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Michaud TJ, Pearse IS, Kauserud H, Andrew CJ, Kennedy PG. Mast seeding in European beech (Fagus sylvatica L.) is associated with reduced fungal sporocarp production and community diversity. Ecol Lett 2024; 27:e14460. [PMID: 38877759 DOI: 10.1111/ele.14460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/16/2024]
Abstract
Mast seeding is a well-documented phenomenon across diverse forest ecosystems. While its effect on aboveground food webs has been thoroughly studied, how it impacts the soil fungi that drive soil carbon and nutrient cycling has not yet been explored. To evaluate the relationship between mast seeding and fungal resource availability, we paired a Swiss 29-year fungal sporocarp census with contemporaneous seed production for European beech (Fagus sylvatica L.). On average, mast seeding was associated with a 55% reduction in sporocarp production and a compositional community shift towards drought-tolerant taxa across both ectomycorrhizal and saprotrophic guilds. Among ectomycorrhizal fungi, traits associated with carbon cost did not explain species' sensitivity to seed production. Together, our results support a novel hypothesis that mast seeding limits annual resource availability and reproductive investment in soil fungi, creating an ecosystem 'rhythm' to forest processes that is synchronized above- and belowground.
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Affiliation(s)
- Talia J Michaud
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Ian S Pearse
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | | | | | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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Bradshaw AJ, Ramírez-Cruz V, Awan AR, Furci G, Guzmán-Dávalos L, Dentinger BTM. Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster. Proc Natl Acad Sci U S A 2024; 121:e2311245121. [PMID: 38194448 PMCID: PMC10801892 DOI: 10.1073/pnas.2311245121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024] Open
Abstract
Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny of Psilocybe using shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage of Psilocybe arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster within Psilocybe.
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Affiliation(s)
- Alexander J. Bradshaw
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
| | - Virginia Ramírez-Cruz
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Ali R. Awan
- Genomics Innovation Unit, Guy’s and St.Thomas’ NHS Foundation Trust, St Thomas’ Hospital, LondonSE1 7EH, United Kingdom
| | | | - Laura Guzmán-Dávalos
- Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Bryn T. M. Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
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3
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Yan C, Hao H, Sha S, Wang Z, Huang L, Kang Z, Wang L, Feng H. Comparative Assessment of Habitat Suitability and Niche Overlap of Three Cytospora Species in China. J Fungi (Basel) 2024; 10:38. [PMID: 38248948 PMCID: PMC10817479 DOI: 10.3390/jof10010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
The plant pathogenic fungus Cytospora is notoriously known for causing woody plant canker diseases, resulting in substantial economic losses to biological forests and fruit trees worldwide. Despite their strong negative ecological impact, the existing and prospective distribution patterns of these plant pathogens in China, according to climate change, have received little attention. In this study, we chose three widely dispersed and seriously damaging species, namely, Cytospora chrysosperma, Cytospora mali, and Cytospora nivea, which are the most common species that damage the Juglans regia, Malus domestica, Eucalyptus, Pyrus sinkiangensis, Populus spp., and Salix spp. in China. We utilized ecological niche modeling to forecast their regional distribution in China under four climate change scenarios (present, SSP 126, SSP 370, and SSP 585). The results show that temperature-related climate factors limit the current distribution ranges of the three species. Currently, the three studied species are highly suitable for northeast, northwest, north, and southwest China. Under future climate scenarios, the distribution ranges of the three species are projected to increase, and the centers of the adequate distribution areas of the three species are expected to shift to high-latitude regions. The three species coexist in China, primarily in the northwest and north regions. The ecological niches of C. chrysosperma and C. nivea are more similar. The distribution range of C. mali can reach the warmer and wetter eastern region, whereas C. chrysosperma and C. nivea are primarily found in drought-prone areas with little rainfall. Our findings can help farmers and planners develop methods to avoid the spread of Cytospora spp. and calculate the costs of applying pesticides to reduce contamination and boost yields.
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Affiliation(s)
- Chengcai Yan
- College of Life Science and Technology, Tarim University, Alar 843300, China;
- Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, Tarim University, Alar 843300, China; (H.H.); (L.H.); (Z.K.)
- The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Tarim University, Alar 843300, China
| | - Haiting Hao
- Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, Tarim University, Alar 843300, China; (H.H.); (L.H.); (Z.K.)
- The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Tarim University, Alar 843300, China
| | - Shuaishuai Sha
- College of Modern Agriculture, Kashgar University, Kashgar 844006, China
| | - Zhe Wang
- Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, Tarim University, Alar 843300, China; (H.H.); (L.H.); (Z.K.)
- The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Tarim University, Alar 843300, China
| | - Lili Huang
- Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, Tarim University, Alar 843300, China; (H.H.); (L.H.); (Z.K.)
- The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Tarim University, Alar 843300, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Xianyang 712100, China
| | - Zhensheng Kang
- Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, Tarim University, Alar 843300, China; (H.H.); (L.H.); (Z.K.)
- The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Tarim University, Alar 843300, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Xianyang 712100, China
| | - Lan Wang
- Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, Tarim University, Alar 843300, China; (H.H.); (L.H.); (Z.K.)
- The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Tarim University, Alar 843300, China
| | - Hongzu Feng
- Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, Tarim University, Alar 843300, China; (H.H.); (L.H.); (Z.K.)
- The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Tarim University, Alar 843300, China
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Substrate affinities of wood decay fungi are foremost structured by wood properties not climate. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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5
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Olds CG, Berta‐Thompson JW, Loucks JJ, Levy RA, Wilson AW. Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11508. [PMID: 36818783 PMCID: PMC9934593 DOI: 10.1002/aps3.11508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/18/2023]
Abstract
PREMISE Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor-efficient and cost-effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once. METHODS We applied a two-step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 Lactarius specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de-noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens. RESULTS The taxonomic identities derived from the nrITS2 sequence data were >90% accurate across all specimens sampled. A phylogenetic analysis of the Lactarius sequences identified 20 MOTUs. DISCUSSION The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.
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Affiliation(s)
- C. Gary Olds
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
- The Department of Integrative BiologyUniversity of Colorado DenverDenverColoradoUSA
| | | | - Justin J. Loucks
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
| | - Richard A. Levy
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
| | - Andrew W. Wilson
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
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DNA Authentication and Chemical Analysis of Psilocybe Mushrooms Reveal Widespread Misdeterminations in Fungaria and Inconsistencies in Metabolites. Appl Environ Microbiol 2022; 88:e0149822. [PMID: 36445079 PMCID: PMC9764976 DOI: 10.1128/aem.01498-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The mushroom genus Psilocybe is best known as the core group of psychoactive mushrooms, yet basic information on their diversity, taxonomy, chemistry, and general biology is still largely lacking. In this study, we reexamined 94 Psilocybe fungarium specimens, representing 18 species, by DNA barcoding, evaluated the stability of psilocybin, psilocin, and their related tryptamine alkaloids in 25 specimens across the most commonly vouchered species (Psilocybe cubensis, Psilocybe cyanescens, and Psilocybe semilanceata), and explored the metabolome of cultivated P. cubensis. Our data show that, apart from a few well-known species, the taxonomic accuracy of specimen determinations is largely unreliable, even at the genus level. A substantial quantity of poor-quality and mislabeled sequence data in public repositories, as well as a paucity of sequences derived from types, further exacerbates the problem. Our data also support taxon- and time-dependent decay of psilocybin and psilocin, with some specimens having no detectable quantities of them. We also show that the P. cubensis metabolome possibly contains thousands of uncharacterized compounds, at least some of which may be bioactive. Taken together, our study undermines commonly held assumptions about the accuracy of names and presence of controlled substances in fungarium specimens identified as Psilocybe spp. and reveals that our understanding of the chemical diversity of these mushrooms is largely incomplete. These results have broader implications for regulatory policies pertaining to the storage and sharing of fungarium specimens as well as the use of psychoactive mushrooms for recreation and therapy. IMPORTANCE The therapeutic use of psilocybin, the active ingredient in "magic mushrooms," is revolutionizing mental health care for a number of conditions, including depression, posttraumatic stress disorder (PTSD), and end-of-life care. This has spotlighted the current state of knowledge of psilocybin, including the organisms that endogenously produce it. However, because of international regulation of psilocybin as a controlled substance (often included on the same list as cocaine and heroin), basic research has lagged far behind. Our study highlights how the poor state of knowledge of even the most fundamental scientific information can impact the use of psilocybin-containing mushrooms for recreational or therapeutic applications and undermines critical assumptions that underpin their regulation by legal authorities. Our study shows that currently available chemical studies are mainly inaccurate, irreproducible, and inconsistent, that there exists a high rate of misidentification in museum collections and public databases rendering even names unreliable, and that the concentration of psilocybin and its tryptamine derivatives in three of the most commonly collected Psilocybe species (P. cubensis, P. cyanescens, and P. semilanceata) is highly variable and unstable in museum specimens spanning multiple decades, and our study generates the first-ever insight into the highly complex and largely uncharacterized metabolomic profile for the most commonly cultivated magic mushroom, P. cubensis.
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Dramani R, Gouwakinnou GN, Houdanon RD, De Kesel A, Minter D, Yorou NS. Ecological niche modelling of Cantharellus species in Benin, and revision of their conservation status. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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8
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Next-Generation Sequencing of Ancient and Recent Fungarium Specimens. J Fungi (Basel) 2022; 8:jof8090932. [PMID: 36135657 PMCID: PMC9503353 DOI: 10.3390/jof8090932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 01/04/2023] Open
Abstract
Fungaria are an unmatched resource for providing genetic data from authoritative, taxonomically-correct fungal species, especially type specimens. These specimens serve to anchor species hypotheses by enabling the correct taxonomic placement of taxa in systematic studies. The DNA from ancient specimens older than 30 years is commonly fragmented, and sometimes highly contaminated by exogenous, non-target fungal DNA, making conventional PCR amplification and Sanger sequencing difficult or impossible. Here, we present the results of DNA extraction, PCR amplification of the ITS2 region, and Illumina MiSeq Nano sequencing of nine recent and 11 ancient specimens, including seven type specimens. The taxa sampled included a range of large and fleshy, to small and tough, or small, melanized specimens of Discina, Gyromitra, Propolis, Stictis, and Xerotrema, with a culture of Lasiosphaeria serving as a positive control. DNA was highly fragmented and in very low quantity for most samples, resulting in inconclusive or incorrect results for all but five samples. Taxonomically-correct sequences were generated from the holotype specimens of G. arctica, G. korshinskii, and G. leucoxantha, from the neotype of G. ussuriensis, and from the positive control. Taxonomic assignments were confirmed through morphology, top BLASTn hits, and maximum likelihood phylogenetic analyses. Though this study was not cost-effective due to the small number of samples submitted and few generating correct sequences, it did produce short DNA barcode fragments for four type specimens that are essential for their correct taxonomic placement in our ongoing systematic studies.
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Nygaard M, Kopatz A, Speed JMD, Martin MD, Prestø T, Kleven O, Bendiksby M. Spatiotemporal monitoring of the rare northern dragonhead ( Dracocephalum ruyschiana, Lamiaceae) - SNP genotyping and environmental niche modeling herbarium specimens. Ecol Evol 2022; 12:e9187. [PMID: 35983172 PMCID: PMC9374565 DOI: 10.1002/ece3.9187] [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: 12/03/2021] [Revised: 05/31/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022] Open
Abstract
The species we have studied the spatiotemporal genetic change in the northern dragonhead, a plant species that has experienced a drastic population decline and habitat loss in Europe. We have added a temporal perspective to the monitoring of northern dragonhead in Norway by genotyping herbarium specimens up to 200 years old. We have also assessed whether northern dragonhead has achieved its potential distribution in Norway. To obtain the genotype data from 130 herbarium specimens collected from 1820 to 2008, mainly from Norway (83) but also beyond (47), we applied a microfluidic array consisting of 96 SNP markers. To assess temporal genetic change, we compared our new genotype data with existing data from modern samples. We used sample metadata and observational records to model the species' environmental niche and potential distribution in Norway. Our results show that the SNP array successfully genotyped all included herbarium specimens. Hence, with the appropriate design procedures, the SNP array technology appears highly promising for genotyping old herbarium specimens. The captured genetic diversity correlates negatively with distance from Norway. The historical-modern comparisons reveal similar genetic structure and diversity across space and limited genetic change through time in Norway, providing no signs of any regional bottleneck (i.e., spatiotemporal stasis). The regional areas in Norway have remained genetically divergent, however, both from each other and more so from populations outside of Norway, rendering continued protection of the species in Norway relevant. The ENM results suggest that northern dragonhead has not fully achieved its potential distribution in Norway and corroborate that the species is anchored in warmer and drier habitats.
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Affiliation(s)
- Malene Nygaard
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
- Natural History Museum and Botanical GardenUniversity of AgderKristiansandNorway
| | | | - James M. D. Speed
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael D. Martin
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Tommy Prestø
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | | | - Mika Bendiksby
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
- Natural History MuseumUniversity of OsloNorway
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Salgado-Salazar C, Thines M. Two new species of Plasmopara affecting wild grapes in the USA. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01813-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Hidden in the tropics: Retiperidiolia gen. nov., a new genus of bird’s nest fungi (Nidulariaceae), and a systematic study of the genus Mycocalia. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01807-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Sharma N, Tapwal A, Verma R, Kumar D, Nepovimova E, Kuca K. Medicinal, nutritional, and nutraceutical potential of Sparassis crispa s. lat.: a review. IMA Fungus 2022; 13:8. [PMID: 35513833 PMCID: PMC9074205 DOI: 10.1186/s43008-022-00095-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Sparassis crispa is an edible mushroom exhibiting a wide range of medicinal properties. It is recognized for therapeutic value because of the high β-glucan content in the basidiomes. The broad range of its reported curative effects include anti-tumour, anti-cancer, immune-enhancing, hematopoietic, anti-angiogenic, anti-inflammatory, anti-diabetic, wound-healing, antioxidant, anti-coagulant, and anti-hypertensive properties. However, most of the studies are conducted on immunomodulatory and anticancer activities. Besides this, it also exhibits anti-microbial properties due to the presence of sparassol. Technology is now available for the cultivation of S. crispa on coniferous sawdust. This review is an attempt to focus on its distribution, taxonomy, chemical composition, medicinal properties, potential applications, and artificial cultivation.
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Affiliation(s)
- Neha Sharma
- Himalayan Forest Research Institute, Conifer Campus, Panthaghati, Shimla, 171013, India
| | - Ashwani Tapwal
- Himalayan Forest Research Institute, Conifer Campus, Panthaghati, Shimla, 171013, India.
| | - Rachna Verma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences , Solan, Himachal Pradesh, 173229, India.
| | - Dinesh Kumar
- School of Bioengineering and Food Technology, Shoolini University of Biotechnology and Management Sciences , Solan, Himachal Pradesh, 173229, India
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003, Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003, Hradec Kralove, Czech Republic.
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Teixeira‐Costa L, Heberling JM, Wilson CA, Davis CC. Parasitic flowering plant collections embody the extended specimen. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Luiza Teixeira‐Costa
- Harvard University Herbaria Cambridge MA USA
- Hanse‐Wissenschaftskolleg – Institute for Advanced Study, Lehmkuhlenbusch 4, 27753 Delmenhorst Germany
| | | | - Carol A. Wilson
- University and Jepson Herbaria University of California, Berkeley, 1001 Valley Life Sciences Building Berkeley CA USA
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Brown SP, Shahrtash M, Tucker AE, Knoepp J, Stokes CE, Baird R. Seasonal disconnects between saprobic and mycorrhizal sporocarp communities in the Southern Appalachian Mountains. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2021.101125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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15
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Baird A, Pope F. ‘Can't see the forest for the trees’: The importance of fungi in the context of UK tree planting. Food Energy Secur 2022. [DOI: 10.1002/fes3.371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Aileen Baird
- School of Geography, Earth & Environmental Sciences Birmingham UK
- Birmingham Institute of Forest Research Birmingham UK
| | - Francis Pope
- School of Geography, Earth & Environmental Sciences Birmingham UK
- Birmingham Institute of Forest Research Birmingham UK
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Lofgren LA, Stajich JE. Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes. Curr Biol 2021; 31:R1312-R1325. [PMID: 34637742 PMCID: PMC8516061 DOI: 10.1016/j.cub.2021.06.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
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Hao T, Elith J, Guillera-Arroita G, Lahoz-Monfort JJ, May TW. Enhancing repository fungal data for biogeographic analyses. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Meineke EK, Daru BH. Bias assessments to expand research harnessing biological collections. Trends Ecol Evol 2021; 36:1071-1082. [PMID: 34489117 DOI: 10.1016/j.tree.2021.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022]
Abstract
Biological collections are arguably the most important resources for investigations into the impacts of human activities on biodiversity. However, the apparent opportunities presented by museum-derived datasets have not resulted in consistent or widespread use of specimens in ecology outside phenological research and species distribution modeling. We attribute this gap between opportunity and application to biases introduced by collectors, curators, and preservation practices and an imperfect understanding of these biases and how to mitigate them. To facilitate broader use of specimen-based data, we characterize collection biases across key axes and explore interactions among them. We then present a framework for determining the bias assessments needed when extracting data from biological collections. We show that bias assessments required by particular ecological studies will depend on the response variables being measured and the predictor axes of interest. We argue that quantification of biases in specimen-derived datasets is needed to facilitate the widespread application of these data.
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Affiliation(s)
- Emily K Meineke
- Department of Entomology and Nematology, University of California, Davis 95616, CA, USA.
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA.
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Hill R, Llewellyn T, Downes E, Oddy J, MacIntosh C, Kallow S, Panis B, Dickie JB, Gaya E. Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives. Front Microbiol 2021; 12:643731. [PMID: 33841366 PMCID: PMC8024981 DOI: 10.3389/fmicb.2021.643731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily Lasiodiplodia, Fusarium, and Aspergillus-while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.
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Affiliation(s)
- Rowena Hill
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Theo Llewellyn
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Elizabeth Downes
- Department for Environment, Food and Rural Affairs, London, United Kingdom
| | - Joseph Oddy
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Catriona MacIntosh
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon Kallow
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
- Division of Crop Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven, Leuven, Belgium
| | - Bart Panis
- Bioversity International, Montpellier, France
| | - John B. Dickie
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
| | - Ester Gaya
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Gómez-Zapata PA, Haelewaters D, Quijada L, Pfister DH, Aime MC. Notes on Trochila (Ascomycota, Leotiomycetes), with new species and combinations. MycoKeys 2021; 78:21-47. [PMID: 36761369 PMCID: PMC9849072 DOI: 10.3897/mycokeys.78.62046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/07/2021] [Indexed: 12/25/2022] Open
Abstract
Studies of Trochila (Leotiomycetes, Helotiales, Cenangiaceae) are scarce. Here, we describe two new species based on molecular phylogenetic data and morphology. Trochilabostonensis was collected at the Boston Harbor Islands National Recreation Area, Massachusetts. It was found on the stem of Asclepiassyriaca, representing the first report of any Trochila species from a plant host in the family Apocynaceae. Trochilaurediniophila is associated with the uredinia of the rust fungus Ceroteliumfici. It was discovered during a survey for rust hyperparasites conducted at the Arthur Fungarium, in a single sample from 1912 collected in Trinidad. Macro- and micromorphological descriptions, illustrations, and molecular phylogenetic analyses are presented. The two new species are placed in Trochila with high support in both our six-locus (SSU, ITS, LSU, rpb1, rpb2, tef1) and two-locus (ITS, LSU) phylogenetic reconstructions. In addition, two species are combined in Trochila: Trochilacolensoi (formerly placed in Pseudopeziza) and T.xishuangbanna (originally described as the only species in Calycellinopsis). This study reveals new host plant families, a new ecological strategy, and a new country record for the genus Trochila. Finally, our work emphasizes the importance of specimens deposited in biological collections such as fungaria.
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Affiliation(s)
- Paula Andrea Gómez-Zapata
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USAPurdue UniversityWest LafayetteUnited States of America
| | - Danny Haelewaters
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USAPurdue UniversityWest LafayetteUnited States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USAHarvard UniversityCambridgeUnited States of America
- Farlow Herbarium and Reference Library of Cryptogamic Botany, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USAHarvard University HerbariaCambridgeUnited States of America
- Faculty of Science, University of South Bohemia, České Budějovice, Czech RepublicUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Luis Quijada
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USAHarvard UniversityCambridgeUnited States of America
- Farlow Herbarium and Reference Library of Cryptogamic Botany, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USAHarvard University HerbariaCambridgeUnited States of America
| | - Donald H. Pfister
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USAHarvard UniversityCambridgeUnited States of America
- Farlow Herbarium and Reference Library of Cryptogamic Botany, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USAHarvard University HerbariaCambridgeUnited States of America
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USAPurdue UniversityWest LafayetteUnited States of America
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Hao T, Guillera-Arroita G, May TW, Lahoz-Monfort JJ, Elith J. Using Species Distribution Models For Fungi. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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22
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Salvador RB, Cunha CM. Natural history collections and the future legacy of ecological research. Oecologia 2020; 192:641-646. [PMID: 32056020 DOI: 10.1007/s00442-020-04620-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/07/2020] [Indexed: 11/29/2022]
Abstract
Natural history collections are now being championed as key to broad ecological studies, especially those involving human impacts in the Anthropocene. However, collections are going through a crisis that threatens their present and future value, going beyond underfunding/understaffing to a more damaging practice: current researchers are no longer depositing material. This seems to be especially true for ecological studies that now benefit from historical collections, as those researchers are not trained to think about voucher specimens. We investigated indexed journals in Ecology and Zoology to assess if they have guidelines concerning voucher specimens. Only 4% of ecological journals presently encourage (but mostly do not require) voucher deposition, while 15% of zoological journals encourage it. In the first place, this goes contrary to scientific standards of reproducibility, since specimens are primary data. Secondly, this erodes the legacy we will leave for future researchers, because if this trend goes on unchecked, it will leave a massive gap in collections' coverage, undermining the quality that is presently acclaimed. The scientific community needs a wakeup call to avoid impoverishing the future value of natural history collections. Training and changing researchers' mindsets is essential, but that takes time. For the moment, we propose a stopgap measure: at the minimum, academic journals should encourage authors to deposit specimens in open collections, such as museums and universities.
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Affiliation(s)
- Rodrigo B Salvador
- Museum of New Zealand Te Papa Tongarewa, 169 Tory Street, Wellington, 6011, New Zealand.
| | - Carlo M Cunha
- Universidade Metropolitana de Santos, Avenida Conselheiro Nébias 536, Santos, SP, 11045-002, Brazil
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23
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Kido A, Hood ME. Mining new sources of natural history observations for disease interactions. AMERICAN JOURNAL OF BOTANY 2020; 107:3-11. [PMID: 31885083 PMCID: PMC6980919 DOI: 10.1002/ajb2.1409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Allyson Kido
- Department of BiologyAmherst CollegeAmherstMassachusettsUSA
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Krah FS, Bates ST, Miller AN. rMyCoPortal - an R package to interface with the Mycology Collections Portal. Biodivers Data J 2019:e31511. [PMID: 30686929 PMCID: PMC6341041 DOI: 10.3897/bdj.7.e31511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/08/2019] [Indexed: 11/12/2022] Open
Abstract
The understanding of the biodiversity and biogeographical distribution of fungi is still limited. The small number of online databases and the large effort required to access existing data have prevented their use in research articles. The Mycology Collections Portal was established in 2012 to help alleviate these issues and currently serves data online for over 4.3 million fungal records. However, the current process for accessing the data through the web interface is manual, therefore slow, and precludes the extensive use of the existing datasets. Here we introduce the software package rMyCoPortal, which allows users rapid, automated access to the data. rMyCoPortal makes data readily available for further computations and analyses in the open source statistical programming environment R. We will demonstrate the core functions of the package, and how rMyCoPortal can be employed to obtain fungal data that can be used to address basic research questions. rMyCoPortal is a free and open-source R package, available via GitHub.
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Affiliation(s)
- Franz-Sebastian Krah
- Bavarian Forest National Park, Grafenau, Germany Bavarian Forest National Park Grafenau Germany.,Technical University of Munich, Freising, Germany Technical University of Munich Freising Germany
| | - Scott T Bates
- Purdue University Northwest, Westville, United States of America Purdue University Northwest Westville United States of America
| | - Andrew N Miller
- University of Illinois Urbana-Champaign, Champaign, United States of America University of Illinois Urbana-Champaign Champaign United States of America
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Meineke EK, Davies TJ, Daru BH, Davis CC. Biological collections for understanding biodiversity in the Anthropocene. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2017.0386. [PMID: 30455204 DOI: 10.1098/rstb.2017.0386] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2018] [Indexed: 12/16/2022] Open
Abstract
Global change has become a central focus of modern biology. Yet, our knowledge of how anthropogenic drivers affect biodiversity and natural resources is limited by a lack of biological data spanning the Anthropocene. We propose that the hundreds of millions of plant, fungal and animal specimens deposited in natural history museums have the potential to transform the field of global change biology. We suggest that museum specimens are underused, particularly in ecological studies, given their capacity to reveal patterns that are not observable from other data sources. Increasingly, museum specimens are becoming mobilized online, providing unparalleled access to physiological, ecological and evolutionary data spanning decades and sometimes centuries. Here, we describe the diversity of collections data archived in museums and provide an overview of the diverse uses and applications of these data as discussed in the accompanying collection of papers within this theme issue. As these unparalleled resources are under threat owing to budget cuts and other institutional pressures, we aim to shed light on the unique discoveries that are possible in museums and, thus, the singular value of natural history collections in a period of rapid change.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Emily K Meineke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - T Jonathan Davies
- Department of Ecology and Evolutionary Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4.,African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2006, South Africa
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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