Notes:
Under oak
No staining of any sort
KOH produces dark brown reaction immediately.
Taste is mild to indiscernible.

collected for IGS!

Species Lists

Images

Proposed Names

-20% (3)
Used references: B-R-B Net Rings with Yellow pore surface to couplet 15b
42% (3)
Recognized by sight
0% (3)
Recognized by sight: beveled margin, dry conditions
60% (2)
Based on chemical features: nrITS and nrLSU sequences
76% (2)
Based on chemical features: nrITS & nrLSU sequences are in good general agreement with obs 250839 and obs 263101

Please login to propose your own names and vote on existing names.

= Observer’s choice
= Current consensus

Comments

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Sorry Igor
By: Geoff Balme (geoff balme)
2017-03-13 05:48:19 PDT (-0700)

I was assuming something different, my now decade old experience playing with sequences and running Paup* have sent me down one kind of rabbit hole with my understanding of these things. But you’re right, I was mainly wanting to know those questions you elaborated.

Thanks for your thorough answer.

I should probably read some more modern papers on the use of these sequences.

Geoff,
By: I. G. Safonov (IGSafonov)
2017-03-12 17:17:02 PDT (-0700)

It would be helpful to know what you mean by A, B and C to respond to your argument.
I am thinking cladistically about boletes, too and all the time, even though I haven’t made a single tree yet (living vicariously through the ones others made). :-)
In my understanding, one doesn’t need any trees to infer the phylogenetic position of 250839, 252208 and 263101. BLASTING of the sequences of these collections gave an unequivocal picture of where these boletes belong, and the gross morphologies are also in good agreement with that picture. They are all Butter Boletes, without a doubt. Whether they are all conspecific and whether they are in turn conspecific with B. aureissimus are two separate questions, answering which will require a bit of time and patience, my friend. At this time I think “yes” for Q. #1 and “no” for Q. #2.
Re “HOW DIFFERENT these segments of DNA can be”, I reckon you are referring to the ITS, as the LSU doesn’t have the requisite barcoding gap for a reliable species resolution (something I came across empirically upon discovering that three distinct red-pored taxa – 206608, 244427 and 251141 – have identical LSU sequences). It won’t be easy to answer this question unless one has several collections that have been determined morphologically to be the same entity. Here we have three (for the purported But. taughannockensis), but I am making a reasonable assumption about the morphology of yours and Renée’s collections only from the posted pix. The good thing is these collections originated from locations separated by great distances, which allows to adequately sample intra-specific variations.
The ITS is a very variable “locus” by default, so 2-3% variability between reliably identified collections of a single entity might be a reasonable figure for some species. I already gave you an example – Sutorius luridiformis from the Urban & Klofac paper. The same authors excluded two collection identified through morphology as S. luridiformis from consideration because “their similarity in both ITS1 and ITS2 is less than 95 %, …exceeding typical levels of within-species sequence variation (Schoch et al. 2012)”. On the other hand (a nice example for Boletus s.s. you asked for), Feng et al. (2012) noted that B. subcaerulescens, B. regineus, B. subalpinus (native to NA only), and B. pinophilus (occurring in NA and Europe), had limited ITS sequence variations, meaning that inter-specific variations for that locus between multiple collection of these taxa are so narrow as to suggest that they are all the same taxon (i.e., no barcoding gap). The authors attributed this phenomenon to adaptive radiation.
I have already mapped out all hetero-sites and ambiguous bases for the three collections and will post them with an accompanying discussion soon in obs 263101 (the thread here is getting a bit long).

I guess
By: Geoff Balme (geoff balme)
2017-03-12 13:32:29 PDT (-0700)

for comparison’s sake, it’s hard to compare A to B without C. I’d like to know HOW DIFFERENT these segments of DNA can be. In other words, would Boletus be 10% different or less than 1% like these are from one another?

I’m definitely thinking cladistically, my training is in that end of phylogenetics (I made millions of trees!) :)

Geoff,
By: I. G. Safonov (IGSafonov)
2017-03-12 13:02:18 PDT (-0700)

Not sure about your call for an outgroup for this situation. In my understanding the term is used in cladistics as a relevant reference. I don’t think one can use a single species (unless it’s a monotypic genus) as an outgroup. The taxonomic and evolutionary status of B. aureissimus is yet to be determined. nrITS and nrLSU sequences of that species do exist (Dr. Ortiz-Santana has them) but haven’t been published in GB yet. I will look into this matter again and report later – a sequence comparison is all we need at this time. It’s time to place your bets now. :-)

Is the outgroup B. aureissiumus?
By: Geoff Balme (geoff balme)
2017-03-12 10:15:38 PDT (-0700)

What are we using for an outgroup?

Geoff,
By: I. G. Safonov (IGSafonov)
2017-03-11 15:22:11 PST (-0800)

I just got molecular data on Renée Lebeuf’s obs 263101, and that’s going to impact my earlier view on the identity of your collection I expressed below…
The ITS and LSU sequences from 250839, 252208 and 262101 are pretty much identical to each other, with just a few hetero-sites and ambiguous characters scattered around. It’s more likely that the three collections represent the same taxon than all of them being a species complex. I think it’s worthwhile to sequence one of the single-copy protein-coding genes (TEF-1 or one of the RPB’s) for the three collections to lend more credence to the single-species theory.

Hmm.
By: Geoff Balme (geoff balme)
2017-03-10 06:30:49 PST (-0800)

thank you for posting the efforts! it looks like you actually foresaw this result in a previous message from Sept.

“Boletus auripes has been sequenced (at least one locus), but surprisingly it missed the two recent phylogenetic studies of the Boletinae/Boletaceae (I am referring to Nuhn et al., 2013, and Wu et al., 2014). Arora and Frank suspected it could be related to Butyriboletus and included it in their Butter Boletes study (2014); however, their findings rule out this connection.”

. . .

DNA sequencing results and discussion (edited 10-Mar-2017)
By: I. G. Safonov (IGSafonov)
2017-03-09 22:04:37 PST (-0800)

> A clean and contiguous nrITS sequence of 690 nucleotides has been obtained for this material and posted in the comment below. There was a hick-up (enzyme slippage) in the forward and reverse reads at the poly-T motif, but the two sequence fragments have been stitched together to give a nice, contiguous sequence. There are two ambiguous characters – a “W” in the poly-T stretch and an “R” in the middle of the ITS2 region. Then there is another ITS haplotype that adds one more “T” to the poly-T motif (unclear if it’s real or not, as insertions and deletions happen frequently during the PCR synthesis in such homopolymeric regions).
> A clean and contiguous nrLSU sequence consisting of the first 961 nucleotides (up to the LR5 region) has been obtained for this material and posted in the comment below.
> There was no need to BLAST these sequences in GenBank. Why? Because I first compared the data to those of obs 250839, Butyriboletus taughannockensis sp. nov., as a follow up to my original supposition that the two entities are likely to be closely related based on their gross morphologies. Sequence alignments revealed that the ITS and LSU traces are 99.1% and 99.6% similar, respectively. The nrITS sequences have 6 mismatching characters (all in the in the ITS2 region!) excluding the 2 aforementioned ambiguous characters, and the nrLSU sequences are only 4 nucleotides off.
> One of the reasons the ITS locus was chosen as the universal DNA barcode marker for fungi is because it has an acceptable barcode gap across multiple phyla (the difference between inter- and intra-specific genetic distances within a group of organisms; no overlap between the two variability ranges is the definition of the gap). However, the LSU barcode gap is quite poor (Schoch, 2012), but this locus is instead quite useful for inferring phylogenetic relationships at the generic level. At the same time, the fact that both the ITS and LSU are not perfectly identical seems to support the notion, however superficially, that 250839 and 252208 are probably not the same species. The ITS2 regions of the two collections are 98.3% similar. Does that exceed the intraspecific variability range for B. taughannockensis? Who knows… For instance, according to Urban & Klofac (2015), the ITS2 sequence similarity for reliably identified Sutorius luridiformis collections can be as low as 98.3%.
> Conclusion: IMO, this collection (252208) is NOT B. taughannockensis, based on both the gross morphologies inferred from the pictures and the DNA data (both loci are very close, but not matching perfectly). But then, morphology aside, one can make a claim that the existing genetic data is insufficient to make any definitive conclusions regarding the nrITS intra- and/or inter-specific variability of 250839 and 252208 (and other similar taxa, if they do exist) simply because the sampling pool is so small (only two collections).

Looking forward
By: Geoff Balme (geoff balme)
2016-11-17 11:52:03 PST (-0800)

to anything you discover!

Follow up
By: I. G. Safonov (IGSafonov)
2016-11-17 10:53:01 PST (-0800)

This collection, which is now in my possession, will be submitted for DNA sequencing (ITS & LSU) in due course.

By: Geoff Balme (geoff balme)
2016-09-18 07:23:40 PDT (-0700)

Is definitely one we looked at. The key in B-R-B removes this specimen due to the lack of any color change when the pore surface is bruised. But it looks like the species we are ready to suggest was not long ago a variety of B. auripes and I can’t stop wondering about some character variability.

Does anyone worry that we’re over-splitting perhaps participating in some serious species multiplication? Darwin did say that varieties should be treated as species, but do we need to be concerned with that?

Even with all the
By: Geoff Balme (geoff balme)
2016-09-18 06:16:23 PDT (-0700)

evidence the world has to offer all we have is BEST GUESS. :)

I am not yet willing to let go of the idea that manuals and experienced experts must be sidelined for molecular studies. Especially since I’ll be long gone before reliable means of doing this on the individual naturalist/enthusiast level are available.

My own work in that field convinced me that these phylogenetic efforts are naive as hell and our “black box” methods of grabbing at sequence data that we barely understand and comparing them without knowledge of intrinsic variability is deeply naive. Every node on EVERY tree we have ever looked at in any journal article is little more than a hypothesis that must be looked at with skepticism. :) Of course we usually make lots of name changes based on them – because that’s the game of taxonomic work these days!

In the end the hierarchic name shifting is of little consequence. Elevating varieties to species, species to genera and genera to families or tribes or any other of the multitude of interstitial levels of nomenclature is not terribly important. Deck chair rearrangement on the Titanic (possibly I should choose a happier vessel)! :)

I am sure that it not yet time to burn the books! :)

I will say, however, that it’ll be a lot of fun to hear what you discover. :)

Man, this was a grumpy rant, sorry about that. In the end I guess we have to decide – are we naively wasting our time or are these things KNOWABLE. :)

Geoff,
By: I. G. Safonov (IGSafonov)
2016-09-17 20:50:06 PDT (-0700)

Just trying to cover the bases before eventually getting some DNA data and subsequent feedback form GenBank: B. aureissiumus and NAB-14 is the best educated guess I can provide at this time. ;-)
Boletus auripes has been sequenced (at least one locus), but surprisingly it missed the two recent phylogenetic studies of the Boletinae/Boletaceae (I am referring to Nuhn et al., 2013, and Wu et al., 2014). Arora and Frank suspected it could be related to Butyriboletus and included it in their Butter Boletes study (2014); however, their findings rule out this connection. I reckon the Golden Foot bolete and its allies, if any, will get their own genus in due course…

That sir
By: Geoff Balme (geoff balme)
2016-09-17 19:48:00 PDT (-0700)

looks like an excellent fit (especially that bottom right shot), and the range data sure can’t hurt! So once a variety of B. auripes – So I chose the NOT SO bright stipe coloration in the key couplet 14. Hmmm.

Thanks for the overtime efforts, Igor!

Ah!
By: Geoff Balme (geoff balme)
2016-09-13 17:23:54 PDT (-0700)
Another book, I’ll start saving my pennies!
Geoff,
By: I. G. Safonov (IGSafonov)
2016-09-13 14:41:44 PDT (-0700)

It seems unlikely that caespitose growth in boletes is genetically coded for, but, on the other hand, it appears that certain species are more prone to grow in fused clusters than others. Perhaps, it’s a function of the environmental pressures and the weather more than anything else.
It’s been ridiculously dry in NJ and the adjacent states, too, for the last three weeks. I don’t even look for shrooms anymore. :-( What’s more worrisome is that the trend is likely to continue indefinitely. All the rain that’s been forecast earlier is either not going to materialize at all or is being pushed off till later. It’s certainly been of the driest summers/years in the NE in recent memory – thanks a lot, La Niña. :-(
I still think your bolete is NAB-14 and mine is another species (the cap color & texture are different). I hope to determine this by sequencing sooner or later. Perhaps NAB-14 has been described and is included in the new bolete book. I will have a chance to discuss this and more with Arleen and Allan in a couple of weeks when I see them at the COMA foray in NY.

Igor
By: Geoff Balme (geoff balme)
2016-09-13 14:09:14 PDT (-0700)

I’d say you’re right, your August observation (of a couple weeks back) looks very like these little critters. The reticulation and pore surface as well as pileus and lack of staining are sure matches.

Are all boletes capable of that fused growth? I notice that yours are stained red-brown where broken as did mine.

I’ll be out again tomorrow and see if any more have come up. IT’s been ridiculously dry though. I’m surprised I’m finding anything.

never mind
By: Matt Welter (mattfungus)
2016-09-12 20:49:25 PDT (-0700)

I figured it out. Its a setting you had at the top of yours or now I can see and didnt fully understand until a few minutes ago.

Sorry to bother you

Matt,
By: I. G. Safonov (IGSafonov)
2016-09-12 20:43:40 PDT (-0700)

What do you mean by “observation preference”?

how do you do observation preference?
By: Matt Welter (mattfungus)
2016-09-12 20:11:57 PDT (-0700)
By: Geoff Balme (geoff balme)
2016-09-12 19:07:05 PDT (-0700)

was one I looked at briefly.

I was not expecting to find so many boletes that are so tricky!
I keep wanting to shoehorn them into the keys.

Wow, Geoff!
By: I. G. Safonov (IGSafonov)
2016-09-12 16:07:44 PDT (-0700)

Some bolete you’ve got yourself there. :-) Thanks for making sure this collection has been preserved! Just like Walter before me, I don’t recognize this taxon, and I also agree with him that it’s not X. illudens. Actually, my first impression was a cross-breed between R. ornatipes and B. auripes, something perhaps closer to what I just collected in upstate NY – obs 250839 that largely went unnoticed. By the way, I don’t think yours and mine are the same, though they might wind up in the same genus.
Anyway, for the heck of it I just checkout the Undescribed Bolete Species Pending Publication section in NAB/BRB, and to my surprise found a close match to your bolete, NAB-14 (p. 354 & p. 363). Bessettes & Roody also thought their find was similar to auripes and ornatipes.

Thank you, Mycowalt!
By: Geoff Balme (geoff balme)
2016-09-12 15:19:58 PDT (-0700)

Too bad I was feeling pretty good about the ID! :)

Geoff
By: walt sturgeon (Mycowalt)
2016-09-12 14:58:42 PDT (-0700)

I don’t recognize this bolete but X. illudens has a broad pseudo reticulum not the fine reticulation shown in your photo.