Volume 17, Number 1, Spring 2007 43

Mushrooming in the Age of DNA: Now Comes the Fun Part Michael Kuo*

Th e fi rst reward of tree study—but one that lasts you to the end of your days—is that as you walk abroad, follow a rushing stream, climb a hill, or sit on a rock to admire the view, the trees stand forth, proclaiming their names to you. Th ough at fi rst you may fi x their identity with more or less conscious eff ort, the easy-to-know species soon become like the faces of your friends, known without thought, and bringing each a host of associations. —D. C. Peattie (1948/1991, p. 156)

I LOVE THIS passage, which comes from Peat- ited from Linnaeus refl ects our understanding of tie’s 1948 A Natural History of Trees of Eastern and natural organisms, not the organisms themselves. Central North America. Peattie’s words capture Hopefully, our understanding is “accurate,” perfectly a sense of familiarity with nature known mean ing that it corresponds with evolution and to many naturalists. Last summer, my wife Kate selection in the natural world—but this happy and I walked through woods in southeastern agreement between nature and is Kentucky, where entire ecosystems are being laid funda mentally out of reach, and never a certainty, to waste by a coal mining practice called moun- since taxonomy is composed of hypotheses, to be taintop removal (if you have Google Earth, zoom supported (or not) by available evidence. I restate in on the region; you can see the devastation from these well known principles here because they are an altitude of 400 miles). We wanted to see what frequently forgotten in biology and especially in might be threatened by destruction , where the hypotheses that underlie tra- of an ancient Appalachian ecosystem known for ditional taxonomy are almost always unstated— its incredible biodiversity, and we spent about probably for good reason, because they are often half an hour walking, looking for mushrooms, ludicrous. To demonstrate this, one need only and cataloguing what we could recognize—a cur- put words to the actual hypothesis that underpins sory, preliminary list. We will be returning with most of the taxonomic keys in mycology: mycologists from Illinois, Ohio, and Tennessee to create a rigorous survey of fungi, but in that 30 1 Displaying a morphological Subgenus minutes we wrote down more than 60 feature whose predictive value Somethings is as far as we know coincidental, names, from Craterellus cornucopioides to a host of since we have no working theory Amanita and Lactarius species that we did not rec- about how the feature is actually ognize at sight. It is a wonderful feeling to know related to natural selection and the names of mushrooms—and while fungophiles speciation. must frequently be content with recog nizing a rather than a species, the feeling that Peattie 1 Not displaying this feature. 2 describes contributed deeply to our enjoyment of those beautiful Appalachian woods. Th is is the essence of the vast majority of But it must be said—not just as an ironic the couplets found in mycological monographs. aside, but as a fundamental matter of science— Cystidia, colors, sporal dimensions, reactions to that the trees and mushrooms do not care what chemicals and reagents, tubes that are individu- their names are. Th e taxonomic system we inher- ally discrete . . . the list, of course, goes on and on, because mycologists have rarely bothered even to * P.O. Box 712, Charleston, IL 61920, mushroom expert think about what selective advantage any of the @yahoo.com. features might provide for an organism; taxo- McIlvainea 17 (1) Spring 2007 43 44 McIlvainea nomic mycology has been predominantly atheo- tidia or the color of the cap can be very useful, retical—which is, frankly, another way of saying of course, when it comes to identifying mush- it has been largely unscientifi c. It sounds odd to rooms—as long as we acknowledge that the pres- claim that an eff ort dependent on highly techni- ence of the cystidia (for example) is as far as we cal monographs, jargon, and advanced micros- know coincidental and prepare ourselves for the copy skills is often “unscientifi c,” but we should possibility that our fl imsy hypothesis will be stood not confuse the trappings of science with science on its head. But keys that have identifi cation, itself, which involves hypothesis and theory. Th is rather than classifi cation, as their sole raison d’être becomes clear if we consider an alternative to the are few and far between in the world of technical key couplet above—one in which a morphologi- mycological publications. Korf’s wonderful “Syn- cal feature’s selective relevance is theorized: optic Key to the Genera of the Pezizales” (1972) is an excellent example of an identifi cation key 1 Rhizomorphs aggregated into a Scleroderma without taxonomic pretenses—as is the Volk & stemlike structure that holds the septentrionale Burdsall (2005) key to Armillaria (in which the

spore-producing machinery high researchers defi ned the species on the basis of enough to avoid being covered with drifting sand on exposed mating studies, then searched for morphological beaches and dunes. characters that might successfully predict the spe- cies) and the den Bakker & Noordeloos (2005) 1 Rhizomorphs present but not 2 key to Leccinum (species defi ned by DNA and aggregated into a stemlike ecology, morphological characters used in part structure since the organism grows in wind-protected for identifi cation). However, the vast majority of environments. keys in mycology (at least, the ones I am familiar with) are taxonomic, not merely identifying but Here we have an actual hypothesis involved defi ning and arranging taxa on the basis of un- with the taxonomy—one that we can test with the theorized morphological features. experiment of further collection and morphologi- Anyone who studies fungi, even casually, cal analysis. If we collect hundreds of Scleroderma is familiar with the taxonomic frustrations that specimens and fi nd that the ones growing in sand permeate the discipline. We are told that Lepiota dunes all manifest the pseudostipe, while speci- americana is really Macrolepiota americana, then mens growing elsewhere do not, we have support- americanus—more closely related ed (not proved!) our hypothesis, especially if we to Agaricus campestris and Coprinus comatus than can correlate this data with other support (mor- to Lepiota cristata. DNA studies like the ones phological or otherwise). Just to be clear, it is not that produced these mind-blowing revisions are the inclusion of the hypothesis in the wording of in vogue, but while I readily concede that a few the couplet that is at issue here; it is the presence DNA studies may be irresponsible and unscien- of a hypothesis at all. It is not as though the many tifi c, most of them are not—or are at the very couplets in mycological monographs referring to least no more irresponsible and unscientifi c than cystidia, for example, merely leave the authors’ what preceded them. In short, the frustration we hypotheses about cystidia unstated in order to feel is the result of having built a huge taxonomic avoid being wordy and repetitive. Th e intent of house of cards on the basis of a fl imsy theory; it mycological taxonomy, according to Korf (2005) is the inability of “comparative morphology” to in a controversial paper that I will discuss in more predict natural relationships consistently that detail below, “was almost always to provide a clas- has created the problem, rather than competing sifi cation that refl ected relationships, deduced evidence from DNA studies, mating studies, or from comparative morphology.” Th is sounds anything else. suspiciously like what I have been describing, and while it is certainly a more presentable form of In the words of one mycologist, we are the idea than “If they look diff erent to me they in a period of transition as far as the must be diff erent,” there is considerable concep- study of mushrooms is concerned. We tual overlap between the two ideas. know the faults of the old system, but Th e use of morphological features like cys- since the new one is still in the forma- Volume 17, Number 1, Spring 2007 45

tive stage undoubtedly many of its faults DNA entered the picture: that mushrooms have have not yet been discovered. evolved with other organisms within ecosystems, and their classifi cation cannot be adequately Some readers will recognize these words, which do accomplished without keeping ecology in the not come from a contemporary mycologist but, foreground. Results from DNA studies support perhaps ironically, from Alexander Smith’s 1949 this idea again and again; if you are interested in introduction to his Mushrooms in Th eir Natural seeing a few examples I recommend the recent Habitat. I quote them here to underscore the fact papers on Leccinum by den Bakker and his col- that Smith—who is generally seen as an iconic laborators (2004, 2005) and a paper by Kretzer representative of micromorphology-based my- and collaborators (1996) on Suillus (full citations cological taxonomy in North America in the last for these works can be found below). century—was immersed at the beginning of his When DNA studies do not support ecologi- career in a similarly frustrating era of taxonomic cal hypotheses, it is often the case that ecological instability as Psalliota, for example, exploded into data is simply missing or too poorly documented Agaricus, Oudesmansiella, and other genera. More to be incorporated into the research. A recent importantly, however, Smith’s words make it clear study of the genus Gymnopilus (Guzmán-Dávalos he understood, at some level, that taxonomy is et al., 2003) is an excellent example, and also perpetually unstable because it is an elaborate hi- serves to underscore some of the points I have erarchy of hypotheses (read: “potential house of been making about morphology-based taxonomy cards”) that may prove to be untenable. and its pitfalls. Th e paper’s title, “Traditional Th ere are many complaints that can be infrageneric classifi cation of Gymnopilus is not lodged about DNA research in mycology. Some supported by ribosomal DNA sequence data,” of these complaints (“I don’t want to have to learn pretty much sums up what the researchers dis- a new name for Lepiota americana,” for example, covered when they sequenced DNA from over 50 or “In the woods, those molecular biologists Gymnopilus specimens. Th e “traditional” way of wouldn’t know a Leccinum from a beer bottle”) looking at Gymnopilus (Romagnesi, 1942; Singer, have more to do with personal misgivings or social 1986; Hesler, 1969) divides the genus into two concerns, and are probably not worth discussing major groups: the Annulati group, which features here. Other complaints—especially the one that mushrooms in which there is a “[v]eil forming a faults some DNA papers for proposing sweep- membranous to densely fi brillose, persistent an- ing taxonomic changes based on molecular data nulus” (quoting Hesler, 1969—the major mono- from something like 10–20 mushrooms—may graph for the genus in North America); and the be more reasonable. But it must be acknowledged Gymnopilus group (“[v]eil absent, or present and that my complaint against comparative morphol- fugacious, not forming a persistent annulus”). ogy—that it (often) lacks any decent theory Th e Gymnopilus group is further subdivided by about natural selection—cannot be maintained Hesler as follows: against molecular biology. Th e theory that an organism’s DNA expresses its genetic identity is 1 Spores 3.5–7 µm long; sect. Microspori one that no scientist would deny, and the quick- if 6-8 :m long, take next est way to demonstrate the massive evidence sup- choice. porting the theory is to try imagining the kind of evidence that would make it unstable: discovery 1 Spores (6-) 7–9 µm long. sect. Gymnopilus of a living organism that has no DNA, or an or- ganism whose DNA appears to code for features Guzmán-Dávalos (1995) later proposed that are not present when the features are present three, rather than two, subdivisions to the in every other organism whose DNA is so coded. Gymnopilus group: On the basis of current evidence, both scenarios are preposterous. 1a Spores 3.5–6.5 µm long. sect. Microspori In my view the most signifi cant fi nding of mycological DNA studies is, frankly, one 1b Spores longer. 2 that should have been “discovered” long before 46 McIlvainea

Some headway might be made by a thorough 2a Spores 6–9 (-10) µm long. Sect. Gymnopilus investigation of collectors’ notes in herbaria, but the kind of rigorous ecological data that might 2b Spores 8–11 (-12) µm long. Sect. Macrospori reliably support conclusions is not likely to be hidden on collection cards, since collectors have I am quoting the “traditional infrageneric never held ecological data to be very signifi cant. classifi cation of Gymnopilus” at length because Mycology, if it is ever going to reach some —with no disrespect intended to those who con- kind of actual understanding of the genus Gym- structed it—it is self-evidently unscientifi c. Entire nopilus, must return to somewhere in the vicinity taxonomic divisions have been erected on the of Square One and a Half and begin to compile basis of whether the ring is “persistent” or not, a robust record of ecological data, accompanied and on diff erences in spore lengths—without by morphological and molecular data (as well as even a passing guess as to how these features data from mating studies). Collectors will need might relate to natural selection and evolution- to document substrates with precision, as well ary history in the genus. Th is is the “comparative as forest types, weather patterns, evidence of morphology” mentioned above by Korf, but the animal (especially insect) activity—in short, the hypothesis-based, deductive reasoning he cham- fullest documentation of ecology possible. Th is pions is simply missing here. Not unstated: miss- way there is a more legitimate, though still un- ing. We did not need a DNA study to tell us that focussed, hypothesis being tested: that the mush- our taxonomic arrangement of Gymnopilus was room has evolved in an ecosystem and that such artifi cial and that the species we named on the data will be integral to understanding the mush- basis of that arrangement are questionable; there room. Subsequent, more specifi c hypotheses will could easily have been a paper entitled “Tradi- undoubtedly suggest themselves as the data come tional infrageneric classifi cation of Gymnopilus is in—including hypotheses regarding the morphol- not supported by anything approaching scientifi c ogy of the mushrooms. Perhaps the scales on hypothesis” long before 2003. the cap of one species represent an adaptation So it should come as no surprise that Guz- to drier ecosystems, handily holding precious mán-Dávalos and her collaborators found no moisture on the mushroom rather than letting DNA support for previous arrangements of the it slide away. Or perhaps the same scales are the genus. Th e results supported dividing the 50+ side-eff ect of an adaptation for a thicker, denser Gymnopilus specimens studied into fi ve groups, cap surface that protects the vital spore-produc- some of which “have no obvious morphological ing below it from increased sunlight. synamorphies that clearly defi ne them,” and the Perhaps a species has developed darker pigments study concludes that “[p]artial veil characters and to hold heat in low-sunlight forests. Yes, I have basidiospore size are highly homoplastic charac- sewn all of these examples out of whole cloth on ters.” the spur of the moment, and the stitchwork is not Th e study does not correlate any ecologi- even particularly adept. But the concept is clear cal data, so we do not know whether the fi ve enough: a robust base of ecological data will allow species groups might be partially or completely us to think this way and restore a sound basis in understood with reference to the ecology of the hypothesis to mushroom taxonomy. mushrooms. I tried to uncover such a possibility Korf’s paper, “Reinventing taxonomy: a cur- by plotting out each species in the study by its mudgeon’s view of 250 years of fungal taxonomy, DNA-defi ned group and by its substrate—but the crisis in biodiversity, and the pitfalls of the while there are hints of a few patterns, they are phylogenetic age,” has become a rallying point not well supported because documentation of for amateurs and professionals who are frustrated substrate in Gymnopilus literature is almost en- with impenetrable, jargon-laden DNA studies tirely insuffi cient. Phrases like “conifer and decid- and long for the good-old days when Lepiota uous logs” or “rotten wood, West Indies” are the americana was Lepiota americana. I disagree with rule (my favorite is: “small excavation near a farm Korf on whether what he calls “comparative mor- house”); more precise information (on “decayed phology” is, in and of itself, sound science—and palm,” for example) is the rare exception. I think he is probably wrong when he says it is Volume 17, Number 1, Spring 2007 47

“clearly impossible to equate DNA sequences every year. Th e number of mushrooms collected with taxonomic insights.” But whether I am right and scrutinized by these two mushroom clubs (comparative morphology usually lacks a sound every year is astounding. theoretical base; DNA studies have one) or Korf What a potential resource for the science! is right (comparative morphology is hypothesis- But, as anyone who has been to a mushroom driven and based on sound theory; DNA studies club’s foray knows, the resource is only a “poten- are not), we are headed, believe it or not, for the tial” one. Th e mushrooms are not picked with an same conclusion. In Korf’s words, “[w]e must col- eye toward documentation of ecological data; they lect, collect, and collect.” are placed on collection tables after being hastily What mycology needs now is data from sorted and identifi ed; the edible mushrooms are collections—especially ecological data, but also removed; someone may make a list of the species data from morphological studies, DNA studies, names that have been applied to the mushrooms and mating studies. Korf documents a sad state . . . and everything is thrown away on Sunday. of aff airs in contemporary academic mycology: Th is is all very fun—but to be honest none of it, grant funding given primarily to DNA studies of even the occasionally produced species list, is very a few crusty and poorly documented specimens useful to science. With just a few changes, how- in herbaria; the “bean-counting mentality” of ever, the process could easily provide mycology uni versities and research institutes that prioritize with lots of invaluable data. faddish publications; the inability of fungal tax- I plan to make my suggestions for mush- onomists to fi nd positions . . . all of this in a fi eld room clubs more specifi c and detailed in further that was never highly popular to begin with and publications and in my lectures, but here I will has been struggling to keep itself afl oat within paint them in broad strokes. At a minimum, biology departments for decades. Some of these three things must happen for mycological society problems may be inherent to academia (this, forays to make more scientifi cally useful contri- anyway, is what my 20 years of experience in aca- butions: collection of ecological data, documen- demic literary studies, where more or less equiva- tation of macromorphology, and preservation of lent problems occur, suggests), but mycology is specimens. very fortunate to have a large body of experienced Documenting the ecology of mushroom and able collectors and enthusiasts outside of aca- collections is fun, and can provide mushroom demia: amateur mycologists, mushroom hunters, clubs with new areas to explore when it comes to and a large network of mycological societies and fi nding speakers and activities. If the Friday night mushroom clubs across the continent. speaker is a club member with tree expertise or a Now comes the fun part. It is up to us, the guest with this expertise from a local university or amateurs, to provide mycology with the mush- department of natural resources, speaking about room data it needs so badly. If the science must the ecosystem and trees in the Saturday foray wait for academics to do it, it will never happen. location, foray participants are better prepared I teach English at a university with over 10,000 to write down information about potential tree students. In my department we have about 300 associations and substrates—perhaps on collec- majors and provide a minimum of two classes tion cards that stress the collection of such infor- for every student on campus; in Biology there are mation rather than simply including a small line two mycology students and two elective courses for “Habitat.” With an eye toward understanding in mycology, one of which is taught every other mushrooms as parts of ecosystems, collection year. In fact Kim and Vince may represent a dis- tables might be organized, not by constantly proportionately high number when compared changing and usually outdated taxonomical to the average number of mycology students schemes but by ecosystems, and labeled “Spruce- at American universities, since the chair of our Fir Zone” or “Cottonwood-Sycamore Lowlands” biology department is a prominent mycologist instead of “Russulaceae” and “Polyporaceae.” who attracts students to the fi eld. However, there Ecological documentation can provide clubs with are two major mycological societies within four activities even in the off -season, since research hours of our school, both of which have a large into a collection site’s ecological history (using membership and hold many meetings and forays sources in local libraries, courthouse records, state 48 McIlvainea archives, and so on) can provide crucial informa- in two-toned sedans with car-top carriers, and tion. call it Lepiota americana. Don’t get me wrong; Th e advent of digital photography has made if there were indeed an offi cial “I Want To Be recording the macromorphology of specimens Alexander Smith Retro Foray,” I would be the much easier, and if one or two club members fi rst to sign up; I am a huge fan of Smith and his were simply to take photographs, from all angles, contemporaries, and North American mycology of each collection while it is still fresh (obviously is inconceivable without their Herculean eff orts a numbering system will be required to keep and genius. everything straight), meticulous journal-style But it is time to move on, as far as the descriptions could be bypassed—though such science of mycology is concerned. We must ac- descriptions would be ideal as an accompaniment cumulate specimens—and it is time to consider to the photos. At a minimum, information that our mushrooms from an ecological perspective. may not be discernible from the photos (odors, I have been framing my argument, so far, in for example) should be documented on the col- terms of the pursuit of the advancement of scien- lection card. tifi c knowledge—but I will close by framing it in Perhaps most importantly, the collections other terms: our planet’s biodiversity crisis. Korf must be dried and saved. If clubs were to add writes: “Curator” to the list of positions, along with “Presi dent,” “Foray Coordinator,” and other tradi- An oft-quoted estimate for fungi is that tional positions, that person (or persons) could be we have described only 4 to 5% of the responsible for drying the specimens, keeping the world’s species, leaving 95% or more numbering system intact, coordinating the digital yet to be recorded. Th e loss of habitats photos and collection cards, and maintaining the is proceeding so swiftly that the prob- club’s herbarium (which sounds fancy but could lem is critical. Unless these habitats are easily consist of a few old fi ling cabinets in a club sampled now we will have lost forever member’s garage). our chance to document the world’s liv- Ideally the process I’m recommending ing biodiversity, to save that in museum would be undertaken for most (even all) of the specimens and, in the case of fungi, mushrooms collected on forays—but this goal is often in culture collections. probably unrealistic. However, members might discuss at a regular meeting what groups of mush- Even the fungi from well-studied areas are rooms seem to be well represented in the club’s subject to habitat loss and potential extinction. regular foray locations and if, for example, many Many of Smith’s mushroom collections, for boletes are regularly collected at the club’s annual example—including type collections for taxa foray to Such-and-Such State Park, the club could that have never (or rarely) been subsequently produce an invaluable resource for mycologists collected—come from locations in Emmet and by going through the process I’m suggesting for Cheboygan counties, in Michigan, that have long boletes alone over the course of several annual since been clear-cut. In one of these locations the forays at the location. logging company left a scrawny swath of trees Mycologist Tom Volk tells his students that standing next to the road in an attempt to hide a mushroom’s name is far from being the most the acres of damage. Somewhere behind these interesting thing about it. Picking a bunch of trees, in what is now a landscape reminiscent mushrooms from a state park, using 40-year-old of Tolkein’s Mordor, Smith collected in 1963 monographs to label them, gawking at them for what he called Leccinum imitatum—and appar- a few days, then throwing them in a dumpster is ently never collected it again. Unfortunately, his lots of fun—but it is also quaint, and a little bit ecological data consisted of two words (“under as- like what Civil War re-enactment clubs do: act pen”), and we may never know much more about out something from the past. We might as well Leccinum imitatum than we do now. wear thick plastic glasses a la 1965, wrap our Th ere is evidence suggesting that cultivated mushrooms in waxed paper pulled from a baking Agaricus bisporus, the common “button mush- roll and twisted at both ends, drive to the forays room” sold in grocery stores, may have “escaped” Volume 17, Number 1, Spring 2007 49 cultivation to threaten native Agaricus popula- Hesler, L. R. 1969. North American species of tions (see Kerrigan et al., 1995)—and while Gymnopilus. New York: Hafner. 117 pp. there are as yet no scientifi c studies to confi rm Kerrigan, R. W., D. B. Carvalho, P. A. Horgen, & these observations, some highly adaptive mush- J. B. Anderson. 1995. Indigenous and intro- rooms—including Amanita thiersii, Morchella ru- duced populations of Agaricus bisporus, the fobrunnea, Stropharia rugosoannulata, and many cultivated button mushroom, in eastern and stinkhorns such as Phallus rubicundus—appear to western Canada: Implications for population be increasing their geographic ranges at alarming biology, resource management, and conser- rates, very possibly assisted by commercial distri- vation of genetic diversity. Canadian Journal bution of substrates like wood chips and sod. of Botany 73: 1925–38. Korf’s warnings about biodiversity cannot Korf, R. P. 1972. Synoptic key to the genera of be ignored, and the time is now for mushroom the Pezizales. Mycologia 64: 937–94. collectors to begin documenting our fungal fl ora. Th is is why Kate and I, along with Midwestern Korf, R. P. 2005. Reinventing taxonomy: A mycologists, are returning to southeastern Ken- curmudgeon’s view of 250 years of fungal tucky. Th e species list we created as we walked taxonomy, the crisis in biodiversity, and the through the woods was fun to produce, and it pitfalls of the phylogenetic age. Mycotaxon was nice to be able to name so many mush- 93: 407–15. rooms—but the list must now be replaced by ac- Kretzer, A., Y. Li, T. Szaro, & T. D. Bruns. 1996. tual documentation of ecology and preservation Internal transcribed spacer sequences from of specimens before that beautiful, diverse, and 38 recognized species of Suillus sensu lato: ancient ecosystem is destroyed. Phylogenetic and taxonomic implications. Mycologia 88: 776–85. ACKNOWLEDGMENTS Peattie, D. C. 1948/1991. A Natural History of Trees of Eastern and Central North America. I wish to thank Ron Meyers, Nicholas Money, Boston: Houghton Miffl in. 606 pp. Patrick Leacock, Richard Korf, Andrew Miller, Romagnesi, H. 1942. Quelques points de tax- and Carol Schmudde (none of whom, of course, onomie. Bulletin Société Mycologique France necessarily agrees with me) for valuable advice on 58: 81–89. this manuscript. Singer, R. 1986. Th e in Modern Tax- onomy. Germany: Koeltz Scientifi c Books. REFERENCES 981 pp. Smith, A. H. 1949. Mushrooms in Th eir Natural Den Bakker, H. C., G. C. Zuccarello, Th . W. Habitat. New York: Hafner Press. 626 pp. Kuyper, & M. E. Noordeloos. 2004. Evolu- Volk, T. J., & H. H. Burdsall. (n.d.) Th e state of tion and host specifi city in the ectomycor- taxonomy of the genus Armillaria. Retrieved rhizal genus Leccinum. New Phytologist 163: March 26, 2007 from the Tom Volk’s Fungi 201–15. Web site: http://botit.botany.wisc.edu/toms_ Den Bakker, H. C. & M. E. Noordeloos. 2005. fungi/arm.html A revision of European species of Leccinum Gray and notes on extralimital species. Per- soonia 18: 511–87. Guzmán-Dávalos, L., G. M. Mueller, J. Cifuen- tes, A. N. Miller, & A. Santerre. 2003. Tra- ditional infrageneric classifi cation of Gym- nopilus is not supported by ribosomal DNA sequence data. Mycologia 95: 1204–14.