Mushrooming in the Age of DNA: Now Comes the Fun Part

Note: This paper appears in McIlvainea 17: 43-49 (2007).

by Michael Kuo

The first 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. Though at first you may fix their identity with more or less conscious effort, the easy-to-know species soon become like the faces of your friends, known without thought, and bringing each a host of associations.

I love this passage, which comes from Peattie's 1948 A Natural History of Trees of Eastern and Central North America. Peattie's words capture perfectly a sense of familiarity with nature known to many naturalists. Last summer, my wife Kate and I walked through woods in southeastern Kentucky, where entire ecosystems are being laid to waste by a coal mining practice called mountaintop removal (if you have Google Earth, zoom in on the region; you can see the devastation from an altitude of 400 miles). We wanted to see what mushrooms might be threatened by destruction of an ancient Appalachian ecosystem known for its incredible biodiversity, and we spent about half an hour walking, looking for mushrooms, and cataloguing what we could recognize--a cursory, preliminary list. We will be returning with mycologists from Illinois, Ohio, and Tennessee to create a rigorous survey of fungi, but in that 30 minutes we wrote down more than 60 mushroom names, from Craterellus cornucopioides to a host of Amanita and Lactarius species that we did not recognize at sight. It is a wonderful feeling to know the names of mushrooms--and while fungophiles must frequently be content with recognizing a genus rather than a species, the feeling that Peattie describes contributed deeply to our enjoyment of those beautiful Appalachian woods.

But it must be said--not just as an ironic aside, but as a fundamental matter of science--that the trees and mushrooms do not care what their names are. The taxonomic system we inherited from Linnaeus reflects our understanding of natural organisms, not the organisms themselves. Hopefully, our understanding is "accurate," meaning that it corresponds with evolution and selection in the natural world--but this happy agreement between nature and taxonomy is fundamentally out of reach, and never a certainty, since taxonomy is composed of hypotheses, to be supported (or not) by available evidence. I restate these well known principles here because they are frequently forgotten in biology and especially in mycology, where the hypotheses that underlie traditional taxonomy are almost always unstated--probably for good reason, because they are often ludicrous. To demonstrate this, one need only put words to the actual hypothesis that underpins most of the taxonomic keys in mycology:

This is the essence of the vast majority of the couplets found in mycological monographs. Cystidia, colors, sporal dimensions, reactions to chemicals and reagents, tubes that are individually discrete . . . the list, of course, goes on and on, because mycologists have rarely bothered even to think about what selective advantage any of the features might provide for an organism; taxonomic mycology has been predominantly atheoretical--which is, frankly, another way of saying it has been largely unscientific. It sounds odd to claim that an effort dependent on highly technical monographs, jargon, and advanced microscopy skills is often "unscientific," but we should not confuse the trappings of science with science itself, which involves hypothesis and theory. This becomes clear if we consider an alternative to the key couplet above--one in which a morphological feature's selective relevance is theorized:

Here we have an actual hypothesis involved with the taxonomy--one that we can test with the experiment of further collection and morphological analysis. If we collect hundreds of Scleroderma specimens and find that the ones growing in sand dunes all manifest the pseudostipe, while specimens growing elsewhere do not, we have supported (not proved!) our hypothesis, especially if we can correlate this data with other support (morphological or otherwise). Just to be clear, it is not the inclusion of the hypothesis in the wording of the couplet that is at issue here; it is the presence of a hypothesis at all. It is not as though the many couplets in mycological monographs referring to cystidia, for example, merely leave the authors' hypotheses about cystidia unstated in order to avoid being wordy and repetitive. The intent of mycological taxonomy, according to Korf (2005) in a controversial paper that I will discuss in more detail below, "was almost always to provide a classification that reflected relationships, deduced from comparative morphology." This sounds suspiciously like what I have been describing, and while it is certainly a more presentable form of the idea than "If they look different to me they must be different," there is considerable conceptual overlap between the two ideas.

The use of morphological features like cystidia or the color of the cap can be very useful, of course, when it comes to identifying mushrooms--as long as we acknowledge that the presence of the cystidia (for example) is as far as we know coincidental and prepare ourselves for the possibility that our flimsy hypothesis will be stood on its head. But keys that have identification, rather than classification, as their sole raison d'etre are few and far between in the world of technical mycological publications. Korf's wonderful "Synoptic Key to the Genera of the Pezizales" (1972) is an excellent example of an identification key without taxonomic pretenses--as is the Volk & Burdsall (2005) key to Armillaria (in which the researchers defined the species on the basis of mating studies, then searched for morphological characters that might successfully predict the species) and the den Bakker & Noordeloos (2005) key to Leccinum (species defined by DNA and ecology, morphological characters used in part for identification). However, the vast majority of keys in mycology (at least, the ones I am familiar with) are taxonomic, not merely identifying but defining and arranging taxa on the basis of untheorized morphological features.

Anyone who studies fungi, even casually, is familiar with the taxonomic frustrations that permeate the discipline. We are told that Lepiota americana is really Macrolepiota americana, then Leucoagaricus americanus--more closely related to Agaricus campestris and Coprinus comatus than to Lepiota cristata. DNA studies like the ones that produced these mind-blowing revisions are in vogue, but while I readily concede that a few DNA studies may be irresponsible and unscientific, most of them are not--or are at the very least no more irresponsible and unscientific than what preceded them. In short, the frustration we feel is the result of having built a huge taxonomic house of cards on the basis of a flimsy theory; it is the inability of "comparative morphology" to predict natural relationships consistently that has created the problem, rather than competing evidence from DNA studies, mating studies, or anything else.

In the words of one mycologist, we are in

a period of transition as far as the study of mushrooms is concerned. We know the faults of the old system, but since the new one is still in the formative stage undoubtedly many of its faults have not yet been discovered.

Some readers will recognize these words, which do not come from a contemporary mycologist but, perhaps ironically, from Alexander Smith's 1949 introduction to his Mushrooms in Their Natural Habitat. I quote them here to underscore the fact that Smith--who is generally seen as an iconic representative of micromorphology-based mycological taxonomy in North America in the last century--was immersed at the beginning of his career in a similarly frustrating era of taxonomic instability as Psalliota, for example, exploded into Agaricus, Oudesmansiella, and other genera. More importantly, however, Smith's words make it clear he understood, at some level, that taxonomy is perpetually unstable because it is an elaborate hierarchy of hypotheses (read: "potential house of cards") that may prove to be untenable.

There are many complaints that can be lodged about DNA research in mycology. Some of these complaints ("I don't want to have to learn a new name for Lepiota americana," for example, or "In the woods, those molecular biologists wouldn't know a Leccinum from a beer bottle") have more to do with personal misgivings or social concerns, and are probably not worth discussing here. Other complaints--especially the one that faults some DNA papers for proposing sweeping taxonomic changes based on molecular data from something like 10-20 mushrooms--may be more reasonable. But it must be acknowledged that my complaint against comparative morphology--that it (often) lacks any decent theory about natural selection--cannot be maintained against molecular biology. The theory that an organism's DNA expresses its genetic identity is one that no scientist would deny, and the quickest way to demonstrate the massive evidence supporting the theory is to try imagining the kind of evidence that would make it unstable: discovery of a living organism that has no DNA, or an organism whose DNA appears to code for features that are not present when the features are present in every other organism whose DNA is so coded. On the basis of current evidence, both scenarios are preposterous.

In my view the most significant finding of mycological DNA studies is, frankly, one that should have been "discovered" long before DNA entered the picture: that mushrooms have evolved with other organisms within ecosystems, and their classification cannot be adequately accomplished without keeping ecology in the foreground. Results from DNA studies support this idea again and again; if you are interested in seeing a few examples I recommend the recent papers on Leccinum by den Bakker and his collaborators (2004, 2005) and a paper by Kretzer and collaborators (1996) on Suillus (full citations for these works can be found below).

When DNA studies do not support ecological hypotheses, it is often the case that ecological data is simply missing or too poorly documented to be incorporated into the research. A recent study of the genus Gymnopilus (Guzmán-Dávalos et al., 2003) is an excellent example, and also serves to underscore some of the points I have been making about morphology-based taxonomy and its pitfalls. The paper's title, "Traditional infrageneric classification of Gymnopilus is not supported by ribosomal DNA sequence data," pretty much sums up what the researchers discovered when they sequenced DNA from over 50 Gymnopilus specimens. The "traditional" way of looking at Gymnopilus (Romagnesi, 1942; Singer, 1986; Hesler, 1969) divides the genus into two major groups: the Annulati group, which features mushrooms in which there is a "[v]eil forming a membranous to densely fibrillose, persistent annulus" (quoting Hesler, 1969--the major monograph for the genus in North America); and the Gymnopilus group ("[v]eil absent, or present and fugacious, not forming a persistent annulus"). The Gymnopilus group is further subdivided by Hesler as follows:

Guzmán-Dávalos (1995) later proposed three, rather than two, subdivisions to the Gymnopilus group:

I am quoting the "traditional infrageneric classification of Gymnopilus" at length because--with no disrespect intended to those who constructed it--it is self-evidently unscientific. Entire taxonomic divisions have been erected on the basis of whether the ring is "persistent" or not, and on differences in spore lengths--without even a passing guess as to how these features might relate to natural selection and evolutionary history in the genus. This is the "comparative morphology" mentioned above by Korf, but the hypothesis-based, deductive reasoning he champions is simply missing here. Not unstated; missing. We did not need a DNA study to tell us that our taxonomic arrangement of Gymnopilus was artificial and that the species we named on the basis of that arrangement are questionable; there could easily have been a paper entitled "Traditional infrageneric classification of Gymnopilus is not supported by anything approaching scientific hypothesis" long before 2003.

So it should come as no surprise that Guzmán-Dávalos and her collaborators found no DNA support for previous arrangements of the genus. The results supported dividing the 50+ Gymnopilus specimens studied into five groups, some of which "have no obvious morphological synamorphies that clearly define them," and the study concludes that "[p]artial veil characters and basidiospore size are highly homoplastic characters."

The study does not correlate any ecological data, so we do not know whether the five species groups might be partially or completely understood with reference to the ecology of the mushrooms. I tried to uncover such a possibility by plotting out each species in the study by its DNA-defined group and by its substrate--but while there are hints of a few patterns, they are not well supported because documentation of substrate in Gymnopilus literature is almost entirely insufficient. Phrases like "conifer and deciduous logs" or "rotten wood, West Indies" are the rule (my favorite is: "small excavation near a farm house"); more precise information (on "decayed stipe palm," for example) is the rare exception. Some headway might be made by a thorough investigation of collectors' notes in herbaria (click here to explore Gymnopilus records in the New York Botanical Garden herbarium, including many scans of original collection notes from Murrill, Hesler, and others)--but the kind of rigorous ecological data that might reliably support conclusions is not likely to be hidden on collection cards, since collectors have never held ecological data to be very significant.

Mycology, if it is ever going to reach some kind of actual understanding of the genus Gymnopilus, must return to somewhere in the vicinity of Square One and a Half and begin to compile a robust record of ecological data, accompanied by morphological and molecular data (as well as data from mating studies). Collectors will need to document substrates with precision, as well as forest types, weather patterns, evidence of animal (especially insect) activity--in short, the fullest documentation of ecology possible. This way there is a more legitimate, though still unfocussed, hypothesis being tested: that the mushroom has evolved in an ecosystem and that such data will be integral to understanding the mushroom. Subsequent, more specific hypotheses will undoubtedly suggest themselves as the data comes in--including hypotheses regarding the morphology of the mushrooms. Perhaps the scales on the cap of one species represent an adaptation to drier ecosystems, handily holding precious moisture on the mushroom rather than letting it slide away. Or perhaps the same scales are the side-effect of an adaptation for a thicker, denser cap surface that protects the vital spore-producing hymenium below it from increased sunlight. Perhaps a species has developed darker pigments to hold heat in low-sunlight forests. Yes, I have sewn all of these examples out of whole cloth on the spur of the moment, and the stitch work is not even particularly adept. But the concept is clear enough: a robust base of ecological data will allow us to think this way, and restore a sound basis in hypothesis to mushroom taxonomy.

Korf's paper, "Reinventing taxonomy: a curmudgeon's view of 250 years of fungal taxonomy, the crisis in biodiversity, and the pitfalls of the phylogenetic age," has become a rallying point for amateurs and professionals who are frustrated with impenetrable, jargon-laden DNA studies and long for the good-old days when Lepiota americana was Lepiota americana. I disagree with Korf on whether what he calls "comparative morphology" is, in and of itself, sound science--and I think he is probably wrong when he says it is "clearly impossible to equate DNA sequences with taxonomic insights." But whether I am right (comparative morphology usually lacks a sound theoretical base; DNA studies have one) or Korf is right (comparative morphology is hypothesis-driven and based on sound theory; DNA studies are not), we are headed, believe it or not, for the same conclusion. In Korf's words, "[w]e must collect, collect, and collect."

What mycology needs now is data from collections--especially ecological data, but also data from morphological studies, DNA studies, and mating studies. Korf documents a sad state of affairs in contemporary academic mycology: grant funding given primarily to DNA studies of a few crusty and poorly documented specimens in herbaria; the "bean-counting mentality" of universities and research institutes that prioritize faddish publications; the inability of fungal taxonomists to find positions . . . all of this in a field that was never highly popular to begin with and has been struggling to keep itself afloat within biology departments for decades. Some of these problems may be inherent to academia (this, anyway, is what my 20 years of experience in academic literary studies, where more or less equivalent problems occur, suggests), but mycology is very fortunate to have a large body of experienced and able collectors and enthusiasts outside of academia: amateur mycologists, mushroom hunters, and a large network of mycological societies and mushroom clubs across the continent.

There is evidence suggesting that cultivated Agaricus bisporus, the common "button mushroom" sold in grocery stores, may have "escaped" cultivation to threaten native Agaricus populations (see the linked page and Kerrigan et al., 1995)--and while there are as yet no scientific studies to confirm these observations, some highly adaptive mushrooms--including Amanita thiersii, Morchella rufobrunnea, Stropharia rugosoannulata, and many stinkhorns such as Phallus rubicundus--appear to be increasing their geographic ranges at alarming rates, very possibly assisted by commercial distribution of substrates like wood chips and sod.

Korf's warnings about biodiversity cannot be ignored, and the time is now for mushroom collectors to begin documenting our fungal flora. This is why Kate and I, along with Midwestern mycologists, are returning to southeastern Kentucky. The species list we created as we walked through the woods was fun to produce, and it was nice to be able to name so many mushrooms--but the list must now be replaced by actual documentation of ecology and preservation of specimens before that beautiful, diverse, and ancient ecosystem is destroyed.

Acknowledgments: I wish to thank Ron Meyers, Nicholas Money, Patrick Leacock, Richard Korf, Andrew Miller, and Carol Schmudde (none of whom, of course, necessarily agrees with me) for valuable advice on this manuscript.

References

Den Bakker, H. C. et al. (2004) Evolution and host specificity in the ectomycorrhizal genus Leccinum. New Phytologist 163: 201-215.

Den Bakker, H. C. & Noordeloos, M. E. (2005). A revision of European species of Leccinum Gray and notes on extralimital species. Persoonia 18: 511-587.

Guzmán-Dávalos, L. et al. (2003). Traditional infrageneric classification of Gymnopilus is not supported by ribosomal DNA sequence data. Mycologia 95: 1204-1214.

Hesler, L. R. (1969). North American species of Gymnopilus. New York: Hafner. 117 pp.

Kerrigan, R. W. et al. (1995). Indigenous and introduced populations of Agaricus bisporus, the cultivated button mushroom, in eastern and western Canada: Implications for population biology, resource management, and conservation of genetic diversity. Canadian Journal of Botany 73: 1925-1938.

Korf, R. P. (1972). Synoptic key to the genera of the Pezizales. Mycologia 64: 937-994.

Korf, R. P. (2005). Reinventing taxonomy: a curmudgeon’s view of 250 years of fungal taxonomy, the crisis in biodiversity, and the pitfalls of the phylogenetic age. Mycotaxon 93: 407-415.

Kretzer, A. et al. (1996). Internal transcribed spacer sequences from 38 recognized species of Suillus sensu lato: Phylogenetic and taxonomic implications. Mycologia 88: 776-785.

Peattie, D. C. (1948/1991). A natural history of trees of eastern and central North America. Boston: Houghton Mifflin. 606 pp.

Romagnesi, H. (1942). Quelques points de taxonomie. Bull. Soc. Mycol. France 58: 81-89.

Singer, R. (1986). The Agaricales in modern taxonomy. Germany: Koeltz Scientific Books. 981 pp.

Smith, A. H. (1949). Mushrooms in their natural habitat. New York: Hafner Press. 626 pp.

Volk, T. J. & Burdsall, H. H. (n.d.) The state of taxonomy of the genus Armillaria. Retrieved March 26, 2007 from the Tom Volk’s Fungi Web site: http://botit.botany.wisc.edu/toms_fungi/arm.html

Cite this page as:

Kuo, M. (2007, March). Mushrooming in the age of DNA: Now comes the fun part. Retrieved from the MushroomExpert.Com Web site: http://www.mushroomexpert.com/kuo_08.html