Collection location: Diamond and Crater Lake, Oregon, USA [Click for map]
These are a pretty good match for C. clandestinus. They were growing with conifers at about 3800ft.
The spores are slightly larger than what Dimitar shows on his site and match the European C. cotoneus that is cited on Michael Kuo’s site.
Spores were ~ 6.9-7.5 X 5.1-6.0 microns.
|I’d Call It That||3.0||3.49||1||(dimitar)|
sum(score * weight) /
(total weight + 1)
|I’d Call It That||3.0||0.00||0|
sum(score * weight) /
(total weight + 1)
>How long before we see the flaws in ITS sequences?
Bioinformatics is a widely used, very complex, and constantly evolving
science. If you have specific and insightful concerns on the subject,
I’d love to hear them.
>And how useful is going to Genbank if you don’t have the DNA of your
specimen in hand?
As I explained earlier — it is very useful, particularly to reject
some names. I tis critical too if you want to develop a deeper sense
of the Genus that you’re trying to call yourself an expert in. You do
not need your own data necessarily. There is plenty of data already.
Basic Local Alignment Search Tool
It finds local areas of matching letters in two strings of letters (your DNA sequences).
All this and more will be part of my “Molecules Demystified” talk…
other than trusting Irene’s instincts due to her long experience collecting and identifying mushrooms in the North, and the graciousness with which she admits any errors or areas of confusion.
It appears that Mary Berbee has mostly collections in her herbaria from the extreme PNW…200 cort sp. from Oluna Ceska’s British Columbia site, alone. But Diamond/Crater Lake is a looooong way from BC down in South Central OR, and may well show Cortinarius sp. that haven’t been collected and documented farther north. The fact that there are no examples of C. melanotus in Genbank just complicates the matter. And gosh, now spore data is relatively worthless, too? How long before we see the flaws in ITS sequences? No system is perfect and all are rife with human error.
If DNA analysis (assuming that happens) of Ron’s specimen is a near perfect match to clandestinus, then that would convince me. But what if it is not? Where does that leave us, esp. since we have no valid DNA data, at this time, on melanotus?
And how useful is going to Genbank if you don’t have the DNA of your specimen in hand? It costs time and money to run these things…not too practical for most. And please, define your terms as you go along…right here would be nice.
yes I will discuss the subject on the MushroomTalk forum dealing with
these matters. Will put several simple and free procedures and
programs that people can use for starters (ClustaW, MAFFT, etc.). Of
course, there is a difference between an “informative tree” and a
“publication grade” tree and many steps in between, using statistical
methods where most folks will probably get lost. But basic things are
very, very easy and useful. Amateurs should get more in touch with
these methods if they enjoy putting names on mushrooms.
if I only knew how to build a tree..
Can you recommend a useful program that does that once we have the sequences?
Well, boys and girls, here is an analysis you can do yourselves and
get a better idea of a possible correctness of a species
hypothesis. When I speak in MSSF on Nov 16 I will touch on the ways
for the informed amateurs to be a bit more “inquisitive” about what is
out there, particularly utilizing GenBank.
1) Go on GenBank and find a trusted European sequence for Cortinarius
2) Blast it.
3) See what comes up from North America. Considering the volume of
collections from the PNW in there (mostly Mary Berbee’s work) you can
see realistically if there is anything in the area that comes close to
C. melanotus (under any name).
NOW, in this particular case, as it turns out, there is no sequence of
Cortinarius melanotus in GenBank. There is actually one from UBC —
Cortinarius melanotus voucher UBC F17139, but when compared to other
collections it is a Dermocybe, so clearly some students didn’t do
their homework before entering data in the public facility.
Anyway, anyone can download data from GenBank and build a little
phylogenetic tree. This will give you a lot better idea as to how many
different species we might be dealing with out there and in many cases
immediately show why European names cannot be used.
In this case, I have build a little tree with publically available
data and you can see that the North American Leprocybe populations are
somewhat different than the European. You can also see that we have a
somewhat large, but fairly condensed group of Cortinarius clandestinus
(originally described by Kauffman from the PNW). Can we squeeze in
Cortinarius melanotus in there, in some of those leaves, hard to say,
particularly because we do not have actually good data for
C. melanotus. But I find it very, very doubtful considering that in
this group we do not cross ways too much with Europe, based on the
data we have so far, which is not too small a dataset. Attached is a
little illustrated tree that I just prepared. I try to encourage
people to be a bit more scrutinizing in a smart way as there are
resources out there that can be utilized.
On my page of clandestinus I have two different species -
at one time I had them different, used even the silly name of
cotoneus, then merged them with clandestinus, but now having had real
data, I can see the two distinct species. The first row is
clandestinus and the second an unnamed Californian CALI-COTONEUS (no PNW collections
in the North!!). Seat of the pants type mycology is hard and extremely
error prone, even when one tinkers with microscopes and spores, so one
has to utilize all other available resources at our disposal. There
are a whole lot of things the average Joe can do here on MO to inject
some sanity into mushroom name calling and I encourage people to do
Bringing attention to C. melanotus was a great thing!! But calling the
above C. clandestinus (by far most likely), a C. melanotus without
more checking is likely to be an error.
I wonder, could this be the same as (at least close to) the european C. melanotus..?
Check Douglas’ pictures and description of obs 52961,
some other photos:
and this description from Funga Nordica:
Cortinarius melanotus Kalchbr.:
“Smell of parsley or radish;
cap tomentose to finely dark scaly, olivaceous brown to olivaceous green, at centre dark blackish brown;
stem with blackish brown veil remnants;
sp 6.5-7.5(-8) x 5-6 μm.
Cap 30-80 mm, hemispherical, later low convex, margin often down-curved, not hygrophanous;
gills medium spaced, pale olivaceous yellowish brownish;
stem 30-80 × 6-12 mm, cylindrical to tapering downwards, firm, whitish yellowish;
flesh whitish yellow to pale olivaceous yellowish;
KOH-reaction red brown on flesh; fluorescence yellow; exsiccates with dark olivaceous brown cap, olivaceouos-brownish gills, olivaceous-yellowish stem and yellow mycelium.
Sp strongly verrucose, strongly dextrinoid.
In Pinus forests on calcareous soil; late summer to autumn; very rare in hemiboreal areas.”
I don’t know if it’s diagnostic, but compared to melanotus, there are some subtle differences in the original description of clandestinus (North American Flora vol.10, part 5):
“gills rather narrow, close, at very first pallid, soon yellowish or with an olivaceous tinge;
a light-green-yellow universal veil;
spores smooth under high magnification, 6-7 × 5-6 μ;
Type collected under Douglas fir and hemlock”
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