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Voller F, Ardanuy A, Taylor AFS, Johnson D. Maintenance of host specialisation gradients in ectomycorrhizal symbionts. THE NEW PHYTOLOGIST 2024; 242:1426-1435. [PMID: 37984824 DOI: 10.1111/nph.19395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/02/2023] [Indexed: 11/22/2023]
Abstract
Many fungi that form ectomycorrhizas exhibit a degree of host specialisation, and individual trees are frequently colonised by communities of mycorrhizal fungi comprising species that fall on a gradient of specialisation along genetic, functional and taxonomic axes of variation. By contrast, arbuscular mycorrhizal fungi exhibit little specialisation. Here, we propose that host tree root morphology is a key factor that gives host plants fine-scale control over colonisation and therefore opportunities for driving specialisation and speciation of ectomycorrhizal fungi. A gradient in host specialisation is likely driven by four proximate mechanistic 'filters' comprising partner availability, signalling recognition, competition for colonisation, and symbiotic function (trade, rewards and sanctions), and the spatially restricted colonisation seen in heterorhizic roots enables these mechanisms, especially symbiotic function, to be more effective in driving the evolution of specialisation. We encourage manipulation experiments that integrate molecular genetics and isotope tracers to test these mechanisms, alongside mathematical simulations of eco-evolutionary dynamics in mycorrhizal symbioses.
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Affiliation(s)
- Fay Voller
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
| | - Agnès Ardanuy
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
- Université de Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, 31320, France
| | - Andy F S Taylor
- Ecological Sciences Group, James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK
| | - David Johnson
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
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2
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Dauphin B, de Freitas Pereira M, Kohler A, Grigoriev IV, Barry K, Na H, Amirebrahimi M, Lipzen A, Martin F, Peter M, Croll D. Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum. Environ Microbiol 2021; 23:6536-6556. [PMID: 34472169 PMCID: PMC9293092 DOI: 10.1111/1462-2920.15752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023]
Abstract
Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore-forming structures but with a massively enlarged genome. We carried out whole-genome sequencing to identify single-nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy-number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome-wide structural variation, lineage-specific recombination and low continent-wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra-specific functional variation in this major symbiosis.
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Affiliation(s)
| | - Maíra de Freitas Pereira
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Annegret Kohler
- INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, USA.,U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Hyunsoo Na
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Mojgan Amirebrahimi
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Francis Martin
- INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Martina Peter
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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3
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Looney BP, Adamčík S, Matheny PB. Coalescent-based delimitation and species-tree estimations reveal Appalachian origin and Neogene diversification in Russula subsection Roseinae. Mol Phylogenet Evol 2020; 147:106787. [PMID: 32165159 DOI: 10.1016/j.ympev.2020.106787] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 11/19/2022]
Abstract
Numerous lineages of mushroom-forming fungi have been subject to bursts of diversification throughout their evolutionary history, events that can impact our ability to infer well-resolved phylogenies. However, groups that have undergone quick genetic change may have the highest adaptive potential. As the second largest genus of mushroom-forming fungi, Russula provides an excellent model for studying hyper-diversification and processes in evolution that drives it. This study focuses on the morphologically defined group - Russula subsection Roseinae. Species hypotheses based on morphological differentiation and multi-locus phylogenetic analyses are tested in the Roseinae using different applications of the multi-species coalescent model. Based on this combined approach, we recognize fourteen species in Roseinae including the Albida and wholly novel Magnarosea clades. Reconstruction of biogeographic and host association history suggest that parapatric speciation in refugia during glacial cycles of the Pleistocene drove diversification within the Roseinae, which is found to have a Laurasian distribution with an evolutionary origin in the Appalachian Mountains of eastern North America. Finally, we detect jump dispersal at a continental scale that has driven diversification since the most recent glacial cycles.
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Affiliation(s)
- Brian P Looney
- University of Tennessee, Department of Ecology and Evolutionary Biology, Knoxville, TN 37996, USA.
| | - Slavomír Adamčík
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 84523 Bratislava, Slovakia
| | - P Brandon Matheny
- University of Tennessee, Department of Ecology and Evolutionary Biology, Knoxville, TN 37996, USA
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4
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Fungal species boundaries in the genomics era. Fungal Genet Biol 2019; 131:103249. [PMID: 31279976 DOI: 10.1016/j.fgb.2019.103249] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
Abstract
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
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Thongbai B, Miller SL, Stadler M, Wittstein K, Hyde KD, Lumyong S, Raspé O. Study of three interesting Amanita species from Thailand: Morphology, multiple-gene phylogeny and toxin analysis. PLoS One 2017; 12:e0182131. [PMID: 28767681 PMCID: PMC5540542 DOI: 10.1371/journal.pone.0182131] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/12/2017] [Indexed: 12/21/2022] Open
Abstract
Amanita ballerina and A. brunneitoxicaria spp. nov. are introduced from Thailand. Amanita fuligineoides is also reported for the first time from Thailand, increasing the known distribution of this taxon. Together, those findings support our view that many taxa are yet to be discovered in the region. While both morphological characters and a multiple-gene phylogeny clearly place A. brunneitoxicaria and A. fuligineoides in sect. Phalloideae (Fr.) Quél., the placement of A. ballerina is problematic. On the one hand, the morphology of A. ballerina shows clear affinities with stirps Limbatula of sect. Lepidella. On the other hand, in a multiple-gene phylogeny including taxa of all sections in subg. Lepidella, A. ballerina and two other species, including A. zangii, form a well-supported clade sister to the Phalloideae sensu Bas 1969, which include the lethal "death caps" and "destroying angels". Together, the A. ballerina-A. zangii clade and the Phalloideae sensu Bas 1969 also form a well-supported clade. We therefore screened for two of the most notorious toxins by HPLC-MS analysis of methanolic extracts from the basidiomata. Interestingly, neither α-amanitin nor phalloidin was found in A. ballerina, whereas Amanita fuligineoides was confirmed to contain both α-amanitin and phalloidin, and A. brunneitoxicaria contained only α-amanitin. Together with unique morphological characteristics, the position in the phylogeny indicates that A. ballerina is either an important link in the evolution of the deadly Amanita sect. Phalloideae species, or a member of a new section also including A. zangii.
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Affiliation(s)
- Benjarong Thongbai
- Centre of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | - Steven L. Miller
- Botany Department, University of Wyoming, Laramie, Wyoming, United States of America
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research; and German Centre for Infection Research (DZIF), partner site Hannover/Braunschweig, Braunschweig, Germany
| | - Kathrin Wittstein
- Department of Microbial Drugs, Helmholtz Centre for Infection Research; and German Centre for Infection Research (DZIF), partner site Hannover/Braunschweig, Braunschweig, Germany
| | - Kevin D. Hyde
- Centre of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Olivier Raspé
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Botanic Garden Meise, Meise, Belgium
- Fédération Wallonie–Bruxelles, Service général de l'Enseignement universitaire et de la Recherche scientifique, Bruxelles, Belgium
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Xing R, Gao QB, Zhang FQ, Fu PC, Wang JL, Yan HY, Chen SL. Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau. J Microbiol 2017; 55:600-606. [PMID: 28674972 DOI: 10.1007/s12275-017-7101-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 11/24/2022]
Abstract
Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.
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Affiliation(s)
- Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.,Key Laboratory of Crop Molecular Breeding of Qinghai Provice, Qinghai, P. R. China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.,Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, P. R. China
| | - Peng-Cheng Fu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China
| | - Jiu-Li Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China
| | - Hui-Ying Yan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.
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Feng B, Liu JW, Xu J, Zhao K, Ge ZW, Yang ZL. Ecological and physical barriers shape genetic structure of the Alpine porcini (Boletus reticuloceps). MYCORRHIZA 2017; 27:261-272. [PMID: 27909816 DOI: 10.1007/s00572-016-0751-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
The Alpine porcini, Boletus reticuloceps, is an ectomycorrhizal mushroom distributed in subalpine areas of Southwest China, central China, and Taiwan Island. This distribution pattern makes it an ideal organism to infer how ectomycorrhizal fungi have reacted to historical tectonic and climatic changes, and to illustrate the mechanism for the disjunction of organisms between Southwest China and Taiwan. In this study, we explored the phylogeographic pattern of B. reticuloceps by microsatellite genotyping, DNA sequencing, ecological factor analysis, and species distribution modeling. Three genetic groups from the East Himalayas (EH), northern Hengduan Mountains (NHM), and southern Hengduan Mountains (SHM), were identified. The earlier divergent SHM group is found under Abies in moister environments, whereas the EH and NHM groups, which are physically separated by the Mekong-Salween Divide, are found mainly under Picea in drier environments. Samples from Taiwan showed a close relationship with the SHM group. High mountains did not form dispersal barriers among populations in each of the EH, NHM, and SHM groups, probably due to the relatively weak host specificity of B. reticuloceps. Our study indicated that ecological heterogeneity could have contributed to the divergence between the SHM and the NHM-EH groups, while physical barriers could have led to the divergence of the NHM and the EH groups. Dispersal into Taiwan via Central China during the Quaternary glaciations is likely to have shaped its disjunct distribution.
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Affiliation(s)
- Bang Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jian Wei Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON , L8S 4K1, Canada
| | - Kuan Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zai Wei Ge
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhu L Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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DNA barcoding of aquatic insects reveals unforeseen diversity and recurrent population divergence patterns through broad-scale sampling in northern Canada. Polar Biol 2016. [DOI: 10.1007/s00300-016-2062-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Sánchez-García M, Henkel TW, Aime MC, Smith ME, Matheny PB. Guyanagarika, a new ectomycorrhizal genus of Agaricales from the Neotropics. Fungal Biol 2016; 120:1540-1553. [PMID: 27890090 DOI: 10.1016/j.funbio.2016.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/29/2016] [Accepted: 08/09/2016] [Indexed: 11/25/2022]
Abstract
A new genus and three new species of Agaricales are described from the Pakaraima Mountains of Guyana in the central Guiana Shield. All three of these new species fruit on the ground in association with species of the ectomycorrhizal (ECM) tree genus Dicymbe (Fabaceae subfam. Caesalpinioideae) and one species has been shown to form ectomycorrhizas. Multi-locus molecular phylogenetic analyses place Guyanagarika gen. nov. within the Catathelasma clade, a lineage in the suborder Tricholomatineae of the Agaricales. We formally recognize this 'Catathelasma clade' as an expanded family Catathelasmataceae that includes the genera Callistosporium, Catathelasma, Guyanagarika, Macrocybe, Pleurocollybia, and Pseudolaccaria. Within the Catathelasmataceae, Catathelasma and Guyanagarika represent independent origins of the ectomycorrhizal habit. Guyanagarika is the first documented case of an ECM Agaricales genus known only from the Neotropics.
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Affiliation(s)
- Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA 95521, USA
| | - Mary Catherine Aime
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Patrick Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
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