Observation 108462: Amanita “sp-60”
When: 2012-08-18
Herbarium specimen reported

Notes: A single large and robust specimen growing on a sandy shoulder of a paved road.
The dried specimen is in the hands of RET.

Proposed Names

ret
81% (1)
Eyes3
Recognized by sight: Within the provisional series “Penetratrices,” this species appears morphologically unique and has apparently unique nrITS (more work needs to be done).
Based on chemical features: This collection is the foundation of the species concept to date. See comments, below.

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Eye3 = Observer’s choice
Eyes3 = Current consensus

Comments

Add Comment
Thank you, Rod,
By: I. G. Safonov (IGSafonov)
2017-04-17 16:41:39 CDT (-0400)

for sharing these details of your research on the Penetratrices
The past is unalterable, the future is unpredictable, and the present is ephemeral (?)…
I see you just proposed a cryptonomen temporarium for this taxon…
Sorry to mention this again, but I am curious if did you do anything with obs 113909? It might be a fresh and unfaded example of 108462.

Yes, Igor. <<___EDITED
By: R. E. Tulloss (ret)
2017-04-17 15:52:10 CDT (-0400)

I have repeatedly created one-gene pseudophylogenies using nrLSU from all taxa of the Vaginatae for which it is available and with the diagnosis of the relevant mushrooms done by a reliable source.

The Penetratrices (now about 10% of the “known” Vaginatae) appear as a largish possible clade and two or three other branches of one or two species each. I used this information (plus known morphology) to create a few stirpes within the proposed series (see website). One little grouping includes “rhacopus-like” taxa with the Penetratrices motif.

It is important that the sampling (collections sampled per species) is very variable in the Vaginatae. We have many sequenced samples of (e.g.) rhacopus and (e.g.) only one from kundabungii. Hence, we know a bit about the “natural variability” of sequences for some taxa, but not for others. We have so many “cards still in the deck”… so many taxa unknown and under-represented in our work.

I should have started on the Vaginatae ten years earlier (or twenty or thirty). But the past appears to be unalterable according to the grandmothers and grandfathers.

All this adds to the uncertainty.

I want to make it very clear that the trees I’ve run-off (using high speed tools rather than “high accuracy” tools) do not show that the “Penetratrices” form a clade. That is one of the reasons why the series is a provisional one.

Very best,

Rod

Hello, Rod
By: I. G. Safonov (IGSafonov)
2017-04-17 15:24:37 CDT (-0400)

Yes, I understand your explanation. The series Penetratrices is distinct from the rest of the sect. Vaginatae by virtue of the unusual LSU motif, but it’s still a provisional series as more phylogenetic support is required to support this “grouping”. How much support? Who knows!
Morphology seems to be variable, but it seems that many species in that series have a certain look about them.
I’ve been wondering if you have “grown” an ITS and/or LSU phylogram of sect. Vaginatae and whether Penetratrices stands out in the tree(s). Yes, it’s only a gene or two, but a 4-5 gene panel may paint a similar picture and we still wouldn’t know to a certainty – may need the whole genome. :-)

Hello, Igor.
By: R. E. Tulloss (ret)
2017-04-17 12:32:29 CDT (-0400)

I only meant to say that gross morphology segregates the species from the A. penetrans, which seemed to me closest to the present taxon within the “penetratrix group” … based on gross morphology.

Another way to say it that may be clearer: Given that the 5-motif or nrLSU is consistent with the present species being in the series Penetratrices, the species is unlike other known taxa in the group due to its gross morphology. From what we have of an nrITS sequence, there is probably genetic difference from other taxa in the Penetratrices; however, the amount of difference is unclear because of the imperfection in the available data.

We have found evidence of a sequestrate species in the Penetratrices. See a new comment on the MO observation for A. kundabungii (MO 196610).

Very best,

Rod

As always, Igor, I am very grateful for your contributions.
By: R. E. Tulloss (ret)
2017-04-17 11:44:30 CDT (-0400)

Please advise, Nina and John about this collection if you haven’t already.

Very best,

Rod

Rod,
By: I. G. Safonov (IGSafonov)
2017-04-17 11:26:56 CDT (-0400)

So, to summarize the info in your comments, the opening motif of the nrLSU region says it’s probably in the ‘penetratrix group’, but the readable portion of the sequence and the gross morphology are less supportive of such a placement.

Of all the representatives of sect. Vaginatae I’ve ever seen/collected in the NJ Pine Barrens, this was clearly one of a kind, but then all of them were pretty distinctive, including the individual members of the dulciarii/vulpecula complex. I would like to point out that you should have obs 113909 (collected later that year at a historically important location in Wharton S.F.), which appears to be morphologically similar. Has that one ever been submitted for sequencing?

As far as 108462 is concerned, it never resurfaced again to my knowledge, though more examples of A. sagittaria have been picked from that location since then during my visits to FPP. We will definitely be on the lookout for more examples of this critter in case the problem with the DNA sequencing has to do with the way the fresh material was processed/preserved.

I can see the resemblance.
By: Debbie Viess (amanitarita)
2017-04-17 11:19:49 CDT (-0400)

That umbo looks like it could be used as a soil battering ram!

I was once tempted to see this entity as similar to A. penetrans.
By: R. E. Tulloss (ret)
2017-04-17 10:53:38 CDT (-0400)

Now I think not. The stem does not appear to extend deeply into the substrate and the cap pigmentation is different…just for starters.

Very best,

Rod

So what we now know…
By: R. E. Tulloss (ret)
2017-04-17 10:48:41 CDT (-0400)

This species produced an nrITS sequence that we rather chaotic in part. Given that we didn’t get a nrLSU and the nrITS seems to be heterogenous, we probably shouldn’t proceed with certainty from the genetic detail we did get. However, one part of the data that was of high quality was the 5’ motif of nrLSU. It was definitively (in my view) of the penetratrix type (“5’-TCTGACCTCAAATCA…”).

Also, the closest matches were all in my local database were from the “penetratrix group.” On the other hand, the closest match was about 15% distant from the sequence we have (such as it is).

We don’t know whether we are just seeing a problem with one sequencing attempt, a problem with the state of the DNA in the material, a problem that will persist because of some issue such as unhomogenized nrITS, or something else.

We will attempt to reseqence if we have any extracted DNA remaining. If that fails, we will re-sample and start from scratch. Of course, the latter will take more time.

Very best,

Rod

Hello, Rod
By: I. G. Safonov (IGSafonov)
2017-04-16 12:10:31 CDT (-0400)

Glad you were able to resolve the problem because I wouldn’t have been able to help you on this one based on what I remember.
I do recall finding this one together with Amanita sagittaria (same date and general location, i.e. shoulder of Rt. 532 near North Gate), but I believe Nina and John took all the collections with them, as the packets contain pictures. In all honesty, I don’t think I started preserving any fungal specimens till the following year.

This corresponds to RET 611-1.
By: R. E. Tulloss (ret)
2017-04-16 11:39:10 CDT (-0400)

As it happens, the collection was made at a time during which either you or Nina put a color photo in the packet with the dried material. Problem resolved.

Very best,

Rod

Hello, Igor.
By: R. E. Tulloss (ret)
2017-04-16 11:28:08 CDT (-0400)

I have two collection from you collected on the same date as this material. But neither is marked as associated with this observer no. Both failed to yield DNA when sampled three years ago. I need clues as to which collection matches this observation. Of course, I will look at the material and see if there is an obvious connection. I will advise if I think I can resolve the issue. As a reference, the two RET accession numbers in question are 610-10 and 611-1.

Very best,

Rod

Thanks for posting the images.
By: R. E. Tulloss (ret)
2012-09-03 19:33:51 CDT (-0400)

R

Created: 2012-09-03 17:57:45 CDT (-0400)
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