Danny’s DNA Discoveries – Lyophyllaceae of the PNW
Unfortunately evolution did not make any uniting feature of this family easy to recognize. The one thing that unites many of them is siderophilous granules in the basidia, which means if you heat a section of gill in acetocarmine, parts of the basidia turn black under a microscope. Needless to say, this is not easy to detect, so no key is going to be able to lead you reliably to this page, and the effect is not even found in every species.
Also unfortunately, Lyophyllum has been split into many almost impossible to differentiate genera, and our sequencing is showing that many more genera will have to be created to avoid lumping many things in this family all into Lyophyllum. Some genera are distinctive and fairly easy to recognize, but most of them are not.
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.
Summary of Interesting Results
Here are some of the newest, most interesting results of the study:
Lyophyllum - click to expand
Greasy capped, white spored, boring greyish-brown mushrooms in two distinct subgenera - either usually large clustered mushrooms or with flesh blackening in age.
Species mentioned: Lyophyllum decastes, shimeji, loricatum, semitale, anthracophilum
Lyophyllum decastes group - "fried chicken" mushrooms, these are large, greasy brown capped, clustered mushrooms with white spores that do no blacken at all even after considerable time. According to the Bellanger paper linked above, Europe has 5 genetic species. So far, I find that we have three. These represent most of one of the two major clades in the genus.
Lyophyllum aff decastes - so far both photographed specimens are tan capped. 1% different in ITS from EU sequences, but EU sequences vary by 1% themselves, so this may or may not be a distinct species. Known from BC, WA and OR. A hardwood species in Europe. Let's note what trees it grows with here.
Lyophyllum shimeji -so far all three photographed specimens are dark greyish brown. Growing with 2-needle pine in Asia and Europe and has been found with 3-needle pine here (in fact, whenever the nearby trees were noted in our local collections, pine was always one of them). Dark brown capped collections like this have been going by the name Lyophyllum loricatum, but that is a poorly understood mushroom very unlikely to occur here, so now we have a proper name for them. Although they say in Europe that you cannot tell L. decastes apart from L. shimeji by cap colour, so far, in our limited sampling, you can, so let's keep investigating that. At first I wondered if ours was a sister species, as all sequences were 2-4 bp different than Asian and EU sequences, but we found a WA sequence that only differed by a single character. Sequenced twice from OR and once from WA.
Lyophyllum "pale spring" - our pale capped spring species. One possible (unsequenced) collection was reported with a strong potato odor. It is very distinct genetically from all other known species, in need of a name. Known from WA, OR and CA. This has been mistaken in the past for the clustered purer chalky white fall species Leucocybe connata, but it is distinct. See below for a discussion of the mystery of Leucocybe connata and Clitocybe dilatata.
Lyophyllum aff decastes, L. shimeji and L. "pale spring" © Jonathan Frank
Lyophyllum anthracophilum EU -smallish species, found in burns, with slightly decurrent gills, and a possibly striate cap margin. It might not have been known from the PNW before now because it was mistaken for the similar Myxomphalia maura, which has an umbilicate cap and gelatinous cap flesh that makes it viscid at first. L. anthracophilum may have a pointy cap, but it won't be umbilicate and it is always dry capped. It was not known from the PNW until one OR sequence popped up matching Bellanger's EU sequences. It is in the non-blackening clade, but is smaller and not clustered unlike the above species. Its features should make it recognizable, although there are no uniting features of Lyophyllum nor most of the other genera on this page. Many have placed it in Tephrocybe because they use that genus for all smallish Lyophyllums, but that's not the correct place for it.
Lyophyllum aff. anthracophilum - very similar except not in burns (at least the few times it was found in WA). Differs by 5 bp and 2 indels.
Lyophyllum anthracophilum © Bruce Newhouse, L. aff. anthracophilum © Jacob Kalichman
Lyophyllum Buck#436 - I believe this to belong to the non-blackening clade, but it grows solitary and is smaller and hopefully does not turn black unlike the following species. This is probably going to be hardest to differentiate from the "More New Genera" species at the bottom of the page, which might be larger.
Lyophyllum Buck#436 © Buck McAdoo
Lyophyllum semitale EU group - these greasy brown capped species blacken in places in age or when bruised, sometimes slowly (give it some time). The gills and flesh might stain differently depending on the species. According to Bellanger, Europe has 15 genetic species. We so far have found 6, all distinct from known EU species. These represent the other major clade of the genus. They have been well studied in North America back in 1983 (unfortunately without colour photographs) and we have 17 species described from the PNW that definitely occur here. I need to do the microscopy to figure out the names of the genetic species below; you can bet there's still a lot of work to be done here. Some of these are large and clustered and look like the L. decastes group except for blackening, so there are lookalikes to the fried chicken mushrooms whose edibility has not been tested, so be careful to look for blackening.
You can read all about the 17 species here. Here are their names: Lyophyllum acutipes, canescentipes, chamaeleon, chondrocephalum, conoideospermum, fistulosum, furfurellum, geminum, gracile, investitum, leptosarx, lubricum, pallidum, piceum, scabrisporum, solidipes and stenosporum.
Now, here are the ones we have genetic information about: (some species are only about 1% apart from each other in ITS so the actual species delineations are not final)
Lyophyllum 'semitale #1' spring - our spring species, found four times in the spring and only once in fall. Only #7 has also been found in the spring. It is a small to medium sized species usually not clustered. Known from WA and OR. Its spores have been measured as averaging ~8.3 x 5.4u, a bit shorter than #7.
Lyophyllum #2 cf pallidum (or solidipes?) - medium to large sized and sometimes clustered species. This species is only 3bp different from #1, and all in ITS2, which is not a lot, but the differences are consistent and the couple of photos we have so far seem morphologically different enough for it to be a different species, so I'll treat it as such. So far only known from OR. One microscopic analysis of a collection seemed to match Lyophyllum pallidum, with the next closest match being L. solidipes.
Lyophyllum #3 cf canescentipes - one large clustered OR collection is between these two species genetically. A microscopic analysis matched it to Lyophyllum canescentipes.
Lyophullum #4 cf palldium (or conoideospermum?) - another medium to large species that clusters. Known from BC, WA, OR and CA. One microscopic analysis of a collection also seemed to match Lyophyllum pallidum, with the next closest match being L. conoideospermum.
Lyophyllum #5 rhombisporum complex - perhaps a pale, small to medium species that doesn't cluster, this matches the type sequence of L. rhombisporum except for 3 bp. That may be enough for it to be a distinct species, but also, there are many collections of L. infumatum, L. macrosporum and L. fuligineofolium that match within a few bp as well. It still needs to be put through the key to see what it might be.
Lyophyllum #6 aemiliae EU - we have found matching ITS DNA to Bellanger's concept of this species, differing in a couple places plus 6 ambiguous locations, that probably represents this species. I don't know if one of our unknown locally described species is the same and might predate this 1998 name.
Lyophyllum 'semitale #7' spring - another spring species, found once so far in WA. The spores average 9.3x5.5u, a bit longer than #1.
blackening Lyophyllum #1 © Yi-Min Wang, L. #2 © Jonathan Frank, L. #3 © Scot Loring
Lyophyllum #4 © NAMA and the Field Museum of Natural History, L. rhombisporum #5 © Bruce Newhouse, L. aemilae #6 © Jacob Kalichman, L. #7 © Yi-Min Wang
Tephrocybe/Sphagnurus/Sagaranella/Myochromella - click to expand
Smaller, hard to identify white spored mushrooms. These smaller mushrooms were separated from Lyophyllum into Tephrocybe, but then they ended up all being in different parts of the tree, so they each ended up in their own genus. As you may have noticed by all the confusing genera on this page, once Lyophyllum was split, it started a chain reaction that makes it tempting to wish that everything on this page would all be lumped back into Lyophyllum.
Species mentioned: Tephrocybe rancida, Sphagnurus paluster, Tephrocybe palustris, Sagaranella tylicolor.
Unfortunately, Tephrocybe was already difficult enough to identify when our three species were split into even harder to recognize three separate genera. Sphagnurus and Sagaranella are somewhat related along with Asterophora, but as some are parasitic and some have finely warty spores, they are being considered as somewhat cryptic separate genera.
Tephrocybe rancida EU - is distinctive enough with dark colours covered in a whitish pruinose, rancid odor and long rooting stem. Our OR sequences differ from EU type area sequences by 3-4 bp.
Sphagnurus paluster NY (Tephrocybe palustris) - a very anonymous little mushroom that can be quite variable, parasitic on mosses. A PQ sequence of this NY mushroom has the same sequence as a WA collection, so we appear to have this species here. It is also found in Europe.
Sagaranella tylicolor EU - finely warty spores are not common and help rescue this one from obscurity, along with notched gills and the fact that it's said to grow on enriched ground (e.g. with animal urine). We have sequenced it from OR matching EU sequences. It appears that other Sagaranella species like Sagaranella tesquorum have the same ITS DNA and may not be distinct species.
Myochromella sp. - a new genus for the PNW was discovered with this WA collection, but it doesn't match either known species. The name translates to "little mouse coloured" mushroom, refering to the greyish colouration.
Tephrocybe rancida © Leah Bendlin, Sphagnurus paluster © Luca Hickey, Sagaranella tylicolor © A and O Ceska, Mycochromella sp. © Jacob Kalichman
Rhizocybe - click to expand
Spring fruiting, usually funnel shaped "Clitocybes" (strongly decurrent gills and indented caps) with abundant rhizomorphs at the base of the stem.
Species mentioned: Rhizocybe vermicularis subsp. americanus, rhizoides, pruinosa, alba. Clitocybe albirhiza.
'Clitocybe' albirhiza ID - very pale orange and white spring mushroom, unfortunately not funnel shaped and therefore not known until now that it needs to be moved to Rhizocybe. It was described from ID and we have an OR sequence.
Rhizocybe sp. (vermicularis subsp. americanus) WA - Funnel shaped cinnamon-orange cap with a wavy margin. Spring conifers. This WA subspecies is said to be a darker orange than the EU type variety. The ITS DNA of a WA and OR sequence are both closer to Rhizocybe alba from China (2%, mostly in ITS1) than they are to Rhizocybe vermicularis (>10%), so our subspecies probably needs to be promoted to species.
Rhizocybe rhizoides TN - discovered in the PNW for the first time at Mt. Rainier in spring 2017, this Tennessee species has a greyish-brown funnel cap (lacking orange tones) with a whitish bloom and a bitter taste. With spring conifers. Our DNA matches the type sequence almost exactly. Since then it appears to have been been found 10 more times in WA and OR in spring 2020 and 2021.
Rhizocybe pruinosa EU - with a paler greyish-brown cap than R. rhizoides supposedly also lacking orange tones although our collection looked somewhat pinkish-orange. It was discovered in the PNW in 2021 on Camano Island WA, matching official EU sequences from the paper that recombined the species into Rhizocybe, except for 10 ambiguous locations where one of the possibilities always matches the EU sequences. It is a subalpine species in the EU, but was found here near sea level. Another probable Rhizocybe from the Cascades is being sequenced now and we'll see if it's the same thing or different.
'Clitocybe' albirhiza © Leah Bendlin, Rhizocybe sp. (vermicularis subsp. americanus) © Jonathan Frank, R. rhizoides © Sava Krstic and Yi-Min Wang, R. pruinosa © Buck McAdoo
Calocybe - click to expand
Colourful Lyophyllums (purple, orange and pink). Most others in the family are boring grey-brown. Attempts to split into Rugosomyces are unnecessary, as all these species are related enough to belong properly in Calocybe.
Species mentioned: Calocybe onychina, fallax, naucoria, carnea, persicolor
Calocybe aff onychina - beautiful purple cap and stem with bright yellow gills, 4 bp and 3 indels from EU sequences, ours may be a sister species.
Calocybe fallax - generally orange, a synonym of Calocybe naucoria, which is a newer name, so I'm not sure why some use that name instead of C. fallax. This EU species has been sequenced in OR. It seems to be a species complex in Europe, but our sequences match official Bellanger sequences so it is likely we have the real thing.
Calocybe cf carnea - generally pink, we don't have local sequences yet to compare with EU sequences to find out if we have the same species as Europe or not. It is thought that the newer Calocybe persicolor is the same species.
Calocybe aff onychina © Michael Beug, C. fallax © Andrew Parker, C. cf carnea © Ben Woo
Asterophora - click to expand
Small parasitic agarics on Russula and Lactarius, either with no gills (very rudimentary) or with more widely spaced gills than the similar 'Collybia'. They may have powdery caps full of asexual spores.
Species mentioned: Asterophora lycoperdoides, parasitica
Asterophora lycoperdoides - gills almost absent, very powdery cap full of asexual spores. This EU species is found worldwide, including here.
Asterophora parasitica - true gills that are more widely spaced than 'Collybia'. This EU species is found in Mexico, so our species is probably the same, although we don't have any local sequences yet to prove it.
Asterophora lycoperdoides © Lauren Ré, A. parasitica © Noah Siegel
Hypsizygus and Ossicaulis - click to expand
Large, wood inhabiting species.
Species mentioned: Hypsizygus tessulatus, Hypsizygus marmoreus, Ossicaulis lignatilis
Hypsizygus tessulatus - the store bought "elm oyster". Fairly large tan cap with water spots being its most distinctive feature. Notched gills. May be farinaceous. Hardwood. Not hygrophanous. This cultivated "elm oyster" also goes by an east coast cultivated name, Hypsizygus marmoreus. Sequences worldwide vary by about 4-6 bp, although all our local sequences match quite well with each other. It is all considered one species, with H. tessulatus being the oldest name.
Ossicaulis aff. lignatilis - pure white, crowded gills of variable attachment. Stem sometimes off centre. Strong fungal-farinaceous odor. Hardwoods. Not hygrophanous. At about 4% different in ITS, our local species sequenced from ID and OR may be a distinct sister species to the European one.
Hypsizygus tessulatus © Kit Scates Barnhart, Ossicaulis aff lignatilis © Jonathan Frank
Atractosporocybe/Tephroderma/etc. - click to expand
Greyish-white clitocybes, difficult to otherwise characterize. Clitocybe sclerotoidea, microscopically similar with large, chalky greyish-white mushrooms and clumps of sclerotia growing parasitically on Helvella belongs in Atractosporcybe.
Species mentioned: Atractosporocybe inornata subsp. occidentalis, Tephroderma fuscopallens, Clitocybe sclerotoidea
Atractosporocybe inornata UK subsp. occidentalis MI - a quite large, chalky grey species, said to have a strongly unpleasant odor (e.g. mouse urine) in Europe, but no odor in western NA, so ours was described as a separate subspecies. ITS DNA from OR matches that from the EU, so there does not appear to be much genetic distinction to support the subspecies, so it should be investigated if odor does indeed correlate to geography and if ours deserves the rank of subspecies.
'Clitocybe' sclerotoidea WA/CA - the paper describing the new genus Atractosporocybe said to consider that the microscopically similar Clitocybe sclerotoidea (described from WA and CA) may properly belong in Atractosporocybe and I can report that two WA sequences show that the species should be renamed. It is recognized by a giant ball of white sclerotia with large greyish-white Clitocybes. The WA sequences are 3% different than A. inornata in ITS, which is closely related.
Atractosporocybe inornata © Jonathan Frank, 'Clitocybe' sclerotoidea © Danny Miller
Tephroderma PNW01 - A smaller grey funnel cap (strongly decurrent gills and a cap that gets depressed in age). Tephroderma was not known from the PNW. The only known species in the world is Tephroderma fuscopallens from France. But this find near Mt. Rainier and Mt. Adams in WA sequences closer to Tephroderma than to any other genus, and kind of looks similar, but at >5% different in ITS it almost definitely constitutes a second species in this so far monotypic genus. However, Tephroderma is a sister genus to Atractosporocybe and I'm not convinced that it needs to be separated.
Tephroderma PNW01 © Michael Beug & NAMA and the Field Museum of Natural History
Gerhardtia - click to expand
Gerhardtia foliicola JP - a greasy, hygrophanous cap that starts out deep red-brown and fades to medium brown. A white stem. It could be mistaken for Rhodocollybia butyracea, but the gills are very crowded and not at all serrated.
This genus was not known from the PNW until it showed up by DNA on a couple WA collections that were either unidentified or misidentified. Matching DNA of this species can be found in Pakistan, China, Japan (where it was described) and South Korea. It seems to have made its way here from SE Asia.
Gerhardtia foliicola © Yi-Min Wang and Connor Dooley
Leucocybe - click to expand
Some white Clitocybes turned out to be more closely related to Lyophyllum and were moved , but which ones? Unfortunately, there's no good morphological way to tell them apart. You just have to learn them. Some are chalky white with a removable bloom.
Species mentioned: Leucocybe candicans, Clitocybe tenuissima, Leucocybe connata, Clitocybe dilatata, Leucocybe salmonilamella
Leucocybe candicans EU (='Clitocybe' tenuissima EU) - a small chalky white forest 'Clitocybe' with a bloom that can be rubbed off exposing a more translucent, greasy cap. It is easily confused with a similar but poisonous grass species, Clitocybe rivulosa (dealbata) as well as the slightly larger forest species Clitocybe phyllophila. We have a local WA sequence as well as eastern North American, Colorado and European sequences that all match.
Leucocybe connata EU - large clusters of chalky white mushrooms in the fall. Sometimes stocky (when it could be mistaken for Lyophyllum "pale spring" above), but often mistakenly referred to as Clitocybe dilatata when found in a slender form with wavy caps. FeSO4 turns violet. We have BC, WA and OR sequences matching this EU species, of both the stocky and slender forms.
We have finally solved one of my most longstanding mysteries. In Europe, where they're apparently smarter than we are, they consider Clitocybe dilatata not to be a unique mushroom, but a junior synonym of the single (non clustered) white Clitocybe phyllophila. It appears they are correct. But dozens of years ago somebody in a North American book somewhere said that Clitocybe dilatata was a slender clustered species with chalky white, wavy caps, and for some reason, it was said to be very poisonous (perhaps just because there is a poisonous white Clitocybe rivulosa/dealbata). Everybody has parroted that information into dozens of guidebooks and online websites. It has long been suspected that what we have been calling Clitocybe dilatata might actually be Leucocybe connata, and therefore not poisonous. This proves it. Perhaps even though the ITS DNA is basically identical, the slender and stocky forms will be considered different forms or varieties of each other, but regardless of that, the important thing is that what we have been calling Clitocybe dilatata is neither a Clitocybe nor poisonous. The one remaining mystery is why 'Citocybe' dilatata is reported with a negative FeSO4 reaction.
'Clitocybe' salmonilamella CA - this is not even pure white like the others and therefore even harder to identify as a Leucocybe. It has a pinkish tan cap with a white rim (like many Clitocybes do) but the pink tinge to the gills helps identify it. This still needs to be renamed to Leucocybe salmonilamella. DNA has been found in OR and WA matching the CA type sequence almost exactly.
Leucocybe candicans © Jacob Kalichman, L. connata (stocky form) © NAMA and the Field Museum of Natural History & (slender, wavy capped 'Clitocybe dilatata' form) © Yi-Min Wang, 'Clitocybe' salmonilamella © Daniel Winkler
Tricholyophyllum and Other Genera - click to expand
These are going to be hard to recognize and three of these four genera don't even have names yet! One recently named genus is Lyophyllaceae Bellanger clade XI from the big paper mentioned in the introduction, which is now known as Tricholyophyllum. A second I am provisionally calling 'Paralyophyllum'.
Species mentioned: Tricholyophyllum brunneum, Lyophyllum turcicum, Clitocybe thujana, Clitocybe subditopoda.
Tricholyophyllum - clade XI in Bellanger's paper (linked above in the introduction) has now got a name, Tricholyophyllum, thanks to the description of the type species in that genus, Tricholyophyllum brunneum. A few of our species appear to be inside that genus.
Tricholyophyllum spp. - these three sequences appear to be inside the clade of this recent genus. These will also be difficult to differentiate from Lyophyllum sp. 'Buck #436' and others, as basically nothing is known about them yet.
Tricholyophyllum sp. iNat 99656740 © Yi-Min Wang, T. sp. Buck #741 © Buck McAdoo, T. sp. iNat 101155508 © Yi-Min Wang
'Paralyophyllum' - proposed new genus name for 'Clitocybe' thujana, 'Lyophyllum' turcicum, etc. - the type sequences of these two species belong in neither Clitocybe nor Lyophyllum, but in a so-far unnamed genus. Here are the species we have in this genus so far:
'Lyophyllum' aff turcicum - does not turn black, and grows solitary. It is going to be hard to differentiate from Lyophyllum sp. 'Buck #436' above (which might be a bit smaller) and species of Tricholyophyllum. It is related to 'Lyophyllum' turcicum (differs by 8 bp and 3 indels from the type sequence) which also needs to be moved to this new genus once it gets a name.
Lyophyllaceae sp. iNat112449743 WA - similar greasy, depressed cap (at least in our one collection), adnate gills, farinaceous smell, strongly farinaceous taste, found with Douglas-fir, western red cedar and rhododendron.
'Clitocybe' thujana WA - The paper "The Pseudoomphalina kalchbrenneri complex in North America" sequenced the WA type of 'Clitocybe' thujana, wondering if it might be a Pseudoomphalina instead, but it turned out to be very far away from both genera, and inside the same as yet unnamed genus that 'Lyophyllum' turcicum is in. It had never been collected in modern times nor photographed, at least in colour, until it was found in WA again, matching the type sequence, so now we have a good colour photo! It is said to have a viscid (that would be unusual for this family) light brown cap and decurrent gills that discolour dingy yellowish. It is definitely very hygrophanous.
'Lyophyllum' aff. turcicum © Yi-Min Wang, 'Paralyophyllum' sp. 112449743 © Jacob Kalichman, 'Clitocybe' thujana © Yi-Min Wang
Lyophyllaceae sp. MO361959 - this WA collection could possibly be distant enough to be in a genus by itself; it was mistaken for Arrhenia (first collection) and Gamundia (second collection).
Lyophyllaceae? sp. MO361959 © Steve Ness, Steve Ness and Sharon Squazzo
Yet another genus
cf 'Clitocybe' subditopoda #1 - a smallish grey/brown strongly hygophanous watery/chalky species, with decurrent gills but perhaps not with as indented a cap. Some collections with a matching sequence have been identified as Clitocybe subditopoda, probably incorrectly, but I can't say for sure if Clitocybe subditopoda is really a Clitocybe and this is a lookalike, or if this is it, needing a name change to a new genus. The first picture is a fall collection, the second is spring.
cf 'Clitocybe' subditopoda #1 © Danny Miller and Yi-Min Wang
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