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Wilson AW, Eberhardt U, Nguyen N, Noffsinger CR, Swenie RA, Loucks JL, Perry BA, Herrera M, Osmundson TW, DeLong-Duhon S, Beker HJ, Mueller GM. Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera. J Fungi (Basel) 2023; 9:788. [PMID: 37623559 PMCID: PMC10455624 DOI: 10.3390/jof9080788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of "splitting" taxa into numerous taxonomic units produces greater barcode gaps when compared to "lumping". The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.
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Affiliation(s)
| | - Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Nhu Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawaiʻi at Mānoa, 3190 Maile Way, St. John 102, Honolulu, HI 96822, USA
| | - Chance R. Noffsinger
- Department of Ecology and Evolutionary Biology, University of Tennessee, Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996, USA
| | - Rachel A. Swenie
- Department of Ecology and Evolutionary Biology, University of Tennessee, Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996, USA
| | | | - Brian A. Perry
- Department of Biological Sciences, California State University East Bay, 25800 Carlos Bee Blvd., Hayward, CA 94542, USA
| | - Mariana Herrera
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
| | - Todd W. Osmundson
- Biology Department, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, USA
| | | | - Henry J. Beker
- Royal Holloway College, University of London, London WC1E 7HU, UK
- Plantentuin Meise, Nieuwelaan 38, B-1860 Meise, Belgium
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Demystifying Hebeloma: introducing hebeloma.org and its database. IMA Fungus 2022; 13:18. [PMID: 36352449 PMCID: PMC9647992 DOI: 10.1186/s43008-022-00105-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
We here announce the launch of the website https://hebeloma.org.
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Bartlett P, Eberhardt U, Schütz N, Beker HJ. Species determination using AI machine-learning algorithms: Hebeloma as a case study. IMA Fungus 2022; 13:13. [PMID: 35773719 PMCID: PMC9245212 DOI: 10.1186/s43008-022-00099-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
The genus Hebeloma is renowned as difficult when it comes to species determination. Historically, many dichotomous keys have been published and used with varying success rate. Over the last 20 years the authors have built a database of Hebeloma collections containing not only metadata but also parametrized morphological descriptions, where for about a third of the cases micromorphological characters have been analysed and are included, as well as DNA sequences for almost every collection. The database now has about 9000 collections including nearly every type collection worldwide and represents over 120 different taxa. Almost every collection has been analysed and identified to species using a combination of the available molecular and morphological data in addition to locality and habitat information. Based on these data an Artificial Intelligence (AI) machine-learning species identifier has been developed that takes as input locality data and a small number of the morphological parameters. Using a random test set of more than 600 collections from the database, not utilized within the set of collections used to train the identifier, the species identifier was able to identify 77% correctly with its highest probabilistic match, 96% within its three most likely determinations and over 99% of collections within its five most likely determinations.
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Affiliation(s)
- Peter Bartlett
- La Baraka, Gorse Hill Road, Virginia Water, Surrey, GU25 4AP, UK
| | - Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany.
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany
| | - Henry J Beker
- , Rue Père de Deken 19, 1040, Bruxelles, Belgium.,Royal Holloway College, University of London, Egham, UK.,Plantentuin Meise, Nieuwelaan 38, B-1860, Meise, Belgium
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Eberhardt U, Kong A, Montoya A, Schütz N, Bartlett P, Beker HJ. Not (only) poison pies - Hebeloma (Agaricales, Hymenogastraceae) in Mexico. MycoKeys 2022; 90:163-202. [PMID: 36760422 PMCID: PMC9849069 DOI: 10.3897/mycokeys.90.85267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/07/2022] [Indexed: 11/12/2022] Open
Abstract
The species of Hebeloma have been little studied in Mexico, but have received attention as edibles and in trials to enhance production of edible fungi and tree growth through inoculation of seedlings with ectomycorrhizal fungi. Here we describe three new species of Hebeloma that are currently known only from Mexico. These species belong to separate sections of the genus: H.ambustiterranum is a member of H.sect.Hebeloma, H.cohaerens belongs to H.sect.Theobromina, while H.magnicystidiatum belongs to H.sect.Denudata. All three species were collected from subtropical pine-oak woodland; all records of H.cohaerens came from altitudes above 2500 m. Hebelomaambustiterranum is commonly sold in the local markets of Tlaxcala as a prized edible mushroom. An additional nine species are reported from Mexico, of which eight are new records for the country: H.aanenii, H.eburneum, H.excedens, H.ingratum, H.neurophyllum, H.sordidulum, H.subaustrale and H.velutipes. First modern descriptions of H.neurophyllum and H.subaustrale, originally described from the USA, are given here.
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Affiliation(s)
- Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Alejandro Kong
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Km 10.5 carretera San Martín Texmelucan-Tlaxcala, San Felipe Ixtacuixtla, Tlaxcala, 90120, Mexico
| | - Adriana Montoya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Km 10.5 carretera San Martín Texmelucan-Tlaxcala, San Felipe Ixtacuixtla, Tlaxcala, 90120, Mexico
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Peter Bartlett
- La Baraka, Gorse Hill Road, Virginia Water, Surrey GU25 4AP, United Kingdom
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Eberhardt U, Schütz N, Bartlett P, Hosaka K, Kasuya T, Beker HJ. Revisiting Hebeloma (Hymenogastraceae, Agaricales) in Japan: four species recombined into other genera but three new species discovered. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01757-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
AbstractHere, we present the results of studies of Japanese Hebeloma collections. The four species described by Imai as Hebeloma (H. fimicola, H. helvolescens, H. humosum, and H. tomoeae) are not from the genus Hebeloma, but are members of Agrocybe, Homophron, or Pholiota. Recombinations are made. Hebelomacrustuliniforme f. microspermum, described by Hongo, is a synonym of H. nanum. Three species of Hebeloma are described as new to science, all currently known only from Japan. Two of these species, H. asperosporum and H. cinnamomeum, are members of H. sect. Denudata while the third species H. citrisporum belongs to H. sect. Velutipes. Japanese records of H. cavipes, H. eburneum, H. hygrophilum, H. subtortum, and H. velutipes are validated. In total, fifteen species of Hebeloma are confirmed from Japan; this is compared with previous checklists.
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Eberhardt U, Schütz N, Bartlett P, Beker HJ. 96 North American taxa sorted - Peck's Hebeloma revisited. Mycologia 2022; 114:337-387. [PMID: 35230235 DOI: 10.1080/00275514.2021.2012063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Charles Horton Peck described some 2700 species of North American fungi in the 19th and early 20th centuries. Among these were 31 species that he described as Hebeloma or that later authors recombined into Hebeloma. These 31 taxa have been analyzed morphologically and molecularly, as far as possible. For six of these species, lectotypes are designated. For twelve species, ITS sequences (some partial) were generated. Thirteen of the species analyzed are Hebeloma, as the genus is delimited today. Of these 13, nine are regarded as 'current', i.e. are names that should be accepted and used. Of the remaining four, three are synonymized with earlier Peck species and one with the generic type H. mesophaeum. Numerous Hebeloma species described from America are synonymized with some of Peck's species, such as H. albidulum, H. album, H. colvinii, H. excedens, H. palustre, H. sordidulum, and H. velatum; Peck's H. album, H. palustre, and H. velatum are earlier names for H. fragilipes, H. clavulipes, and H. dunense, respectively. All three names were in current use and described from Europe. The 18 species that are not Hebeloma belong to a range of genera: Agrocybe, Hemistropharia, Inocybe, Inosperma, Naucoria, and Pholiota; three species that were not previously recombined into their respective genera are here recombined and one species, Hebeloma commune is synonymized with Pholiota lenta. Two taxa, that are not Hebeloma, remain unresolved. Sixty later Hebeloma taxa described from North America are revised and synonymized with Peck species and seven with H. mesophaeum, 36 of these supported by ITS (some partial) sequence data. Updates on two species, H. petrakii and H. remyi, from Europe, are also given, and a lectotype and epitype selected for the latter.
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Affiliation(s)
- Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Peter Bartlett
- La Baraka, Gorse Hill Road, Virginia Water, Surrey GU25 4AP, United Kingdom
| | - Henry J Beker
- Rue Père de Deken 19, B-1040 Bruxelles, Belgium; Royal Holloway College, University of London, Egham, United Kingdom; Plantentuin Meise, Nieuwelaan 38, B-1860 Meise, Belgium
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