, conifer species with an especially large ring too. It resembles the hardwood species A. cepistipes and A. gallica above. Armillaria gemina PQ sequences from back east are very similar in ITS, but as that species is not known from the PNW, there shouldn't be any confusion.
Kim's study only used WNA sequences but called them all by the name of the EU species, A. ostoyae - even though our name, A. solidipes, is much older. Other people say they are the same thing and that we should use the older name A. solidipes. Still others have said rather definitively that they are different species, and that here out west we should use the name A. solidipes. EU sequences that supposedly represent A. ostoyae vary by as much as a couple % amongst themselves, and our local sequences of A. solidipes are similar, but a couple % different than the EU sequences, so the DNA is inconclusive.
The upshot is I am calling our mushrooms Armillaria solidipes until somebody can demonstrate why I shouldn't. It is possible that A. solidipes is something different than we think, since it was described without reference to the large ring the photos show. I would love a CO type sequence to verify what it is, and if it is something different, we need to figure out what to call the pictured species and whether or not A. solidipes is present in the PNW.
Armillaria solidipes © Jonathan Frank
Armillaria 'mellea PNW01' - stocky, pale colouration and in large clusters on hardwoods. Usually not bulbous at the bottom of the stem like the rest of the species are. CA and the PNW have a unique sister species from the EU A. mellea. So does the east coast. Our west coast sequences seem to differ by up to 3% in ITS, but there are up to 3 long indels, and usually all the differences can be explained by 5 or fewer actual differences.
Armillaria 'mellea PNW01' © Christian Schwarz and Michael Beug
Armillaria (Desarmillaria) tabescens EU - as the only species without a partial veil and ring, and sitting alongside the other species in the genus, some give it its own genus, Desarmillaria. There is more than 1% variation in ITS throughout Europe of this species. Recently, rumour has it that it is present in the PNW, so we need local collections to see how they match up against EU sequences.
Flammulina - click to expand
This is what Enoki looks like in the wild, and the amazing morphologic change into a all-white, needle-thin, long stemmed mushroom with a pinprick head is an astonishing example of how environmental conditions can change a species. They are on the small side (<5 cm), with a dark velvety stem when mature (and difficult to ID before then). Somewhat viscid orange-brown cap that is not hygrophanous, growing on hardwood. Not uncommon year round. Japanese growers (who are usually heavy consumers) of this mushroom in Nagano were found to have much lower cancer rates than those in other Japanese provinces.
Species mentioned: Flammulina velutipes, filiformis, lupinicola, populicola, rossica.
Flammulina filiformis China - we thought our most common local species was F. velutipes which was also, supposedly, the cultivated Enoki mushroom. Recently it was reported that Enoki is really F. filiformis, which we confirmed by sequencing Enoki from a local grocery. Well, it turns out the species most commonly found in the wild in the PNW is also F. filiformis. Worldwide sequences can vary by over 1% (10 differences or so) but it all seems to be the same species. Some of our collections have only 4 differences in ITS from the type sequence.
Flammulina velutipes EU - only a single collection from southern OR seems to sequence to be this, but it has a chunk of 8 characters missing compared to EU sequences plus a couple other indels. We should look for more collections.
Flammulina lupinicola CA - this former variety of F. velutipes is very close in ITS to F. velutipes, but can usually be distinguished in a tree. Common in CA, it has been sequenced once from southern OR.
Flammulina populicola CA - often on aspen or cottonwood. West coast sequences vary by as much as 4 bp from each other. Verified from southern OR, the paratype sequence is from AK so it appears to be all up and down the coast.
Flammulina rossica Russia - These species will usually need to be distinguished microscopically, but this one might have a relatively pale cap colour (although not always as shown in the examples pictured here). We have sequences from China which probably represent this species. Again, ITS sequences within China vary by over 1% (as many as 10 differences) so Flammulina as a genus does appear to commonly have intra-species variation in ITS higher than normal. We have two WA sequences that are basically identical to each other, so we are not yet showing any genetic diversity in our sequences.
Flammulina filiformis © Yi-Min Wang, F. populicola © Jonathan Frank, F. rossica © Buck McAdoo
Strobilurus - click to expand
Tiny (~1 cm) mushrooms on conifer cones or the ground with close gills and two-toned orange stems. (Baeospora myosura is similar with crowded gilled and a pinkish stem on cones. Many other similar Marasmiineae mushrooms have more distant gills and although they may have a two-toned stem, are usually found on the ground or debris other than cones).
Species mentioned: Strobilurus kemptonae, trullisatus, lignitilis, albipilatus, occidentalis, wyomingensis.
Strobilurus trullisatus WA (=S. kemptonae WA) - found on Douglas fir cones. Pleurocystidia capitate and thick walled. Often pale capped.
Strobilurus albipilatus NY? (S. lignitilis AK) - usually found on different cones or on the ground, with thin walled capitate pleurocystidia, often at high elevations. Perhaps tan or brown capped (but may be pale or grey). This is not as common as previously believed, because it turns out S. occidentalis, described next, doesn't have to be on spruce cones (many collections of that have been incorrectly identified as this). We have the type sequence from AK of S. lignitilis and it matches all of our collections that we call S. albipilatus, an older name from NY and assumed to be the same species. But are they the same? Rumour has it back in NY the species looks a little different, so we need east coast sequences, or ideally their type sequence, to prove it. If it is shown that S. albipilatus is not the same thing, we will have to start using the name S. lignitilis for our collections instead of S. albipilatus.
Strobilurus occidentalis AK - I have discovered that it does not only grow on spruce cones as commonly believed but on non-Douglas fir cones or on the ground, without capitate pleurocystidia. Perhaps grey capped, but may be pale or tan or brown. It is a often a coastal species. The subalpine Rocky Mountain species S. wyomingensis cannot be differentiated by ITS.
Strobilurus wyomingensis WY - found in the subalpine in the Rockies in Idaho. It cannot be differentiated by ITS from S. occidentalis, the coastal species, but it has larger spores.
Strobilurus trullisatus © Stephen Russell, S. albipilatus © Lauren Ré, S. occidentalis (on a spruce cone and on the ground) © Danny Miller and Yi-Min Wang
Xerula, Gloiocephala, Rhizomarasmius, etc. - click to expand
These genera typically have spherical cap cuticles like Marasmius.
Gloiocephala - all white, a few rudimentary vein-like gills, with cap and short stem but only a few mm across growing on sedges.
Rhizomarasmius - small (<1 cm across) mushrooms growing on the ground with adnate to decurrent gills and downy stems that darken towards the base. Resembles many other marasmioids in the Omphalotaceae and Marasmiaceae, but those species either smell of garlic or don't have a cellular cap cuticle nor downy stems. (Sequences of this genus appear to be inside Gloiocephala, which may be polyphyletic, so many more sequences are going to be needed of both of them and other related genera to sort out the proper names of these species).
'Marasmius' epiphyllus - rudimentary vein-like gills and white cap (like Gloiocephala), long brown two-toned stem (like Rhizomarasmius), but seemingly needing its own genus.
Oudemansiella/Xerula/Paraxerula - long rooting stem like Caulorhiza and Rhodocollybia.
Species mentioned: Paraxerula americana. Oudemansiella longipes. Gloiocephala caricis. Marasmius caricicola, epiphyllus. Rhizomarasmius epidryas, undatus.
'Marasmius' (Gloiocephala) caricis EU (='Marasmius' caricicola MI?) - a tiny white mushroom (a few mm across) with a tiny white stem (that may be off centre like a pleurotoid) on sedges. The few gills are rudimentary and fold-like. This/these belong in Gloiocephalus. No photos or sequences yet from anywhere, but there is an east coast name and a European name, so if our collections match one of those, it already has a name. It was reported at least once from BC back in the 70s.
Rhizomarasmius epidryas EU - on dryas stems, small (<1 cm across) mushrooms growing on the ground with adnate to decurrent gills and downy stems that darken towards the base. Resembles many other marasmioids in the Omphalotaceae and Marasmiaceae, but those species either smell of garlic or don't have a cellular cap cuticle nor downy stems. Three EU sequence of R. epidryas are almost 2% different from each other, but I haven't seen the chromatograms to see if the sequences are closer than they appear or if this is a species that really has some genetic variation. No local sequences yet, but it was reported from BC and across the arctic back in the 80's.
Sequences of Rhizomarasmius appear to be inside Gloiocephala, which may be polyphyletic, so many more sequences are going to be needed of both of them and other related genera to sort out the proper names of these species.
'Marasmius' aff. epiphyllus EU/'Marasmius' subvenosus NY - rudimentary vein-like gills and white cap (like Gloiocephala), long brown two-toned stem (like Rhizomarasmius), but seemingly needing its own genus, at least according to an ITS tree. Our one WA sequence differs by 5 bp and 2 indels from EU sequences of 'Marasmius' epiphyllus, but it also lacks a second repeating copy of a large chunk of ITS1 that seems to be duplicated in all EU sequences. I don't know how significant a change that is, but it seems prudent to suspect our local species is not the same. The east coast 'Marasmius' subvenosus (no known sequences) is thought to be a synonym, so it should be investigated if that is not really a synonym, but in fact what our species is. Or perhaps our west coast species in unique.
Paraxerula americana WY (=Xerula americana, =Oudemansiella americana) - long rooting stem like Caulorhiza and Rhodocollybia, found in Idaho. A single Idaho Rocky Mountain report from the 70s was part of the description of the Wyoming species O. longipes var. americana which is now O. americana, but the Rocky Mountain sequences we have from CO and NM are labeled Paraxerula americana, also described from WY. It turns out that there really are three lookalike genera: Oudemansiella, Xerula and Paraxerula, and that our species belongs in Paraxerula.
'Marasmius' (Physalacriaceae gen. nov.) aff. epiphyllus © Luca Hickey
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