Courtesy M. G. Wood. MYCOLEGIUM: Making Sense New genera: of a ll t he Ne w horn of plenty or deluge? Mushroom Names Else C. Vellinga and Thomas W. Kuyper [email protected]

n 2014 and the first Text box #1 – Some definitions six months of 2015 – a monophyletic group consisting of a common ancestor and all its descendants. alone, more than 20 (plural: genera) – a monophyletic group of that have (preferably) new genera were morphological characters in common. I monophyletic – a genus is called monophyletic when all its members share a proposed. Contrary to what most recent common ancestor that is not shared by species outside that many people would expect, these genera genus (the red and blue blocks in Fig. 1 represent monophyletic groups). are not restricted to some faraway exotic A single species is monophyletic by definition. locale where the have novel paraphyletic – a genus is called paraphyletic, when only by including members character combinations, no, these new of another genus or other genera, all its members share a common ancestor genus names are for familiar species that (the green block in Fig. 1 represents a paraphyletic genus). occur in North America and Europe and polyphyletic – a genus is called polyphyletic as a more advanced case of that we have been calling by the name and the members of the genus are scattered over widely different “” for a long time. (example: with M. androsaceus falling inside , This creation of new genera is not and M. minutus outside the family ). restricted to the boletes. The numbers sister group – the closest relative of a clade or species in a phylogenetic tree for the gilled mushroom species are (the red block in Fig. 1 is a sister group to the blue-green clade). comparable: we counted around 24 new genera published in that same time (plural: taxa) – any taxonomic unit from forma to . period, most of them white-spored, species of a genus – the species that is the name-bearing type of a genus with six new genera for species we used (example: comatus is the type species of the genus Coprinus; when to call , five new genera in the Coprinus was split up, the name Coprinus stayed with C. comatus, and the , and three new ones in the other parts of the genus, got new names). The type species is not Psathyrella family. However, there were necessarily the most typical for the genus. only two new brown-spored genera. And the largest genus by far, Cortinarius, was not affected. Most of these genera are for existing species, only a few, such as Cercopemyces crocodilinus from the Rocky Mountains (Baroni et al., 2014; and see the spring 2015 issue of FUNGI), are for newly discovered species. Here we will try to explain what triggered this flood of new genera. We’ll also have a critical look at what is necessary to make good, solid, acceptable genera. On that basis we can also look Figure 1. An example of a phylogenetic tree with the terminal branches each critically whether these new genera are, representing an individual species. The blue and the red parts of the tree at least for the time being, warranted. represent monophyletic groups. The green part is not monophyletic, but We give references to the original paraphyletic, as the green and the blue together are monophyletic. The red articles in which the research we cover clade is sister to the green/blue clade. (from Wikimedia) here is described; many of those are freely accessible, so you can see for Some historical background with the underlying principle that what yourself how this type of science is done. Up to the mid 1990s mushroom we recognized represented a natural Definitions of some of the terms we use genera were recognized and described system and that system was the result throughout this article are in Text box #1. based on morphological characters, of evolution. These classifications were FUNGI Volume 8:4 Winter 2015 35 of course subjective and prone to a lot characters that could be used to gauge your family tree one could conclude of debate. Different traditions reigned the value of certain characters for that your cousin is your closest on the different continents: in genus definitions. What to do with relative, though in reality it is your Europe included and , those characters that were incongruent brother. So trees that are based whereas in the USA these were three was a big problem. Was it more exclusively on taxa of a certain area different genera, and in important that all species in a genus had (e.g., the northern hemisphere), North America included the colorful amyloid than that they all were while the group itself has a much species that were in their own ectomycorrhizal or had an annulus? broader geographical distribution, genus in Europe. Those were unanswerable questions, as in the case of some bolete trees, Name changes happened, also in the though, of course; taxonomists would are suspect. past. An example is the turkey tail, now argue about these issues, but nobody 2. Is your tree a gene tree, based on known as versicolor, which has could claim victory. one piece of DNA only, or is it resided in 12 different genera since its Molecular changes based on a critical examination of a initial naming in 1753 (Linnaeus, 1753). fungal systematics number of different genes? And if it Alexander Smith was upset by the is based on one piece of DNA only, With the advance of molecular flood of new genera created by Singer is that a piece that is known to be methods to make many copies of pieces who worked in the neotropics where the very variable and very helpful at the of DNA that could then be analyzed did not fit the descriptions species level but not so much for and sequenced, and the development of of the temperate genera. Smith (1968) genus recognition? The nrITS region larger and faster computers that could thought that “When we have made a (a spacer region that sits in between deal with larger and more complicated critical study from an adequate sample genes that do not show much data sets, mushroom systematics of a population, such as that of North variation among species) is very changed dramatically. America for the gill fungi, I believe that good at discriminating mushroom These methods made it possible to the generic concepts will be found to be species (not all, but many; it is compare genetic markers (for instance rather self-evident.” therefore used as the so-called bar pieces of spacer regions in between Mushroom fruitbodies do not have code region. But while it is very genes, and genes that code for the a wealth of morphological characters, good at species, that means there is household chores in the cells, but not so they did not lend themselves very a lot of variation among species, and those that make the pigments) and we well to phylogenetic studies based on it is much harder to use for species could formulate hypotheses for the morphology as developed by Hennig groups that are not so closely evolution of these pieces of DNA. These (1950; 1965). There were simply no related. The nrITS region is not hypotheses are in general presented recommended as the sole marker as a phylogenetic tree, in which each for genus recognition. Unfortunately terminal branch is a sample or a (or should we say of course) some collection. The more different pieces of mycologists still do base genera on DNA that are used to make these trees, trees derived from ITS data alone. the more species and specimens are A further advantage of making trees included, and the higher the statistical based on a number of (say 5–8) support for the branches on the tree is, genes, is that it allows evaluation of the better this hypothesis will represent alternative classifications in case the the true path of evolution. The tree various genes provide contradictory might become a species tree instead of information. If statistical support for a gene tree. These trees are similar to the final tree is low, an attempt can the family trees one can build for their be made to analyze the causes for ancestors, though here the terminal that lack of congruence. branches represent an individual person. These phylogenetic trees are used to The first revolutionary results determine what good species are, and Coprinus, the inky cap genus, was one also for the circumscription of genera. of the first genera to be analyzed with Figure 2. A phylogenetic tree with 5 As indicated above, one needs to look these new methods, and to everybody’s terminal monophyletic taxa. This tree carefully at the tree, and be aware of a surprise this genus turned out to be represents many different monophyletic few things: polyphyletic, with Coprinus comatus genera: a; a and b together; a, b and c 1. Which taxa are included in the tree? and its close allies closely related to together; a, b, c, and d together, and all One can only draw conclusions Lepiota, and the rest of the genus not five together. A paraphyletic genus is about the taxa that are included in monophyletic, but clearly separating formed by the d-e combination, or by the study, not about those that are into three groups (Hopple and Vilgalys, c, d and e; the combination of a and e not there – it is like making a family 1999). These results were based on the in one genus can be called polyphyletic. tree without your twin brother who analyses of one gene region only, and If a and b together are recognized as fled home at the age of 14 and has also the three new genera Parasola, a genus, c, d, and e should each be never been heard of again; from Coprinopsis, and Coprinellus ended up considered a genus as well. 36 FUNGI Volume 8:4 Winter 2015 make them stand out, and nobody had sister to Lacrymaria, but does not share Text box #2 – Bolete genera expected this (see also Redhead, 2001). the ornamented spores with that genus, described or names put to The new genus Parasola (for Coprinus quite to the contrary it has pale smooth use since 2000 relevant for plicatilis etc.) is morphologically well spores with a hardly visible germ pore, defined, but Psathyrella conopilus has to and cystidia with crystals on the top; North America be placed into it (Larsson and Örstadius, now it is placed in the genus Homophron Alessioporus – Gelardi et al., 2014 2008). The other two are much vaguer (Örstadius et al., 2015). Baorangia – Wu et al., 2015 and more diverse in their characters The second big discovery from these (Redhead et al., 2001). It took until this early studies was that many gasteroid Borofutus – Hosen et al., 2013 year, 2015, before three new genera were and secotioid species really are closely Bothia – Halling et al., 2007 split off from Psathyrella (Örstadius related to and recently derived from – Arora and Frank, 2014 et al., 2015) to make that genus gilled or pored mushrooms. This had – Vizzini, 2014a monophyletic. Psathyrella spadicea is a been a bone of contention among Corneroboletus – Zeng et al., 2012 Crocinoboletus – Zeng et al., 2014 Cyanoboletus – Vizzini, 2014e – Vizzini, 2014f Harrya – Halling et al., 2012a Hortiboletus – Vizzini, 2015 Hourangia – Zhu et al., 2015 Imleria – Vizzini, 2014b Imperator – Assyov et al., 2015 Lanmaoa – Wu et al., 2015 Neoboletus – Vizzini, 2014h Parvixerocomus – Wu et al., 2015 Pseudoaustroboletus – Li et al., 2014b Pseudoboletus – Šutara, 1991 Pulchroboletus – Gelardi et al., 2014 Retiboletus – Binder and Bresinsky, 2002 Rheubarbariboletus – Vizzini, 2015 Rubroboletus – Zhao et al., 2014 Rugiboletus – Wu et al., 2015 Suillellus – Murrill 1909; Vizzini, 2014g – Halling et al., 2012b Veloporphyrellus – Li et al., 2014a – Šutara, 2008 – Li et al., 2011

inside the genus Psathyrella making that genus paraphyletic [in other words this early study would not pass our bar!] (Padamsee et al., 2008). The Coprinus study really represented a landmark: it caused a storm of protest, and it took a long time to get used to these revolutionary results and ideas. Nowadays these placements and genera are all mainstream and accepted, but it took a while! Coprinus comatus has characters in common with Lepiota, but the spores with their almost black walls and the germ pore in the really

FUNGI Volume 8:4 Winter 2015 37 (in evolutionary times) secotioid and gasteroid taxa can evolve. Text box #3 – Gilled mushroom genera described 2014–2015, family they belong to, evidence provided, and the reference Interpretation of phylogenetic trees The genera of boletes and of gilled Albomagister – s.str. – multigene – Sánchez-Garcia et al., 2014 mushrooms that were described in the Atractosporocybe – position not clear yet – multigene – Alvarado et al., 2015 last year or so are listed in text boxes #2 Bonomyces – for Clitocybe sinopica – no supporting evidence – Vizzini, 2014c and #3; there are many more new genera Calocybella – Lyophyllaceae – LSU and ITS – Vizzini et al., 2015 in the gilled mushrooms proposed Cercopemyces – close to and – multigene – this century – many more than we can Baroni et al., 2014 analyze here in depth. There is hardly any Ciboamyces – – LSU and ITS – Hao et al., 2014 group where there have not been new Clitocella – – multigene – Kluting et al., 2014 genera or new arrangements. But here, Corneriella – Tricholomataceae s.str. – multigene – Sánchez-Garcia et al., 2014 we’d like to focus on a few groups and Crassisporium – – multigene – Matheny et al., 2015 show the approaches of different authors. Cryptomarasmius – Physalacriaceae – LSU and ITS – Jenkinson et al., 2014 First up are the Entolomataceae and Homophron – – multigene – Örstadius et al., 2015 , followed by Trametes, and lastly Hygrophorocybe – for Clitocybe nivea – no supporting evidence – Vizzini, 2014d we’ll stop by the Tricholomataceae. Kauffmania – Psathyrellaceae – multigene [name will probably to change] – Entolomataceae Örstadius et al., 2015 Pink spores that are box-shaped, have – position not clear yet – multigene – Alvarado et al., 2015 angles, bumps or ridges – those char- Myochromella – Lyophyllaceae – multigene – Hofstetter et al., 2014 acterize the Entolomataceae. There are Pogonoloma – for spinulosum, position not clear yet – multigene – two main groups: species with spores Sánchez-Garcia et al., 2014 with bumps or longitudinal ridges, Pseudolaccaria – position not clear yet – LSU and ITS – Lavorato et al., 2015 and the species with more box-shaped Pseudotricholoma – Tricholomataceae s.str. – multigene – Sánchez-Garcia et al., 2014 angular spores. Rhizocybe – position not clear yet – multigene – Alvarado et al., 2015 There are two main issues to resolve Romagnesiella – Strophariaceae – multigene – Matheny et al., 2015 in this family, having to do with the two Sagaranella – Lyophyllaceae – multigene – Hofstetter et al., 2014 different spore types that are present. We start with the bumpy and ridged spores. Sphagnurus (=Bryophyllum Vizzini) – Lyophyllaceae – no evidence provided – Traditionally the species with the Redhead, 2014b ridged spores (shaped like American Tephrocybella – Lyophyllaceae – ITS – Vizzini in Crous et al., 2015 footballs but a polygon in transverse Typhrasa – Psathyrellaceae – multigene – Örstadius et al., 2015 view), are in the genus (the miller, sweetbread, is a good example), and the ones with the bumpy spores in . Unfortunately these two groups that are so easy to recognize morphologically under the microscope, do not each form a monophyletic group; Clitopilus is monophyletic in phylogenies based on a set of quite different pieces of DNA, but Clitopilus is surrounded by Rhodocybe members (Fig. 3). For such a situation there are two solutions: either lump all together into one genus (in this case it would be called Clitopilus), or recognize the five different clades as Figure 3. Schematic phylogenetic tree of Clitopilus and Rhodocybe, based on Co- separate genera (Clitopilus, Rhodocybe, David et al. (2009). Clitopilus is monophyletic, Rhodocybe is paraphyletic. , Clitopilopsis, and the newly named Clitocella). Both solutions mycologists, who held strong opinions (Moncalvo et al. 2000 and 2002), have been proposed (Co-David et al., in which direction evolution had Gastroboletus species have to be divided 2009 for the Clitopilus option; Kluting et gone (were the puffballs and truffles over several bolete genera (Nuhn et al., al., 2014 for the five-genus option). We primitive or advanced?). So, indeed, 2014), and Gastrosuillus laricinus is should also keep in mind that this group Nivatogastrium nubigenum is a just a morphological variant of is relatively species poor in comparison species (Redhead, 2014; Siegel et grevillei (Baura et al., 1992; Kretzer to the other, much bigger clade in the al., 2015), Lycoperdon, Bovista, and and Bruns, 1997). These are just a few family, Entoloma s.l. Calvatia are gasteroid examples that suggest how quickly Entoloma itself is the other component 38 FUNGI Volume 8:4 Winter 2015 of the Entolomataceae; recognized as one huge genus in Europe by various Text box #4 – Criteria for solid work and genus recognition: authors (e.g., Noordeloos, 1992), but split up into smaller units (Nolanea, 1. All genera that are recognized have to be monophyletic, not only the Leptonia, Pouzaromyces, Entoloma etc.) one that is the focus of the study, but also the group it is leaving and here in North America (e.g., Largent, the group it ends up in. (A good example: when Macrolepiota was split 1994; Baroni et al., 2011). Again, the into core Macrolepiota with M. procera as its type, and a second group molecular-phylogenetic approach containing M. rachodes, the latter was moved to that in has shown that the smaller genera as itself was only monophyletic by including Endoptychum agaricoides; proposed by the American authors are bad example: by splitting Coprinus up into 4 genera, 3 of them ended not all monophyletic; the conclusion drawn by the European authors is that within Psathyrella, making that genus paraphyletic). Entoloma is best considered one big 2. The phylogenetic tree has to be based on more than one gene. genus (Co-David et al., 2009). Here in North America the conclusion was 3. The coverage of the phylogenetic tree has to be wide, in terms of that there should be more genera, so species, and geographic distribution of the taxa, and should include was proposed for the basal type species of genera that are being included. group of Entoloma which has spores that are bumpy, but which are not 4. The branching of the phylogenetic trees has to be sufficient statistically as boxy as those in Entoloma proper, supported (a measure of how realistic the pattern is). Weak support neither as irregularly bumpy as in Rhodocybe (Baroni et al., 2011). (or even absence of statistical support) indicates that alternative The comparison of both sister groups classifications cannot be rejected. And so the advice is: “in dubiis abstine,” raises a further question: should we when in doubt refrain from proposing new genera. treat them in comparable ways? That is, if we split Clitopilus into five genera, 5. Phylogenetic methods often allow more than one formal classification does that force us to split Entoloma; with monophyletic groups. Therefore, the list of options should be or alternatively, if we decide not to discussed, and arguments for the final decision given. (A good example: split Entoloma, does that force us to the Trametes example). recognize a broadly circumscribed Clitopilus? Or can both decisions with regard to generic delimitation be considered separately? resulting in small genera; some of several groups of scientists. There is a these (new) genera are monophyletic, well-resolved phylogeny of the group Xerula and its relatives: what to do but Hymenopellis, the genus in which based on five different gene regions, on when morphology and molecules X. megalospora and X. furfuracea are which everybody agrees, but how the clearly tell different stories placed, is paraphyletic (Petersen & data are interpreted depends on the We have an interesting problem here Hughes, 2010). Other authors maintain people. Justo and co-author (Justo and that resembles the situation around fewer and larger, monophyletic genera Hibbett, 2011; Justo, 2014) opted for a Rhodocybe and Psathyrella: a group of that represent the ITS/LSU phylogenies large genus Trametes, whereas Welti et mushrooms that has in common very (e.g., Hao et al., 2012; Qin et al., 2014a). al. (2012) proposed the option of small distinct morphological characters, but is in that case the genera and then, of course, also had to does not form a monophyletic group in name to use for X. megalospora and X. make a new genus. Justo (2014) gives phylogenetic trees based on two gene furfuracea. Here, it might be useful to good insight into the process of reaching regions (ITS and LSU). We are talking make phylogenies based on a wider range his conclusion of one genus as the about and her look- of genes to solve these problems in a ultimate and best solution! There is one alikes. They definitely do not belong in more satisfactory way. silver lining to this cloud of difference: Xerula as those species with the long We like to maintain that genera the two groups agreed on the position setae on the cap and form their should pass the criterion of betulina: that species should own monophyletic group, well away (see also text box #4 for more criteria be named . The from these species with the glutinous cap for solid work), and applaud the use of downside of the one-genus option is cuticles. But the beautiful porcelain-like Oudemansiella for these species. Tests that the orange-red species that are so Oudemansiella mucida from Europe, to evaluate the different scenarios of easily recognized as , are now and the tropical species O. canarii fall in more or less inclusive genera can also within Trametes. the middle of the X. megalospora group. be done, but in the mycological practice These examples show that how the Again, it is a matter of taste and choice of the last years these are unfortunately data are interpreted and where to draw how to solve such a problem. One group hardly executed. genus borders is still very much subject of researchers uses first morphological Turkey tails: a different approach? to taste and human insight. That has characters, and then the delimitations not changed with the arrival of these Trametes, turkey tails and their as presented in the phylogenetic trees, new techniques and methods; these relatives have also been studied by FUNGI Volume 8:4 Winter 2015 39 provide strict criteria for recognition combinations, and the focus of most of What can we make from all these of monophyletic groups but do not these is on European species. Because changes? Should we rejoice, because provide unambiguous answers for of those slightly different approaches, the rise of new fungal genera is a ranking of such groups. History and it is hard to see how these different long overdue process? Or should we tradition still determine to some extent pieces of the puzzle fit together become frustrated, because many of what is done with the data. Some of (Alvarado et al., 2015; Musumeci them are premature? It is currently so the current practices can therefore and Contu, 2010; Vizzini et al., 2012; easy to download sequences from a be better understood in the light of Vizzini and Ercole, 2012). public database and have new genera previous classifications. The ultra- One big surprise did turn up: the published without peer review – is that rapid and extensive splitting of the small species (C. cirrhata, a good development? Our title reflects boletes is a good example of that C. tuberosa, and C. cookei) fall in the that there may well be difference of phenomenon. We recognize, and middle of Clitocybe – that would opinion to what extent these changes have been recognizing, the genera toll an end of the genus Collybia, indicate scientific progress. Leccinum, , and , as Gymnopus, , and It is clear that recognizing genera is alongside Boletus. Now it is clear that had already left that the work of humans, and as such there Boletus species are spread out over the genus. But in case you are indeed will be difference of opinion and insight. bolete tree around these other already unhappily surprised by this merger: We strongly advise everybody active named units; Boletus species do not try to explain in words how you can in the field adhere to our guidelines form a monophyletic group (Nuhn recognize a large specimen of Collybia as outlined in text box #4, and not to et al., 2013; Wu et al., 2014). Hence, cirrhata from a small specimen of make new genera without providing many new genera are characterized Clitocybe candicans. A microscope them with a family home. Taking a step to accommodate the species formerly will not help you, as they are virtually back, and contemplating the merging of placed in Boletus (see text box #2 for identical in all microscopical characters. genera, instead of making new ones, is the new bolete genera of 2014 and The other development is the also our recommendation. Ask yourself 2015). If we had not started splitting ultimate slimming of the family the question: would it be best to have the boletes up into smaller units, who Tricholomataceae. In the past all one large genus Boletus or do you want knows, we would still call all of them species with light spores and lacking seven genera (Wu et al., 2014), or are Boletus, and this avalanche of new the distinctive characters of the Amanita you most satisfied with hundreds of names would not have happened. The family, the wax caps, or the parasol genera, each with only a few species, name Boletus is now reserved for the mushrooms, were thrown into the which is the unavoidable outcome of type species of the genus, , garbage can that represented that family. the current splitting snowball (see text and its closest relatives. Many of the More than 90 genera were listed by box #2)? eastern North American species still Singer (1986) in his all-encompassing But, what is the average amateur have to be placed in these new genera, overview of the . Now, eight mycologist to do with all the new but Boletus bicolor has already moved are left (Sánchez-Garcia et al., 2014). names? Several, or possibly even many, to Baorangia, Sutorius accommodates But a good family home has not yet names are definitely here to stay, and Tylopilus eximius, and Harrya been found for all these remaining we have to learn them. Keeping track chromapes replaces Tylopilus chromapes. genera, and that is also applicable to of all these changes is not so easy – Most western species are already those new genera that have been split there is a lot of literature! But, you accommodated in the new genera. off from Clitocybe et al. in recent years. are not on your own, there are many Tricholomataceae: family matters Again, as in Trametes, it might be people who are following the newest a good idea to step back and to see developments, and who make name We cannot avoid talking about whether perhaps bigger units do changes on popular web sites, such as families as well. For several of the represent solid monophyletic groups, MushroomObserver.org. newly proposed genera we have which can be named. In this case, All these changes mean that our indicated that the exact position is not one has to take many steps back, knowledge is also changing: we are yet known (text box #3), that has to do to the whole of what is called the gaining more and more insight in with the fact that those white-spored Tricholomatoid clade by Matheny et the relationships of our beloved groups are still not very well sorted al. (2007) in their big overview of the mushrooms, and that is a development out, and this represents a wide open gilled mushrooms. Besides the slimmed we only can applaud! research field. There are quite a few version of the Tricholomataceae, the different studies dealing with species References Cited Lyophyllaceae, the Entolomataceae, the that have white spores, decurrent Alvarado, P., G. Moreno, A. Vizzini, Marasmiaceae, Clitocybe and some of gills, and very little else in terms of G. Consiglio, J.L. Manjón, and its split-offs, and other orphaned genera character. In fact, most of the other L. Setti. 2015. Atractosporocybe, fall into this clade. Naming this big clade “characters” are negative characters Leucocybe and Rhizocybe: three “Tricholomataceae” might be a good (no cystidia, no differentiated new clitocyboid genera in the solution, but not one that everybody will structure, no amyloid reactions, Tricholomatoid clade (Agaricales) happily and readily accept! etc.). But all these studies use slightly with notes on Clitocybe and . different markers, and different species Conclusions Mycologia 107: 123–136. http://

40 FUNGI Volume 8:4 Winter 2015 dx.doi.org/10.3852/13-369 57: 1276–1292. http://dx.doi. Jenkinson, T.S., B.A. Perry, R.E. Schaefer, Arora, D., and J.L. Frank. 2014. org/10.1016/j.ympev.2010.10.004 and D.E. Desjardin. 2014. Clarifying the butter Boletes: a new Gelardi, M., G. Simonini, E. Ercole, and Cryptomarasmius gen. nov. genus, Butyriboletus, is established A. Vizzini. 2014. Alessioporus established in the Physalacriaceae to accommodate Boletus sect. and Pulchroboletus (, to accommodate members of Appendiculati, and six new species ), two novel genera for Marasmius section Hygrometrici. are described. Mycologia 106: 464– Xerocomus ichnusanus and X. Mycologia 106: 86–94. http://dx.doi. 480. http://dx.doi.org/10.3852/13-052 roseoalbidus from the European org/10.3852/11-309 Assyov, B., J.-M. Bellanger, P. Bertéa, R. Mediterranean basin: molecular and Justo, A. 2014. of Turkey tails Courtecuisse, G. Koller, M. Loizides, morphological evidence. Mycologia and related . Mycophile G. 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