The North American Mycoflora Project ~ without a sequenced specimen it is a rumor ~
Else C. Vellinga, Department of Plant and Microbial Biology/UC Herbarium
University of California, Berkeley, CA 94720
email: ecvellinga [at] comcast.net
The idea of a North American Mycoflora project came up in several articles and presentations in the last few years (Matheny & Vellinga 2009, Bruns 2011, Bruns & Beug 2011), and a meeting of amateur and professional mycologists was held mid July 2012 in New Haven (CT) about this subject.
In short, a mycoflora would provide keys and descriptions for all macrofungi in North America.
The current article is based on a talk given at the NAMA foray in Scotts Valley, California, on 14 December 2012.
The outline is as follows:
- the goals of the NAmFlora project
- what needs to be done to reach the goals
- which great tools we have
- how we can contribute.
The goals we envision for a North American Mycoflora are the following:
- A modern flora with keys, descriptions, and lots of photos based on dried collections that are accompanied by photos, notes of the fresh specimens, data on habitat, location and date, and with DNA sequence data
- Available on the web, portable, free, and easy to update. Besides being a tool to identify mushrooms (obviously), this will also provide insight in distributions, habitat, rarity, and with that base line data for conservation purposes; furthermore, it will produce a great sequence database for ecological studies.
Europe is blessed with several series of floras and monographs; some examples are the series Fungi of Switzerland edited by Breitenbach & Kränzlin; Funga Nordica now in its second edition edited by Knudsen & Vesterholt, the Dutch Flora Agaricina Neerlandica, and the Italian series Fungi Europaei. There is nothing comparable in the U.S. or Canada. Contributors to the European books mentioned above come from the professional mycological world, but each series also has contributing amateur mycologists (e.g. Parra – the author of the Agaricus volume in the Fungi Europaei series is a veterinarian, Breitenbach was a shop owner, and Kees Uljé who did the Coprinus part for FAN trained and practiced as a street paver). This involvement of amateur mycologists is also clear when we look at new species – in Europe in the last 10 years the number of species described by non-professional mycologists is greater than the number of species described by people who have mycology as their profession.
I know first hand how challenging a flora project is. I have been one of the editors of the Dutch flora for boletes and gilled mushrooms, Flora Agaricina Neerlandica, since its early years. This project was started in the 1980s, with the idea that in four years time, 1983–1987, all mushrooms would have been done – provided with descriptions based on the collections available in the herbarium (all with notes), original line drawings of the microscopic characters and critical notes. So far, six volumes have been published, but many groups still remain to be worked on. We were and are still a small group of collaborators on this project, but we do have the advantage that there are well-annotated voucher specimens in the central herbarium, that there is an actively participating mycological society, and that the mycoflora in general is well known and well researched.
The scope of a similar North American project is five to ten times that for the Netherlands in numbers of species, with much less ground work done, especially in terms of annotated collections, with big swatches of the area severely under-inventoried and under-collected, a small number of active fungal taxonomists, and probably many new species to be discovered. Nevertheless, it can be and should be done.
Some reasons for making a mycoflora for North America
The existing “Flora of North America” which also included parts on fungi, was written almost a century ago, and it does not cover all genera. An example is provided by Overholts’ Pholiota treatment (1924), which covers species now considered in other genera, such as Conocybe and Pholiotina. There are no figures or pictures of the species in this work, at all.
Taxonomy went on after that, and many systematic works have been published, but few of these contain color photos, and only the very latest publications include molecular data. The existing literature is scattered, and not freely accessible, and for many mushroom groups there is only European literature.
Chanterelles were called by the name of the European species C. cibarius, which we now know not to occur in North America. A quick look at the Cantharellus literature shows that in the last 15 years seven articles in which new species and varieties are described were published in four different journals. Only the oldest paper uses solely morphological data, in all other cases molecular data are used as well. To identify a western species four different articles have to be consulted, as the latest paper does not contain a key to all western species (Arora & Dunham 2008).
Despite the many articles, there are still undescribed big charismatic chanterelle species in the U.S.
This brings us to another set of reasons to work on a North American mycoflora, namely that European names are used for North American species, though we slowly come to realize that the species in North America are in many cases different from the ones in Europe with the same names (there are also a few American species names used in Europe, such as Russula pectinatoides).
There is no checklist for North American species, so we don’t know how many species there are, nor what their distribution and relative abundance might be. A paper from 2007 based on lists compiled from the literature came up with an estimate of 10,000 species, of which 65% would be unique to North America, and 35% shared with other parts of the world (Mueller et al. 2007). From the collection data entered at Mycoportal (see below), a checklist of 6,977 species could be distilled. However, how realistic are these numbers?
For Russula we know that as of 2005, 329 species were described from the U.S., with 87 additional European names in use; a total of 416 taxa. Bart Buyck, the world expert on Russula (pers. com.) estimates that there are at least 1000 species of Russula, possibly 2,000 species, in North America.
The 27 lepiotoid species described from California cover a long period, with a recent upsurge in numbers. However, at least as many western species are still waiting description. And the situation for the east of the USA for this particular mushroom group is probably not that different. In other words for Lepiotas a doubling of the number of species can be expected. And this is possibly true for many groups for which no modern (regional or national) monograph exists.
This would mean an estimate of 20,000 species of macrofungi for North America!
What do we need to do to make a mycoflora?
It is clear that a lot needs to be done, before we can even start working on a flora.
-Much more sampling and vouchering of all groups and in all parts of the country has to be done. At the moment it is clear that many people photograph mushrooms, but that they do not keep specimens for further study. People have to be trained, and instructed, as the data and collections have to be useful for the work on hand, and data have to be detailed.
-All those collections have to be sequenced and these data have to be analyzed. Existing herbarium records, collections and the literature need to be assembled and scrutinized.
-From all those data, monographs have to be created.
-It would be good to set some short-term goals – start with some small genera for which many data are already available, and come up with a strategy for the long term.
-And last, but actually the first requisite for most of the work that has to be done, is finding funding.
Money is a huge bottleneck. Costs for a sequence per collection have gone down considerably, and the work has got much easier over the last 15 years, but still, the chemicals involved are expensive, and labor costs have to be taken into account as well. Herbarium space comes with a price tag. The actual work of the systematists involved is not even considered when we start making calculations about cost.
New species and type collection studies
It is apparent from the Russula example that there is a huge backlog of new species to be described. The few mycologists that are doing systematic work in North America cannot do this. Funding for such work has been extremely difficult to get, though work in the tropics has been funded regularly. The numbers of new species described for the U.S. and Canada over the last five years shows an increase over that period, but these numbers are still extremely low as is shown in the following table:
|2009||1 gilled mushroom species and 2 boletes, 1 polypore, and 2 truffles||6 TOTAL||6 publications|
|2010||20 species of gilled mushroom and boletes, 2 polypores, and 4 truffles||26 TOTAL||14 publications|
|2011||15 gilled mushrooms, 4 chanterelles, 1 polypore, 2 earth stars, 1 truffle||23 TOTAL||13 publications|
|2012||11 gilled mushrooms, 4 polypores, 14 + 9 morels, 2 sequestrate species||40 TOTAL||11 publications|
|2013*||28 gilled species, 3 chanterelles, 1 hydnoid, 3 truffles||35 TOTAL|
*up to 1 October 2013
Another way to look at the numbers of species that are described is to look at one genus, and compare the number of new species described from the USA with those described in Europe. The genus Russula has a strong history of research in Europe, and that shows in the numbers. Since 2000, 43 new Russula species were described for Europe; in contrast, only 10 were described from the USA in that same period (five by Raymond Fatto, and the other five by Buyck et al.). From Bart Buyck’s assessment of the total number of species in the USA and Canada, we can conclude that there are many more new species than these numbers suggest.
At this pace, a snail’s pace, it will take 780 years to describe the minimum number of 600 new Russula species that are out there….. Even if all our efforts are focused on Russula, and 10 new species are described per year, it will take at least 60 years to get them all done. I will not live to see that day.
BUT, if all of us, NAMA members, active mycologists, and serious mushroom lovers, describe one species each year, the job is done in less than 10 years! This implies that many people need to be recruited and trained.
We have to realize that deciding that a species is new for science, and that it has to be named, can be a long and arduous process that involves first of all a thorough revision of the literature, comparison of the material in hand of the supposedly new species with that of those that have been described already, based on morphological and preferably molecular characters. All the evidence has to be weighed and the decision made, culminating in a publication.
Part of this process is the study of type collections – the pivotal collection indicated by the author of a new species that have been preserved for this purpose: that other researchers themselves can check the characters of the newly described species.
There is a huge need to re-examine the species that have been described in the past. Many names have not been in use since the species were described, and for many of the older species microscopical data are lacking. The ideal would be to have both morphological and molecular data, but for the older specimens, described for instance by Peck over a century ago, this will not always be possible, as DNA degrades over time.
It is also very important that those data are interpreted and put in the context of present day knowledge and classifications. Fortunately there are many examples of this work. For Russula, Buyck & Adam?ik have started a series of type studies, as for a third of the species (around 100 species) microscopical data are not available (one example is the article by Adam?ik & Buyck 2011). For the western lepiotaceous fungi, some old names given by Murrill a century ago, have been resurrected, such as L. castanescens Murrill and L. fuliginescens Murrill (Vellinga & Sundberg 2008; Vellinga 2010); we were also fortunate to find a name in the literature (viz. Lepiota maculans Peck) for a very characteristic pink-spored and pink staining Lepiota, found in the Great Smoky Mountains National Park (Birkebak et al. 2011). Publication of type studies, or having that information on a nomenclature web site such as Mycobank or Index Fungorum should be mandatory.
Voucher specimens and sequence data
Many mushroom clubs keep lists for their forays and fairs, and these are great for internal use, but if we want to talk across the continent and be sure we are talking about the same species, not just the same name, we need to have specimens to get back to. Amanita muscaria in the southeast is definitely not the same species as the ones in Alaska, and we know that for a fact, because dried collections (voucher specimens) have been extensively studied and compared with each other (Geml et al. 2008). The western North American Helvella lacunosa, a very common species, was shown to be in fact a complex of at least three species, each with its own ecology, all different from the European Helvella lacunosa which also turned out to be a tangled web of several species (Nguyen et al. 2013). The only way to be sure about the specimens’ real identity is by examining these dried specimens, and getting data, microscopical, macroscopical, and molecular data, and carefully compare them with those from specimens from a wide area. Other common species that are in fact a group of several species are Pluteus cervinus, and Laccaria laccata. It is even doubtful whether the latter occurs in North America! And I can go on and on giving you example after example. If we had not started sequencing these common and so-called widespread species, we would have been kept in the dark, and underestimated species diversity and richness.
Again collections are key to the study of these species, and sequence data a must.
Brandon Matheny and his students at the University of Tennessee at Knoxville have produced sequence data for 66 type specimens, the oldest one collected 75 years ago. These data are deposited in GenBank. One of the findings is that some species described by Hesler & Smith in the genus Pholiota have identical ITS sequences. This work also gets rid of some superfluous names! By sequencing the type of a Pholiota species from Mount Shasta in northern California, we can link modern collections of a common spring fungus to a name that had not been used since its creation, 45 years ago!
The tools at hand
Fortunately we live in a time that there are many tools available, notably on the web, to help with the many tasks ahead. Which tools do we have?
The NAMA voucher program
NAMA has around 1,200 individual members (the affiliated clubs have a total of 10,000 members), and a great voucher program, in which the collections of the annual national forays are dried and preserved in the herbarium of the Field Museum in Chicago. Since 1997 vouchers have been kept, whereas before that time, lists were made. The numbers of new species observed never leveled off, and the total stands now over 4,000 (lichens and slime molds are not included in this count). That number is probably on the low side, as we now know that some names represent more than one species, such as the often collected Pluteus cervinus and Laccaria laccata.
Another great citizen scientists project is Mushroom Observer (MO), where one can post observations of mushrooms, and can comment and help others with their identifications. Over 4,000 people from all over the world contribute to this website, with more than 135,000 observations of 10,460 taxa (as of 1 October 2013). You can manage your data there as well, make lists of certain fungi or an area, and add as many details and photos as you like!
But, to put the numbers of MO contributors in perspective, birds enjoy a much bigger crowd; 16 times as many people participated in the 2011 Christmas bird count, though the total number of bird species observed in the USA is only 914, less than a tenth of the total number of taxa in MO. In other words there are many more mushroom species to observe for an average person than birds. And remember, those Christmas bird counts – they are rumors, just flying rumors, without vouchers and definitely without a sequence!
Mycoportal is the central database where over 35 institutions keep the records of their fungal collections, as part of the MaCC project (Macrofungi Collections Consortium) – almost 1.5 millions data are already there, and the numbers keep growing everyday! The database is easy to search, and provides links to images, GenBank entries and much more. See also the contribution by Thiers et al. in this issue of McIlvainea.
Online sources for nomenclature and literature
I’ll just list here some of the resources that are now available on line, for everybody to use.
First the two main nomenclature databases:
– Index Fungorum (www.indexfungorum.org), one of the three depositories for new species descriptions
– MycoBank (www.mycobank.org), also one of the three depositories for new species descriptions.
These two nomenclature databases give much more information than only the bare facts of when where and by whom taxa were described; links to the original literature are provided on Indexfungorum, and MycoBank often gives modern descriptions and illustrations.
Some literature websites:
– Cyber Liber (www.cybertruffle.org.uk/cyberliber/index.htm) for e.g. the first 106 Mycotaxon volumes, Grevillea, and Saccardo’s Sylloge Fungorum (the latter under ‘Catalogues’), and many other publications
– Botanicus Digital Library (http://www.botanicus.org) which offers a scanned version of the North American Flora, and many other old publications; this is part of the Biodiversity Heritage Library project www.biodiversitylibrary.org, and linked to by www.archive.org/. Here you can find the original description of Amanita muscaria published in 1753!
– the French national library’s website (http://gallica.bnf.fr) for books by Fries and other 19th century authors (especially the French ones)
– the Digital Library of the Royal Botanic Garden in Madrid (http://bibdigital.rjb.csic.es/ing/) for many old periodicals
– Google Books is also a good place to start, but books can still be under copyright, and not freely accessible
– The Fungi of California website, Mykoweb.com, has sections devoted to literature, and hosts pdfs of many important works.
Many journals are online, and though the full text is often not freely accessible, the abstracts are. Older issues are often free. Mycologia (www.mycologia.org) is particularly important for North American mycology, with the older issues at www.jstor.org.
Search engines are great these days, and will help you find what you are looking for (and otherwise there might be a helpful soul at a university close to you…)
Genbank (www.ncbi.nlm.nih.gov/genbank/) is THE place for sequence data, freely accessible for everyone, and it also offers various tools. One that is most useful is called BLAST, which lets you compare sequences. You put yours in, and the program comes up with a list of close to less close hits. This gives you an idea about the identity of your sequence, with the caveat that there is no quality control on identification, so look critically at the outcome.
On line keys
There are two compelling reasons to have the ultimate product, the flora, on line. One is that it will be easy to update.
The Funga Nordica’s first edition was sold out, and out of date in a few years, so in 2012 a second edition, with much more information was printed. Now we have two big sets of books on the shelves, instead of one.
A second reason is that on line keys can be much more user friendly than the traditional printed dichotomous keys. Photos of the important characters help the user decide which character state to choose, you can often use all the characters you see, and leave out the ones that you don’t know about, and you can start with whatever character you have. A great example is this key, made by Andy Miller for a select number of Xylariaceae: www.discoverlife.org/mp/20q?guide=Xylariaceae.
Other more traditional keys on line can be found at www.Mushroomexpert.com and the keys of the Pacific Northwest Key Council (www.svims.ca/council/).
Suggestions for involvement and contributions
I want to end with some suggestions of projects everybody can do, to get the project going:
- Focus on one genus, collect & keep vouchers, annotate, photograph, publish! An example is given by the Western Pennsylvania Mushroom Club, which focuses on Amanita species and has set up a protocol to work with. More information on how to collect and keep vouchers is in the article by Thiers et al. in this issue of McIlvainea.
- Inventory a park, collect & keep vouchers, publish the results (e.g. in NAMA’s newsletter The Mycophile!)
- As a club, keep vouchers of the specimens collected during forays, or for a fair; team up with a local university or museum for space. Several Canadian mushroom societies do this already; specimens are vouchered and sequenced!
- Research the old literature for species described in your area and revisit those places. Try to find the species described a century ago!
- Participate in the MaCC project by interpretation of written labels and notebooks, find a herbarium close to you that participates (see mycoportal.org for an overview)
- Tell your friends and neighbors about mushrooms and the mycoflora project, as name recognition and public relations are badly needed. A great way to do so is by having mushrooms on hand, or out of season to have one of those beautiful mushroom books on your coffee table. Wear your mushroom t-shirts with pride and be ready to talk mushrooms any moment!
The only way to get this project off the ground is by participation of many, financial contributions from some big donors, and the will to start.
You can’t leave footprints in the sands of time if you’re sitting on your butt.
And who wants to leave butt prints in the sands of time?
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- Birkebak J, Vellinga EC, Franco-Molano AE, Wood MG, Matheny PB. 2011. Lepiota maculans, an unusual mushroom rediscovered after 105 years. Southeastern Naturalist 10: 267–274.
- Breitenbach J, Kränzlin F. 1984–2000. Fungi of Switzerland 1–5 Kränzlin F. 2005. Fungi of Switzerland 6.
- Bruns TD. 2011. President’s corner. Working toward a North American mycobiota for macrofungi – what’s stopping us? Inoculum 62 (4): 1–3.
- Bruns TD, Beug MW 2012. Working toward a North American Mycoflora for Macrofungi. McIlvainea 21.
- Buyck B, Adam?ik S. 2011. Type studies of Russula species described by W.A. Murrill 1. R. roseiisabellina, R. sericella and R. obscuriformis. Mycotaxon 115: 131–144.
- Geml J, Tulloss RE, Laursen GA, Sazanova NA, Taylor DL. 2008. Evidence for strong inter- and intracontinental phylogeographic structure in Amanita muscaria, a wind-dispersed ectomycorrhizal basidiomycete. Molecular Phylogenetics and Evolution 48: 694–701.
- Knudsen H, Vesterholt J (eds). 2008. Funga Nordica. Nordsvamp, Copenhagen. 965 pp.
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- Matheny PB, Vellinga EC. 2009. A North American flora for mushroom-forming fungi. Inoculum 60 (5): 28–29.
- Mueller GM, Schmit JP, Leacock PR, Buyck B, Cifuentes J, Desjardin DE, Halling RE, Hjortstam K, Iturriaga T, Larsson K-H, Lodge DJ, May TW, Minter D, Rajchenberg M, Redhead SA, Ryvarden L, Trappe JM, Watling R, Wu Q. 2007. Global diversity and distribution of macrofungi. Biodiversity and Conservation 16: 37–48. DOI 10.1007/s10531-006-9108-8
- Nguyen NH, Landeros F, Garibay-Orijel R, Hansen K, Vellinga EC. 2013. The Helvella lacunosa species complex in western North America: cryptic species, misapplied names and parasites. Mycologia 105: 1275–1286. DOI: 10.3852/12-391
- Thiers BM, Wilson N, Halling RE. 2013. Making scientific vouchers of North American macrofungi: how documenting the fungi you encounter contributes to the Mycoflora of North America. McIlvainea 22.
- Vellinga EC. 2010. Lepiotaceous fungi in California, U.S.A. Leucoagaricus sect. Piloselli. Mycotaxon 112: 393–444.
- Vellinga EC, Sundberg WJ. 2008. Lepiotaceous fungi in California, U.S.A. 6. Lepiota castanescens. Mycotaxon 103: 97–108.
Citation: Vellinga, EC (2013) The North American Mycoflora Project: without a sequenced specimen it is a rumor. McIlvainea 22 (2-10): V22/north_american_mycoflora.html
Editor: Michael W. Beug
Publisher: North American Mycological Association
Published: October 12, 2013
Copyright: © 2013 Else C. Vellinga.