Boletus Edulis and the Whole Genome Testing Revolution
In late 2022 the Dentinger Lab at the University of Utah published a revolutionary study on the Boletus edulis clade of super-choice mushrooms (collectively “Porcini”). The results have the world of bolete taxonomy and nomenclature in an uproar. We have decided to adopt the more radical half of the study for Bolete Filter purposes, but will hold off on the other half due to some doubts I will outline below.
This link will take you to a video talk Dr. Dentinger gave for the foraging community, which was headlined by a panel of the same renowned authors and experts we rely on for the Bolete Filter data. The results he presented create an uproar in several ways, including all of these:
Many distinct Porcini species had been accepted across North America on the basis of region and morphology (visible characteristics). The new work merges several of those into mega-species that may look different on the outside but have the same DNA, and often have a larger range.
To use an easy analogy, Canis lupus familiaris presents obvious morphological distinctions between Bulldogs, Beagles, Schnauzers, and St. Bernards, but they all have the same genetic code until you get down to individual specimens. The same thing applies to all the disparate forms of B. edulis. And to Homo sapiens, but that’s a whole other point.
The new work includes DNA on several 19th century herbarium samples, obtained through cutting edge sequencing techniques that somehow squeezed usable DNA blood from the ancient holotype stones.
Early mycology heroes like Charles Horton Peck published hundreds of mushrooms with names and ID’s that form the basis of what we use today. People hurried to test those original finds as soon as DNA technology became available, only to discover that they’d been subjected to various insults like being stored in mothballs or formaldehyde, on shelves next to other mushrooms, exposed to direct sunlight, and in dusty old rooms that certain obnoxious pests always manage to penetrate. Add that to the natural degradation of DNA over time, and you will see the problem. No one managed to isolate long enough strands of DNA to make even tentative stabs at comparing those ancient and insulted samples to modern finds. Until now.
The Dentinger Lab has developed and/or adopted some cutting edge approaches that yielded usable DNA bits. The issue? Those bits do not match up to the published descriptions, and those descriptions often correspond to holotypes with a different name. Arrrgh! It creates problems that go to the very heart of field mycology; the effort to put names on specimens found in the field, so that foragers can run to the books and find out more.
The new work changes our understanding of Porcini evolution, expansion rates, and other factors in ways that challenge our understanding of what it means to be a “species” as well as what it means to have a geographic range.
Sit back and watch folks. The ivory tower of mycology is crumbling on one side, the stones are being used to build a new wing, and arguments are underway about the wisdom of both efforts. Plus the inevitable fights about whether the new architecture will work. Outsiders will have every right (and opportunity) to laugh. Just don’t do it in from of the people on the inside who care very, very much about every iota of change. It isn’t worth the nose they’ll snap at, nor the ear they will lecture into agony.
All humor aside, the Dentinger paper raises fundamental questions about how mycologists have viewed both evolution and reproduction in the Porcini group. The implications reach even further. If it’s true for Porcini, why not other mushrooms?
The new work changes our assumption that (i) the old descriptions accurately reflect what Peck et. al. found in the field, and (ii) the sample from the field made its way to an herbarium box with the proper label. What happens when you have an unreliable chain of custody? What happens in the event of an obvious mistake? And what are academic nomenclature conventions meant to accomplish in the first place?
Put simply, anyone who compares the herbarium names to the written descriptions can see that some of the specimens got mixed up between the time from when they were described to when they were plucked from the shelves for DNA testing in the 2020’s. See below for more details. This reality raises a fundamental question: Which is more true: the descriptions that Peck wrote and taught to his students as Name X and Name Y, or the names typed onto the herbarium labels? What happens when the DNA in the Name X box corresponds to a mushroom that looks like Name Y, and the stuff in the Y box corresponds to the description of X?
Understand: academic mycologists do not really care about names any more than astronomers care about whether a star is called Ursa Major or HD 102956. Amateurs with home telescopes (like foragers in the field) have the opposite point of view. We want, first and foremost, to be told that “ABC light is named this, XYZ light is named that, and you can learn more about both by looking at these references…” Thus Ursa Major is a magnificent name because it is easy to remember and can help the amateur to orient his telescope according to the map. Same with B. variipes to name one example. Professional astronomers/mycologists are just as happy to use the letters and numbers approach. They care about stars versus galaxies, relative motions, and what the data can say about the nature of the cosmos in general; or about phylogenetic trees and what the data reveals about history, nature, and evolution.
To continue the analogy, one might define nomenclature as the spoken name of each mushroom, and taxonomy as the distinct biological nature and relationship of each mushroom in relation to all of the others. Nomenclature matters immensely to foragers and only in passing to academics; while taxonomy consumes the professionals has only an [ahem] academic interest to the rest of us. One can argue about my definitions, but they serve to illustrate the point. The new work could technically require radical changes to the names of well known mushrooms, even to the point of simply swapping one name for another. Those changes are a [shrug] from the academic point of view; and yet they would throw the foraging and publishing worlds into long term and expensive chaos.
So should we just start over again, and scrap the original names and descriptions created by Peck, Frost, Murrill, etc. because they do not match the DNA-proven species? Out with the old and in with the new, since they failed to imagine the amount of documentation their descendants would have preferred? Where does that stop, and how should we raise up new names?
Should we assume the ancient holotypes were misfiled, and retype the labels so the DNA-proven species will match the descriptions? Who makes that decision, and according to what rules? What happens the next time when the human error is a little less obvious, or the cost of switching names less severe? And while we are at it, what exactly were the procedures used back in the day, and why not scrap the specimens completely if the link from field to storage box can’t be relied on?
Should we close our eyes to the actual science, and accept the use of clade-level names like “Porcini” that refer to groups rather than species? Don’t laugh at this idea! Aren’t most of us doing that already for morels, chanterelles, and other beloved edibles that now contain species we cannot distinguish with the naked eye?
The radical findings we are going to adopt into the Bolete Filter
The Dentinger paper uses whole genome testing rather than relying on individual genes. That makes the results orders of magnitude more accurate than anything done before. The comparisons of “Sample A” to “Sample B” aren’t locked in stone; they’re cast into blocks of stainless steel. Annealed blocks encased in imperishable crystal. Thus we have incorporated all of the following changes into the entries on this site:
1. B. edulis is a cross-continental species that can display as many facial distinctions as Pointers versus Poodles, or Chihuahuas compared to Chow Chows. Notes about this merger will appear in the “Science Notes” section of the merged entry. But here is the bottom line. The entry for B. edulis will now include all the [ahem] breeds formerly known as:
- the European B. edulis (yes, it is indeed a transcontinental species);
- the northeastern B. edulis var. clavipes;
- the northeastern B. chippewaensis;
- the Rocky Mountains B. rubriceps; and
- California’s B. grandedulis.
2. B. variipes var. fagicola is a separate species, which presents an issue because there is a totally different mushroom that’s already called B. fagicola. This site will call it “B. variipes-fagicola” until something better comes along (i.e., get rid of the “var.” and replace it with a dash). Note that many finds of B. atkinsonii (another legitimate and separate species) have been proven to be B. variipes-fagicola, a nice piece of trivia you can use to show off for friends. “I would call this B. atkinsonii, but that species is very hard to distinguish from B. variipes-fagicola…”
4. The common and much loved B. separans turns out to be two lookalike species, which will be noted in the text.
5. B. gertrudiae is merged into B. nobilis. The yellow band at the top does not denote a separate species.
6. Five new and as yet unnamed species have also been identified, which will go up on the site as soon as they have been formally published.
- The rare, Rocky Mountains species that should be called B. Mottiae (see below);
- a truly lovely southern species;
- a Canadian species;
- a California species and
- a B. separans lookalike from the Northeast.
The changes we will hold off on adopting for now
1.What we all know as B. variipes will not be merged into the long forgotten B. leptocephalus (link goes to Peck’s description), and what we all know as B. nobilissimus will not be merged into B. variipes.
Right about now you are going, “huh?!” In brief, Peck published a species called B. variipes in 1888, and then another species he called B. leptocephalus in 1898. The first is extremely common and well known, and the second is a name that history forgot. Both and Riedel published the much rarer but well accepted B. nobillisimus in 2000. Dr. Dentinger’s work proves – irrefutably – that the accepted nobillisimus match the DNA of the herbarium holotype for variipes, while the many thousands of accepted variipes finds match to the holotype for leptocephalus. Thus one could argue we have to start calling “variipes” “leptocephalus,” and “nobillisimus” “variipes.” Never mind the century and a half of books, training, accepted usage, etc.
I resist this because (1) B. variipes is one of the few species we’ve all felt comfortable identifying, so changing that name would cause enormous confusion, (2) nobillisimus is rare, while leptocephalus was so rare as to be totally forgotten, (3) Peck’s description of B. variipes matches the thing we call by that name, but not the thing we call B. nobillisimus, and thus (4) it makes much more sense to connect nobillisimus to leptocephalus. And yet the DNA evidence is irrefutable. I believe we can solve all this confusion by accepting a blunder with the herbarium labels. Somehow the holotype for B. variipes got tagged with the label for leptocephalus, and vice versa. Nice, simple, clean, and oh so very human.
This would explain why we (including all of Peck’s students and other mycology heirs) have been so consistent about variipes finds for the past 135 years. And it would prevent the chaos that would be caused by changing one name, and giving the original name to another species entirely. So why doesn’t it happen as a matter of course? Well, remember that names have very little importance to professional mycologists, who’d be just as happy to use number and letter codes. Demanding an exception to the nomenclature rules just for the sake of the general public, however… That could cause academics some extra work.
But wait, there’s more! Assume my “switched labels” theory is true. Doesn’t that mean nobillisimus should be renamed leptocephalus to complete the story? Yessss, but… Do we really want to impose the long forgotten name over an accepted one based on a DNA fragment we know was misfiled? I truly have no idea how all this will play out in the end, and will maintain the old status quo by continuing to use the names B. variipes and B. nobillisimus until a firm consensus is reached. Notes about the nomenclature confusion will be added to the text of each species with a link to this article.
Same issues in a somewhat less confusing format. B. frustulosus is another Peck species from the late 19th century, this time collected while he was visiting down in Alabama and Mississippi. Peck also came across a mushroom he called B. pinophilus, named after a European lookalike. He distinguished the two by emphasizing “the deeply cracked surface of the pileus [cap] as the most notable feature of [B. frustulosus]… The deep chinks with sloping sides cause [the cap’s surface] to appear like  polygonal pyramids.”
B. pseudopinophilus is a Southern species erected in recent years, when DNA testing became advanced enough to prove that it differs from the lookalike European species B. pinophilus. Needless to say, B. pseudopinophilus does not have deep cracks in the cap unless (as one local expert told me) “all the 19th century collections happened to be of sun-bleached and sun-beaten fruiting bodies.“ Which someone like Peck would have recognized instantly.
In other words, the descriptions do not match. Not. At. All. Add in Peck’s knowledge of the European lookalike, plus the finds he and many others called by the European name, and it seems clear we have another foul up at the human level, with the wrong sample making its way into the herbarium (or the wrong label being applied at the herbarium, which seems less likely). And then there’s a spicy extra detail in none of the literature. I am informed that locals occasionally find an as-yet-unpublished crypto species, with pale coloration and a deeply fissured cap. If that does prove to be a separate species, it would complete the picture of another “wrong label” confusion exactly like the one that occurred with B. variipes and B. leptocephalus.
A PERSONAL ASIDE: All of that is fascinating and fun, but do not let the details hide the essential problem. How would/should things work if I’m wrong, and no samples were lost at all? Go ahead and assume that (a) Peck found a series of what he would have called B. pinophilus if they hadn’t been so butchered by environmental factors, (b) published those finds as a new species because he made an uncharacteristic and humiliating professional error, and (c) the herbarium sample tested in the 2020’s was exactly the same one that he found. Question: Should the mushroom now be called by that defective name, or should the world use the name devised to say, “this looks like the European species but is genetically distinct;” which is how this species was actually found? For that matter, does the word should really have any place when it comes to discussing nomenclature conventions? You and I (the people who care deeply about nomenclature) would say yes. Ivory tower academics (who care vastly more about taxonomy, but also write the nomenclature rules) would much rather eliminate such fuzzy concerns as should and ought to.
And again. The much loved Pacific coast Queen Bolete (B. regineus) was separated out of the King Bolete (B. edulis) in 2008. And that was correct, because we now know that the two are genetically distinct. Since then B. regineus has become a well known species with thousands of finds by extremely happy foragers. Meanwhile, back in 1975 Harry Thiers erected another, exceedingly rare mushroom he called B. mottiae; which got a different name because it’s description had very little to do with the B. edulis that Thiers new exceedingly well. The only recorded mottiae finds since then have been isolated, much disputed ones in the Rocky Mountains. Indeed, B. mottiae is so rare that we have not been able to find a photo for the site! Testing now proves that there are indeed two species… but it also proved that the mottiae holotype actually has regineus DNA. Thus the rules would normally require us to rename regineus as mottiae. But there is a twist! Those weird Rocky Mountains finds were likewise proven to be a separate species… but one with no DNA that has been located in any herbarium. So the rules say that it will need to be published as a new species with a new name. Summing up, the common regineus is supposed to vanish into the rare mottiae despite the description, and the rare finds hitherto identified as mottiae get a new name, with a description that matches what Thiers wrote back in 1975.
It seems obvious how all this happened. Thiers really did find a new species, and published it just the way he should. But something funny happened on the way to the herbarium, so the original B. mottiae sample got replaced with one from the relatively common B. regineus (then thought to be a variant on B. edulis). A completely understandable, human level blunder that caused no one any harm… unless and until you and I are required to dance a topsy turvy nomenclature jig.
Bottom line: This site will not participate in the massive confusion all of these name changes would cause unless and until the academic community insists that public and publishing madness is the price of scientific sanity.
Take the above with several grains of salt
Please remember that this is an amateur site, run by uncredentialed hobbyists, for the benefit of a general public that only wants some kind of key to narrow down the possibilities into a manageable number of vaguely similar species. We try our best to reflect new understandings at the academic level, but it is not our actual goal.