Notes:
Oak woods. Manage to dig up the stem so that some of the volva is intact. Stem buried > 1.5 inch. Compare with obs 22537 and 22610. Unlike 22610 this one has volval material that is white.

Images

Copyright © 2009 Dave in NE PA
Copyright © 2009 Dave in NE PA
Copyright © 2009 Dave in NE PA
Copyright © 2009 Dave in NE PA

Proposed Names

46% (3)
Recognized by sight
ret
92% (2)
Based on chemical features: The nrITS is rather remote from anything in GenBank (min. gen. dist. 6.39%). The nrLSU is moderately distant from anything in GenBank.

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= Observer’s choice
= Current consensus

Comments

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The addition or subtraction of characters is usually ignores (although not altered).
By: R. E. Tulloss (ret)
2021-05-21 12:24:46 CDT (-0500)

Dr. Hughes explained that this “stuttering” occurs in nature and in PCR. it is simply treated as a chaaracter of a certain region in a certain sequence from a certain species and neither attributed to nature nor to PCR. We can’t tell where it came from.

If you see it you reported, if it is common in sequeces for one locus in one species and not in the same locus from another it may be a character of the species if it shows up in sequences from multiple labs.

Rod

Looked at the description…
By: Dave W (Dave W)
2021-05-21 10:45:12 CDT (-0500)

of LSU variants within the species concept A. crassiputamen. One particularly interesting variation (to me, at least) is the variable length of multi T repeats. With a few of my NAMP ITS sequences that I examined, there were instances in which one extra of the same repeating character was a difference between my submission and one previously stored on GenBank. Igor has explained to me that it is not allowable to remove a character form a sequence. But, in at least a couple of these instances (with my NAMP submissions) removing an “extra” repeated character resulted in the rest of the sequence matching the one which has the one fewer repeated character. Of course, it’s natural to wonder about such a thing. Like you say, Rod, thought bubbles rising. Does it make sense to suppose that a particularly high peak in the chromatogram may be misinterpreted by the software as “two” peaks? Or maybe two consecutive high peaks as a single peak?

“Thought bubbles rising.”
By: R. E. Tulloss (ret)
2021-05-21 10:17:45 CDT (-0500)

Amanita is very old, with a projected common ancestor to Caesareae and Vaginatae well back in the Cretaceous (plus or minus a very large number of years). Our view is a bit distorted because wwe are looking at ITS and LSU which are both much more variable (less conserved) that was thought when they were selected for a barcode and for phylogenetic use respectively.

I have found one group of apparently separate species that share almost identical LSU sequences. (The LSUs are separable by havine very sparse (but distince) patterns of SNPs as their only differences. This is why using protein-coding genes for phylogeny seems wiser. If you choose the right ones, and this has been done a number of times, you can get loci that have sufficient variation for phylogeny, but are not so wild as the ribosomal RNA sequences and occur only once in the genome in contrast to the multiple copies of the rRNA loci.

Nevertheless, it is very natural to hypothesize that species that basically “share” a “common” LSU may also share a relatively recent ancestor. The group in question is getting larger as we review more DNA. Its description is on the technical tab of the WAO page for A. crassiputamen.

Very best.

Rod

I wonder if…
By: Dave W (Dave W)
2021-05-19 19:46:54 CDT (-0500)

the molecular diversity among the Vaginatae may be indicative of this group undergoing some sort of rapid evolution?

Excellent!
By: Dave W (Dave W)
2021-05-19 19:18:37 CDT (-0500)

I’ll certainly be on the look-out for this type!

We got a GB accession number and I’ve posted it here.
By: R. E. Tulloss (ret)
2021-05-19 19:12:53 CDT (-0500)

It’s amazing that, while we get repeats of now known sequences these days, we are still finding sequences that appear to be only rather distantly related to presently sequenced species of the Vaginatae.

Very best,

Rod

Thanks, Rod.
By: Dave W (Dave W)
2021-01-07 15:21:53 CST (-0600)

Yes, I should have also linked this original post to the corrected one. Corrected observation is obs 444575.

Now that I’m confident about where I had found this, I can make the extra effort to find it again.

Corrected collection site is in obs 444575.
By: R. E. Tulloss (ret)
2021-01-07 14:58:34 CST (-0600)

R

Well, Rod…
By: Dave W (Dave W)
2020-09-25 21:57:20 CDT (-0500)

if you’re willing to come charging out of your corner ready to continue the fight, I’ve got more stuff here to hit you with :-)

I’ll certainly keep my eyes open for this one. Yeah… quite awhile ago. In 2009 I was really just starting to collect/preserve for study. I wish I would have made a better record of the location. The photo of the spores is kinda dim. But, it’s good enough to see the spores are ellipsoid to broadly ellipsoid, which is notable within the Vaginatae.

Thanks Rod, always a pleasure.

Well, you did it again, David.
By: R. E. Tulloss (ret)
2020-09-25 14:17:46 CDT (-0500)

So this time, I have no choice :) , I have to name it for you. So many years of torturing me with new species. Finally, I have to fight back. :)

The DNA data had good signal strength and very little in the way of ambiguity. I’m not even sure there was any accept in the “dirty ends” of the reads. And, guess what? It’s brown. Good luck finding it again!

Wow. Nevertheless, I am IMPRESSED. HOLY MACKEREL, MAN. THIS ONE DATES BACK ELEVEN YEARS! Oh, it has been a long day.

Be safe.

Very best,

Rod

Thanks David,
By: groundhog
2014-04-25 15:22:47 CDT (-0500)

This material has been accessioned to Rod’s herbarium.
-Naomi